BIOMOLECULES

Chemical Make-Up of Living Things

• Elements = basic units of matter

• Most living things are made up of 4 elements
o Carbon
o Hydrogen
o Oxygen
o Nitrogen

Atoms

• The smallest functional units of matter that form all chemical substances
• Cannot be further broken down into other substances by ordinary means
• Each specific type of atom is a chemicalelement

Chemical Bonds and Molecules

• Molecule = Two or more atoms bonded together

• Molecular formula
o Contains chemical symbols of the elements in the molecule (C6H12O6)
o Subscript indicates how many of each atom are present (H2O has two hydrogens, 1
oxygen)
• Compound = Any molecule composed of two or more elements
o N2 and O2 are examples of molecules that are not compounds

Three subatomic particles

• Protons
o positive charge (+)
o found in nucleus
• Neutrons
o neutral
o found in nucleus
• Electrons
o negative charge (−)
o found in orbitals
• Protons and electrons are present in equal numbers, giving the atom no net charge
• The number of neutrons can vary

What are biomolecules ?

= Molecules within living organisms

• Carbohydrates
• Lipids
• Proteins
• Enzymes
• Nucleic acids
• ATP
The Carbon Atom
• Organic molecules contain carbon
• Organic molecules are abundant in living organisms
• Macromolecules are large, complex organic molecules

Carbon

• Carbon has 4 electrons in its outer shell

• Needs 4 more electrons to fill the shell
• It can make up to four bonds
o Usually single or double bonds
• Carbon can form nonpolar or polar bonds
o Molecules with polar bonds are water soluble
o Molecules with nonpolar bonds (like hydrocarbons) are not very water soluble

Functional Groups

• Groups of atoms with special chemical features that are functionally important

• Each type of functional group exhibits the same properties in all molecules in which it occurs

Carbohydrates
• Most abundant class of organic molecules found in nature.
• Carbon, Hydrogen, Oxygen
• General formula: Cn(H2O)n
• Breakdown of carbohydrates provides energy that sustains animal life.
• Carbohydrates are the metabolic precursors of virtually all other biomolecules

Functions

• A store of chemical energy

• Structural components in cells
• Based on function we can distinguish three types of carbohydrates :
o Simple sugars e.g. glucose, fructose, galactose
o Storage carbohydrates e.g. starch, glycogen
o Structural carbohydrates e.g. cellulose, chitin, pectin, gums, mucilages,
glycosaminoglycans

a) Simple Sugars – Monosaccharides

• Mono-single sacchar = sugar
• Simple sugars in which carbon ,hydrogen and oxygen occur in the ratio (CH2O)
• Have between 3 – 7 C atoms in their carbon chains
• Major nutrient for cells
• Can be produced by photosynthetic organisms from CO2 ,H20 and sunlight
Monosaccharides = Simplest sugars

• Most common are 5 or 6 carbons

o Pentoses: Ribose C5H10O5, Deoxyribose (C5H10O4)
o Hexose: Glucose (C6H12O6)
• Different ways to depict structures
o Ring
o Linear

Monosaccharides

• Store energy in their chemical bonds which is harvested by cellular respiration.

• Their carbon skeletons are raw materials for other organic molecules.
• Can be incorporated as monomers into disaccharides and polysaccharides

How do monosaccharides differ ?

• The number of carbons

• The way in which the atoms are grouped together to form a functional group.
• The way in which the atoms or groups are arranged in space.

Some monosaccharides of interest:

Glucose = C6H12O6

• Made by plants during photosynthesis

• Glucose is the main fuel for the brain - tested in blood and urine as indicators for diabetes
o In animals, released from breakdown of glycogen in the liver

Fructose and Galactose (C6H12O6)

• Isomers (same formula, different atomic arrangement)

• This gives different chemical and biochemical properties
• Fructose: fruit sugar
• Galactose: slow conversion in liver. Main food source -
combined with a glucose molecule to form lactose

b) Disaccharides
• Most common and simplest type of oligosaccharides
• Composed of two monosaccharides
• Linked by a glycosidic bond
• Examples:
o Glucose + glucose → maltose
o Glucose + galactose → lactose
o Glucose + fructose → sucrose
c) Polysaccharides
• Many monosaccharides linked together to form long polymers
• Differ in
o nature of their component monosaccharides
o length of their chains
o amount of chain branching that occurs.
• Examples:
o Energy storage – starch, glycogen
o Structural – cellulose, chitin, glycosaminoglycans

Polysaccharide – Cellulose

• Straight chain polymer (2000 –3000 units)

• Shape and construction of the polymer allows close packing of chains into fibres
• Main substance in the walls of plant cells (structural)
o Used to make paper, cardboard
o Biofuel crops
• Humans can’t digest cellulose but important part of fibre in diet

Polysaccharide - Starch

• Polymer of glucose – important storage material in plants

• Composed of two components
o Amylose – linear chain of glucose in alpha 1-4 linkage –poorly soluble in water and
forms a helical structure.
o Amylopectin – highly branched glucose polymer – branches occur every 12-30
glucose residues. The linear linkages are alpha (1-4) whereas the branch points are
alpha (1-6)

Polysaccharide - Glycogen

• Branched chain polymer of glucose

o Highly branched molecule - branch points occurring every 8-12 glucose units.
• Major storage polysaccharide in animals
• Found mainly in liver (10% of mass) and skeletal muscle ( 1-2% of mass) as granules.
• Readily hydrolysed by enzyme to release the glucose
• Associated in cells with three times its own weight of water -highly hydrated.

Other polysaccharides and derivatives

Pectins
• Found in plant cell walls
• Galactose + galacturonic acid, bound by calcium

Chitin
• Chemically related to cellulose
• In walls of fungi hyphae and also exoskeletons of arthropods
 Mucopolysaccharides
• Also called glycosaminoglycans
• Occur in vertebrate connective tissue, lubricants in joints

Lipids
What are lipids?

• Contain C, H, O (Some contain Phosphorous and nitrogen)

• Diverse group of organic compounds that are insoluble in water (hydrophobic).
• Will dissolve in non polar solvents (ethanol, ether).
• Classification:
o Simple lipids – animal fats, vegetable oils, waxes
o Phospholipids
o Steroids

Fat - an essential nutrient

Biological roles of fat include :

• Source of energy
• Insulation of important organs
• Transport of vitamins A,E,D,K
• Source of essential fatty acids
• Source of steroids and hormones
• Structural role in membranes

Fatty acid
• Fats/oils are esters formed between fatty acids and an alcohol called glycerol to form ester
links (-COO-)
• The fatty chain of the molecule is a water insoluble (hydrophobic),oil soluble non polar chain
of variable length.
• Made entirely of carbon and hydrogen atoms and ends in a methyl group.
• The acid end of the molecule is a water soluble (hydrophilic) polar, weak organic acid known
as a carboxyl group.
Triacylglycerol (Triglyceride)

• Main form of fat in the human diet.

• Main storage form of fat in the body
• Made of a glycerol molecule and 3 fatty acids
• The fatty acids are attached to the glycerol backbone by a loss of
water
• The fatty acids can be saturated or unsaturated.

Fatty acid (summary)

• Building block of triacylglycerols and phospholipids.

• Range in length from 2-22 carbons.
• Straight chains –no branching.
• Usually an even number of carbon atoms.
• Hydrogens are attached to the carbons forming a hydrocarbon chain.
• The acidic group (COOH) is also present.

Common fatty acids

• C2 = Acetic acid
• C4 = Butyric acid
• C12 = Lauric acid
• C14 = Myristic acid
• C16 = Palmitic acid
• C18 = Stearic acid

How do fatty acids differ ?

• Fatty acids differ in

o The number of carbons on the backbone .
o The number of hydrogens in the chain.
o The number of double carbon carbon bonds (C=C).
Carbon number and number of double bonds determine the chemical and physical
properties of the fatty acid.
➢ Saturated Fats.
➢ Unsaturated Fats.

Fatty acids

a) Saturated – all carbons linked by single bonds, Tend to be

solid at room temperature
b) Unsaturated – contain one or more double bonds, Tend to
be liquid at room temperature (known as oils), Cis forms
naturally; trans formed artificially, Trans fats are linked to
disease
 a) Saturated fatty acids
• Maximum number of hydrogens attached to the carbons i.e. carbons are saturated with
hydrogens.
• Usually found in animal based foods.
• Solid at room temperature i.e. they have high melting points.
• Melting point increases with increasing number of carbons in the chain.

b) Unsaturated Fats

Monounsaturated
• Has one carbon carbon double bond in its structure.
• The insertion of a double bond results in the removal of two hydrogens from the chain.
• Usually a liquid at room temperature
• Found in vegetable oils particularly olive oil.

Polyunsaturated Fatty Acids (PUFA)

• Have more than one double carbon carbon bond in their structure.
• Can have 2,3 4,5,6 double carbon carbon bonds along the backbone of the fat
• Found in plant foods and oily fish
• Usually a liquid at room temperature.

Common unsaturated fatty acids

C18:1 = Oleic acid

C18:2 = Linoleic acid

C18:3 = Linolenic acid

C20:4 = Arachidonic acid

C20:5 = EPA (eicosapentaenoic acid )

C22:6 = DHA (docosahexaenoic acid)

Essential fatty acids

• These are fatty acids that cannot be made by the body and must be taken in the diet.
• Include ?
18:2 linoleic acid
18:3 linolenic acid

What does the body do with fatty acids?

• Saturated fatty acids less than 16 carbons provide energy and heat.
• The shorter the fatty acid the more readily it burns (oxidises) and the more easily we can
digest it.
• Saturated fatty acids between 16 and 18 carbons generate energy, are used to construct
membranes or are stored in larger molecules called Triacylglycerols.
What about the unsaturated fatty acids ?

• Our body uses unsaturated fatty acids also to construct membranes.

• In addition, the body can lengthen and insert more double bonds into these fatty acids. The
resulting highly unsaturated molecules have important functions in key organs like the brain,
sense organs, adrenals glands and testes.
• Enzyme controlled processes can change these unsaturated molecules into hormone like
substances that regulate many functions (eicosanoids)

Simple Lipids: Fats and Oils

• Aggregate into globules as they are hydrophobic
o Also known as triglycerides or triacylglycerols
o Formed by bonding glycerol to 3 fatty acids
• Fats and oils the same except for their physical state at 20⁰C
o Fat – solid
o Oils – liquid

Fats
• Fats are important for energy storage
o 1 gram of fat stores more energy than 1 gram of glycogen or starch
• Fats can also be structural, providing cushioning and insulation

Phospholipids
• Formed from glycerol, two fatty acids and a phosphate group
• Phospholipids are amphipathic molecules
o Phosphate head – polar / hydrophilic
o Fatty acid tail – nonpolar / hydrophobic

Phospholipids
• Second major class of lipids
• Make up less than 5% of the total lipids found in food
and our body.
• Major structural components of cells and
intracellular membranes in living organisms.
• Similar to triglycerides but have only 2 fatty acids
attached to the glycerol molecule.
• The third position on the glycerol is occupied by a
phosphate and a charged group.

Cholesterol - what is it ?

• Hard waxy lipid substance that melts at 149 o C.

• It consists of 27 carbons arranged in four ring structures.
• Can be made from 2 carbon precursors which come from the breakdown of sugars, fats, and
proteins.
 What does the body do with the cholesterol ?

• Cholesterol compensates for changes in membrane fluidity keeping it within narrow limits for
optimal membrane function.
• It makes steroid hormones like male and female sex hormones, aldosterone, cortisol,
cortisone.
• It makes Vitamin D
• It makes Bile salts

Steroids

• Four interconnected rings of carbon atoms

• Usually insoluble in water

• Example: Cholesterol

• Tiny differences in structure can lead to profoundly different, specific biological properties

Estrogen versus testosterone

Proteins
• Proteins are made of monomers called amino acids.
• Amino acids contain C, H, O, N, & S

What are proteins?

• Macromolecules containing the elements carbon, hydrogen, oxygen and nitrogen.

• All proteins contain nitrogen and this makes them different to carbohydrates and lipids.
• Built from a linear sequence of amino acids
• Different proteins have different shapes and the shape is closely related to its function.
Shape is particularly important if the protein is an enzyme.

Amino Acids
• Each amino acid consists of: an amino group (NH2)
o a carboxyl group (COOH)
o a hydrogen atom (H)
o a variable group called R
• ALL these groups are attached to a central carbon (alpha
carbon )

R group

• 20 different types - making 20 different amino acids

• R groups determine the chemical properties of the amino acids
• The R groups vary and make the amino acids different to each other.
• They also affect the way the amino acid bonds with another amino acid.
• Glycine is the simplest amino acid with a hydrogen atom forming its R group:
Remember….

• Proteins are LARGE organic molecules made up of amino acid monomers to create long
polypeptide chains

• They contain Carbon, Hydrogen, Oxygen, Nitrogen (some also contain Sulphur and Phosphorus).

Proteins

• Composed of carbon, hydrogen, oxygen, nitrogen, and small amounts of other elements, notably
sulfur

• Building blocks of proteins are amino acids

o 20 different amino acids

o Common structure with variable sidechain that determines structure and function

Functions of Proteins

1. Structural support

2. Storage (of amino acids)

3. Transport (e.g. haemoglobin)

4. Signalling (chemical messengers)

5. Movement (contractile proteins)

6. Defence against foreign substances (antibodies)

7. Catalysis of biochemical reactions (enzymes)

Amino acids
• There are 20 amino acids that commonly occur in proteins.
• Amino acids are soluble and they all have the same basic structure.
• They always contain: An amino group – NH2 –this is basic, a carboxyl group – COOH – this is
acidic.

20 amino acids – but many thousands of different proteins –how?

• Amino acids are like letters in the alphabet- and the proteins are like words.
• Nature makes many different proteins from twenty amino acids in the same way we can
make a dictionary full of words from just twenty six letters.
• One difference – proteins contain many more amino acids than words contain letters.

POLYPEPTIDE CHAINS

• Amino acids join together by a reaction between the amino group of one amino acid and the
carboxyl group of another amino acid.

• This is a condensation reaction and a molecule of water is lost. The bond formed is called a peptide
link/bond.

• Polypeptides are broken down by hydrolysis

Peptide Bond =Peptide bonds are covalent bonds between two amino acids.

• Peptide bond = covalent bond that links the carboxyl group of one amino acid to the amino
group of the next
• Repeating sequence –N-C-C-N-C-C as a backbone
• Ranges in length from a few monomers to more than a thousand

Further reactions form polypeptides (could contain thousands of amino acids). A protein is made up
of one or more polypeptide chains.

Polypeptide chain = polymer of many amino acids joined by peptide bonds

PROTEIN STRUCTURE

• Polypeptides are just strings of amino acids but they fold up to form the complex three
dimensional structure of working proteins.
• To help understand protein structure,it is broken down into four levels:
o primary
o secondary
o tertiary
o quaternary

Primary structure

• This is the specific sequence of amino acids that make up the

polypeptide chain. The primary structure is specific to each
protein. It is coded for by the DNA of the cell.

Primary structure

• Amino acid sequence

• Encoded directly by genes

Secondary structure

• The secondary structure of a protein forms when the

polypeptide chain takes up a particular shape through
folding. The most common shapes are an α helix or a β
pleated sheet. They are stable structures maintained by
hydrogen bonding between different groups of amino
acids.

Tertiary structure

• The secondary structure is then folded further to form a complex shape. The folding is
irregular and results from the formation of
different bonds between the amino acids.
The R groups play an important role in
determining and maintaining the specific
shape of the protein molecule.
• There are 4 main types of bonds that can
form.
Quaternary

• This is where the protein consists of more than one polypeptide chain. The chains may be of
one or different types.
• Protein can be formed from several copies of the same polypeptide Or may be multimeric –
composed from different polypeptides
• Examples include:
Haemoglobin
Collagen

Five factors that promote protein folding and stability

• Hydrogen bonds

• Ionic bonds and other polar interactions

• Hydrophobic effects

• Van der Waals forces

• Disulfide bridges

Protein-protein interactions

• Many cellular processes involve steps in which two or more different proteins interact
• Specific binding at surface
• Use first four factors to bind
o Hydrogen bonds
o Ionic bonds and other polar interactions
o Hydrophobic effects
o Van der Waals forces
Functions of proteins in cells

Structural role

Protein name Function

Collagen Strength in cartilage and tendons

Elastin Flexibility with strength in ligaments and

blood vessels

Keratin Feathers, claws, nails, horns, Scales, wool,

quills, hooves, outer layer of skin

Ossein Support in bone

Histones Bind to DNA

Transmembrane proteins Channels for the movement

of molecules across the cells

Protection

Example Role in the organism

Immunoglobulins Antibodies - immune system defence

Mucin Keep respiratory surface moist/protect

stomach from acid

Fibrinogen /prothrombin Blood clotting Dr Siobhán McCarthy

Movement

Example Role in the organism

Actin/myosin Muscle contraction

Flagellin Protein in an appendage used by bacteria for

locomotion

Kinesin Cilia in animals

 Catalysts

Example Role in the organism

Protease Breaks down protein

Lipase Breaks down lipids

Amylase Breaks down starch

Nuclease Breaks down nucleic acids

Hormones

Example Role in the organism

Growth hormone Stimulates growth of bone and muscle

Thyroxine Controls the amount of energy we use at

rest

Insulin Controls blood glucose levels

Anti-diuretic hormone Controls amount of water lost in the urine

Nucleic Acids
• Responsible for the storage, expression, and transmission of genetic information
• Two classes
o Deoxyribonucleic acid (DNA) - Stores genetic information encoded in the sequence of
nucleotide monomers
o Ribonucleic acid (RNA) - Decodes DNA into instructions for linking together a specific
sequence of amino acids to form a polypeptide chain

Nucleic acid monomer is a nucleotide

• Made up of phosphate group, a five-carbon sugar (either ribose or deoxyribose), and a single
or double ring of carbon and nitrogen atoms known as a base
• Nucleotides are linked into polymer by a sugar-phosphate backbone A nucleotide

Nucleotides

• Sugars = 5 carbons :deoxyribose, ribose

• Bases - 2 rings = purines
o adenine (A)
o guanine (G)
1 ring = pyrimidines
o cytosine (C),
o thymine (T)
o uracil (U) A+T, G+C
ATP (Adenosine Triphosphate)

• Nucleotides have other metabolic functions

• Adenosine + 3 phosphate groups = ATP
• ATP = an energy carrier in the cell
 PROCARYOTES
Procaryotes

• They are unicellular organisms (single cell)and have a much

simpler structure than eucaryotes.
• Their small size (1-10um) gives them a high surface area to
volume ratio. This eliminates the need for extensive internal
membrane networks.
• Because they are very small ,they also possess a small
volume of cytoplasm for their genetic material to control,
therefore their metabolism is extremely fast.

Two categories of procaryotes:

• Bacteria
o Small cells, 1 micrometer to 10 micrometer in diameter
o Very abundant in environment and our bodies
o Vast majority are not harmful to humans
o Some species cause disease
• Archaea
o Also small cells, 1 micrometer to 10 micrometer in diameter
o Less common
o Often found in extreme environments

Characteristics of procaryotic cells

• Nuclear material lacks a membrane.

• Absence of cell organelles –single structure for multiple functions.
• Small size –less than 10um
• Ribosomes are different
• Reproduction by a process called binary fission – no mitosis or meiosis.

Cell Shape and Arrangement

Five major shapes

• Spheres – cocci
• Rods – bacilli
• Comma-shaped – vibrios
• Spiral-shaped flexible – spirochaetes
• Spiral-shaped rigid – spirilli

Occur as single cells, pairs, or filaments

Cell arrangement

• Bacteria grow in characteristic arrangements from random single cells to complex

assemblages formed when bacteria divide and fail to separate from each other.
• Pairs of spherical cells - diplococci
• chain of spherical cells- streptococci
• cluster of cells -staphylococci
Grouping bacteria according to requirement for oxygen

• Aerobic bacteria require oxygen

• Anaerobic bacteria cannot tolerate oxygen
• Facultative anaerobic bacteria can use oxygen or not

Grouping according to how they obtain their energy

• Heterotrophs = Organisms that require at least one organic compound, and often more
• Autotrophs = Produce all or most of their own organic compounds

Procaryotic Cell Structure

Typical bacterial cell
• Inside the plasma membrane:
o Cytoplasm – contained within plasma membrane
o Nucleoid region – where DNA is located
o Ribosomes – synthesize proteins
• Outside the plasma membrane:
o Cell wall – provides support and protection
o Glycocalyx – traps water, gives protection, help
evade immune system
o Appendages – pilli (attachment), flagella
(movement)

Glycocalyx/capsule
• Viscous material surrounding some bacteria. It is made of polysaccharide or polysaccharide-
polypeptide complex.
• Slime capsule
o Definite structure- attached firmly to cell wall.
• Slime layer
o Disorganised- without a definite shape-loosely attached

Functions of glycocalyx:

Protection:

• Binds water –prevents dehydration.

• Reservoir of stored food.
• Can determine the pathogenicity of bacteria.

Adherence:

• Streptococcus mutans – human teeth

• Ecoli –digestive system
• Bacteria –urinary tract infections.
Cell Wall Structure
• Most have rigid cell wall outside the plasma membrane

• Maintain cell shape and help protect against attack

• Also help avoid lysis in hypotonic solutions

• Archaea and some bacteria use protein

• Most bacteria use peptidoglycan

Composition of cell wall

• Cell wall composition varies widely amongst bacteria and is one of the most useful ways to
identify particular bacteria.
• Complex structure
• Strength due to Peptidoglycan (composed of amino acids and sugars)

Gram Stain

A Danish physician Hans Christian Gram in 1884 used a staining and washing technique to
differentiate between two forms of bacteria that differ in their cell wall composition.

Gram positive

• Relatively thick peptidoglycan layer

• Purple dye held in thick layer
• Cells are stained purple
• Vulnerable to penicillin that interferes in cell wall synthesis

Gram negative

Less peptidoglycan and a thin outer envelope of lipopolysaccharides

• Lose purple stain but retain final pink stain

• Cells are stained pink
• Resists penicillin and requires other antibiotics

Examples of gram positive and gram negative bacteria

• Gram positive
o Staphylococcus aureus, Streptococcus, Lactobacillus, Listeria , Clostridium
• Gram negative
o E.coli , Salmonella, Neisseria, Pseudomonas, Acetobacter

Plasma membrane
• Boundary between the cell and the extracellular environment

• Functions:

o Membrane transport in and out of cell, with selective permeability

o Cell signaling using receptors
o Cell adhesion
 • Structure: phospholipid bilayer +Protein no cholesterol

Motility
• Allows cells to move to favorable conditions

• Respond to chemical signals

• Swim, twitch, glide or adjust flotation

Flagella

• Swimming

• Different from eukaryotic flagella

• Like an outboard motor

• Differ in number and location of flagella

Pili

• Twitch or glide across surfaces

• Threadlike structures on surface of cell

• Shorter, thinner (3-10um in diameter),straighter and more numerous than flagella

• Also play important roles in bacterial reproduction and disease processes

Cytoplasm
• This is where cell growth and metabolism is carried out.
• Gel like substance
• Contains structures like ribosomes, nucleic acid and plasmids
• Composed of : water,enzymes,nutrients,waste and gases

Nucleoid
• Region of the cytoplasm where strands of DNA are found.
• Single strand of DNA - no proteins attached
• No membrane
Plasmids
• Fragments of DNA which occur in the cytoplasm independently of the nucleoid.
• Circular
• Can replicate independently of the chromosome.
• 5 -100 genes.
• Gives the bacterium the ability to synthesise new products

Reproduction
• Binary fission – divide by splitting in two

• A process by which a cell divides to produce two equal size progeny cells

• Basis for widely used method of detecting and counting bacteria in samples

o Place measured volume of sample into plastic dishes of agar

o Each single cells will form a visible colony

• Can also use fluorescent dye that binds bacterial DNA to directly count bacteria

Surviving Harsh Conditions

• Akinetes

o Found in aquatic filamentous cyanobacteria

o Develop when winter approaches
o Survive winter and produce new filaments in spring

• Endospores

o Tough protein coat

o Amazingly long dormant span
o Found in some Gram-positive bacteria
o Bacillus anthracis, Clostridium botulinum, Clostridium tetani

Ways of increasing variation in a bacterial population

Horizontal Gene Transfer = Organism receives genetic material from another organism without being
the offspring of that organism

a) Transformation = DNA released from a dead bacterium into the environment is taken up by
another bacteria
b) Transduction = A virus transfers genetic information from one bacterium to another
c) Conjugation = Direct physical interaction transfers genetic material from donor to recipient
cell
 a) Transformation:
• Uptake of naked DNA and its incorporation into bacterial chromosomes.
• No cell to cell contact
• Cells can be made able to take up the foreign DNA by

a) chemical treatment

b) cold shock

c) High voltage shock

b) Transduction
• Bacteriophage infects donor cell and destroys it.
• Most viral particles carry virus DNA
• 1 in 10,000 carry bacterial DNA by mistake
• Bacteriophage can then transfer this DNA to
another bacterium.

c) Conjugation
• Transfer of genes between two bacterial cells that are temporarly joined by a pilus.
• One bacterium acts as the donor and transfers DNA to a recipient cell

Endosymbiosis

• Procaryotes are far older and more diverse than eucaryotes.

• It is thought that eucaryotic cell organelles like nuclei,mitochondria and chloroplasts are
derived from procaryotic cells that became incorporated inside larger procaryotic cells
• This idea is called endosymbiosis

Evidence that supports endosymbiosis theory

• Organelles contain circular DNA,like bacterial cells

• Contain 70S ribosomes like bacteria
• Organelles have double membranes as though a single membraned cell had been engulfed
and surrounded by a larger cell.
• Organelles reproduce by binary fission, like bacteria
• Organelles are very like some bacteria that are alive today
 EUCARYOTES
1. Procaryotic cell
• Archaebacteria
• Eubacteria

2. Eucaryotic cell

• Animalia
• Plantae
• Fungi
• Protista

Components

• Cell wall (plants only)

• Cell membrane (plasma membrane/plasmalemma)
• Protoplasm: All internal contents of cell., Made up of nucleus & cytoplasm
• Cytoplasm made up of cytosol (fluid matrix)& organelles

Organelles

• Mitochondria
• Golgi apparatus
• Rough & smooth endoplasmic reticulum
• Ribosomes
• Lysosomes
• Centrioles
• Chloroplasts
• Vacuoles
• Peroxisomes

Nucleus
Functions:

• Controls genetic material (genes)

• Controls all cell activities by controlling protein synthesis
• DNA sends messages in form of mRNA

DNA -> mRNA -> pores in nuclear envelope -> cytoplasm -> ribosomes -> protein synthesis

Structure:

• Largest organelle (3-25µm in diameter)

• Enclosed by double membrane = nuclear envelope
• Perforated by pores of about 100nm in diameter
• Contains chromosomes (DNA & protein)
• Each species has a characteristic number of chromosomes e.g. humans - 46 per cell
• Normally appear as chromatin (unwound DNA)
 • Nucleus contains structures called nucleolus (nucleoli) = sites of ribosome synthesis
è Contains RNA, DNA & proteins

Ribosomes
Function:

• Sites of protein synthesis

• Translation of mRNA to particular sequence of amino acids proteins

Structure:

• 2 subunits of RNA & protein

• Join & become functional when attached to mRNA
• 1000s to millions per cell
• 2 types:
o Free Ribosomes (cytosol)
o Bound Ribosomes (attached to ER)
• Proteins made by bound ribosomes used in membrane production or exported
(e.g.hormones)

Endoplasmic Reticulum (ER)

Structure:

• Extensive network of internal membranes

• Surround tubules & sacs = cisternae

2 types:

1. Rough ER: Studded with ribosomes

2. Smooth ER: no ribosomes attached

Functions of Rough ER:

1. Secretion of proteins

Proteins produced by ribosomes enter ER, modified to glycoproteins, & then leave in vesicles

2. Production of membranes

Functions of Smooth ER:

1. Synthesis of lipids (e.g. steroids)

2. Carbohydrate metabolism (e.g. glucose in the liver)

3. Detoxification of drugs & poisons (e.g. in liver)

4. Pump Ca2+ ions from cytosol (e.g. muscle cells)

Golgi Apparatus
Structure:

• Stack of flattened membranous sacs

• Membranes of cisternae at opposite ends of stack are
different

1. Cis face: Receiving end

2. Trans face: Shipping end

• Products modified in stages from cis to trans face

• Vesicles depart from trans face & fuse with plasma
membrane to exit cell
• Large number in secretory cells

Functions:

• Receive transport vesicles from ER

• Centre of manufacturing, warehousing, sorting & shipping
• Products of ER are modified, stored, tagged & shipped out
• Modification of proteins
• Manufacture of some molecules e.g.polysaccharides
• Addition of molecular ID tags

Lysosomes
• Membrane enclosed bag of digestive enzymes

Functions:

- Intracellular digestion

- Destruction of fats, proteins, carbohydrates, nucleic acids

- Engulf other organelles -> renewal of cell

- Nutrition in unicellular organism (phagocytosis)

- Macrophages destroy bacteria by phagocytosis

- Excessive leakage can destroy cell

Vacuoles
Large membrane enclosed sac

3 types:

- Food vacuole (formed by phagocytosis)

- Contractile vacuole (unicellular organisms)

- Central vacuole (plants)

 • Vacuoles are part of the endomembrane system
o Nuclear envelope, rough ER, smooth ER, vesicles, Golgi, lysosomes, tonoplast

Functions:

• Storage of organic compounds (e.g. seeds)

• Storage of inorganic compounds (e.g. K+, Cl-)
• Function as lysosome in plant cells
• Disposal sites for metabolic by products
• Contain pigments (e.g. petals)
• Contain poisons

Mitochondria
• May be from 1 to 1000s depending on cell
• Enclosed by double membrane
• Outer membrane smooth, inner membrane
convoluted
• Infoldings = cristae
• Mitochondrial matrix and inner membrane contain enzymes for respiration

Function:

• Site of cellular respiration

• Sugars, fats etc. +O2 -> chemical energy
• Contain ribosomes: produce membrane proteins & enzymes
• Contain some DNA
• Possibly evolved from aerobic bacteria

Chloroplasts
Structure:

• Member of family of plantorganelles =Plastids

• Leucoplasts = colourless, found in dividing cells
• Amyloplasts = store starch (e.g. potatoes)
• Chromoplasts = pigmented
• Chloroplasts =green
• Contain chlorophyll
• Bounded by double membrane
• Contain membranous system arranged into flattened sacs = thylakoids
• Thylakoids may be stacked to from Grana
• These are embedded in a fluid matrix =stroma
• Contain ribosomes & some DNA

Cell Wall
• Found in plants only*
• *Procaryotes, fungi and some protists also have cell walls
• 0.1 to several µm thick
• Fibres made of cellulose embedded in matrix of polysaccharides & proteins
 • Secreted from vesicles produced by Golgi

Functions:

• Protection
• Maintain shape of cell
• Prevent excessive uptake of water

Extracellular Matrix (ECM)

• Animal cells

Structure:

• Glycoproteins (mainly)
• Collagen forms strong fibres outside cells
• Some cells attached to ECM by fibronectins – glue that sticks ECM to PM

Integrins bind ECM on one side & cytoskeleton on other

Functions:

• Support & anchorage for cells

• Communication: integrins transmit mechanical stimuli between cells interior and exterior

Cytoskeleton
Network of fibres throughout cytoplasm

Functions:

-Mechanical support

-Maintain cell shape

-Hold organelles in place

- May be involved in locomotion

3 types: Microtubules, microfilaments, intermediate filaments

1. Microtubules:

- Straight, hollow, thick (~25nm dia.) rods

- Wall constructed from protein, tubulin

- May radiate from centrosome in animal cells

- Locomotion of flagellae and cilia

- Strengthening of tissues e.g. windpipe

2. Microfilaments:

- Solid rods, narrow (~7nm dia.)

- Made from protein actin

- Important in muscle contraction

- Also functions in support

- Present in microvilli of plasma membrane

- Movement of Pseudopodia

- Cytoplasmic streaming in plant cells

3. Intermediate Filaments:

- Large variety of types of intermediate size

- More permanent

- Important in maintaining shape and fixing organelles e.g. axons of nerve cells

Cilia & Flagella

• Specialised arrangement of microtubules
• Locomotive appendages
• Contain a core of microtubules, covered in an extension of PM
• Each contains 9 pairs of microtubules in a ring with 2 single microtubules in middle (‘9+2’)

Flagella

• Long (10-200µm), whip-like structure

• Diameter about 0.25 µm
• Only one or a few per cell
• Found in some protists and sperm cells
• Usually undulates, driving cell same direction as axis of flagellum

Cilia

• Shorter (2 - 20 µm), more numerous on surface of cell

• Same diameter as flagella
• Found in some Protists (e.g. Paramecium) & in certain tissues e.g. ciliated lining of windpipe
• Back & forth motion
Cell Junctions
Plants: PM of adjacent cells separated by cell walls, so how do cells transfer material?

è Plasmodesmata… water & solutes can pass freely

Animals: 3 types

1. Tight junction: Membranes of adjacent cells fused

2. Desmosomes (anchoring junctions): Functions like rivets fastening cells together

3. Gap junctions (communicating junctions): Channels between cells. Wide enough for salts, sugars,
Aas and other small molecules to pass through. Common in embryos
 MENDEL AND GENETICS
Genetics
= The study of heredity – transmission of characteristics from one generation to another

• Concerned with study of genes – units of heredity that control characteristics of organisms

Mendel’s Laws of Inheritance

• Gregor Mendel, 1822 to 1884
• Entered monastery and became a priest
• Historic experiments with pea plants
• His paper was ignored at the time, but his findings were independently rediscovered years
later

Garden Pea, Pisum sativum

Several advantageous properties:

• Many different variable traits

• Normally self-fertilizing

o Female gamete fertilized by male gamete from same plant

o Easy to breed true-breeding lines (exhibit the same trait)

• Large flowers make crosses easy when desired

o Cross-fertilization or hybridization

• Character: a heritable feature, such as flower colour, that varies among individuals
• Trait: each variant for a character, such as purple or white flowers
• Mendel looked at inherited characters in an ‘either-or’ rather than ‘more-or-less’ manner
• A variable = a characteristic or trait found in individuals of a species
• Discontinuous variables: clearly defined categories with no intermediates
• Continuous variables: Intermediates. E.G. heights of humans

Self-fertilising

• Self-fertilisation is prevented if making a cross between pea plants with contrasting

characters
• Anthers of 1 plant are dissected & transferred to carpel of other plant
• Progeny self-fertilise naturally

• Pea plants used were grown from seed that came from plants that were pure-bred (i.e. when
crossed with itself, offspring will resemble parents for a given trait)
• Recorded numbers of individuals in each class
• Established ratios of contrasting characters of subsequent generations
Single-factor cross
• Where the experimenter follows only a single trait
• P generation = True-breeding parents

F1 generation = Offspring of P cross Monohybrids (if parents differ in one trait)

F2 generation = F1 self-fertilizes, Recessive trait reappears

Monohybrid crosses
• Single characteristic e.g. tall vs dwarf
• Pure breeding tall plants and crossed with pure-breeding small plants (Parents or P
generation)
• Offspring are the F1 generation (first filial)
• These are hybrids (i.e. not pure-bred)
• Allowed F1 generation to self-pollinate to produce F2 generation (2nd filial)
• F2 generation included both tall & dwarf plants in ratio of 3 tall to 1 dwarf (3:1)
• Realised that there must be 2 independent factors for each characteristic that was conserved
through lineage

Example:

• Dwarf characteristic that disappeared in F1 reappeared in F2

• Controlling factor for dwarf remained intact but wasn’t expressed in the presence of a factor
for tall
• Must be 2 independent factors
• One factor comes from 1 parent the other factor comes from other parent

Mendel’s three important ideas (#1 and 2)

• Traits are dominant and recessive Dominant variant is displayed in hybrids

• Recessive variant is masked by dominant
• Genes and alleles = Particulate mechanism of inheritance
o His “unit factors” are genes
o Every individual has two genes for a character
o A gene has two variant forms, or alleles

Mendel’s three important ideas (#3)

Segregation of alleles

• Two copies of a gene carried by an F1 plant segregate (separate) from each other, so that
each sperm or egg carries only one allele
• F2 traits follow approximately 3:1 ratio
• Mendel’s Law of Segregation = Two copies of a gene segregate from each other during the
transmission from parent to offspring.
Genotype and phenotype
Genotype – The genetic composition of an individual

• TT – homozygous dominant
• tt – homozygous recessive
• Tt – heterozygous

Phenotype – Physical or behavioral characteristics that are the result of gene expression

• TT and Tt are tall

• tt is dwarf

Homozygous and Heterozygous

Homozygous: identical alleles for a characteristic. E.G. Pea plant homozygous for purple flowers (PP).
Pea plant homozygous for white flowers (pp)

Heterozygous: different alleles for a characteristic. E.G. Pp

Punnett square
Step 1. Write down genotypes of parents

• Male parent: Tt
• Female parent: Tt

Step 2. Write down the possible gametes that each parent can make

• Male gametes: T or t
• Female gametes: T or t

Creating a Punnett square

Step 3. Create an empty Punnett square.

Step 4. Fill in the possible genotypes.

Results of a Punnett square

Step 5. Determine relative proportions of

genotypes and phenotypes.

• Genotype ratio = TT:Tt:tt

§ 1:2:1
• Phenotype ratio = tall:dwarf
§ 3:1
Modern interpretation
1. Alternative versions of genes (different alleles) account for variations in inherited characters.

The gene for flower colour exists in 2 versions, 1 for purple, 1 for white.

Each gene has locus but DNA can vary in its sequence of info. So 2 DNA variations at flowercolour
locus

2. For each character, an organism inherits 2 alleles, 1 from each parent

In homologous pair, there is one chromosome from each parent

3. If 2 alleles differ, one, the dominant allele is fully expressed in organism’s appearance; the other
(recessive allele) has no noticeable effect E.G. purple is dominant over white : F1

4. Two genes for each character segregate during gamete production (meiosis)

Sex cells only receive 1 gene from each pair

50% of gametes receive each allele

This is Mendel’s LAW OF SEGREGATION

Mendel’s First Law

1. Law of segregation: The characters of an organism are controlled by pairs of alleles which separate
in equal numbers into different gametes as a result of meiosis

Testcross

• A dwarf pea plant must be tt

• A tall pea plant could be either TT or Tt, so genotype must be determined by a testcross

• Cross the unknown individual (TT or Tt) to a homozygous recessive individual (tt)

If some offspring are dwarf, unknown individual must have been Tt

If all offspring are tall, unknown individual was TT

Summary

• Mendel – father of genetics

• Information is passed to offspring via genes
• Different versions of genes exist (alleles) and account for variations in inherited characters
Dihybrid crosses
Dihybrid cross

• Mendel derived law of segregation (50% of alleles from each parent) by carrying out
monohybrid crosses
• What would happen in a mating of parental varieties differing in 2 characters – a dihybrid
cross??
• E.G. Seeds may be either yellow or green
o Seeds may be either round or wrinkly
• From looking at monohybrid crosses, Mendel knew that yellow seed is dominant (Y) and
green seed is recessive (y)
• Also, round is dominant [R] and wrinkly is recessive [r]
• Will Y and R alleles always stay together, generation after generation? Will the 2
characteristics be transmitted to offspring as a package?
• Or are seed colour & seed shape inherited independently of each other?
• Do the cross!

• F1 generation: genotype is YyRr and phenotype is yellow and round

• 2 pairs of alleles segregate independently of each other. So, genes are packaged into
gametes in all possible allelic combinations, as long as each gamete has one allele for each
gene (or character)
• Alleles combine & make up the phenotypes in the F2 generation in a 9:3:3:1 ratio
• Each character is independently inherited. In dihybrids, 2 alleles for seed colour segregate
independently of 2 alleles for seed shape

→ Law of independent assortment

2 or more pairs of alleles segregate independently of each other as a result of meiosis

Relationship between genotype & phenotype is rarely simple….

• Mendel studied characters that were determined by one gene, for which there are only 2
alleles, one completely dominant over the other
• Most heritable characters can be more complex

Dominance

• Phenotype of dominant allele is expressed

• Phenotype of heterozygote & homozygote are indistinguishable
• A dominant allele does not subdue or mute or change a recessive allele in any way
• Just because an allele is dominant, doesn’t mean it is more common
Co-dominance

• Phenotypes of both alleles are expressed

• MN blood groups
• M: produces antigen M on red blood cells
• N: produces antigen N on RBC
• MN: produces M and N antigens on RBC
• In co-dominance, the heterozygote has character of both parents

Incomplete dominance

• Phenotype is intermediate between dominant & recessive traits

• Occurs where a single dominant allele doesn’t make enough gene product to control
characteristic completely
• E.G. Snapdragons: Cross homozygous red flowers with homozygous white flowers, get pink
flowers!
• F2 generation segregate into red, pink and white in ratio 1:2:1
• Heterozygote has phenotype intermediate between 2 parents characters

Dominance/recessive relationships

1. Range from complete dominance, through various degrees of incomplete dominance, to co-
dominance

2. Reflect how specific alleles are expressed in phenotype & do not involve ability of 1 allele to
subdue another

3. Do not determine the relative abundances of alleles in a population

Multiple Alleles

• Genes which exist in more than 2 allelic forms e.g. human blood groups
• A, B, AB, O: based on substance coating RBC
• A type blood: A substance
• B type blood: B substance
• AB type blood: both A and B substances
• type blood: neither substances

4 blood groups arise from various combinations of 3 different alleles of 1 gene

→ IA IB i

• 6 possible phenotypes:
Pleiotropy

• Most genes have multiple phenotypic effects

• Pleiotropy : the ability of a gene to affect an organism in many ways

Recessively inherited disorders

• Many human disorders follow Mendelian patterns of inheritance

• Recessively inherited disorder turns up only in the homozygous individuals who inherit one
recessive allele from each parent
• Don’t have disorder : Aa or AA
• Have disorder: aa
• Heterozygotes are carriers because they can transmit the disorder to offspring
o Cystic fibrosis: One in 25 Caucasians is a carrier; one in every 2500 are homozygous
recessive
o Normal gene codes for a membrane protein in lungs.
o Recessive homozygotes have build up of mucus in lungs, pancreas & other organs

Dominantly inherited disorders

• Lethal dominant alleles are less common than lethal recessives

• One example is a certain type of bone growth disorder resulting in dwarfism
(achondroplasia)
o 1 in 10,000 people has this disorder
o Heterozygous individuals have the dwarf phenotype
o Therefore, if you don’t have disorder you are homozygous for recessive allele

Multifactorial Disorders

• Diseases that have both genetic and environmental influences

• e.g. heart disease, diabetes
Genetics
Learning Objectives

• Explain why X-linked recessive traits are more likely to occur in males.
• Describe how Drosophila fruit flies can be useful in genetic experiments
• Define what a mutation is
• Explain how mutations can increase genetic variation

Disease genes can be recessive or dominant, autosomal or sex-linked

• Many of the alleles causing human genetic disease are recessive, like Cystic Fibrosis
• But some are dominant, like Huntington disease
o Huntington disease has an autosomal dominant inheritance pattern
o Gene is on one of 22 pairs of autosomes
• Disease genes can also be found on the sex chromosomes

Linkage
• Each chromosome is made up of 100s – 1000s of genes linked together in a linear sequence
• Genes on the same chromosome will usually be inherited together and are described as
linked
• Expt on sweet pea: plants homozygous for purple flower & long pollen grains were crossed
with plants homozygous for red flower & round pollen grain

→ Offspring had purple flowers & long pollen

→ F1 generation selfed. Expect pairs of alleles would segregate independently of each other
in 9:3:3:1

• Didn’t happen. Instead they represented original parents (purple/long, red/round)

• Independent assortment didn’t occur
• Genes are linked on same chromosome

Morgan’s Experiments Showed a Correlation Between a Genetic Trait and the Inheritance of a Sex
Chromosome in Drosophila

• Thomas H. Morgan, 1866 to 1945, first geneticist to receive Nobel Prize

• Found a mutant male fly with white eyes rather than the normal red eyes

• Testcross results suggested a connection between alleles for eye color and sex

• X-linked gene the first to be located on a specific chromosome

Suitable for genetic experiments

• Each pair of flies produces hundreds of offspring. A new generation can be bred every 2
weeks
• Only have 4 chromosomes
• Easy to handle & look after
• Can be sexed quickly

Sex linkage

• Sex chromosomes also have genes for other characters unrelated to sex
• Characters on the X chromosome are sex-linked characters
• Fathers pass sex-linked characters onto daughters
• Mothers pass sex-linked characters onto both sons &

Sex chromosomes

• In humans: 22 pairs of autosomal chromosomes; 1 pair of sex chromosomes

• Female: XX
Male: XY
• If Y genes are present in offspring, testes develop → male
• If Y genes are absent in offspring, ovaries develop →?

X-linked traits 1

• In humans, X chromosome is larger and carries more genes than the Y chromosome
• Genes found on the X but not the Y are X-linked genes
o Sex-linked genes are found on one
o sex chromosome but not the other
• Males are hemizygous for X-linked genes
• Example: Hemophilia A

X-linked traits 2

• Hemophilia A is caused by recessive X-linked gene

• Disease allele (Xh-A)
o encodes defective version of a clotting protein
GENETIC VARIATION

Genetic recombination

• Meiosis & random fertilisation create genetic variation

• Genetic recombination: production of offspring with new combinations of traits inherited
from 2 parents
• Recombinants are a result of cross-over or trading of DNA between adjacent chromatids
• Crossing-over occurs in Prophase I of meiosis
• Recombination also occurs in linked genes aswellas unlinked genes

Mutations

• Genetic variation can result from independent assortment, crossing over in chromosomes
and mutations
• Mutation: change in structure, arrangement or quantity of DNA in chromosomes
• Occur randomly &
• Mutation is detected by a marked difference in characteristics of offspring from parents
• Chromosome mutation: change in structure or number of chromosomes
• Gene mutation: change in structure of gene
• Somatic mutations occur in cells in body other than germ cells (reproductive organs)
• Somatic mutations are not passed onto offspring, germ cell mutations can be

Chromosome mutations

• Euploidy & aneuploidy

• Euploidy: Having full complement of chromosomes. Can sometimes get alteration in number
of whole sets of chromosomes. Rare in animals
• Aneuploidy: Variation in chromosomal number.Part of a chromosome is deleted, or
duplicated or broken off & added to a different chromosome
• Example - Down syndrome: extra chromosome 21 (trisomy 21)

Gene mutations

• Gene: sequence of nucleotide pairs that code for amino acids

• Changes can occur in this coding
• Gene mutations can occur spontaneously or can be due to environmental factors such as
exposure to radioactive rays that break up DNA

Consequence of mutations

• Occasionally beneficial
• Brings about genetic variation
• Mutations can often be lethal or disadvantageous

Summary

• X- linked genes are found on the X chromosome but not the Y chromosome.
• Recessive X- linked alleles in humans can cause disorders which are more likely to occur in
males
• Mutations are another form of genetic variation
• Mutations can be in genes or chromosomes