Tab 1

BIOCHEMISTRY
Lecture | s.y 2024-2025

WEEK 2: INTRODUCTION TO gene and its role in the transfer of

information in the cell.
BIOCHEMISTRY
II.I. THREE MAIN TYPES OF BIOCHEMISTRY
I. THE SCIENCE OF BIOCHEMISTRY
1.​ PLANT BIOCHEMISTRY
➔​ It deals with the structures and -​ involves the study of the biochemistry
functions of cellular components of autotrophic organisms such as
such as proteins, carbohydrates, photosynthesis and other
lipids, nucleic acids, and other plant-specific biochemical
biomolecules. processes.
➔​ Among the vast number of different
biomolecules, many are complex and 2.​ GENERAL BIOCHEMISTRY
large molecules (known as -​ encompasses both plant and animal
polymers), consisting of similar biochemistry.
repeating subunits (known as
monomers). 3.​ HUMAN/MEDICAL/MEDICINAL
BIOCHEMISTRY
II. HISTORY OF BIOCHEMISTRY -​ focuses on the biochemistry of
humans and medical illnesses.
➔​ In 1828, Friedrich Wöhler published a
paper on urea synthesis, proving that III. CHEMICAL BASIS OF LIFE
organic compounds can be created
artificially.
➔​ The dawn of biochemistry may have
been the discovery of the first
enzyme, diastase (today called
amylase), in 1833 by Anselme Payen.
➔​ Eduard Buchner contributed the first
demonstration of a complex
biochemical process outside of a cell
in 1896: alcoholic fermentation in cell
extracts of yeast.
➔​ Although the term “biochemistry”
seems to have been first used in 1882,
it is generally accepted that the ➔​ The biomolecules such as proteins
formal coinage of biochemistry found in living organisms are
occurred in 1903 by Carl Neuberg, a compounds based on carbon.
German chemist. ➔​ The third most abundant element of
➔​ Another significant historic event in living organisms is carbon.
biochemistry is the discovery of the
➔​ Carbon is the basis of all biochemical pairs of electrons to form a covalent
compounds, therefore carbon is bond.
essential for Earth's life. ➔​ Compounds containing mainly
➔​ The discipline of organic chemistry carbon and hydrogen are considered
best explains the properties of organic compounds while inorganic
biomolecules, such as form and compounds are compounds
chemical reactivity. composed mostly of elements other
than carbon and hydrogen.
III.I. CARBON IS IMPORTANT TO LIFE ➔​ A structural formula indicates a
molecule's composition and
➔​ Cells consist of many complex approximate structure and shape.
molecules, called macromolecules, Single bonds, double bonds, and
including proteins, nucleic acids (RNA triple bonds are covalent bonds in
and DNA), carbohydrates, and lipids. which two bonded atoms share one,
➔​ For all these macromolecules the two, or three pairs of electrons,
fundamental component is carbon. respectively.
The carbon atom has unique
properties that allow it to form III. III. FUNCTIONAL GROUPS
covalent bonds with as many as four
different atoms, making this versatile ➔​ The chemical reactions of
element ideal for serving as the biomolecules are dictated by the
macromolecules' basic structural functional groups they contain.
component, or "backbone." ➔​ The first carbon atom attached to the
functional group is called alpha
STRUCTURE OF CARBON carbon; the second is beta carbon;
the third, is gamma carbon, and so
on.
➔​ A functional group can be classified
as primary, secondary, or tertiary,
depending on whether it is
connected to one, two, or three
carbon atoms.

IV. MANY BIOMOLECULES ARE POLYMERS

➔​ In cells (proteins, polysaccharides,

and nucleic acids), the principle
III.II. CHEMICAL BONDING
biomolecules are polymer chains of
amino acids, monosaccharides, and
➔​ Ionic compounds contain both
nucleotides, respectively.
positively and negatively charged
➔​ Biopolymers are formed by
ions resulting in a complete zero
condensation reactions in which
charge.
water is removed from the reacting
➔​ Most covalent compounds consist of
monomer units.
molecules, groups of atoms in which
at least two atoms share one or more
➔​ Each unit of a biopolymer's monomer STRUCTURE OF STARCH

is called a residue. IV.III. LIPIDS AND MEMBRANES

IV. I. PROTEINS

➔​ Proteins make up much of the cell's

chemical reactions.
➔​ Proteins are also the major structural
constituents of most cells and tissue
➔​ Proteins are also called polypeptides
because they consist of amino acids
that are bound together by peptide
bonds.
➔​ Lipids are a complex group of
➔​ Peptide bonds are essentially amide
biomolecules, consisting primarily of
bonds formed by condensation of
hydrogen and carbon, that is,
carboxyl groups and amino groups of
hydrocarbons.
consecutive amino acids in the
➔​ A fatty acid is the principal building
polymer chain.
block of many lipids. The cell
membrane's most common
PEPTIDE LINKAGE BETWEEN AMINO ACIDS
structural lipid — glycerophospholipid
— contains 2 fatty acids, glycerol, and
a group of polar heads.

GLYCEROPHOSPHOLIPID

IV.II. POLYSACCHARIDES

➔​ Polysaccharides are polymers of DOUBLE PHOSPHOLIPID BILAYER OF CELL MEMBRANE

simple sugars called
monosaccharides (e.g. glucose).
➔​ Diverse polysaccharides perform
either structural (cellulose) or energy
storage (glycogen, starch) functions.
➔​ The polysaccharides and
monosaccharides were among the
first biomolecules examined by
organic chemists.
 IV.IV. NUCLEIC ACIDS V. THE ENERGETICS OF LIFE

➔​ Nucleic acids are constituted by ➔​ In animals, energy is derived from the

monomer units of nucleotides. breakdown of fuel molecules by
➔​ Nucleotides themselves contain a processes referred to as catabolism.
monosaccharide, a nitrogen base, In turn, the energy released from
and one or more groups of catabolism is used to drive
phosphates. biosynthetic processes collectively
➔​ All nucleotides are held together by referred to as anabolism.
phosphodiester bonds where one ➔​ Energy flows within biological
group of phosphates is attached to systems are covered by the discipline
two units of sugar in the polymer's known as bioenergetics
backbone. ➔​ The energy required for the work and
➔​ Nucleotides play a key role in the biosynthesis of human and animal
transmission of information in all cellular structures is derived from the
organisms (DNA). The RNA can also dietary organic molecules.
perform structural and enzymatic
functions. STRUCTURE AND BONDING
I. THE PERIODIC TABLE
NUCLEOTIDE STRUCTURE

➔​ The nucleus contains positively

charged protons and uncharged
neutrons.
PHOSPHODIESTER LINKAGE IN RNA ➔​ The electron cloud is composed of
negatively charged electrons.

➔​ Elements in the same row are similar

in size.
➔​ Elements in the same column have II. SECOND ROW ELEMENTS
similar electronic and chemical
properties. ➔​ Since each of the four orbitals
available in the second shell can hold
two electrons, there is a maximum
capacity of eight electrons for
elements in the second row.
➔​ The second row of the periodic chart
consists of eight elements, obtained
by adding electrons to the 2s and
three 2p orbitals.

➔​ An s orbital has a sphere of electron

density and is lower in energy than
the other orbitals of the same shell.
➔​ A p orbital has a dumbbell shape
and contains a node of electron III. REVIEW OF BONDING
density at the nucleus. It is higher in
energy than an s orbital. ➔​ Bonding is the joining of two atoms in
a stable arrangement.
➔​ Through bonding, atoms attain a
complete outer shell of valence
electrons.
➔​ Through bonding, atoms attain a
stable noble gas configuration.
➔​ Since there is only one orbital in the ➔​ Ionic bonds result from the transfer of
first shell, and each shell can hold a electrons from one element to
maximum of two electrons, there are another.
two elements in the first row, H and ➔​ Covalent bonds result from the
He. sharing of electrons between two
nuclei.
➔​ An ionic bond generally occurs when
elements on the far left side of the
periodic table combine with
➔​ Each element in the second row of elements on the far right side,
the periodic table has four orbitals ignoring noble gases.
available to accept additional ➔​ A positively charged cation formed
electrons: one 2s orbital, and three 2p from the element on the left side
orbitals. attracts a negatively charged anion
formed from the element on the right
side. An example is sodium chloride,
NaCl.
 V. REVIEWS OF LEWIS STRUCTURE

IV. BONDING IN MOLECULAR HYDROGEN (H2) ➔​ Lewis structures are electron dot
representations for molecules. There
➔​ Hydrogen forms one covalent bond. are three general rules for drawing
➔​ When two hydrogen atoms are joined Lewis structures:
in a bond, each has a filled valence 1.​ Draw only the valence electrons.
shell of two electrons. 2.​ Give every second-row element an
octet of electrons, if possible.
3.​ Give each hydrogen two electrons.

➔​ Second-row elements can have no

more than eight electrons around
them. For neutral molecules, this has
two consequences: ➔​ The number of electrons “owned” by
◆​ Atoms with one, two, or three different atoms is indicated in the
valence electrons form one, following examples:
two, or three bonds,
respectively, in neutral
molecules.
◆​ Atoms with four or more
valence electrons form
enough bonds to give an octet.
This results in the following
equation:

◆​ When second-row elements

form fewer than four bonds
their octets consist of both
bonding (shared) and
nonbonding (unshared)
electrons. Unshared electrons
are also called lone pairs.
 VI. ISOMERS ➔​ Parentheses are used around similar
groups bonded to the same atom.
➔​ In drawing a Lewis structure for a
molecule with several atoms,
sometimes more than one
arrangement of atoms is possible for

VIII.I. EXAMPLES OF CONDENSED STRUCTURES

a given molecular formula.

➔​ Both are valid Lewis structures and
both molecules exist. These two
compounds are called isomers.
➔​ Isomers are different molecules
having the same molecular formula.
Ethanol and dimethyl ether are
constitutional isomers.

VII. EXCEPTIONS TO THE OCTET RULE

VII.I. ELEMENTS IN GROUPS 2A AND 3A
VIII.II. EXAMPLES OF CONDENSED STRUCTURES
CONTAINING C-O DOUBLE BOND

VII.II. ELEMENTS IN THE THIRD ROW

IX. SKELETAL STRUCTURES

VIII. DRAWING ORGANIC MOLECULES -
CONDENSED STRUCTURES
➔​ Assume there is a carbon atom at
the junction of any two lines or at the
➔​ All atoms are drawn in, but the
end of any line.
two-electron bond lines are generally
➔​ Assume there are enough hydrogens
omitted.
around each carbon to make it
➔​ Atoms are usually drawn next to the
tetravalent.
atoms to which they are bonded.
➔​ Draw in all heteroatoms and
hydrogens directly bonded to them.

IX.I. EXAMPLES OF SKELETAL STRUCTURES FLUID MOSAIC MODEL

WEEK 3: THE CELLS

CELL MEMBRANE
I. CELL STRUCTURES AND FUNCTIONS

➔​ The cell structure consists of

individual components with specific
functions that are essential for the
processes of life. These components
are: the cell wall, cell membrane
cytoplasm, nucleus, and cell
organelles.

I.I CELL MEMBRANE

I.II. CELL WALL

➔​ Barrier for cell contents
➔​ Double phospholipid layer
➔​ A cell wall is defined as the non-living
◆​ Hydrophilic heads
component, covering the outmost
◆​ Hydrophobic tails
layer of a cell.
➔​ Other materials in the cell membrane
➔​ It is a rigid and stiff structure
◆​ Protein
surrounding the cell membrane.
◆​ Cholesterol
➔​ It provides shape and support to the
◆​ Glycoproteins
cells and protects them from
mechanical shocks and injuries.
➔​ It is present exclusively in eukaryotic ➔​ The nucleus is surrounded by the
plants, fungi, and a few prokaryotic nuclear envelope that separates the
organisms. DNA from the rest of the cell.

I.V. CELL ORGANELLE

I.III. CYTOPLASM

➔​ The cytoplasm is a thick, clear,

jelly-like substance present inside the
cell membrane.
➔​ Most of the chemical reactions within
a cell take place in this cytoplasm.
➔​ The cell organelles such as
endoplasmic reticulum, vacuoles,
mitochondria, and ribosomes are
suspended in this cytoplasm.
Nucleolus The nucleolus is the site of
ribosome synthesis. Also, it is
involved in controlling cellular
activities and cellular
reproduction

Nuclear The nuclear membrane protects

Membrane the nucleus by forming a
boundary between the nucleus
and other cell organelles

Chromosomes Chromosomes play a crucial role

in determining the sex of an
individual. Each human cells
contain 23 pairs of
I.IV. NUCLEUS
chromosomes

➔​ The nucleus contains the hereditary Endoplasmic The endoplasmic reticulum is

Reticulum involved in the transportation of
material of the cell, the DNA.
substances throughout the cell. It
➔​ It sends signals to the cells to grow, plays a primary role in the
mature, divide, and die.
 metabolism of carbohydrates, ➔​ Examples of prokaryotes are bacteria
synthesis of lipids, steroids, and and archaea.
proteins. ➔​ Examples of eukaryotes are protists,
fungi, plants, and animals
Golgi Bodies Golgi bodies are called the cell’s
post office as it is involved in the (everything except prokaryotes).
transportation of materials within
the cell

Ribosome Ribosomes are the protein

synthesizers of the cell

Mitochondria The mitochondrion is called “the

powerhouse of the cell”. It is
called so because it produces
ATP – the cell’s energy currency

Lysosomes Lysosomes protect the cell by

engulfing the foreign bodies
entering the cell and helps in cell
renewal. Therefore, it is known as
the cell’s suicide bags

Chloroplast Chloroplasts are the primary ➔​ The common features of prokaryotic

organelles for photosynthesis. It and eukaryotic cells are:
contains the pigment chlorophyll
◆​ DNA
Vacuoles Vacuoles store food, water, and ◆​ Plasma membrane
other waste materials in the cell ◆​ Cytoplasm
◆​ Ribosomes

I.VI. MITOCHONDRIA
III. WATER REACTION MEDIUM IN THE CELL
III.I. PROPERTIES OF WATER

HYDROGEN BONDING

II. PROKARYOTIC AND EUKARYOTIC CELLS

➔​ Is a special type of dipole-dipole
➔​ There are two broad types of cells: attraction
◆​ Prokaryotic ➔​ An important component of the three
◆​ Eukaryotic major macromolecules in
➔​ Prokaryotic cells lack internal cellular biochemistry
bodies (organelles), while eukaryotic
cells possess them.
 ➔​ The H-bonding is responsible for the HIGH HEAT OF VAPORIZATION
structure and properties of proteins
(enzymes).
➔​ Hydrogen bonding between water
molecules makes water an extremely
cohesive liquid.

COHESION

➔​ It is the attraction of molecules to

other molecules of the same kind.

ADHESION
UNIVERSAL SOLVENT

➔​ Is when water is attracted to other

➔​ dissolve other polar molecules and
substances.
ionic compounds.
➔​ water readily dissolves hydrophilic
HIGH SURFACE TENSION
compounds.
➔​ Nonpolar molecules experience
hydrophobic interactions in water

HYDROPHOBIC INTERACTIONS

➔​ Hydrophobic interactions describe

the water-hydrophobic relations (low
water-soluble molecules).
➔​ Hydrophobic molecules are nonpolar
and usually have a long chain of
carbons that do not interact with
molecules of water
HIGH SPECIFIC HEAT
NUCLEOPHILIC NATURE OF WATER pH <7 is acidic, pH > 7 is basic or alkaline

1 change in pH units equals a 10-fold

change in [H+]

WEEK 4: AMINO ACIDS

I. AMINO ACIDS AS BUILDING BLOCKS OF
PROTEIN

➔​ A nucleophile is a species (an ion or

PROTEIN
a molecule) which is strongly
➔​ Greek word, "proteios," meaning
attracted to a region of positive
primary.
charge
➔​ Make up 3/4th of total dry body
➔​ Nucleophiles are negatively charged
weight
or have unshared pairs of electrons
➔​ Contains the major components of C,
--> attack electrophiles during
H , O, and N, while S and P minor
substitution or addition reactions.
components
➔​ Examples of nucleophiles: are oxygen,
➔​ Distinguished by nitrogen
nitrogen, sulfur, carbon, water (weak)
➔​ Commonly contain 20 types of amino
➔​ Important in condensation reactions,
acids
where hydrolysis reactions are
favored.
I.I. TYPES AND FUNCTIONS OF PROTEIN
e.g. protein ------> amino acids
➔​ In the cell, these reactions only occur
in the presence of hydrolases ROLE EXAMPLES FUNCTIONS

➔​ Condensation reactions usually use

Digestive Amylase, Breakdown
ATP and exclude water to make the Enzyme lipase, pepsin nutrients in food
reactions more favorable into small pieces
that can be readily
absorbed
IONIZATION OF WATER
Transport Hemoglobin Carry substances
➔​ Pure water ionizes slightly and can throughout the
act as an acid (proton donor) or body in blood or
lymph
base (proton acceptor).
Structure Actin, tubulin, Build different
2H2O ---> H3O+ + OH-, but usually written keratin structures, like the
cytoskeleton

H2O ---> H+ + OH-

Hormone Insulin, Coordinate the
Signaling glucagon activity of different
pH OF WATER/pH SCALE body systems

Defense Antibodies Protect the body

pH = - log [H+], so at equilibrium
from foreign
pathogens
pH = -log (1.0 x 10-7) = 7
Contraction Myosin Carry out muscle
 contractions

Storage Legume Provide food for the

storage early development
proteins, egg of the embryo or
white the seedling
(albumin)

I.II. AMINO ACIDS

I.II.I. STRUCTURE OF AMINO ACIDS

➔​ The building blocks of proteins

➔​ Also used as single molecules in ➔​ The α carbon is chiral or asymmetric
biochemical pathways (4 different groups are attached to
➔​ Two functional groups: the carbon; the exception is glycine.)
◆​ carboxylic acid group ➔​ Amino acids exist as stereoisomers
◆​ the amino group on the alpha (same molecular formula, but differ
(𝛂) carbon in arrangement of groups).
➔​ Have different side groups (R) ◆​ Designated D(right) or L(left).
◆​ Properties dictate the behavior ◆​ Amino acids used in nature are
of amino acids of L configuration.
◆​ Structure of R also influences ◆​ α amino group orientation
solubility determines
●​ NH3+ on left = L
●​ NH3+ on right = D

➔​ Both the –NH2 and the –COOH groups

in an amino acid undergo ionization
in water.
➔​ At physiological pH (7.4), a zwitterion
➔​ There are 20 standard amino acids
forms
called α -amino acids because they
◆​ Both + and – charges
all have an amino (NH3+) group and a
◆​ Overall neutral
carboxyl group (COOH) attached to
◆​ Amphoteric
C-2 carbon (α -carbon).
●​ The amino group is
protonated
●​ Carboxyl group is
deprotonated
➔​ Soluble in polar solvents due to ionic
character
 I.II.II. STANDARD AMINO ACIDS ➔​ Aromatic (bulky, neutral, polarity
depends on R)

➔​ Basic
◆​ Acidic
●​ R group = carboxylic
acid
●​ Donates H+
●​ Negatively charged
I.II.III. CLASSIFICATION OF AMINO ACIDS

CLASSIFIED BY THE STRUCTURE OF R

➔​ Nonpolar (hydrophobic, neutral,
aliphatic)

◆​ Basic
●​ R group = amine
●​ Accepts H+
●​ Positively charged
●​ Ionizes at pH 6.0

➔​ Polar (hydrophilic, neutral, typically

H-bond)
 I.II.IV. AMINO ACID ORGANIZATION

I.II.V. STEREOCHEMISTRY OF AMINO ACIDS

➔​ All amino acids (except glycine) are

optically active

➔​ Fischer projections: