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A polymer is a long molecule consisting of many repeated monomers.

Carbohydrates/ polysaccharides (Polymers)

Proteins (Polymers)

Text

Nucleic acids (Polymers)

Lipids (Monomers)

• A condensation reaction or more specifically a dehydration reaction occurs when two

monomers bond together through the loss of a water molecule.
• Polymers are disassembled to monomers by hydrolysis, a reaction that is essentially the
reverse of the dehydration reaction.

Carbohydrates

Ratio 1:2:1 = 1 carbon, 2 hydrogen,1 oxygen.

Alpha: The Hydroxyl OH group of C1 in the opposite side of OH of C6. Beta: The OH group of C1 in
the same side of OH of C6.

Polysaccharide
Monosaccharide Disaccharide Oligosaccharide
(Glycan)

Maltotriose: 3 Glucose Homopolysaccharide

• Less than 20 monosaccharide
Glucuse Maltose: Two glucose •Contain only single type
of monosaccharide
•Starch: Storage from in
plants (alpha)
•Unbtanched glucose
polymer: Amylose
Lactose: Galactose +
Galactose
Glucose
•Branched glucose
polymer: Amylopectin
•Glycogen: Storage form
in animals (liver and
Sucrose: Glucose + muscle cells)
Fructose •Dextran: Bacteria and
Fructose • Formed by plantsm not by yeast
animal or human.
•Cellulose: structural
componant in plants
(unbranched) (Beta
confuguration)

Hetropolysaccharide
• Contain two or more types of
monosaccharide
 • A disaccharide is formed when a dehydration reaction joins only two monosaccharides.
• This covalent bond is called a glycosidic linkage.

Lipids

Hydrolyzable non Hydrolyzable

(can broken down) (cannot broken down)

Triglycerol "energy Prostaglandins

storage"
"eicosanoids 20 carbons"
Phospholipids
Steroids
Sphingolipid "nerve
cells"

Waxes Fat soluable vitamins

 Structural lipids

•Phospholipids
•Glycerophospholipids
•Sphingolipida
•Waxes

Signaling lipids

•Terpenes and Terpenoids

•Steroids
•Prostaglandins
•Fat soluble vitamins

Energy storage

•Triaclyglycerols
•Free fatty acids and Saponification

• Glycerol is a three-carbon alcohol with a hydroxyl group attached to each carbon.

• A fatty acid consists of a carboxyl group attached to a long carbon skeleton.
• Saturated fatty acids have the maximum number of hydrogen atoms possible and no double
bonds.
• Unsaturated fatty acids have one or more double bonds.
• Fats made from saturated fatty acids are called saturated fats, and are solid at room
temperature, most animal fats are saturated.
• Fats made from unsaturated fatty acids are called unsaturated fats or oils, and are liquid at
room temperature. Plant fats and fish fats are usually unsaturated.

Phospholipids
• In a phospholipid, two fatty acids and a phosphate group are attached to glycerol.
• The two fatty acid tails are hydrophobic, but the phosphate group and its attachments
form a hydrophilic head

Steroids are lipids characterized by a carbon skeleton consisting of four fused rings.
Cholesterol, an important steroid, is a component in animal cell membranes. “membrane fluidity”
Accumulation of cholesterol in arterial wall “atherosclerosis” hardening of wall.

Prostaglandins
• Powerful effects on smooth muscle function, sleep-wake cycle and elevation of body
temperature associate with fever and pain.
• Nonsteroidal anti-inflammatory drugs “NSAIDs” like aspirin, ibuprofen.

Fat soluble vitamins

 Vitamin A Vitamin D Vitamen E Vitamin K

Carotene
Cholecalciferol Tocopherols and
Retinol: the storage Phylloquinone
liver, kidney Tocotrienols
form of vitamin A

Important contributor
vision, growth,
Bone to the development of Clotting factor
immune function.
cancer and aging

Proteins

Amino acids are molecules that contain two functional groups: an amino group (NH2) and a carboxyl
group (COOH).
Amino acids differ in their properties due to differing side chains, called R groups.

Except for glycine, all amino acids are chiral (chiral means bounded to four group), and except for
cysteine, all of them have an (S) absolute configuration. L-amino acids are the only ones found in
eukaryotic proteins.
• Polypeptides are polymers built from the same set of 20 amino acids.
• A protein may consist of one or more polypeptides.

Nonpolar: according to side chains (R groups): (alkyl group)

Polar:

Only two of the 20 amino acids have negative charges on their side chains at physiological pH 7.4,
those two are aspartic acid and glutamic acid. The remaining three amino acids have positively
charged nitrogen atoms.

• Amino acids are linked by peptide bonds.

• A polypeptide is a polymer of amino acids.
Polypeptide cleaved by hydrolysis or trypsin:
• Hydrolysis nonspecific.
• Trypsin is a protease enzyme, so remember that enzymes have a preference for certain
structures based on the active site. When proteins are cleaved by trypsin, only residues with
Lysine or Arginine nearby the C terminus are cut.

Four Levels of Protein Structure

• The primary structure of a protein is its unique sequence of amino acids.
• Secondary structure, found in most proteins, consists of coils and folds in the polypeptide
chain (α helix, β sheets). Result from hydrogen bonds.
• Tertiary structure is determined by interactions among various side chains (R groups).
Hydrophobic interactions and hydrogen bonds cause protein to collapse into its proper three dimensional structure.
The formation of a disulfide bridge happens on the exterior of a cell.
• Quaternary structure results when a protein consists of multiple polypeptide chains. (not all
proteins have quaternary structure).
Proteins can be divided into fibrous and globular proteins, and both result of protein folding.
• Collagen is a fibrous protein consisting of three polypeptides coiled like a rope.
• Hemoglobin is a globular protein consisting of four polypeptides: two alpha and two beta
chains.

Alterations in pH, salt concentration, temperature, or other environmental factors can cause a
protein to unravel.
• This loss of a protein’s native structure is called denaturation.
• A denatured protein is biologically inactive.

Chaperonins are protein molecules that assist the proper folding of other proteins.

All amino acids with charged side chains are hydrophilic,

At highly acidic pH values, amino acids tend to be positively charged. At highly alkaline pH values,
amino acids tend to be negatively charged.
Increase temp. will destroy the 2o 3o 4o structures. (unfolded)
Change the pH surrounding a protein is that you have disruption of ionic bonds, will destroy the 3o 4o
structures.
Chemical denaturants often disrupt the hydrogen bonding within a protein. And remember that
hydrogen bonds contribute to secondary, tertiary, all the way up to quaternary structure.
Enzyme destroy 1o structure; break the bonds between the individual amino acids.

Non-Enzyme protein
1. Receptors/Ion channels: receptor like insulin, ion channel like calcium.
2. Transport: hemoglobin pick up the oxygen from the lungs and then delivers to tissues.
 3. Motor: myosin, kinesin, dynein. And myosin specifically is a protein responsible for generating
the forces exerted by contracting muscles, kinesin and dynein are motor proteins that are
responsible for intracellular transport.
4. Antibodies: are protein components of the adaptive immune system whose main function is to
find foreign antigens and target them for destruction.

Level of protein
structure Interactions that stabilize the structure
Primary Covalent bond (amide/peptide bond)
Secondary Hydrogen bonds
Ionic bonds, disulfide bonds, hydrophobic interactions, hydrogen
Tertiary bonding
Ionic bonds, disulfide bonds, hydrophobic interactions, hydrogen
Quaternary bonding

Nucleic Acid

• Deoxyribonucleic Acid (DNA)

• Ribonucleic Acid (RNA)

DNA found in chromosomes in the nucleus of eukaryotic cells, although some is also present in
mitochondria and chloroplasts.
DNA provides directions for its own replication: Adenine with Thymine via two hydrogen bonds,
Guanine with Cytosine via three hydrogen bonds so it needs more energy to break G-C down.

Nucleotides: nitrogenous base, a 5-C pentose sugar (Ribose) and a phosphate group (PO43-).
The portion of a nucleotide without the phosphate group is called a nucleoside.
Deoxyribose means the ribose with the 2’ – OH
group replaced by -H. If the pentose is deoxyribose
then it will be DNA, if the pentose is ribose, the
nucleic acid is RNA.

Nitrogenous base: linked by hydrogen bond.

– Pyrimidines 1 rings (cytosine, thymine, and uracil)
have a single six-membered ring.
– Purines 2 rings (adenine and guanine) have a six-
membered ring fused to a five-membered ring.

DNA is generally double-stranded dsDNA and RNA is generally single-stranded ssRNA.

Exceptions to this rule may be seen, especially in viruses.
In the DNA double helix, the two backbones run in opposite 5’ → 3’ directions from each other, an
arrangement referred to as antiparallel.

Telomeres act as buffer zone, protect chromosomes from sticking to others.

What happens is that with each time the chromosomes replicate? the telomeres get a little bit shorter
and shorter and shorter, so there's an enzyme known as telomerase and telomerase is able to
lengthen telomeres and bring them back to their original length. because the chromosomes replicated
many, many times, let's just get rid of the telomeres, so the chromosomes will actually not be able to
replicate, and so the cell will not divide again, and it will kind of die.

Single Copy Moderately Repeative Highly Repeative

DNA that's somewhat repetitive is Contains no genes, and because it

Most of the important genes are
found, well at least in mammals and contains no genes, it is not
going to be single copy
in insects, near the centromeres transcribed and not translated, and
highly repetitive DNA has an even
higher rate of mutation than DNA
Transcribed and translated but then that's somewhat repetitive
Transcribed and translated there might also be parts of the
repetitive DNA that don't contain
genes, and those parts are not
transcribed and translated Telomeres are sections of highly
Low mutation rate repetitive DNA, purpose is to
basically act as a buffer zone for the
important part of the chromosome
Mutation rate higher than single copy

DNA replication

Topoisomerases correct “over winding” ahead of replication forks by breaking, swiveling, and
rejoining DNA strands.
Helicases are enzymes that untwist/unwind the double helix at the replication forks. (break down
hydrogen bonds)
Single-strand binding protein binds to and stabilizes single-stranded DNA until it can be used as a
template. (prevent the hydrogen bonds occur again)
Enzymes called DNA polymerases catalyze the elongation of new DNA at a replication fork. (only
synthesize in the 5’ to 3’)
Primase create RNA primase, required to start replication.
DNA ligase join Okazaki fragments.

Leading strand: is copied in a continuous fashion, in the same direction as the advancing replication
fork. This parental strand will be read 3’ to 5’ and its complement will be synthesized in a 5’ to 3’
manners.
Lagging strand: is copied in a direction opposite the direction of the replication fork. On this side of the
replication fork, the parental stand has 5’ to 3’ polarity. DNA polymerase cannot simply read and
synthesize on this strand. How does it solve this problem? Small strands called Okazaki fragments
are produced.

DNA transcription

• Transcription is the first step in gene expression. It involves copying a gene's DNA sequence
to make an RNA molecule.
• Transcription is performed by enzymes called RNA polymerases, which link nucleotides to
form an RNA strand (using a DNA strand as a template).
• Transcription has three stages: initiation, elongation, and termination.
• In eukaryotes, RNA molecules must be processed after transcription: they are spliced and
have a 5' cap and poly-A tail put on their ends.
• Transcription is controlled separately for each gene in your genome.

The main enzyme involved in transcription is RNA polymerase, which uses a single-stranded DNA
template to synthesize a complementary strand of RNA. Specifically, RNA polymerase builds an RNA
strand in the 5' to 3' direction, adding each new nucleotide to the 3' end of the strand.

Stages of transcription
1. Initiation. RNA polymerase
binds to a sequence of DNA
called the promoter, found near
the beginning of a gene. Each
gene (or group of co-transcribed
genes, in bacteria) has its own
promoter. Once bound, RNA
polymerase separates the DNA
strands, providing the single-
stranded template needed for
transcription.
 2. Elongation. One strand of
DNA, the template strand, acts
as a template for RNA
polymerase. As it "reads" this
template one base at a time,
the polymerase builds an RNA
molecule out of
complementary nucleotides,
making a chain that grows
from 5' to 3'. The RNA
transcript carries the same
information as the non-
template (coding) strand of
DNA, but it contains the base
uracil (U) instead of thymine
(T).

3. Termination. Sequences
called terminators signal that
the RNA transcript is
complete. Once they are
transcribed, they cause the
transcript to be released from
the RNA polymerase. An
example of a termination
mechanism involving
formation of a hairpin in the
RNA is shown below.

• In bacteria, RNA transcripts can act as

messenger RNAs (mRNAs) right away. In
eukaryotes, the transcript of a protein-coding
gene is called a pre-mRNA and must go
through extra processing before it can direct
translation.
• Eukaryotic pre-mRNAs must have their ends
modified, by addition of a 5' cap (at the
beginning) and 3' poly-A tail (at the end).
• Many eukaryotic pre-mRNAs undergo splicing.
In this process, parts of the pre-mRNA (called
introns) are chopped out, and the remaining
pieces (called exons) are stuck back together.

These modifications of pre mRNA share several functions:

• They seem to facilitate the export of mRNA.
 • They protect mRNA from hydrolytic enzymes.
• They help ribosomes attach to the 5’ end.

Initiation (start) codon: AUG Termination (stop) codons: UGA, UAA, UAG

DNA translation

Translation is complex process that requires mRNA, tRNA, ribosomes, amino acids, and energy in the
form of GTP.
Translation occurs in the cytoplasm in prokaryotes and eukaryotes. In prokaryotes, the ribosomes
start translating before the mRNA is complete; in eukaryotes, however, transcription and translation
occur at separate times and in separate locations within the cell.

tRNAs, are molecular "bridges" that connect mRNA codons to the amino acids they encode. One end
of each tRNA has a sequence of three nucleotides called an anticodon, which can bind to specific
mRNA codons. The other end of the tRNA carries the amino acid specified by the codons.

Ribosomes are the structures where polypeptides (proteins) are built. They are made up of protein
and RNA (ribosomal RNA, or rRNA). Each ribosome has two subunits, a large one and a small one,
which come together around an mRNA.
Flexible pairing at the third base of a codon is called wobble and allows some tRNAs to bind to more
than one codon.

Steps of translation:
1. In initiation, the ribosome assembles
around the mRNA to be read and the
first tRNA (carrying the amino acid
methionine, which matches the start
codon, AUG).
2. Elongation is the stage where the
amino acid chain gets longer. In
elongation, the mRNA is read one
codon at a time, and the amino acid
matching each codon is added to a
growing protein chain. During
elongation, the ribosome moves in
the 5’ to 3’ direction along mRNA.
3. Termination is the stage in which the
finished polypeptide chain is
released. It begins when a stop
codon (UAG, UAA, or UGA) enters
the ribosome, triggering a series of
events that separate the chain from
its tRNA and allow it to drift out of the ribosome.
Binding sites during elongation
• A site holds the incoming aminoacyl-tRNA complex.
• P site holds the tRNA that carries the growing polypeptide chain, it is also where the first
amino acid binds.
• E site is where the now inactivated (uncharged) tRNA pauses transiently before exiting the
ribosome.

Three types of RNA polymerases

• RNA polymerase I is located in the nucleolus and synthesizes rRNA.
• RNA polymerase II is located in the nucleus and synthesizes hnRNA (pre-processed mRNA)
and some small nuclear RNA (snRNA).
• RNA polymerase III is located in the nucleus and synthesizes tRNA and some rRNA.

Differences in translation between prokaryotes and eukaryotes

Prokaryotic mRNA start with non-coding region and then after we have the Shine-Dalgarno sequence;
is the site that the ribosome’s going to recognize and bind to. And then after the Shine-Dalgarno
sequence, we have another noncoding region. And then we have our start codon, which is typically
AUG, so that tells us to start. And so the ribosome's going to start translating, it's going to read this
entire section, put together the corresponding polypeptide chain, until it hits the stop codon, which
tells it to stop translating. And then we have another noncoding region.
In eukaryotic mRNA, the five prime cap is actually the ribosomal binding site in eukaryotes. So that
means that in eukaryotes, the ribosome's going to recognize this particular part and bind to it. So after
the five prime cap, we have this other noncoding region which the ribosome's not going to translate.
And then the ribosome is going to hit the start codon again. AUG tells it to start, and it's going to start
translating, so it's going to translate this entire section until it hits the stop codon. And then we have
another noncoding region. And then we hit something that looks different than what we've seen in the
prokaryotic mRNA called the poly-A tail. And the poly-A tail is a bunch of nucleotides that are all A's,
or adenines. And the purpose of both the five prime cap, and the poly-A tail is to prevent this mRNA
from being degraded by enzymes. So it acts as kind of a signal that does not allow enzymes to break
it down or degrade it. And so you might be wondering, well, what about prokaryotic mRNA?
How come they don't have anything similar to prevent them from being degraded. And the brief
answer to that question is that in prokaryotic cells, transcription, and translation, both happen in the
same place. So prokaryotic cells don't exactly have a nucleus. They have this cytosol and
transcription and translation are happening in the same place. And not only are they happening in the
same place, but they can actually be happening at the same time. So you can have a piece of mRNA
that's being formed, and while it's being formed, a ribosome will attach to it and being to translate it.
But, in eukaryotic cells, things are a little bit different. So transcription happens in the nucleus, and
translation happens in the cytoplasm where there are ribosomes. And so the mRNA, after it's made,
has to travel, from the nucleus to the cytoplasm to where the ribosomes are. And so because it's
traveling this relatively large distance, it's going to encounter a lot of different things, including
enzymes that might break it down. And so it needs this extra protection to prevent it from being
damaged in any way. In prokaryotic cells, the first amino acid in the chain is always formylmethionine.
DNA repair
The DNA can be damaged in a number of ways such as exposure to chemicals or radiation. Any
defect in the genetic code can cause an increased risk of cancer.
Mutated genes that cause cancer are termed oncogenes which develop from mutation of proto-
oncogenes.
Tumor suppressor genes code for proteins that reduce cell cycling or promote DNA repair; mutations
of tumor suppressor genes can also lead to cancer.
The mutation in the lagging strand is higher than the leading strand.
Replication errors and DNA damage are actually happening in the cells of our bodies all the time. In
most cases, however, they don’t cause cancer, or even mutations. That’s because they are usually
detected and fixed by DNA proofreading and repair mechanisms. Or, if the damage cannot be fixed,
the cell will undergo programmed cell death (apoptosis) to avoid passing on the faulty DNA.
Mutations happen, and get passed on to daughter cells, only when these mechanisms fail. Cancer, in
turn, develops only when multiple mutations in division-related genes accumulate in the same cell.

DNA damage repair

Mismatch repair,
pathways, which
Proofreading, which corrects which fixes mispaired
detect and correct
errors during DNA replication bases right after DNA
damage throughout
replication
the cell cycle

DNA polymerases are the enzymes that build DNA in cells.

During DNA replication (copying), most DNA polymerases can
“check their work” with each base that they add. This process is
called proofreading. If the polymerase detects that a wrong
(incorrectly paired) nucleotide has been added, it will remove
and replace the nucleotide right away, before continuing with
DNA synthesis.

Many errors are corrected by proofreading, but a few slip

through. Mismatch repair happens right after new DNA has been
made, and its job is to remove and replace mis-paired bases
(ones that were not fixed during proofreading).

Repair processes that help fix damaged DNA include:

• Direct reversal: Some DNA-damaging chemical
reactions can be directly "undone" by enzymes in the
cell.
• Excision repair: Damage to one or a few bases of DNA
is often fixed by removal (excision) and replacement of
the damaged region. In base excision repair, just the
damaged base is removed. In nucleotide excision
repair, as in the mismatch repair we saw above, a
patch of nucleotides is removed.
• Double-stranded break repair: Two major pathways,
non-homologous end joining and homologous
recombination, are used to repair double-stranded
breaks in DNA (that is, when an entire chromosome
splits into two pieces).

UV rays cause the formation of pyrimidine dimers.

Mutation at nucleotide level

Point Frameshift
mutation mutation

Silent: no effect on protein synthesis. result from nucleotide addetion or

deletion, and change the reading
frame of subsequent codons.

Nonsence: produce a
premature stop codon.

Missense: produce a codon

that codes for a different
amino acid.

Conservative mutations are where the new

amino acid is of the same type as the
original.

Nonconservative mutation is one with a

new amino acid is of a different type from
the original.

Mistakes during translation and transcription may not have an effect that cause mutation gene.
Mutation occurs usually at the DNA level.
Frameshift mutation has more significant effect on the cell than point mutation.

Chromosomal mutation “large scale mutation”

Deletion mutation
•occur when a large segment of DNA is lost from a
chromosome. Small deletion mutation are considered
frameshift mutation.
Duplication mutation
•occur when a segment of DNA is copied multiple times in the
genome
Inversion mutation
•occur when a segment of DNA is reversed within the
chromosome.
Insertion mutation
•occur when a segment of DNA is moved from one chromosome
to another. Small insertion mutations are considered
frameshift mutations.
Translocation mutation
•occur when a segment of DNA from one chromosome is
swapped with a segment of DNA from another chromosome.
 Mutagen
Endogenous: comes from
inside body.
Reactive oxygen species
Exogenous: comes from
outside body.
Intercalators

Carcinogens
Tobacco
UV radiations

• Sickle cell disease is non-conservative missense mutation, instead of glutamate, it produces

valine.
o Which cannot adequately carry O2.
o Natural resistance to malaria.
• A transition is a point mutation in which a purine is substituted for another purine, or a
pyrimidine is substituted for a pyrimidine.
Genetics
• Genes come in different versions, or alleles, with dominant alleles being expressed over
recessive alleles. Recessive alleles are only expressed when no dominant allele is present.
• In most sexually reproducing organisms, each individual has two alleles for each gene (one
from each parent). This pair of alleles is called a genotype and determines the organism's
appearance, or phenotype. Sex determined by 23rd pair of chromosomes.
• Each human being possesses two copies of each chromosome, called homologues.
• A person will inherit two alleles for all genes (except for male sex chromosomes).
• If only one copy of an allele is needed to express a given phenotype, the allele is said to be
dominant. If two copies are needed, the allele is said to be recessive.
• Homozygous means both alleles are the same for a given gen, if the alleles are different, it
will be heterozygous genotype. Hemizygous genotype describes a situation in which only one
allele is present for a given gene, as in case for parts of the X chromosome in males.

Patterns of dominance
Complete Incomplete
Codominance
dominance dominance
•only one dominant •more than one •hetrozygote
and one recessive dominant allele expresses a
allele exist for a exist for a given phenotype that is
given gene. gene. intermediate
•the presence of one •ex, AB blood type. O between the two
dominant allele will is recessive, both A homozygous
mask the recessive and B dominant. genotype.
allele. •ex, red flowe
crossed with a white
flowe results in pink
flowes.

Darker pigment usually dominance than bright pigment, for example, blue eyes has a recessive allele.

Punnett squares

Homozygous parents Heterozygous parents

Cross between two is known as a dihybrid cross.

• Human phenotypes—and phenotypes of other organisms—also vary because they are

affected by the environment.
• Boveri and Sutton's chromosome theory of inheritance states that genes are found at specific
locations on chromosomes, and that the behavior of chromosomes during meiosis can
explain Mendel’s laws of inheritance.

Sex-linked traits
Traits carried on the X-chromosome are called Sex-linked traits.
Female XX, Male Xy (Hemizygous)

A human male has two sex chromosomes, the X and the Y. Unlike the 44 autosomes (non-sex
chromosomes), the X and Y don’t carry the same genes and aren’t considered homologous.
Y chromosome is much shorter and contains many fewer genes. has just 70 protein-coding genes,
about half of which are active only in the testes (sperm-producing organs).

SRY (gene) is found on the Y chromosome and encodes a protein that turns on other genes required
for male development.
• XX embryos don't have SRY, so they develop as female.
• XY embryos do have SRY, so they develop as male.

X-linked genetic disorders

• Hemophilia
• Color blindness
• Baldness
• Muscular dystrophy

Males are more susceptible to sex-linked conditions than females.

Women who are heterozygous for disease alleles are said to be carriers, and they usually don't
display any symptoms themselves.
where "recombinants" are offspring that do not show the parental phenotype.

Euploid, meaning that it contains chromosomes correctly organized into complete sets (eu- = good).
If a cell is missing one or more chromosomes, it
is said to be aneuploid (an- = not, "not good").
Two common types of aneuploidy have their
own special names:
• Monosomy is when an organism has
only one copy of a chromosome that
should be present in two copies (2n−1)
• Trisomy is when an organism has a
third copy of a chromosome that should
be present in two copies (2n+1)
Organisms with more than two complete sets of
chromosomes are said to be polyploid.
Disorders of chromosome number are caused by
nondisjunction, which occurs when pairs of
homologous chromosomes or sister chromatids fail to
separate during meiosis I or II (or during mitosis).

Mitosis. Nondisjunction can also happen during mitosis.

In humans, chromosome changes due to nondisjunction
during mitosis in body cells will not be passed on to
children (because these cells don't make sperm and
eggs). But mitotic non-disjunction can cause other problems: cancer cells often have abnormal
chromosome numbers.

Genetic disorders caused by aneuploidy

Human embryos that are missing a copy of any
autosome (non-sex chromosome) fail to develop to
birth. In other words, human autosomal monosomies
are always lethal. That's because the embryos have
too low a "dosage" of the proteins and other gene
products that are encoded by genes on the missing
chromosome.
Most autosomal trisomies also prevent an embryo
from developing to birth. However, an extra copy of
some of the smaller chromosomes (13, 15, 18, 21, or
22) can allow the affected individual to survive for a
short period past birth, or, in some cases, for many
years. When an extra chromosome is present, it can
cause problems in development due to an imbalance
between the gene products from the duplicated chromosome and those from other chromosomes.
The most common trisomy among embryos that survive to birth is Down syndrome, or trisomy 21.

DNA is also found in the mitochondria present in most plant and animals cells, as well as in
the chloroplasts of plant cells.
Non-nuclear DNA is often inherited uniparentally, meaning that offspring get DNA only from the male
or the female parent, not both. In humans, for example, children get mitochondrial DNA from their
mother (but not their father).
Control of gene expression on prokaryotes
the Lac Operon. An operon is a unit of genomic
DNA containing a cluster of genes that are under
control of a single regulatory signal, otherwise
known as a promoter. And these genes are co-
transcribed into a single mRNA strand and either
translated together or undergo trans-splicing to
create single mRNA's that are translated
separately. So, basically, genes in an operon are
expressed either altogether or not at all. Now,
the operon that I've drawn here happens to
represent the lac operon, and the lac operon is
an example of an inducible set of genes which
are responsible for importing and breaking down
the sugar molecule lactose to use as a source of
energy.
Operons include both inducible and repressible systems, and offer a simple on-off switch for gene
control in prokaryotes, particularly E. coli.
• Structural gene: codes for the protein of interest.
• Operator site: a nontranscribable region of DNA that is capable of binding a repressor protein.
• Promoter site: similar in function to promoters in eukaryotes; it provides a place for RNA
polymerase to bind.
• Regulator gene: codes for a protein known as the repressor.

Control of gene expression on eukaryotes

DNA is packed into chromosomes in the form of chromatin, also known as supercoiled DNA. And so,
chromatin is made up of DNA, histone proteins, and non-histone proteins. And there are repeating
units in chromatin, called nucleosomes, which are made up of 146 base pairs of double helical DNA
that is wrapped around a core of eight histones. And there are four different types of histones within
this structure of eight that named H2A, H2B, H3, and H4.
• Heterochromatin is tightly coiled DNA which make it inaccessible to the transcription
machinery, so these genes are inactive.
• Euchromatin is looser, the transcription machinery can access the genes of interest, so these
genes are active.
Acetylation occurs at the amino terminal tails of these histone proteins by an enzyme called histone
acetyltransferase. And this is a reversible modification, so the acetylation of histones is sort of kept in
balance by another enzyme that removes these acetyl groups, which is called histone deacetylase.
The acetylation of histones leads to uncoiling of this chromatin structure, and this allows it be
accessed by transcriptional machinery for the expression of genes. On the flip side of this, histone
deacetylation leads to a condensed, or closed structure of the chromatin, and less transcription of
those genes. When these modifications that regulate gene expression are inheritable, they are
referred to as epigenetic regulation.
Cell
Cell membrane exhibits selective permeability, allowing some substances to cross it more easily than
others (semi-permeable).
It made up by phospholipids bilayer which have three major
components. The first is a phosphate head group. The second is
a glycerol backbone, and the third are two fatty acid tails.
Phospholipids are amphipathic molecules, containing
hydrophobic and hydrophilic regions.

The Permeability of the Lipid Bilayer

• Small, nonpolar molecules (ex: oxygen and carbon
dioxide) can pass through the lipid bilayer and do so by
squeezing through the phospholipid bilayers. They don't
need proteins for transport and can diffuse across
quickly.
• Small, polar molecules (ex: water): This is a little more
difficult than the molecule type above. Recall that the
interior of the phospholipid bilayer is made up of the
hydrophobic tails. It won’t be easy for the water
molecules to cross, but they can cross without the help of
proteins. This is a somewhat slower process.
• Large, nonpolar molecules (ex: carbon rings): These
rings can pass through but it is also slow process.
• Large, polar molecules (ex: simple sugar - glucose) and
ions: The charge of an ion, and the size and charge of large polar molecules, makes it too
difficult to pass through the nonpolar region of the phospholipid membrane without help.

The main three things that make up the cell membrane:

1. Phospholipid
2. Cholesterol inserts itself between phospholipids. It maintains the fluidity of our cell
membranes. So as temperatures become lower, cholesterol will help increase the fluidity. And
as temperatures become higher, cholesterol will help reduce the fluidity of the cell membrane.
3. Protein
• Peripheral proteins are bound to
the surface of the membrane
(usually attached to integral
proteins) for example, a
hormone might be a peripheral
protein, and it might attach to the
cell, make the cell do something,
and then leave. “easy to remove”
• Integral proteins penetrate the
hydrophobic core of the lipid
bilayer

Cells recognize each other by binding to surface molecules, often carbohydrates, on the plasma
membrane. Membrane carbohydrates may be covalently bonded to lipids (forming glycolipids) or
more commonly to proteins (forming glycoproteins) for signaling. Gluco = sugar.

Integral protein
• Channel protein, and like the name kind of implies, there's a channel, or hole, inside the
protein that lets things pass through. So for example, if there is some sort of ion-- let's say this
is an Na+ ion, a sodium ion, this is outside the cell. Channel proteins generally don't require
energy, so there's no energy needed. Sometimes we call energy ATP. And another thing
that's special about channel proteins is you'll notice that it will go with the concentration
gradient. So out here, there's a lot, and inside, there's very little. So it'll pump from where
there's a lot of sodium into where there's very little.
 • Carrier protein. And like the name implies, it carries substances into the cell. I kind of picture it
like a baseball glove. So if there's a molecule that's outside the cell and the cell actually
needs this molecule-- so what the carrier protein will do is it'll actually protect this substance
so that it can enter the cell safely. It can also do this in reverse. It can take something inside
the cell and pump it outside the cell. And this type of protein is really important, because
unlike channel proteins, carrier proteins can go against the concentration gradient because
say your cell has a lot of chloride ions, and your body needs more to perform a certain
process. So what your body can do is it can bring more chloride ions into your cell, even
though your cell already has a lot of chloride ions. So carrier proteins can sometimes use
energy or ATP.

Cell membrane fluidity

Factors affects the fluidity:
1. Temperature. Low temp: will decrease the fluidity, phospholipids are actually going to start
clustering together really closely. High temp: phospholipids have a little more energy. So
they're going to move around a little bit more and cause themselves to have more of a
distance between each other. So you'll notice that the distance between phospholipids is now
much greater than what it was over here, at low temperatures, which is very, very small. So
this increased distance allows our fluidity to increase, because there's much more room for
the cell membrane to move around.

2. Cholesterol. The presence of cholesterol increases the distance between some of the
phospholipids. At high temperatures, as the distance between
the phospholipids increases, the fluidity can also increase and
our phospholipids are already pretty far apart but just like
before, the cholesterol will insert itself into the membrane at
random places. And what this will actually do is it will cause the
phospholipids to pull themselves closer together, because they
kind of want to attach to that cholesterol. So the fluidity actually decreases at high temp. with
cholesterol. When the temperature gets too low, the fluidity will increase a little with presence
of cholesterol.
3. Saturated and unsaturated fatty acids. Fatty acids are what make up the phospholipid tails.
Saturated fatty acids are chains of carbon atoms that have single bonds between them. This
makes them straight and easy to pack tightly. Unsaturated fats are chains of carbon atoms
that have some double bonds between them. Double bonds create kinks in the chain, making
them not as easy to pack tightly.

Membrane dynamic
1. Rotational: phospholipid rotates on its axis to interact with its immediate neighbors.
2. Lateral: phospholipid moves around in one leaflet. Since we're not actually switching between
leaflets in this type of movement, this is actually pretty fast. “need ATP”
3. flip-flop: phospholipids moves between both leaflets of the bilayer in transverse movement.
“no catalyst so it is slowly”
Catalyzed transbilyer movement.
This catalyst that we use in lateral or this protein, is actually called flippase, move phospholipids from
the outer leaflet to the inner leaflet and it is pretty fast. Floppase uses ATP, what floppase does is it
actually brings a phospholipid on the inner leaflet to the outer leaflet. So it does the opposite of what
flippase does, this is also pretty fast, because it uses a catalyst. The last one that is catalyzed does
something really interesting. It actually brings a phospholipid from the inner leaflet to the outer leaflet
and one from the outer leaflet to the inner leaflet. And this is what we call scramblase. And this
actually does not need ATP. It doesn't require that extra input of energy. And again, because it is
catalyzed, it is pretty fast.

Cell communication
There are a few different types of cell-cell interactions. Some of these interactions are meant for big
molecules that enter and exit the cell called, endocytosis (entering the cell) and exocytosis (exiting
the cell). For smaller particles like amino acids, water, ions and other solutes there are different types
of direct contact between the cells called gap junctions.

Exocytosis is a process used by the cell to take out its trash and to incorporate
proteins into the cell membrane. During exocytosis, the phospholipid bilayer of the
cell membrane surrounds the waste proteins, creating a bubble-like structure called
a vesicle. Vesicles are frequently used in the cell for transportation of molecules
across the cell membrane. Exocytosis is also used to integrate new proteins into the
cell membrane. In this process, the new protein is formed inside the cell, and
migrates to phospholipid bilayer of the vesicle. The vesicle, containing the new
protein as a part of the phospholipid bilayer, fuses with the cell membrane. This allows the protein to
be directly integrated into the cell membrane when the vesicle, in the same way as with waste
proteins, fuses and opens with the cell membrane.

Endocytosis is the opposite process of exocytosis. Endocytosis brings molecules into the cell. These
molecules are important for the survival of the cell, such as glucose.
There are three different styles of endocytosis: 1) phagocytosis,
2) pinocytosis, and 3) receptor-mediated endocytosis.

Phagocytosis is the process similar to eating, where the cell

engulfs a molecule in order to move it to the interior of the cell.
For example, white blood cells recognize pathogens, such as
viruses or bacterial cells, outside of the cell and will use
phagocytosis to bring it in to destroy it!

If phagocytosis is how the cell eats, then pinocytosis is how the

cell drinks. Pinocytosis engulfs dissolved ions and other solutes
in the liquid medium surrounding the cell. pinocytosis is not specific
to what is carried into the cell, whereas phagocytosis can be highly
specific.
Receptor-mediated endocytosis is very specific with respect to what
is imported into the cell. It’s actually a bit like a lock-and-key system.

Cell junction “often occur in epithelial tissue”

There are many different ways that cells can connect to each other.
The three main ways for cells to connect with each other are: gap
junctions, tight junctions, and desmosomes.

• Gap junctions are essentially tubes that join two cells together. These
tubes create a connection that allows for the transport of water and ions to
and from the connecting cells. The tubes also help to spread
electrochemical signals that are produced by action potentials that occur
in the nervous system (neurons) and in cardiac cells that make your heart
beat.

• Tight junctions are different from gap junctions because they are the
connections that form when cells are squished up against one another. In this
case, the cell membranes are connected, but the contents of each cell are not
connected in any way. There are no tubes here, but there is an impermeable
layer in between the cells. These types of cell connections are useful in places
that need to contain certain fluids, like in the bladder, the intestines or the
kidneys.

• Desmosomes cell membranes are connected by thread like substances that

connect the cells across the space in between cells, physically hold the cells
together, but do not allow fluids or materials to pass from the inside of one
cell to the next. These connections are also attached to the scaffolding of the
cell, called the cytoskeleton, to help with structural support. The space in
between the cells allows for water and solutes to flow freely between each cell without
compromising the connection. This is convenient for areas of our body that experience high
stress like in our skin or our intestines because the space in between the cells offer flexibility
that the other junctions can’t.

A signal transduction pathway is a series of steps by which a signal on a cell’s surface is converted
into a specific cellular response.
Ligand can be again a hormone, a neurotransmitter, it'll bind to a protein and that protein will tell other
proteins inside the cell about what's going on. And this signal is propagated throughout the cell
causing the cell to perform a specific function.
There are three main types of membrane receptors:
1. G protein-coupled receptors
2. Receptor tyrosine kinases (RTK)
3. Ion channel receptors

G-protein coupled receptors are only found in eukaryotes and they comprise of the largest known
class of membrane receptors. In fact humans have more than 1,000 known different types of GPCRs,
and each one is specific to a particular function. They are a very unique membrane receptor and they
are the target of around 30 to 50% of all modern medicinal drugs. In fact, the ligands that bind range
from things like light sensitive compounds to odors, pheromones, hormones and even
neurotransmitters. GPCRs can regulate the immune system, growth, our sense of smell, of taste,
visual, behavioral and our mood. Including things like serotonin and dopamine.
The most important characteristic of GPCRs is that they have seven transmembrane alpha helices.
G-proteins in general are specialized proteins which have the ability to bind GTP and GDP. In other
words they are able to bind guanosine triphosphate and
guanosine diphosphate. Alpha, beta and gamma subunits
together is making our G-protein. GDP binds to the alpha
subunit in inactive situation and bind GTP instead when
becomes active.
Ligand binds to GPCR > CPCR undergoes
conformational change > alpha subunit exchanges GDP
to GTP > target protein relay signal via 2nd messenger >
GTP hydrolyzed to GDP to back normal.
A very common example of GPCR function in our cell
actually involves epinephrine or adrenaline.

Enzyme linked receptors: most common receptor

tyrosine kinases which are membrane receptors that
attach phosphates to tyrosines and regulate cell growth,
differentiation and survival. They can bind and respond
to ligands such as growth factors.
When this signaling molecule binds to an RTK they
cause neighboring RTKs to associate with each other
forming what we call a cross-linked dimer.
Ex, regulating surface proteins called ephrin. Another
thing that RTKs are famous for is they can also bind hormones most
famously insulin.

Ion channel receptors

A ligand-gated ion channel receptor acts as a gate when the receptor
changes shape.
• When a signal molecule binds (ligand) to the receptor, the gate
allows specific ions, such as Na+ or Ca2+.

Points
• Some receptors are intracellular, found in the cytosol or nucleus
of target cells.
• Small or hydrophobic chemical messengers such as steroid
and thyroid hormones can readily cross the membrane and
activate their receptors.
• Protein kinases transfer phosphates from ATP to protein, a
process called phosphorylation.
• Protein phosphatases remove the phosphates from proteins,
a process called dephosphorylation.
• Second messengers are small, nonprotein, water-soluble
molecules or ions that diffuse in the cell.
• Cyclic AMP and calcium ions are common second messengers
• Cyclic AMP (cAMP) is one of the most widely used second
messengers.
• Adenylyl cyclase, an enzyme in the plasma membrane, converts ATP to cAMP in response
to an extracellular signal.
• Calcium ions (Ca 2+) act as a second messenger in many pathways.
• Calcium is an important second messenger because cells can regulate its concentration.
Membrane transportation

Transportation

Passive Active
"not using energy" "using energy"

2o using indirectly energy

Facilitated 1o using directly energy
Simple diffusion Osomosis Filteration Endocytosis and
diffusion Na/K pump
Exocytosis

Facilitated diffusion is simple diffusion for large, polar or charged molecules. It requires integral
membrane proteins to serve as channels for these substrates.
Carriers or channels proteins. Carriers, the chloride for
example binds with carriers protein, then it will undergoes
conformational change, finally will release this chloride inside
the cell and the carrier protein will restore its shape to bind
another molecule.

Osmosis is a specific kind of simple diffusion that concerns

water; water will move from a region of lower solute
concentration to one of higher solute concentration. That is, it
will move from a region of higher water concentration down its
gradient to a region of lower water concentration.
“Solute mean the dissolved particles which is the less inside
the cell”
• Tonicity is the ability of a solution to cause a cell to
gain or lose water.
• Isotonic solution: Solute concentration is the same as
that inside the cell; no net water movement across the
plasma membrane.
• Hypertonic solution: Solute concentration is greater
than that inside the cell; cell loses water.
• Hypotonic solution: Solute concentration is less than that inside the cell; cell gains water.

Active transport results in the net movement of a solute against its concentration gradient “the down
its concentration means move from high solute concentration to low” and it requires energy but the
source of energy can vary.
1. Primary active transport uses ATP or another energy molecule to directly transport molecules
across a membrane. “Ex, maintains the membrane potential of neurons in the nervous
system = Na/K pump”
2. Secondary active transport “coupled transport” is not
direct coupling to ATP hydrolysis. “Ex, the kidney”
When both particles flow the same direction across the
membrane, it is termed symport. When the particles flow in
opposite directions, it is called antiport.
Na/K pump: the Na+ high concentration outside the cell, and
K+ high concentration inside the cell. And less positive inside
the cell, more positive outside the cell and this based on the
ratio, every time the ATP hydrolysis, three sodium pomp out
and two potassium pomp in. But sometime ions can continue
to "leak" in, in order to maintain the -70 millivolt potential
difference between the cytoplasm and the extracellular fluid.
Exocytosis: occurs when secretory vesicles
fuse with the membrane, releasing material
from inside the cell to the extracellular
environment. “important for nervous system
and intercellular signaling”

Endocytosis: occurs when the cell

membrane invaginates and engulfs material
to bring it into the cell. The material
encased in a vesicle.
• Pinocytosis is the endocytosis of
fluids and dissolved particles.
• Phagocytosis is the ingestion of large solids such as bacteria. Phagocytosis is a critical part of
the immune system. Several types of cells of the immune system perform phagocytosis, such
as neutrophils, macrophages, dendritic cells, and B lymphocytes.
Uses
Transport Molecules moved energy? Example transporter/disease
Simple
diffusion Small, nonpolar No Pulmonary edema
Facilitated
diffusion Polar molecules, larger ions No GLUT4 / Diabetes Mellitus Type II
Molecules moving against Sodium-potassium pump, proton
Primary active their gradient coupled to the pump / atrial fibrillation, acid
transport hydrolysis of ATP Yes reflux
Secondary Molecule going with +
active molecule going against Sodium-calcium exchanger,
transport gradient Yes SGLT2

Cell
The cell is the basic unit of structure / function: simplest collection of matter
that can live.
1. Eukaryotic cell: Protists, fungi, animals, and plants.
2. Prokaryotic cell: Bacteria and Archaea.

Eukaryotic cells are characterized by having:

• DNA in a nucleus that is bound by a
• membranous nuclear envelope.
• Membrane-bound organelles.
• Cytoplasm in the region between the plasma
membrane and nucleus.
• Divide by mitosis.

Prokaryotic cells are characterized by having:

• No nucleus.
• DNA in an unbound region called the nucleoid.
• No membrane-bound organelles.
• Cytoplasm bound by the plasma membrane.
• Divide by binary fission.
Eukaryotic Cell
Organelle Function
Nucleus DNA Storage
Mitochondrion Energy production
Smooth Endoplasmic
Reticulum (SER) Lipid production; Detoxification
Rough Endoplasmic Protein production; in particular for
Reticulum (RER) export out of the cell
Golgi apparatus Protein modification and export
Lipid Destruction; contains oxidative
Peroxisome enzymes
Lysosome Protein destruction

Nucleus holds our DNA. A membrane called the nuclear envelope surrounds the nucleus, and its job
is to create a room within the cell to both protect the genetic information and to house all the
molecules that are involved in processing and protecting that info. This membrane is actually a set of
two lipid bilayers. Proteins channels known as nuclear pores form holes in the nuclear envelope. The
nucleus itself is filled with liquid (called nucleoplasm) and is similar in structure and function to
cytoplasm. It is here within the nucleoplasm where chromosomes (tightly packed strands of DNA
containing all our blueprints) are found.
Within the nucleus is a small subspace known as the nucleolus. It is not bound by a membrane, so it
is not an organelle. This space forms near the part of DNA with instructions for making ribosomes, the
molecules responsible for making proteins. Ribosomes are assembled in the nucleolus, and exit the
nucleus with nuclear pores.

Mitochondria: ATP (adenosine triphosphate) is the energy currency of the cell, and is produced in a
process known as cellular respiration. two lipid bilayers that separate the mitochondrial contents from
the cytoplasm. We refer to them as the inner “not permeable for small molecules” and outer
mitochondrial membranes “permeable for small molecules”. If we cross both membranes we end up in
the matrix, where pyruvate is sent after it is created from the breakdown of glucose (this is step 1 of
cellular respiration, known as glycolysis).The space between the two membranes is called the
intermembrane space, and it has a low pH (is acidic) because the electron transport chain embedded
in the inner membrane pumps protons (H+) into it. Energy to make ATP comes from protons moving
back into the matrix down their gradient from the intermembrane space.
It contains their own DNA.

Endoplasmic reticulum is a plasma membrane found inside the cell

that folds in on itself to create an internal space known as the Smooth Rough
lumen. This lumen is actually continuous with the perinuclear
space, so we know the endoplasmic reticulum is attached to the It doesn't has
It has ribosomes
nuclear envelope. ribosomes

Protein synthesis in cytoplasm might end up in:

• Nucleus. Lipids synthesis
• As in cell Protein synthesis
• Mitochondria. membrane and
steroids
• Peroxisomes.
• Stay in the cytoplasm. Metabolizes
carbs
Protein synthesis in ER:
• Secreted into the extracellular environment.
• Become integral protein. Aid in detox of
drugs
• Might remain in the endoplasmic reticulum, Golgi
apparatus, or lysosomes.
Stores calcium
The protein created from RNA segment will find itself inside the lumen of the rough endoplasmic
reticulum, where it folds and is tagged with a (usually carbohydrate) molecule in a process known as
glycosylation that marks the protein for transport to the Golgi apparatus.

The Golgi apparatus consists of flattened membranous sacs called cisternae.

Functions of the Golgi apparatus:
• Modifies products of the ER.
• Manufactures certain macromolecules (some polysaccharides).
• Sorts and packages materials into transport vesicles.

Different molecules actually have different fates upon entering the Golgi:
• Cytosol: the proteins that enter the Golgi by mistake are sent back into the cytosol.
• Cell membrane: proteins destined for the cell membrane are processed continuously. Once
the vesicle is made, it moves to the cell membrane and fuses with it. Molecules in this
pathway are often protein channels which allow molecules into or out of the cell, or cell
identifiers which project into the extracellular space and act like a name tag for the cell.
• Secretion: some proteins are meant to be secreted from the cell to act on other parts of the
body. Before these vesicles can fuse with the cell membrane, they must accumulate in
number, and require a special chemical signal to be released.
• Lysosome: The final destination for proteins coming through the Golgi is the lysosome.
Vesicles sent to this acidic organelle contain enzymes that will hydrolyze the lysosome’s
content.

The lysosome is the cell’s recycling center. These organelles are spheres full of enzymes ready to
hydrolyze. These disposal enzymes only function properly in environments with a pH of 5.

Autophagy Crinophagy

"Self-eating"
Digest molecules Digest excess
that are part of the secretory products.
cell or other cells.

For example, excess

Macrophages of the hromons will be
immune system. broken down by the
lysosomes.

Peroxisomes are oxidative organelles. Peroxisomes are specialized metabolic, compartments

bounded by a single membrane. Peroxisomes produce hydrogen peroxide and convert it to water.
Unlike the lysosome, which mostly degrades proteins, the peroxisome is the site of fatty acid
breakdown.
Tissue formation in Eukaryotic cells
Epithelial Connective Musscle Nervous
tissue tissue tissue tissue
Support the body and provides
Cover the body and line its cavities,
a framework for the epithelial
providing protection, involved in
cells to carry out their
absorpation, seceretion and sensation.
functions.

Stroma: Bone, catilage,

tendons, ligaments, adipose
1. Simple: have one layer of cells, ex, tissue "no fibers", and blood
Alevoli in lung. "no fibers". Areolar.
2. Stratified: have multiple layers, ex,
Esophagus for protection.
3. Pseudostratified: Appear to have
multiple layers but in reality, only
one layer.

Avascular: they get nutrients from the

underlying tissue

Cytoskeleton provides structure to the cell and helps it to maintain its shape, also a conduit for the
transport of materials around the cell.
• Microfilaments are the thinnest part of the cytoskeleton, and are made of actin [a highly-
conserved protein that is actually the most abundant protein in most eukaryotic cells].
Actin is both flexible and strong, making it a useful protein in cell movement. In the heart,
contraction is mediated through an actin-myosin system.
• Microtubules are small tubes made from the protein tubulin. These tubules are found in
cilia and flagella, structures involved in cell movement. They also help provide pathways
for secretory vesicles to move through the cell, and are even involved in cell division as
they are a part of the mitotic spindle, which pulls homologous chromosomes apart.
• intermediate filaments smaller than the microtubules, but larger than the microfilaments,
the intermediate filaments are made of a variety of proteins such as keratin and/or
neurofilament. They are very stable, and help provide structure to the nuclear envelope
and anchor organelles.
All these are made up of protein.

Prokaryotic cells/ Bacteria

1. Bacteria “modern”
2. Archaea “primitive”

Shapes of bacteria:
1. Spherical “Cocci”
2. Rod-shaped “Bacilli”
3. Spiral

• An important feature of nearly all prokaryotic cells is their cell wall, which maintains cell
shape, provides physical protection, and prevents the cell from bursting in a hypotonic
environment (i.e. water)
• Eukaryote cell walls are made of cellulose (plants) or chitin (fungus) (Chitin: polymer of
glucosamine) Bacterial cell walls are made of peptidoglycan, a network of sugar polymers
cross-linked by polypeptides.
• Archaea contain polysaccharides and proteins but lack peptidoglycans.
 • Using the Gram stain, scientists classify many bacterial
species into Gram-positive and Gram-negative groups
based on cell wall composition.
• Gram-negative bacteria have less peptidoglycan and an
outer membrane that can be toxic, and they are more likely
to be antibiotic resistant.
• Prokaryotes reproduce quickly by binary fission.

Binary fission, or prokaryotic fission, is the form of asexual

reproduction and cell division used by all prokaryotes. It requires
fewer events than mitosis, so it can proceed more rapidly. E.coli can
replicate every 20 mins under ideal growth conditions. No mitotic
spindle forms in bacteria. Perhaps more importantly, DNA replication
actually happens at the same time as DNA separation during binary
fission (unlike in mitosis, where DNA is copied during S phase, long
before its separation in M phase).

Archaea
Some archaea live in extreme environments and are called extremophiles.
Extreme halophiles live in highly saline environments. Extreme
thermophiles thrive in very hot environments.
Methanogens live in swamps and marshes and produce methane
as a waste product. Obligate

Bacteria
• Cell membrane, cytoplasm, and some have flagella or
fimbriae.
• Production of vitamin K in the intestine by bacteria which
important for production of plasma proteins necessary for
blood clotting. This example of symbiotes “both humans Anaerobic
and bacteria benefit from the relationship”.
• Chlamydia trachomatis, a common sexually transmitted
infection, lives inside cells of the reproductive tract. This
example of pathogens. Aerotolerant Facultative
• Bacteria that require oxygen for metabolism are termed
obligate aerobes, does not require oxygen, are called
anaerobes.

Anaerobic
1. Obligate: need an oxygen-free environment to live, they cannot grow in places with
oxygen.
2. Aerotolerant: do not use oxygen to live, but can exist in its presence for a period of time.
3. Facultative: use fermentation to grow in places without oxygen, but use aerobic
respiration in places with oxygen.
Types of cell wall are determined by the Gram
staining process with a crystal violet stain.
1. Gram positive: absorb the crystal, it will
appear deep purple.
2. Gram negative: does not absorb the
crystal, it will appear pink-red. “very
thin”.

Bacterial growth follows a predictable pattern:

Lag phase
•The bacteria adapt to new local conditions.

Exponetial •Growth then increases exponentially.

(log) phase

Stationary •As resources are reduced, growth levels off.

phase

Death •As resources become insufficient, bacteria undergo a death phase.

phase

Viruses do not fit the definition of living things because they are acellular. They are composed of
genetic material, a protein coat, and sometimes an
envelope containing lipids.
“Considered obligate intracellular parasites”
• The genetic information may be circular or
linear, single or double stranded and composed
of either DNA or RNA.
• Capsid made of smaller subunits called
capsomeres.
Bacteriophages are viruses target bacteria, they do
not actually enter bacteria; rather, they simply inject
their genetic material.

How the viruses infect a specific set of cells: Structure of

1. Binding to specific receptors on the host cell. bacteriophage
2. Enveloped viruses fuse with the plasma
membrane of a cell. “HIV”
3. Bacteriophage use tail fibers to anchor themselves to the cell membrane.
Lytic and Lysogenic cycles of bacteriophage
• Lytic: replication very fast, kill the host
cell. It produces new phages called
virulent phages.
• Lysogenic: takes longer, replicates
without destroying the host.

Retroviruses “HIV”: enveloped, single-stranded

RNA “fusion with plasma membrane”
• Retroviruses use reverse
transcriptase to copy their RNA
genome into DNA.
• HIV (human immunodeficiency virus) is
the retrovirus that causes AIDS
(acquired immunodeficiency
syndrome).

Subviral particles “smaller than viruses”

• Viroids: circular RNA molecules that infect plants and disrupt their growth. “Human = Hepatitis
D”
• Prions: made up only by proteins, no genetic material. It causes brain diseases in mammals,
propagate by converting normal proteins “alpha helical structure” into mutated proteins “beta
pleated sheet”.

Vaccines are harmless derivatives of pathogenic microbes that stimulate the immune system to
mount defenses against the actual pathogen. Viral infections cannot be treated by antibiotics.

Cellular division
Autosomal cells are diploid (2n), which means that they contain two copies of each chromosome.
Germ cells are haploid (n), containing only one copy of each chromosome. In human, these numbers
are 46 and 23, respectively.

The cell cycle consists of four stages: G1, S, G2, M. The first three stages are known as interphase
“the longest part of cell cycle” 90% of their time in interphase. Cell that not divide spend all of their
time in an offshoot of G1 called G0. G0 stage, the cell is simply living and serving its function, without
any preparation for division, ex, neurons in brain.

• G1 Cell create organelles for energy and protein production

“mitochondria, ribosomes, and endoplasmic reticulum” while also
increasing their size.
• S “Synthesis of DNA” The cell replicates its genetic material so that
each daughter cell will have identical copies. After replication, each
chromosome consists of two identical chromatids that are bound
together at a specialized region known as the centromere.
• G2 The cell checks to ensure that there are enough organelles and
cytoplasm to divide between two daughter cells. Make sure that DNA
replication proceeded correctly to avoid passing on an error to
daughter cells.
• M consists of mitosis itself along with cytokinesis. Mitosis is divided
into four phase: prophase, metaphase, anaphase, and telophase.
Cytokinesis is the splitting of the cytoplasm and organelles into two
daughter cells.

In autosomal cells, division results in two genetically identical daughter cells. In germ cells,
the daughter cells are not equivalent.
Cell cycle control: there are two check points, the first, between G1 and S, the second, between G2
and M. The molecules responsible for the cell cycle are known as cyclins and cyclin-dependent
kinases, or CDKs. All the different types are always present in a cell, but their default form, or their
default function, is for them to be inactive. In order to be activated, CDKs require the presence of the
right cyclins. The main protein in control of cycle is known as p53.

Loss of cell cycle control: one of the most common mutations found in cancer is mutation of the
gene that produces P53 which will bind DNA directly to produce proteins that block the progression of
the cell cycle. One of those proteins include p21. P21 will function to inhibit CDK. So the CDK will not
be able to activate DNA replication or activate mitosis. RB is another protein that is associated with
the function of P53, and these proteins are considered tumor suppressor genes.

Haploid gametes (sperm and egg cells) combine to form a diploid zygote “46 chromosomes or you
could say it has 23 pairs of homologous chromosomes.”

Mitosis
Meiosis I
meiosis in humans is a division process that
takes us from a diploid cell—one with two sets of
chromosomes—to haploid cells—ones with a
single set of chromosomes. In humans, the
haploid cells made in meiosis are sperm and
eggs. When a sperm and an egg join in
fertilization, the two haploid sets of chromosomes
form a complete diploid set: a new genome. Using
a two-step division process. Homologue pairs
separate during a first round of cell division, called
meiosis I. Sister chromatids separate during a
second round, called meiosis II.
In anaphase I, the homologues are pulled apart
and move apart to opposite ends of the cell. The sister chromatids of each chromosome, however,
remain attached to one another and don't come apart.
Finally, in telophase I, the chromosomes arrive at opposite poles of the cell. In some organisms, the
nuclear membrane re-forms and the chromosomes decondense, although in others, this step is
skipped—since cells will soon go through another round of division, meiosis II. Cytokinesis usually
occurs at the same time as telophase I, forming two haploid daughter cells.

Meiosis II

During prophase II, chromosomes condense and

the nuclear envelope breaks down, if needed. The
centrosomes move apart, the spindle forms
between them, and the spindle microtubules
begin to capture chromosomes.
The two sister chromatids of each chromosome
are captured by microtubules from opposite
spindle poles. In metaphase II, the chromosomes
line up individually along the metaphase plate. In
anaphase II, the sister chromatids separate and
are pulled towards opposite poles of the cell.
In telophase II, nuclear membranes form around
each set of chromosomes, and the chromosomes
decondense. Cytokinesis splits the chromosome
sets into new cells, forming the final products of
meiosis: four haploid cells in which each
chromosome has just one chromatid. In humans,
the products of meiosis are sperm or egg cells.

• Apoptosis is programmed or controlled

cell suicide.
• Apoptosis prevents enzymes from leaking
out of a dying cell and damaging neighboring cells.

Apoptosis can be triggered by:

• An extracellular death-signaling ligand.
• DNA damage in the nucleus.
• Protein misfolding in the endoplasmic reticulum.
Plant vs Animal cells
Both plant and animal cells are eukaryotic, so they contain membrane-bound organelles like the
nucleus and mitochondria.
However, plant cells and animal cells do not look exactly the same or have all of the same organelles,
since they each have different needs. For example, plant cells contain chloroplasts since they need to
perform photosynthesis, but animal cells do not.

• Both animal and plant cells have

mitochondria, but only plant cells have
chloroplasts. Plants don’t get their sugar
from eating food, so they need to make
sugar from sunlight. This process
(photosynthesis) takes place in the
chloroplast. Once the sugar is made, it is
then broken down by the mitochondria to
make energy for the cell. Because animals
get sugar from the food they eat, they do not
need chloroplasts: just mitochondria.
• Both plant and animal cells have vacuoles. A
plant cell contains a large, singular vacuole
that is used for storage and maintaining the
shape of the cell. In contrast, animal cells
have many, smaller vacuoles.
• Plant cells have a cell wall, as well as a cell
membrane. In plants, the cell wall surrounds
the cell membrane. This gives the plant cell
its unique rectangular shape. Animal cells
simply have a cell membrane, but no cell
wall.
• In plant cell there is tunnels called plasmodesmata to
communicate with neighboring cells, in animal cell
called gap junction.

Cellular respiration

Adenosine triphosphate, or ATP, is a small, relatively simple molecule. It can be thought of as the
main energy currency of cells. The energy released by hydrolysis (breakdown) of ATP is used to
power many energy-requiring cellular reactions.
ATP is hydrolyzed to ADP in the following reaction:
ATP + H2O ⇋ ADP + Pi + energy
Like most chemical reactions, the hydrolysis of ATP to ADP is
reversible. The reverse reaction, which regenerates ATP from ADP
and Pi.

The energy is used by glucose to produce 38 ATP with heat as a

byproduct to warm up the cell.

1. Glycolysis – anaerobic – produces 2 ATPs net and 2 NADH.

“occurs in cytosol”
2. Krebs cycle – aerobic – produces 2 ATPs and 6 NADH.
3. Electron transport chain – aerobic – produces 34 ATPs.
Fermentation: An anaerobic pathway for breaking down glucose
Some organisms are able to continually convert energy without the presence of oxygen. They
undergo glycolysis, followed by the anaerobic process of fermentation to make ATP.
• Muscle cells can continue to produce ATP when oxygen runs low using lactic acid
fermentation. However, this often results in muscle fatigue and pain.

Aerobic Anaerobic
Reactants Glucose and oxygen Glucose
ATP and lactic acid (animals); or
Products ATP, water, CO2 ATP, ethanol, and CO2 (yeast)
Cytoplasm (glycolysis) and
Location mitochondria Cytoplasm
Glycolysis (anaerobic), Krebs
Stages cycle, oxidative phosphorylation Glycolysis, fermentation
ATP
produced Large amount (36 ATP) Small amount (2 ATP)

Oxidation is losing electron, reduction is gaining electron.

O is more electronegativity than H so it will hogging the electrons from H that will make O in reduction
state and H will be oxidized.
Glycolysis

We use 2 ATPs to
produce net 2 ATPs

Glucose gets
rearranged, and two
phosphate groups are
attached to it. The
phosphate groups
make the modified The glucose splits
sugar—now called into two 3 carbons
fructose. molecules called
pyruvates

Two ATP molecules and

one NADH are made.
Because this phase
takes place twice, once
for each of the two
three-carbon sugars, it
makes four ATP “net 2
ATP uses up” and two
NADH overall.

At the end of glycolysis, we’re left with two ATP, two NADH, and two pyruvate molecules. If oxygen is
available, the pyruvate can be broken down (oxidized) all the way to carbon dioxide in cellular
respiration, making many molecules of ATP.
What happens to the NADH? It can't just sit around in the cell, piling up. That's because cells have
only a certain number of NAD+ molecules, which cycle back and forth between oxidized (NAD+) and
reduced (NADH) states: NAD+ + 2e- + 2H+ ⇌ NADH + H+
Glycolysis needs NAD+ to accept electrons as part of a specific reaction. If there’s no NAD+ around
(because it's all stuck in its NADH form), this reaction can’t happen and glycolysis will come to a halt.
So, all cells need a way to turn NADH back into NAD+ to keep glycolysis going.
There are two basic ways of accomplishing this.
1. When oxygen is present, NADH can pass its electrons into the electron transport chain,
regenerating NAD+ for use in glycolysis. (Added bonus: some ATP gets made!)
2. When oxygen is absent, cells may use other, simpler pathways to regenerate NAD+. In these
pathways, NADH donates its electrons to an acceptor molecule in a reaction that doesn’t
make ATP but does regenerate NAD+ so glycolysis can continue. This process is
called fermentation.

Krebs/Citric acid cycle

v Pyruvate oxidation
At the end of glycolysis, we have two pyruvate molecules that still contain lots of extractable energy.
In eukaryotes, this step takes place in the matrix, the innermost compartment of mitochondria. In
prokaryotes, it happens in the cytoplasm. Overall, pyruvate oxidation
converts pyruvate—a three-carbon molecule—into acetyl CoA—a two-
carbon molecule attached to Coenzyme A—producing an NADH and
releasing one carbon dioxide molecule in the process.
 • Two molecules of pyruvate are converted into two molecules of acetyl CoA.
• Two carbons are released as carbon dioxide—out of the six originally present in glucose.
• 2 NADH are generated from NAD+.
Why make acetyl CoA? Acetyl CoA serves as fuel for the citric acid cycle in the next stage of cellular
respiration. The addition of CoA helps activate the acetyl group, preparing it to undergo the necessary
reactions to enter the citric acid cycle.

v Krebs cycle

1. Acetyl CoA joins with a four-carbon molecule, oxaloacetate, releasing the CoA group and
forming a six-carbon molecule called citrate.
2. Isocitrate is oxidized and releases a molecule of carbon dioxide, leaving behind a five-carbon
molecule. During this step, NAD+ is reduced to form NADH.
3. Reducing NAD+ to NADH and releasing a molecule of carbon dioxide in the process. The
remaining four-carbon molecule picks up Coenzyme A.
4. The remaining four-carbon molecule undergoes a series of additional reactions, first making
an ATP molecule—or, in some cells, a similar molecule called GTP then reducing the electron
carrier FAD to FADH2 and finally generating another NADH.

Overall, one turn of the citric acid cycle releases two carbon dioxide molecules and produces
three NADH, one FADH2, and one ATP or GTP. The citric acid cycle goes around twice for each
molecule of glucose that enters cellular respiration because there are two pyruvates—and thus, two
acetyl CoA. As—made per glucose.

Oxidative phosphorylation
Oxidative phosphorylation is made up of two closely connected components: the electron transport
chain and chemiosmosis. In the electron transport chain, electrons are passed from one molecule to
another, and energy released in these electron transfers is used to form an electrochemical gradient.
In chemiosmosis, the energy stored in the gradient is used to make ATP.
The electron transport chain is a collection of membrane-embedded proteins and organic molecules,
most of them organized into four large complexes labeled I to IV. In eukaryotes, many copies of these
molecules are found in the inner mitochondrial membrane. In prokaryotes, the electron transport chain
components are found in the plasma membrane.
All of the electrons that enter the transport chain come from NADH and FADH2 molecules produced
during earlier stages of cellular respiration: glycolysis, pyruvate oxidation, and the citric acid cycle.

Overall, what does the electron transport chain do for the cell? It has two important functions:
• Regenerates electron carriers. NADH and FADH2 pass their electrons to the electron
transport chain, turning back into NAD+ and FAD. This is important because the oxidized
forms of these electron carriers are used in glycolysis and the citric acid cycle and must be
available to keep these processes running.
• Makes a proton gradient. The transport chain builds a proton gradient across the inner
mitochondrial membrane, with a higher concentration of H+ in the intermembrane space and a
lower concentration in the matrix. This gradient represents a stored form of energy, and, as
we’ll see, it can be used to make ATP.

NADH is very good at donating electrons in redox reactions (that is, its electrons are at a high energy
level), so it can transfer its electrons directly to complex I, turning back into NAD+. As electrons move
through complex I in a series of redox reactions, energy is released, and the complex uses this
energy to pump protons from the matrix into the intermembrane space. Each NADH yields 2.5 ATP.
FADH2 is not as good at donating electrons as NADH (that is, its electrons are at a lower energy
level), so it cannot transfer its electrons to complex I. Instead, it feeds them into the transport chain
through complex II, which does not pump protons across the membrane. Each FADH2 yields 1.5 ATP.
“Note: Study cellular respiration from MCAT book, irreversible stages and enzymes”

In lactic acid fermentation, NADH transfers its electrons directly to pyruvate, generating lactate as a
byproduct. The bacteria that make yogurt carry out lactic acid fermentation, as do the red blood cells
in your body, which don’t have mitochondria and thus can’t perform cellular respiration.
Lactic acid produced in muscle cells is transported through
the bloodstream to the liver, where it’s converted back to
pyruvate and processed normally in the remaining reactions
of cellular respiration.

Alcohol fermentation, in which NADHNADHN, A, D,

H donates its electrons to a derivative of pyruvate, producing
ethanol.
Going from pyruvate to ethanol is a two-step process. In the
first step, a carboxyl group is removed from pyruvate and
released in as carbon dioxide, producing a two-carbon
molecule called acetaldehyde. In the second step, NADH
passes its electrons to acetaldehyde, regenerating NAD+ and
forming ethanol.

Many bacteria and archaea are facultative anaerobes,

meaning they can switch between aerobic respiration and
anaerobic pathways (fermentation or anaerobic respiration)
depending on the availability of oxygen. This approach allows
lets them get more ATP out of their glucose molecules when
oxygen is around—since aerobic cellular respiration makes
more ATP than anaerobic pathways—but to keep metabolizing
and stay alive when oxygen is scarce.
Other bacteria and archaea are obligate anaerobes, meaning
they can live and grow only in the absence of oxygen. Oxygen
is toxic to these microorganisms and injures or kills them on
exposure.
Gluconeogenesis
To keep our blood glucose levels constant we have to eat a meal “feed state” for breaking down
glycogen “glycogenolysis” but unfortunately only lasts for about 10 to 18 hours in our body. Our body
has come up with a second way called gluconeogensis.

Glycogenesis and Glycogenolysis.

Glycogen, a branched polymer of glucose, represents a storage form of glucose. Glycogen synthesis
and degradation occur primarily in liver “to maintain a constant level of glucose in the blood” and
skeletal muscle “provide glucose to the muscle during vigorous exercise”, although other tissues store
smaller quantities. Glycogen is stored in the cytoplasm as granules.

Plants also store excess glucose in long alpha linked chains of glucose called starch.

Glycogenesis, is the production of glycogen using two main enzymes:

1. Glycogen synthase, which creates alpha 1,4 glycosidic links between glucose molecules. It is
activated by insulin in liver and muscle.
2. Branching enzyme, which moves a block of oligoglucose from one chain and adds it to the
growing glycogen as a new branch using an alpha 1,6 glycosidic link.

Glycogenolysis, is the breakdown of glycogen using two main enzymes:

1. Glycogen phosphorylase, which removes single glucose 1-phosphate molecules by breaking
alpha 1,4 glycosidic links. In the liver, it is activated by glucagon to prevent low blood sugar;
in exercising skeletal muscle, it is activated by epinephrine and AMP to provide glucose for
the muscle itself.
2. Debranching enzyme, which moves a block of oligoglucose from one branch and connects it
to the chain using an alpha 1,4 glycosidic link. It also removes the branchpoint, which is
connected via an alpha 1,6 glycosidic link, releasing a free glucose molecule.

Gluconeogensis occurs in both the cytoplasm and mitochondria, predominantly in the liver. There is a
small contribution from the kidneys.
Most of gluconeogenesis is simply the reverse of glycolysis, using the same enzymes. The three
irreversible steps of glycolysis must be bypassed by different enzymes:
• Pyruvate carboxylase converts pyruvate into oxaloacetate, which is converted to
phosphoenolpyruvate by phosphoenolpyruvate carboxykinase PEPCK. Together, these
two enzymes bypass pyruvate kinase. Pyruvate carboxylase is activated by acetyl-CoA from
beta oxidation; PEPCK is activated by glucagon and cortisol.
• Fructose – 1,6-bisphosphatase converts fructose 1,6 bisphosphate to fructose 6-
phosphate, bypassing phosphofructokinase-1. This is the rate-limiting step of gluconeogensis.
It is activated by ATP directly and glucagon indirectly (via decreased levels of fructose 2,6-
 bisphosphate). It is inhibited by AMP directly and insulin indirectly (via increased levels of
fructose 2,6-bisphosphate).
• Glucose-6-phosphatase converts glucose 6-phosphate to free glucose, bypassing
glucokinase. It is found only in the endoplasmic reticulum of the liver.

Endocrine system

The endocrine system consists of organs, known as glands, that secrete hormones. Hormones are
signaling molecules that are secreted directly into the bloodstream to travel to a distant target tissue.
At that tissue, hormones bind to receptors, including a change in gene expression or cellular
functioning.

Classification of hormones by chemical structure:

1. Peptide hormones “proteins hormones” are made up of amino acids, ranging in size from
quite small (such as ADH) to relative large (such as insulin). Made in RER > Golgi > Vesicles.
Because peptide hormones are charged and cannot pass through the plasma membrane,
these hormones must bind to an extracellular receptor “2o messenger”. And they can travel
freely in the bloodstream and usually do not require carriers because are generally water-
soluble. The effect of peptide hormones are usually rapid but short-lived.
2. Steroid hormones are derived from cholesterol “lipids” and are produced primarily by the
gonads and adrenal cortex. Because steroid hormones are derived from nonpolar molecule,
they can easily cross the cell membrane. Their receptors are usually intracellular (in the
cytosol) or intranuclear (in the nucleus) “1o messengers”. And they have to carried by proteins
in the bloodstream to be able to travel around the body because they are not water-soluble.
The effect of steroid hormones are slower but longer-lived than peptide hormones because
steroid hormones cause alteration in the amount of mRNA and protein present in a cell.
3. Amino acid-derivative hormones are less common than peptide and steroid hormones, but
include some of the most important hormones. It derived from tyrosine “amino acid” but what
makes this different from the peptide hormones are made up of a singular modified tyrosine
amino acid. Epinephrine and norepinephrine have extremely fast onset but are short-lived,
like peptide hormones. Thyroxine and triiodothyronine have slower onset but a longer
duration, like steroid hormones.

Classification of hormones by target tissue:

1. Direct hormones, are secreted and then act directly on a target tissue. For example, insulin
released by the pancreas causes increased uptake of glucose by muscles.
2. Tropic hormones, require an intermediary to act. For example, gonadotropin-releasing
hormone (GnRH) from hypothalamus stimulates the release of lucteinizing hormone (LH) and
follicle-stimulating hormone (FSH). LH then acts on the gonads to stimulate testeosterone
production in the male and estrogen production in the female. GnRH and LH do not cause
direct changes in the physiology of muscle, bone, and hair follicles.
Hypothalamus
The bridge between the nervous and endocrine systems. By regulating the pituitary gland through
tropic hormones.

It interacts with pituitary in different ways:

Interaction with anterior pituitary
Gonadotropin-releasing hormone (GnRH) –> follicle-stimulating hormone (FSH) and luterinizing
hormone (LH)
Growth hormone-releasing hormone (GHRH) –> growth hormone (GH)
Thyroid-releasing hormone (TRH) –> thyroid-stimulating hormone (TSH)
Corticotropin-releasing factor (CRF) –> adrenocorticotropic hormone (ACTH)
Prolactin-inhibiting factor (PIF) –> decrease prolactin secretion “exception, the hypothalamus stop
releasing dopamine the prolactin is secreted”

Interaction with posterior pituitary

The posterior pituitary contains the nerve terminals of neurons with cell bodies in the hypothalamus,
the posterior pituitary receives and stores two hormones produced by the hypothalamus.
• Oxytocin is a hormone that stimulates uterine contractions during labor as well as milk
letdown during lactation.
• Antidiuretic hormone (ADH) increases reabsorption of water in the collecting ducts of the
kidneys.

Products of the anterior pituitary:

FLAT PEG
FSH (Follicle Stimulating Hormone)
LH (Leutinizing Hormone)
ACTH (Adrenocorticotropic Hormone)
TSH (Thyroid Stimulating Hormone)
Prolactin
Endorphins: decrease the perception of pain.
Growth Hormones.
FLAT are all tropic hormones, while the three hormones in PEG are all direct hormones.

Thyroid
It has two major functions: setting basal metabolic rate and calcium homeostasis. It mediated the first
effect by releasing triiodothyronine (T3) and thyroxine (T4) and both produced by the iodination of the
amino acid tyrosine in the follicular cells of the thyroid, whereas calcium levels are controlled by
calcitonin which produced by C-cells “parafollicular cells”.
Increased amounts of T3 and T4 will lead to increased cellular respiration. This leads to a greater
amount of protein and fatty acid turnover by speeding up both synthesis and degradation of these
compounds. High plasma levels of thyroid hormones will lead to decreased TSH and TRH synthesis;
prevents excessive secretion of T3 and T4.
• Hypothyroidism which thyroid hormones are secreted in insufficient amounts or not at all.
This condition is characterized by lethargy, decreased body temperature, slowed respiratory
and heart rate, cold intolerance, and weight gain.
• Hyperthyroidism results from an excess of thyroid hormone which may result from a tumor
or thyroid overstimulation. This condition is characterized by heightened activity level,
increased body temperature, increased respiratory and heart rate, hear intolerance, and
weight loss.

Calcitonin acts to decrease plasma calcium levels in three ways:

1. Increased calcium excretion from the kidneys.
2. Decreased calcium absorption from the gut.
3. Increased storage of calcium in the bone.

Parathyroid glands
The hormone produced is parathyroid hormone (PTH), serves as an antagonistic hormone to
calcitonin, raising blood calcium levels, decreases excretion of calcium by the kidneys, increases
absorption of calcium in the gut (via vitamin D), and increases bone resorption.

Adrenal cortex
Secretes corticosteroids “steroid hormones” that can be divided into three functional classes:
glucocorticoids, mineralocorticoids, and cortical sex hormones.

Glucocorticoids are steroid hormones that regulate glucose levels. In addition, these hormones also
affect protein metabolism. Cortisol and cortisone, these hormones raise blood glucose by increasing
gluconeogenesis and decreasing protein synthesis. Cortisol and cortisone can also decrees
inflammation and immunologic responses. Cortisol is also known as a stress hormone because it is
released in times of physical or emotional stress. This increases blood sugar and provides a ready
source of fuel in case of the body must react quickly to a dangerous stimulus.
Corticotropin-releasing factor (CRF) from the hypothalamus promotes release of adrenocorticotropic
hormone (ACTH) from the anterior pituitary, which promoted release of glucocorticoids from the
adrenal cortex.

Mineralocorticoids are used in a salt and water homeostasis; their most profound effects are on the
kidneys. Aldosterone increases sodium reabsorption in the distal convoluted tubule and collecting
duct of the nephron. Water follows the sodium cations into the bloodstream, increasing blood volume
and pressure.

Cortical sex hormones “androgens and estrogens”: because males already secrete large quantities
of androgens in the tested, adrenal testosterone plays a small role in male physiology. However,
females are much more sensitive to disorder of cortical sex hormone production.

Adrenal medulla
It is responsible for the production of the sympathetic hormones epinephrine and norepinephrine
“catecholamines”. All their effects are centered on the fight-or-flight response. Epinephrine can
increase the breakdown of glycogen to glucose (glycogenolysis) in both liver and muscle, as well as
increase the basal metabolic rate. Both hormones will increase heart rate, dilate the bronchi, and alter
blood flow to supply the systems that would be used in a sympathetic response.

Pancreas
Islets of Langerhans contain three distinct types of cells: alpha cells secrete glucagon, beta cells
secrete insulin, and delta cells secrete somatostatin.
• Glucagon is secreted during times of fasting. When glucose levels run low, the secretion of
glucagon stimulates degradation of protein and fat, conversion of glycogen to glucose, and
 production of new glucose via gluconeogenesis. When blood glucose concentrations are
high, glucagon release is inhibited.
• Insulin is antagonistic to glucagon and is therefore secreted when blood glucose levels are
high. Insulin induces muscle and liver cells to take up glucose and store it as glycogen for
later use. In excess, insulin will cause hypoglycemia, which is characterized by low blood
glucose concentration. Underproduction, insufficient secretion, or insensitivity to insulin all
can result in diabeted mellitus, which is clinically characterized by hyperglycemia (excess
glucose in the blood).
• Somatostatin is an inhibitor of both insulin and glucagon secretion. It is produced by the
hypothalamus, where it functions to decrease growth hormone secretion in addition to its
effects on insulin and glucagon.

Gonads
• The testes secrete testosterone in response to stimulation by gonadotropins (LH and FSH).
Testosterone causes sexual differntiation of the male during gestation and also promoted the
development and maintenance of secondary sex characteristics in males, such as axillary
and pubic hair, deepening of the voice, and muscle growth.
• The ovaries secrete estrogen and progesterone in response to gonadotropins. Estrogen is
involved in development of the female reproductive system during gestation ans also
promotes the development and maintenance of secondary sex characteristics in females,
such as axillary and pubic hair, breast growth, and the body fat redistribution.

Pineal gland
It secretes the hormone melatonin, blood levels of melatonin are at least partially responsible for the
sensation of sleepiness.
HDL vs LDL
Cholesterol travels through the blood on proteins called “lipoproteins.” Two types of lipoproteins carry
cholesterol throughout the body:
• LDL (low-density lipoprotein), sometimes called “bad” cholesterol, makes up most of
your body’s cholesterol. High levels of LDL cholesterol raise your risk for heart disease and
stroke.
• HDL (high-density lipoprotein), or “good” cholesterol, absorbs cholesterol and carries it
back to the liver. The liver then flushes it from the body. High levels of HDL cholesterol can
lower your risk for heart disease and stroke.
When your body has too much LDL cholesterol, the LDL cholesterol can build up on the walls of your
blood vessels. This buildup is called “plaque.” As your blood vessels build up plaque over time, the
insides of the vessels narrow. This narrowing blocks blood flow to and from your heart and other
organs. When blood flow to the heart is blocked, it can cause angina (chest pain) or a heart attack.

Hematologic system
By using centrifuge in the lab, we can separate the blood into its components, based on density. By
volume, blood is about 55% liquid “plasma” and 45% cells “erthrocytes, leukocytes, and platelets.”
Plasma an aqueous mixture of nutrients, salts, respiratory gases, hormones, and blood proteins.

Plasma: 90% is H2O, 8% is protein “ex, Albumin, antibody, fibrinogen, clotting factors”, 2% is
hormones, electrolytes, nutrients.
Serum is similer to plasma except, it does not contain fibrinogen + clotting factors.

Hematocrit is a measurement of how much of

the blood sample consists of red blood cells.
= Volume of RBC/ Total volume.
Polycythemia: Hematocrit is very high. Anemia:
Hematocrit is very low.
A normal hemoglobin between 13.5 and 17.5 for
males and between 12.0 and 16.0 for females.
A normal hematocrit between 41 and 53% for
males and between 36 and 46% for females.
• Plasma, the liquid component of blood, can be isolated by spinning a tube of whole blood at
high speeds in a centrifuge. The denser cells and platelets move to the bottom of the tube,
forming red and white layers, while the plasma remains at the top, forming a yellow layer.
Some of the molecules found in the plasma have more specialized functions. For example,
hormones act as long-distance signals, antibodies recognize and neutralize pathogens, and
clotting factors promote blood clot formation at the site of wounds. (Plasma that’s been
stripped of its clotting factors is called serum.) Lipids, such as cholesterol, are also carried in
plasma, but must travel with escort proteins because they don’t dissolve in water.

• Red blood cells, or erythrocytes, are specialized cells that circulate through the body and
deliver oxygen to tissues. In humans, red blood cells are small and biconcave (thinnest in the
center, just 777 - 888 μm in size), and do not contain mitochondria or a nucleus when mature.
These characteristics allow red blood cells to effectively perform their task of oxygen
transport. Small size and biconcave shape increase the surface area-to-volume ratio,
improving gas exchange, while lack of a nucleus makes additional space for hemoglobin, a
key protein used in oxygen transport. Lack of mitochondria keeps red blood cells from using
any of the oxygen they’re carrying, maximizing the amount delivered to tissues of the body. In
the lungs, red blood cells take up oxygen, and as they circulate through the rest the body,
they release the oxygen to the surrounding tissues. Red blood cells also play an important
role in transport of carbon dioxide, a waste product, from the tissues back to the lungs. Some
of the carbon dioxide binds directly to hemoglobin, and red blood cells also carry an enzyme
that converts carbon dioxide into bicarbonate. The bicarbonate dissolves in plasma and is
transported to the lungs, where it's converted back into carbon dioxide and released. Red
blood cells have an average life span of 120 days. Old or damaged red blood cells are broken
down in the liver and spleen, and new ones are produced in the bone marrow. Red blood cell
production is controlled by the hormone erythropoietin, which is released by the kidneys in
response to low oxygen levels. This negative feedback loop ensures that the number of red
blood cells in the body remains relatively constant over time.

• Platelets, also called thrombocytes, are cell fragments involved in blood clotting. They are
produced when large cells called megakaryocytes break into pieces, each one
making 2000 - 3000 platelets as it comes apart. Platelets are roughly disc-shaped and small,
about 222 - 444 μm in diameter. When the lining of a blood vessel is damaged (for instance, if
you cut your finger deeply enough for it to bleed), platelets are attracted to the wound site,
where they form a sticky plug. The platelets release signals, which not only attract other
platelets and make them become sticky, but also activate a signaling cascade that ultimately
converts fibrinogen, a water-soluble protein present in blood plasma, into fibrin (a non-water
soluble protein). The fibrin forms threads that reinforce the platelet plug, making a clot that
prevents further loss of blood. Thrombopoietin, which is secreted by the liver and kidney and
stimulates mainly platelet development.

• White blood cells, also called leukocytes, are much less common than red blood cells and
make up less than 1%1%1, percent of the cells in blood. Their role is also very different from
that of red blood cells: they are primarily involved in immune responses, recognizing and
neutralizing invaders such as bacteria and viruses. White blood cells are larger than red blood
cells, and unlike red blood cells, they have a normal nucleus and mitochondria. White blood
cells come in five major types, and these are divided into two different groups, named for their
appearance under a microscope.
1. One group, the granulocytes, includes neutrophils, eosinophils, and basophils, all of which
have granules in their cytoplasm when stained and viewed on a microscope.
2. The other group, the agranulocytes, includes monocytes and lymphocytes, which do not
have granules in the cytoplasm.
Granulocytes: “neutrophils, eosinophils, and basophils” are so named because they contain a variety
of compounds that are toxic to invading microbes, and their contents can be released through
exocytosis. Granular leukocytes are involved in inflammatory reactions, allergies, pus formation, and
destruction of bacteria and parasites.

The agranulocytes, which do not contain granules that are released by exocytosis, consist of
lymphocytes and monocytes. Lymphocytes are important in the specific immune response, the
body’s targeted fight against particular pathogens, such as viruses and bacteria.
Lymphocyte maturation takes place in one of three locations. Those lymphocytes that mature in the
spleen or in lymph nodes are referred to as B-cells, and those that mature in the thymus are called T-
cells. B-cells are responsible for antibody generation, whereas T-cells kill virally infected cells and
activate other immune cells.

Monocytes, which phagocytize foreign matter such as bacteria. Most organs of the body contain a
collection of these phagocytic cells; once they leave the bloodstream and enter an organ, monocytes
are renamed macrophages. Each organ’s macrophage population may have a specific name, as well.
In the central nervous system, for example, they are celled microgila; in the skin, the are called
langerhans cells; in bone, they are called osteoclasts.

Hematopoiesis:
Blood antigens
Red blood cells express surface proteins celled antigens. The two major antigen families relevant for
blood groups are the ABO antigens and the Rh factor.
The red blood cells contain a glycolipids molecules called “AB or A, or B”, The A (IA) and B (IB) are
dominant alleles, and O (i) is recessive allele. For example,The A blood type may be IAIA or IAi.

Blood Type Genotype(s) Antigens Antibodies Can Donate Can Receive

Produced Produced to… from…
A IAIA, IAi A anti-B A, AB A, O
B IBIB, IBi B anti-A B, AB B, O
AB IAIB A and B none AB only A, B, AB, O
“universal
recopient”
O ii none anti-A and A, B, AB, O O only
anti-B “universal
donor”

Rh factor is also a surface protein expressed on red blood cells, Although at one time it was thought
to be a single antigen, it has since been found to exist as several variants. When left unmodified, Rh-
positive (Rh+) “have protien” or Rh-negative (Rh-) “not having protein” refers to the presence or
absence of a specific allele called D. Rh-positivity follows autosomal dominant inheritance; one
positive allele is enough for the protein to be expressed.

Unlike for the ABO groups, a Rh-negative individual will not normally produce antibodies against
antigen D. However, if they one ever exposed to antigen D, then their immune system kicks in and
begins forming antibodied.

If the fetus ends up being Rh-positive and the mother is Rh-negative, how will this affect the
pregnancy?
• During the first pregnancy, some of the red blood cells of the fetuc that have the antigen D Rh
factor can leak into the mother’s blood. This will cause the mother’s immune system to
produce antibodies against antigen D. However, since the fetal red blood cells usually leak
during child birth, this will not affect that fetus.
• When the woman becomes pregnant again, the antigen D antibodies can now cross the
placenta and enter the blood stream of the fetus. If the fetus is Rh-positive, the antibodies will
bind onto the red blood cells and lyse them. The lysing eelease dangerous chemicals into the
fetal blood. This is known as Rh-incompatibility.

Immune system
The two main classes of the immune system are the innate immune system and the adaptive immune
system, or “acquired immunity”.
The innate immune system is made of defenses against infection that can be activated immediately
once a pathogen attacks. The innate immune system is essentially made up of barriers that aim to
keep viruses, bacteria, parasites, and other foreign particles out of your body or limit their ability to
spread and move throughout the body. The innate immune system includes:
 • Physical Barriers
such as skin, the gastrointestinal tract, the respiratory tract, the nasopharynx, cilia, eyelashes
and other body hair.
• Defense Mechanisms
such as secretions, mucous, bile, gastric acid, saliva, tears, and sweat.
• General Immune Responses
such as inflammation, complement, and non-specific cellular responses. The inflammatory
response actively brings immune cells to the site of an infection by increasing blood flow to
the area. Complement is an immune response that marks pathogens for destruction and
makes holes in the cell membrane of the pathogen.

The innate immune system is always general, or nonspecific, meaning anything that is identified as
foreign or non-self is a target for the innate immune response. The innate immune system is activated
by the presence of antigens and their chemical properties.
Anatomy
• Bone marrow produces all of the leukocytes that participate in the
immune system through the process of hematopoiesis.
• Spleen is a location of blood storage and activation of B-cells
“humoral immunity”, which turn into plasma cells to produce
antibodies as part of adaptive immunity. T cells, another class of
adaptive immune cells, mature in the thymus, a small gland just in
front of the pericardium, the sac that protects the heart. T-cells are the
agents of cell-mediated immunity because they coordinate the
immune system and directly kill virally infected cells.
• Lymph nodes filter lymph and provide a place for immune cells to
communicate and mount an attack; B-cells can be activated here as
well.

Cells of the Innate Immune System

The following cells are leukocytes of the innate immune system:
• Phagocytes, or Phagocytic cells: Phagocyte
means “eating cell”, which describes what
role phagocytes play in the immune
response. Phagocytes circulate throughout
the body, looking for potential threats, like
bacteria and viruses, to engulf and destroy.
• Macrophages: Macrophages, are efficient
phagocytic cells that can leave the
circulatory system by moving across the
walls of capillary vessels. The ability to roam
outside of the circulatory system is
important, because it allows macrophages
to hunt pathogens with less limits.
Macrophages can also release cytokines in
order to signal and recruit other cells to an
area with pathogens.
• Mast cells are found in mucous membranes and connective tissues, and are important for
wound healing and defense against pathogens via the inflammatory response. When mast
cells are activated, they release cytokines and granules that contain chemical molecules to
create an inflammatory cascade. Mediators, such as histamine, cause blood vessels to dilate,
increasing blood flow and cell trafficking to the area of infection. The cytokines released
during this process act as a messenger service, alerting other immune cells, like neutrophils
and macrophages, to make their way to the area of infection, or to be on alert for circulating
threats.
• Neutrophils are phagocytic cells that are also classified as granulocytes because they contain
granules in their cytoplasm. These granules are very toxic to bacteria and fungi, and cause
them to stop proliferating or die on contact. Neutrophils are typically the first cells to arrive at
the site of an infection because there are so many of them in circulation at any given time.
They are very short-lived “a bit more than five days”. Dead neutrophil collections are
responsible for the formation of pus during an infection.
 • Eosinophils are granulocytes target multicellular parasites.
Eosinophils secrete a range of highly toxic proteins and free
radicals that kill bacteria and parasites. The use of toxic
proteins and free radicals also causes tissue damage during
allergic reactions, so activation and toxin release by
eosinophils is highly regulated to prevent any unnecessary
tissue damage.
• Basophils are also granulocytes that attack multicellular
parasites. Basophils release histamine, much like mast
cells. The use of histamine makes basophils and mast cells
key players in mounting an allergic response.
• Natural Killer cells (NK cells), do not attack pathogens
directly. Instead, natural killer cells destroy infected host
cells in order to stop the spread of an infection. Infected or
compromised host cells can signal natural kill cells for
destruction through the expression of specific receptors and
antigen presentation.
• Dendritic cells are antigen-presenting cells that are located
in tissues, and can contact external environments through
the skin, the inner mucosal lining of the nose, lungs,
stomach, and intestines. Since dendritic cells are located in
tissues that are common points for initial infection, they can
identify threats and act as messengers for the rest of the
immune system by antigen presentation. Dendritic cells also
act as bridge between the innate immune system and the
adaptive immune system.

Histamine causes inflammation by inducing vasodilation and the

movement of fluid and cells from the bloodstream into tissues.
Inflammation is particulary useful against extracellular pathogens,
including bacteria, fungi, and parasites.

The complement system (also called the complement cascade) is a

mechanism that complements other aspects of the immune
response. Typically, the complement system acts as a part of the
innate immune system, but it can work with the adaptive immune
system if necessary.
The complement system is made of a variety of proteins that, when
inactive, circulate in the blood. When activated, these proteins come
together to initiate the complement cascade, which starts the
following steps:
• Opsonization: Opsonization is a process in which foreign particles are marked for
phagocytosis. All of the pathways require an antigen to signal that there is a threat present.
Opsonization tags infected cells and identifies circulating pathogens expressing the same
antigens.
• Chemotaxis: Chemotaxis is the attraction and movement of macrophages to a chemical
signal. Chemotaxis uses cytokines and chemokines to attract macrophages and neutrophils
to the site of infection, ensuring that pathogens in the area will be destroyed. By bringing
immune cells to an area with identified pathogens, it improves the likelihood that the threats
will be destroyed and the infection will be treated.
• Cell Lysis: Lysis is the breaking down or destruction of the membrane of a cell. The proteins
of the complement system puncture the membranes of foreign cells, destroying the integrity
of the pathogen. Destroying the membrane of foreign cells or pathogens weakens their ability
to proliferate, and helps to stop the spread of infection.
• Agglutination: Agglutination uses antibodies to cluster and bind pathogens together, much like
a cowboy rounds up his cattle. By bringing as many pathogens together in the same area, the
cells of the immune system can mount an attack and weaken the infection. Other innate
 immune system cells continue to circulate throughout the body in order to track down any
other pathogens that have not been clustered and bound for destruction.

Adaptive Immune
Unlike the innate immune system, which attacks only based on the identification of general threats,
the adaptive immunity is activated by exposure to pathogens, and uses an immunological memory to
learn about the threat and enhance the immune response accordingly. The adaptive immune
response is much slower to respond to threats and infections than the innate immune response,
which is primed and ready to fight at all times.
The adaptive immune system relies on fewer types of cells to carry out its tasks: B cells and T cells.
Both B cells and T cells are lymphocytes that are derived from specific types of stem cells, called
multipotent hematopoietic stem cells, in the bone marrow. After they are made in the bone marrow,
they need to mature and become activated. Each type of cell follows different paths to their final,
mature forms.

B cells
After formation and maturation in the bone marrow (hence the name “B cell”), the naive B cells move
into the lymphatic system to circulate throughout the body. In the lymphatic system, naive B cells
encounter an antigen, which starts the maturation process for
the B cell. B cells each have one of millions of distinctive surface
antigen-specific receptors that are inherent to the organism’s
DNA. For example, naive B cells express antibodies on their cell
surface, which can also be called membrane-bound antibodies.
When a naive B cell encounters an antigen that fits or matches
its membrane-bound antibody, it quickly divides in order to
become either a memory B cell or an effector B cell, which is
also called a plasma cell. Antibodies can bind to antigens
directly.
The antigen must effectively bind with a naive B cell’s
membrane-bound antibody in order to set off differentiation, or
the process of becoming one of the new forms of a B cell.
Memory B cells express the same membrane-bound antibody as the original naive B cell, or the
“parent B cell”. Plasma B cells produce the same antibody as the parent B cell, but they aren’t
membrane bound. Instead, plasma B cells can secrete antibodies. Secreted antibodies work to
identify free pathogens that are circulating throughout the body. When the naive B cell divides and
differentiates, both plasma cells and memory B cells are made.
B cells also express a specialized receptor, called the B cell receptor (BCR). B cell receptors assist
with antigen binding, as well as internalization and processing of the antigen. B cell receptors also
play an important role in signaling pathways. After the antigen is internalized and processed, the B
cell can initiate signaling pathways, such as cytokine release, 7 to communicate with other cells of the
immune system.

T cells
Once formed in the bone marrow, T progenitor cells migrate to the thymus (hence the name “T cell”)
to mature and become T cells. While in the thymus, the developing T cells start to express T cell
receptors (TCRs) and other receptors called CD4 and CD8 receptors. All T cells express T cell
receptors, and either CD4 or CD8, not both. So, some T cells will express CD4, and others will
express CD8.
Unlike antibodies, which can bind to antigens directly, T cell receptors can only recognize antigens
that are bound to certain receptor molecules, called Major Histocompatibility Complex class 1 (MHCI)
and class 2 (MHCII). These MHC molecules are membrane-bound surface receptors on antigen-
presenting cells, like dendritic cells and macrophages. CD4 and CD8 play a role in T cell recognition
and activation by binding to either MHCI or MHCII.
T cell receptors have to undergo a process called rearrangement, causing the nearly limitless
recombination of a gene that expresses T cell receptors. The process of rearrangement allows for a
lot of binding diversity. This diversity could potentially lead to accidental attacks against self cells and
molecules because some rearrangement configurations can accidentally mimic a person’s self
molecules and proteins. Mature T cells should recognize only foreign antigens combined with self-
MHC molecules in order to mount an appropriate immune response.
Three types of mature T cells: Helper T cells, Cytotoxic T cells, and T regulatory cells.
• Helper T cells express CD4, and help with the activation of TC cells, B cells, and other
immune cells. It is secreting chemicals known as lymphokines.
• Cytotoxic T cells express CD8, and are responsible for removing pathogens and infected host
cells.
• T regulatory cells express CD4 and another receptor, called CD25. T regulatory cells help
distinguish between self and nonself molecules, and by doing so, reduce the risk of
autoimmune diseases.
Because the adaptive immune system can learn and remember specific pathogens, it can provide
long-lasting defense and protection against recurrent infections. When the adaptive immune
system is exposed to a new threat, the specifics of the antigen are memorized so we are
prevented from getting the disease again. The concept of immune memory is due to the body’s
ability to make antibodies against different pathogens. A good example of immunological memory
is shown in vaccinations. A vaccination against a virus can be made using either active, but
weakened or attenuated virus, or using specific parts of the virus that are not active. Both
attenuated whole virus and virus particles cannot actually cause an active infection. Instead, they
mimic the presence of an active virus in order to cause an immune response, even though there
are no real threats present. By getting a vaccination, you are exposing your body to the antigen
required to produce antibodies specific to that virus, and acquire a memory of the virus, without
experiencing illness. Some breakdowns in the immunological memory system can lead to
autoimmune diseases. Molecular mimicry of a self‐antigen by an infectious pathogen, such as
bacteria and viruses, may trigger autoimmune disease due to a cross-reactive immune response
against the infection. One example of an organism that uses molecular mimicry to hide from
immunological defenses is Streptococcus infection.

Attribute Innate Immunity Adaptive Immunity

Response Time Fast: minutes or hours Slow: days

Only specific for molecules and Highly specific! Can discriminate between
molecular patterns associated with pathogen vs. non-pathogen structures, and
general pathogens or foreign miniscule differences in molecular
Specificity particles structures

Macrophages, Neutrophils, Natural

Killer Cells, Dendritic Cells, T cells, B cells, and other antigen
Major Cell Types Basophils, Eosinophils presenting cells

Antimicrobial peptides and proteins,

Key Components such as toxic granules Antibodies

Not as good as the innate immune system,

but still pretty good at determining which is
Innate immunity is based on self vs. which. Problems in self vs. nonself
Self vs. Nonself nonself discrimination, so it has to be discrimination result in autoimmune
Discrimination perfect diseases
 Attribute Innate Immunity Adaptive Immunity

Immunological Memory used can lead to faster response

Memory None to recurrent or subsequent infections

Limited: Receptors used are standard

and only recognize antigen patterns. Highly diverse: can be customized by
Diversity and No new receptors are made to adapt genetic recombination to recognize
Customization the immune response epitopes and antigenic determinants.

Antibodies (also called immunoglobulins Ig) can carry out many different jobs in the body. Just as
antigens can be displayed on the surface of cells or can float freely in blood, chyle (lymphatic fluid), or
air, so tooo can antibody binds to an antigen, the response will depend on the location. For antibodies
secreted into body fluids, there are three main possibilities: first, one bound to a specific antigen,
antibodies may attract other leukocytes to phagocytize those antigens immediately. This is called
opsonization. Second, antibodies may cause pathogens to clump together or agglutinate, forming
large insoluble complexed that can be phagocytized. Third, antibodies can block the ability of a
pathogen to invade tissues, essentially neutralizing it.

For cell-surface antibodies, the binding of antigen to a B-cell causes activation of that cell, resulting in
its proliferation and formation of plasma and memory cell. In contrast, when antigen binds to
antibodies on the surface of a mast cell, it causes degranulation (exocytosis of granule contents),
allowing the release of histamine and causing an inflammatory allergic reaction.

Antibodies are Y-shaped molecules that are made up of two identical heavy chain and two identical
light chains. “Disulfide linkages and noncovalent interactions hold the heavy and light chains together”
Antibodies isotypes:
• IgM
• IgD
• IgG
• IgE
• IgA