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BIOCHEMISTRY (CHM3)
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BIOCHEMISTRY MIDTERMS CHEM
WEEK 7 PROTEINS
Characteristics of Proteins:
• A protein is a naturally-occurring,
unbranched polymer in which the
monomer units are amino acids.
• Proteins are the most abundant molecules
in cells after water, accounting for about
15% of a cell’s overall mass.
• Elemental composition: Proteins contain
Carbon (C), Hydrogen (H), Nitrogen (N),
Oxygen (O), and most also contain Sulfur
(S).
• The average nitrogen content of proteins
is 15% by mass.
• Also present are Iron (Fe), phosphorus
(P), and some other metals in some
specialized proteins.
Amino Acids: The Building Blocks for Proteins:
• Amino acid: An organic compound that
contains both an amino (-NH2) and
carboxyl (-COOH) groups attached to the
same carbon atom.
• The position of the carbon atom
is Alpha (α).
• The - NH2 group is attached at the
alpha (α) carbon atom.
• The - COOH group is attached at
the alpha (α) carbon atom.
• R = side chain – varying in size, shape,
charge, acidity, functional groups present,
hydrogen-bonding ability, and chemical
reactivity.
• More than 700 amino acids are
known.
• Based on common “R” groups,
there are 20 standard amino acids.
• All amino acids differ from one another
by their R-groups.
• Standard amino acids are divided into four
groups based on the properties of R-
groups:
1. Non-polar amino acids: R-groups are
non-polar.
• Such amino acids are
hydrophobic (water-
fearing) and insoluble in
water.
• Eight of the 20 standard
amino acids are non-
polar.
• When present in proteins, they
are located in the interior of the
protein where there is no polarity.
1. Polar amino acids: R-groups are polar.
• Three types: Polar
neutral, Polar acidic, and
Polar basic.
• Polar-neutral: Contains
polar but neutral side
chains – Seven amino
acids belong to this
category.
• Polar acidic: Contain a
carboxyl group as part of
the side chains – Two
amino acids belong to
this category.
• Polar basic: Contain an
amino group as part of
the side chain – Two
amino acids belong to
this category.
Nomenclature:
• Common names assigned to the amino
acids are currently used.
• Three-letter abbreviations are widely used
for naming:
• The first letter of the amino acid
name is compulsory and
capitalized, followed by the next
two letters not capitalized, except
in the case of Asparagine (Asn),
Glutamine (Gln), and Tryptophan
(Trp).
• One-letter symbols are commonly used for
comparing amino acid sequences of
proteins:
• Usually, the first letter of the
name.
• When more than one amino acid
has the same letter, the most
abundant amino acid gets the 1st
letter.
• Both types of abbreviations are given in
the following slides.
Non-polar Amino Acids:
• Glycine (Gly)
• Alanine (Ala)
• Valine (Val)
• Leucine (Leu)
• Isoleucine (Ile)
• Proline (Pro)
• Phenylalanine (Phe)
• Methionine (Met)
• Tryptophan (Trp)
Polar Neutral Amino Acids:
• Serine (Ser)
• Cysteine (Cys)
• Threonine (Thr)
• Asparagine (Asn)
• Glutamine (Gln)
• Tyrosine (Tyr)
Polar Acidic and Basic Amino Acids:
Polar Acidic Amino Acids:
• Aspartic Acid (Asp)
• Glutamic Acid (Glu)
Polar Basic Amino Acids:
• Histidine (His)
• Lysine (Lys)
• Arginine (Arg)
Chirality and Amino Acids:
• Four different groups are attached to the α-
carbon atom in all of the standard amino acids
except glycine.
• In glycine, the R-group is
hydrogen.
• Therefore, 19 of the 20 standard amino acids
contain a chiral center.
• Chiral centers exhibit enantiomerism (left- and
right-handed forms).
• Each of the 19 amino acids exists in left and
right-handed forms.
• The amino acids found in nature as well as in
proteins are L-isomers.
• Bacteria do have some D-amino
acids.
• With monosaccharides, nature
favors D-isomers.
• The rules for drawing Fischer projection
formulas for amino acid structures:
• The — COOH group is put at the
top, the R group at the bottom to
position the carbon chain
vertically.
• The — NH2 group is in a horizontal position.
• Positioning — NH2 on
the left - L isomer.
• Positioning — NH2 on the right -
D isomer.
Acid-Base Properties of Amino Acids:
• In pure form, amino acids are white
crystalline solids.
• Most amino acids decompose before they
melt.
• They are not very soluble in water.
• Amino acids exist as Zwitterions: An ion
with both positive and negative charges on
the same molecule, resulting in a net zero
charge.
• Carboxyl groups give up a proton
to acquire a negative charge.
• Amino groups accept a proton to
become positively charged.
• Amino acids in solution exist in three
different species (zwitterions, positive
ions, and negative ions) - Equilibrium
shifts with changes in pH.
• Isoelectric point (pI) – pH at which the
concentration of Zwitterion is maximum,
resulting in a net charge of zero.
• Different amino acids have
different isoelectric points.
• At the isoelectric point, amino
acids are not attracted towards an
applied electric field because they
have a net zero charge.
Cysteine: A Chemically Unique Amino Acid
• Cysteine is the only standard amino acid
with a sulfhydryl group (—SH group).
• The sulfhydryl group imparts cysteine a
chemical property unique among the
standard amino acids.
• In the presence of mild oxidizing agents,
cysteine dimerizes to form a cystine
molecule.
• Cystine consists of two cysteine
residues linked via a covalent
disulfide bond.
Peptides:
• Under proper conditions, amino acids can
bond together to produce an unbranched
chain of amino acids.
• The length of the amino acid chain can
vary from a few amino acids to many
amino acids.
• Such a chain of covalently-linked amino
acids is called a peptide.
• The covalent bonds between amino acids
in a peptide are called peptide bonds.
Types of Peptides:
• Dipeptide: bond between two amino acids.
• Oligopeptide: bond between
approximately 10 - 20 amino acids.
• Non-amino acid components may
be organic or inorganic prosthetic
groups.
• Lipoproteins contain lipid
prosthetic groups.
• Glycoproteins contain
carbohydrate groups.
• Metalloproteins contain a specific
metal as a prosthetic group.
Primary Structure of Proteins:
The primary structure of proteins is the first
level of protein structure and refers to the order
in which amino acids are linked together in a
protein.
• Every protein has its own unique amino
acid sequence.
• Frederick Sanger (1953) sequenced and
determined the primary structure for the
first protein - Insulin.
• Proteins of the same organism always
have the same sequence (e., cows, pigs,
etc.).
• Insulin from different sources (pigs, cows,
sheep, humans) is similar, but some
differences exist.
• Due to these differences, insulin
may show some variation in
reactions over time.
• Currently, human insulin is produced from
genetically engineered bacteria.
Secondary Structure of Proteins:
The secondary structure of proteins refers to the
arrangement of atoms of the backbone in space.
The two most common types are the alpha-helix
(α-helix) and the beta-pleated sheet (β-pleated
sheet).
• The peptide linkages are essentially
planar, allowing only two possible
arrangements for the peptide backbone for
the following reasons:
• For two amino acids linked
through a peptide bond, six atoms
lie in the same plane.
• The planar peptide linkage
structure has considerable
rigidity, therefore rotation of
groups about the C–N bond is
hindered.
• Cis–trans isomerism is possible
about the C–N bond, with the
trans isomer being the preferred
orientation.
Alpha-helix (α-helix):
• A single protein chain adopts a shape that
resembles a coiled spring (helix).
• Hydrogen bonding occurs between the
same amino acid chains (intra-molecular).
• The structure resembles a coiled helical
spring.
• R-groups are positioned outside of the
helix due to insufficient room for them to
stay inside.
Beta-Pleated Sheets:
• Involve completely extended amino acid
chains.
• Hydrogen bonding occurs between two
different chains, both inter- and/or
intramolecular.
• Side chains may be positioned either
below or above the axis of the sheet.
Tertiary Structure of Proteins:
The tertiary structure of proteins refers to the
overall three-dimensional shape of a protein. It
results from the interactions between amino acid
side chains (R groups) that are widely separated
from each other.
Four Types of Interactions:
1. Disulfide bond: A covalent, strong bond
formed between two cysteine groups.
2. Electrostatic interactions: These involve
the formation of salt bridges between
charged side chains of acidic and basic
amino acids.
• Examples include - OH, - NH2, -
COOH, - CONH2 groups.
1. Hydrogen bonding: Occurs between
polar, acidic, and/or basic R groups. For
hydrogen bonding to occur, the hydrogen
must be attached to oxygen (O), nitrogen
(N), or fluorine (F).
2. Hydrophobic interactions: These occur
between non-polar side chains and
contribute significantly to the overall
stability of the protein structure.
Protein Classification Based on Shape:
There are three types of proteins: fibrous, globular,
and membrane.
Fibrous Proteins:
• Protein molecules with elongated shapes.
• Generally insoluble in water.
• Typically exhibit a single type of
secondary structure.
• Tend to have simple, regular, linear
structures.
• Often aggregate together to form
macromolecular structures such as hair,
nails, and tendons.
Globular Proteins:
• Protein molecules with peptide chains
folded into spherical or globular shapes.
• Generally water-soluble due to
hydrophobic amino acid residues in the
protein core.
• Function as enzymes and intracellular
signaling molecules.
Membrane Proteins:
• Associated with cell membranes.
• Insoluble in water due to hydrophobic
amino acid residues on the surface.
• Play key roles in transporting molecules
across the membrane.
Examples of Fibrous Proteins:
• Alpha-Keratin:
• Provides protective coatings for
organs.
• Major protein constituent of hair,
feather, nails, horns, and turtle
shells.
• Mainly made of hydrophobic
amino acid residues.
• The hardness of keratin depends
on the presence of - S-S- bonds,
which make nails and bones hard.
• Collagen:
• Most abundant proteins in
humans, comprising 30% of total
body protein.
• Major structural material in
tendons, ligaments, blood vessels,
skin, bones, and teeth.
• Predominant structure is a triple
helix.
• Rich in proline (up to 20%),
which is important for
maintaining structure.
Examples of Globular Proteins:
• Myoglobin:
• An oxygen storage molecule in
muscles.
• Monomeric protein with a single
peptide chain containing one
heme unit.
• Binds one oxygen molecule and
has a higher affinity for oxygen
than hemoglobin.
• Oxygen stored in myoglobin
molecules serves as a reserve
oxygen source for working
muscles.
• Hemoglobin:
• An oxygen carrier molecule in
blood.
• Tetrameric protein (four peptide
chains), each with a heme group.
• Can transport up to four oxygen
molecules at a time.
• The iron atom in heme interacts
with oxygen for transport.
Protein Classification Based on Function:
Proteins play crucial roles in most biochemical
processes, and their functional diversity far
exceeds that of other biochemical molecules. The
versatility of proteins in terms of function stems
from their ability to bind small molecules
specifically and strongly, to bind other proteins
and form fiber-like structures, and to integrate into
cell membranes.
Major Categories of Proteins Based on
Function:
1. Catalytic Proteins:
• Enzymes are best known for their
catalytic role.
• Almost every chemical reaction
in the body is driven by an
enzyme.
1. Defense Proteins:
• Immunoglobulins or antibodies
are central to the functioning of
the body's immune system.
1. Transport Proteins:
• Bind small biomolecules, such as
oxygen and other ligands, and
transport them to other locations
in the body, releasing them on
demand.
1. Messenger Proteins:
• Transmit signals to coordinate
biochemical processes between
different cells, tissues, and
organs.
• Examples include insulin and
glucagon, which regulate
carbohydrate metabolism, and
human growth hormone, which
regulates body growth.
1. Contractile Proteins:
• Necessary for all forms of
movement.
Immunoglobulins, also known as antibodies, are
glycoproteins produced in response to the invasion
of microorganisms or foreign molecules. Here are
some key points about immunoglobulins:
• They function as a protective response
against invading microorganisms or
foreign molecules by binding to specific
antigens.
• Immunoglobulins bind to antigens via the
variable region of the immunoglobulin,
utilizing hydrophobic interactions, dipole-
dipole interactions, and hydrogen bonds.
Immunoglobulins play a crucial role in the
immune response by recognizing and neutralizing
specific antigens, thus aiding in the body's defense
against pathogens and foreign substances.
Lipoproteins:
Lipoproteins are conjugated proteins that contain
lipids in addition to amino acids. Here are some
key points about lipoproteins:
• Major Function: Their major function is
to help suspend lipids and transport them
through the bloodstream.
• Plasma Lipoproteins: There are four
major classes of plasma lipoproteins:
a. Chylomicrons: These transport dietary
triacylglycerols from the intestine to the liver and
adipose tissue.
b. Very-low-density lipoproteins
(VLDL): They transport triacylglycerols
synthesized in the liver to adipose tissue.
c. Low-density lipoproteins (LDL): LDLs
transport cholesterol synthesized in the liver to
cells throughout the body.
d. High-density lipoproteins (HDL): HDLs
collect excess cholesterol from body tissues and
transport it back to the liver for degradation to bile
acids.
Lipoproteins play a crucial role in lipid
metabolism and the transportation of lipids within
the body. They are essential for maintaining lipid
homeostasis and overall metabolic health.
WEEK 8 NUCLEIC ACIDS
Nucleotides: Building Blocks of Nucleic Acids
Return to TOC
Nucleic Acids: Polymers in which repeating unit
is nucleotide
• A Nucleotide has three components:
• Pentose Sugar: Monosaccharide
• Phosphate Group (PO4 3-)
• Heterocyclic Base
• Phosphate Sugar Base
Pentose Sugar
• Ribose is present in RNA and 2-
deoxyribose is present in DNA
• Structural difference:
• a —OH group present on carbon
2’ in ribose
• a —H atom in 2-deoxyribose
• RNA and DNA differ in the identity of the
sugar unit in their nucleotides.
Nitrogen-Containing Heterocyclic Bases
• There are a total five bases (four of them
in most of DNA and RNAs)
• Three pyrimidine derivatives - thymine
(T), cytosine (C), and uracil (U)
• Two purine derivatives - adenine (A) and
guanine (G)
• Adenine (A), guanine (G), and cytosine
(C) are found in both DNA and RNA.
• Uracil (U): found only in RNA
• Thymine (T) found only in DNA.
Phosphate
• Phosphate - third component of a
nucleotide, is derived from phosphoric
acid (H3PO4)
• Under cellular pH conditions, the
phosphoric acid is fully dissociated to give
a hydrogen phosphate ion (HPO4 2-)
Nucleotide Formation
• The formation of a nucleotide from sugar,
base, and phosphate is visualized below.
• Phosphate attached to C-5’ and
base is attached to C-1’ position
of pentose
Primary Nucleic Acid Structure
• Sugar-phosphate groups are referred to
as nucleic acid backbone - Found in all
nucleic acids
• Sugars are different in DNA and RNA
Primary Structure
• A ribonucleic acid (RNA) is a nucleotide
polymer in which each of the monomers
contains ribose, a phosphate group, and
one of the heterocyclic bases adenine,
cytosine, guanine, or uracil
• A deoxyribonucleic acid (DNA) is a
nucleotide polymer in which each of the
monomers contains deoxyribose, a
phosphate group, and one of the
heterocyclic bases adenine, cytosine,
guanine, or thymine.
Primary Structure
• Structure: Sequence of nucleotides in
DNA or RNA
• Primary structure is due to changes in the
bases
• Phosphodiester bond at 3’ and 5’ position
• 5’ end has free phosphate and 3’ end has a
free OH group
• Sequence of bases read from 5’ to 3’
Comparison of the General Primary Structures
of Nucleic Acids and Proteins
• Backbone: - Phosphate-Sugar- Nucleic
acids
• Backbone: - Peptide bonds - Proteins
The DNA Double Helix
• Nucleic acids have secondary and tertiary
structure
• The secondary structure involves two
polynucleotide chains coiled around each
other in a helical fashion
• The polynucleotides run anti-parallel
(opposite directions) to each other, i., 5’
- 3’ and 3’ - 5’
• The bases are located at the center and
hydrogen bonded (A=T and G≡C)
• Base composition: %A = %T and %C =
%G
• Example: Human DNA contains
30% adenine, 30% thymine, 20%
guanine, and 20% cytosine
DNA Sequence
• The sequence of bases on one
polynucleotide is complementary to the
other polynucleotide
• Complementary bases are pairs of bases in
a nucleic acid structure that can hydrogen-
bond to each other.
• Complementary DNA strands are strands
of DNA in a double helix with base
pairing such that each base is located
opposite its complementary base.
• Example:
• List of bases in sequential order in the
direction from the 5’ end to 3’ end of the
segment:
• 5’-A-A-G-C-T-A-G-C-
T-T-A-C-T-3’
• Complementary strand of this sequence
will be:
• 3’-T-T-C-G-A-T-C-G-A-A-T-G-
A-5’
Base Pairing
• One small and one large base can fit
inside the DNA strands:
• Hydrogen bonding is stronger
with A-T and G-C
• A-T and G-C are called
complementary bases
Practice Exercise
• Predict the sequence of bases in the DNA
strand complementary to the single DNA
strand shown below:
• 5’ A–A–T–G–C–A–G–C–T 3’
• Answer:
• 3’ T–T–A–C–G–T–C–G–A 5’
Replication of DNA Molecules
• Replication: Process by which DNA
molecules produce exact duplicates of
themselves
• Old strands act as templates for the
synthesis of new strands
• DNA polymerase checks the correct base
pairing and catalyzes the formation of
phosphodiester linkages
• The newly synthesized DNA has one new
DNA strand and one old DNA strand
DNA Polymerase Directionality
• DNA polymerase enzyme can only
function in the 5’-to-3’ direction
• Therefore, one strand (top; leading strand)
grows continuously in the direction of
unwinding
• The lagging strand grows in segments
(Okazaki fragments) in the opposite
direction
• The segments are later connected by DNA
ligase
• DNA replication usually occurs at
multiple sites within a molecule (origin of
replication)
• DNA replication is bidirectional from
these sites (replication forks)
• Multiple-site replication enables rapid
DNA synthesis
Chromosomes
• Upon DNA replication, the large DNA
molecules interact with histone proteins to
fold long DNA molecules.
• The histone–DNA complexes are called
chromosomes:
• A chromosome is about 15% by
mass DNA and 85% by mass
protein.
• Cells of different kinds of organisms have
different numbers of chromosomes.
• Example: Number of
chromosomes in a human cell 46,
• The process involves excision of
one or more exons.
Transcriptome
• Transcriptome: All of the mRNA
molecules that can be generated from the
genetic material in a genome.
• Transcriptome is different from a
genome.
• Responsible for the biochemical
complexity created by splice
variants obtained by hnRNA.
The Genetic Code
The base sequence in a mRNA determines the
amino acid sequence for the protein synthesized.
The base sequence of an mRNA molecule involves
only 4 different bases - A, C, G, and U.
Codon: A three-nucleotide sequence in an mRNA
molecule that codes for a specific amino acid.
Based on all possible combination of bases A, G,
C, U, there are 64 possible codes.
Genetic code: The assignment of the 64 mRNA
codons to specific amino acids (or stop signals). 3
of the 64 codons are termination codons (“stop”
signals).
Characteristics of Genetic Code:
• The genetic code is highly degenerate:
• Many amino acids are designated
by more than one codon.
• Arg, Leu, and Ser - represented
by six codons.
• Most other amino acids -
represented by two codons.
• Met and Trp - have only a single
codon.
• Codons that specify the same
amino acid are called synonyms.
• There is a pattern to the arrangement of
synonyms in the genetic code table.
• All synonyms for an amino acid
fall within a single box unless
there are more than four
synonyms.
• The significance of the “single
box” pattern - the first two bases
are the same.
• For example, the four synonyms
for Proline - CCU, CCC, CCA,
and CCG.
• The genetic code is almost universal:
• With minor exceptions, the code
is the same in all organisms.
• The same codon specifies the
same amino acid whether the cell
is a bacterial cell, a corn plant
cell, or a human cell.
• An initiation codon exists:
• The existence of “stop” codons
(UAG, UAA, and UGA) suggests
the existence of “start” codons.
• The codon - coding for the amino
acid methionine (AUG) functions
as initiation codon.
Anticodons and tRNA Molecules
During protein synthesis, amino acids do not
directly interact with the codons of an mRNA
molecule. tRNA molecules serve as intermediaries
to deliver amino acids to mRNA. Two important
features of the tRNA structure are:
• The 3’ end of tRNA is where an amino
acid is covalently bonded to the tRNA.
• The loop opposite to the open end of
tRNA is the site for a sequence of three
bases called an anticodon.
Anticodon: A three-nucleotide sequence on a
tRNA molecule that is complementary to a codon
on an mRNA molecule.
Translation: Protein Synthesis
Return to TOC
Translation is a process in which mRNA codons
are deciphered to synthesize a protein molecule.
The ribosome, an rRNA-protein complex, serves
as the site of protein synthesis. It contains 4 rRNA
molecules and ~80 proteins, packed into two
rRNA-protein subunits (one small and one large).
The mRNA binds to the small subunit of the
ribosome.
Five Steps of Translation Process:
1. Activation of tRNA: Addition of specific
amino acids to the 3’-OH group of tRNA.
2. Initiation of protein synthesis: Begins with
the binding of mRNA to the small
ribosomal subunit such that its first codon
(initiating codon AUG) occupies a site
called the P site (peptidyl site).
3. Elongation: Adjacent to the P site in an
mRNA-ribosome complex is A site
(aminoacyl site), and the next tRNA with
the appropriate anticodon binds to it.
4. Termination: The polypeptide continues to
grow via translocation until all necessary
amino acids are in place and bonded to
each other.
5. Post-translational processing: Gives the
protein the final form it needs to be fully
functional.
Efficiency of mRNA Utilization:
• Polysome (polyribosome): A complex of
mRNA and several ribosomes.
• Many ribosomes can move simultaneously
along a single mRNA molecule.
• The multiple use of mRNA molecules
reduces the amount of resources and
energy that the cell expends to synthesize
needed protein.
• In the process, several ribosomes bind to a
single mRNA, forming polysomes.
Mutations
Return to TOC
Mutation:
• An error in base sequence reproduced
during DNA replication.
• Errors in genetic information are passed
on during transcription.
• The altered information can cause changes
in the amino acid sequence during protein
synthesis, thereby altering protein
function.
• Such changes have a profound effect on
an organism.
Mutagens
Mutations are caused by mutagens, substances, or
agents that cause a change in the structure of a
gene:
• Radiation and chemical agents are two
important types of mutagens.
• Ultraviolet, X-ray, radioactivity, and
cosmic radiation are mutagenic and can
cause cancers.
• Chemical agents can also have mutagenic
effects.
• For example, HNO2 can convert
cytosine to uracil.
• Nitrites, nitrates, and
nitrosamines can form nitrous
acid in cells.
• Under normal conditions, mutations are
repaired by repair enzymes.
Nucleic Acids and Viruses
Viruses:
• Tiny disease-causing agents with an outer
protein envelope and inner nucleic acid
core.
• They cannot reproduce outside their host
cells (living organisms).
• Invade their host cells to reproduce and, in
the process, disrupt the normal cell’s
operation.
• Virus invades bacteria, plants, animals,
and humans.
• Many human diseases are of viral
origin, e., Common cold,
smallpox, rabies, influenza,
hepatitis, and AIDS.
Vaccines:
• Inactive virus or bacterial envelope.
• Antibodies produced against inactive viral
or bacterial envelopes will kill the active
bacteria and viruses.
Viruses:
• Viruses attach to the host cell on the
outside cell surface, and proteins of the
virus envelope catalyze the breakdown of
the cell membrane, forming a hole.
• Viruses then inject their DNA or RNA
into the host cell.
• The viral genome is replicated, and
proteins coding for the viral envelope are
produced in hundreds of copies.
• Hundreds of new viruses are produced
using the host cell replicated genome and
proteins in a short time.
Recombinant DNA and Genetic Engineering
Recombinant DNA Production using a Bacterial
Plasmid:
1. Dissolution of cells:
• E. coli cells of a specific strain
containing the plasmid of interest
are treated with chemicals to
dissolve their membranes and
release the cellular contents.
1. Isolation of plasmid fraction:
• The cellular contents are
fractionated to obtain plasmids.
1. Cleavage of plasmid DNA:
• Restriction enzymes are used to
cleave the double-stranded DNA.
1. Gene removal from another organism:
• Using the same restriction
enzyme, the gene of interest is
removed from a chromosome of
another organism.
1. Gene–plasmid splicing:
• The gene (from Step 4) and the
opened plasmid (from Step 3) are
mixed in the presence of the
enzyme DNA ligase to splice
them together.
1. Uptake of recombinant DNA:
• The recombinant DNA prepared in step 5
is transferred to a live E. coli culture
where they can be replicated, transcribed,
and translated.
Three Important Aspects of the Naming Process:
1. Suffix - ase identifies it as an enzyme (e.,
urease, sucrase).
2. The type of reaction catalyzed is often
used as a prefix (e., oxidase, hydrolase).
3. The identity of the substrate is often used
in addition to the type of reaction (e.,
glucose oxidase, pyruvate carboxylase).
Six Major Classes of Enzymes
• Enzymes are grouped into six major
classes based on the types of reactions
they catalyze:
a. Oxidoreductases: Oxidation-reduction
reactions.
b. Transferases: Functional group transfer
reactions.
c. Hydrolases: Hydrolysis reactions.
d. Lyases: Reactions involving addition or
removal of groups from double bonds.
e. Isomerases: Isomerization reactions.
f. Ligases: Reactions involving bond
formation coupled with ATP hydrolysis.
Specific Enzyme Examples
• Oxidoreductase: Catalyzes oxidation-
reduction reactions, with coenzymes that
are either oxidized or reduced as
substrates.
• Transferase: Catalyzes the transfer of
functional groups between molecules,
with subtypes like transaminases and
kinases.
• Hydrolase: Catalyzes hydrolysis
reactions, essential in processes like
digestion.
• Lyase: Catalyzes addition or removal of
groups to form or break double bonds.
• Isomerase: Catalyzes isomerization
reactions, rearranging atoms within
molecules.
• Ligase: Catalyzes the formation of bonds
between molecules, requiring ATP
hydrolysis for energy input.
These characteristics and classifications help us
understand the diverse roles enzymes play in
biological systems and their importance in
biochemical reactions.
Models of Enzyme Action
Enzyme Active Site:
• The active site is a relatively small part of
an enzyme's structure directly involved in
catalysis.
• It's where the substrate binds to the
enzyme, formed by the folding and
bending of the protein.
• Typically, it's located in a crevice-like
area of the enzyme, and some enzymes
may have more than one active site.
Enzyme-Substrate Complex:
• This complex is essential for enzyme
activity.
• It's an intermediate reaction species
formed when the substrate binds with the
active site.
• The favorable orientation and proximity of
the substrate to the active site facilitate a
fast reaction.
Two Models for Substrate Binding to Enzyme:
1. Lock-and-Key Model:
• Enzyme has a pre-determined
shape for the active site.
• Only a substrate with a specific
shape can fit and bind with the
active site.
1. Induced Fit Model:
• Substrate contact with the
enzyme causes a change in the
shape of the active site.
• This model allows for a small
change in space to accommodate
the substrate, similar to how a
hand fits into a glove.
Forces That Determine Substrate Binding:
• Substrate binding to the enzyme is
influenced by various forces, including
hydrogen bonding, hydrophobic
interactions, and electrostatic interactions.
Enzyme Specificity:
• Absolute Specificity:
• An enzyme catalyzes a particular
reaction for only one substrate.
• Urease is an example of an
enzyme with absolute specificity.
• Stereochemical Specificity:
• Enzymes can distinguish between
stereoisomers based on their
chiral properties.
• For example, L-amino-acid
oxidase catalyzes reactions of L-
amino acids but not D-amino
acids.
• Group Specificity:
• Enzymes recognize structurally
similar compounds with the same
functional groups.
• Carboxypeptidase is an enzyme
that cleaves amino acids one at a
time from the carboxyl end of a
peptide chain.
• Linkage Specificity:
• Enzymes recognize a particular
type of bond irrespective of the
structural features nearby.
• Phosphatases, for instance,
hydrolyze phosphate-ester bonds
in all types of phosphate esters.
Factors That Affect Enzyme Activity
Temperature:
• Higher temperature increases the kinetic
energy of molecules, leading to more
collisions between reactants and higher
enzyme activity.
• Optimum temperature is the temperature
at which the rate of enzyme-catalyzed
reaction is maximum.
• Human enzymes typically have an
optimum temperature around 37°C (body
temperature). Higher temperatures (e.,
during fever) can lead to decreased
enzyme activity due to denaturation.
pH:
• Changes in pH can significantly affect
enzyme activity.
• Drastic pH changes can result in protein
denaturation.
• Most enzymes have optimal activity in the
pH range of 7 - 7, which is close to
neutral.
• However, there are exceptions like
digestive enzymes:
• Pepsin has an optimum pH of 2.
• Trypsin has an optimum pH of
8.
Substrate Concentration:
• Enzyme activity increases with increased
substrate concentration at a constant
enzyme concentration.
• Substrate saturation occurs when the
substrate concentration reaches its
maximum rate, and all active sites are
filled.
• Turnover number refers to the number of
substrate molecules converted to product
per second per enzyme molecule under
conditions of optimum temperature and
pH.
Enzyme Concentration:
• Enzymes are not consumed in the
reactions they catalyze.
• At a constant substrate concentration,
enzyme activity increases with an increase
in enzyme concentration.
Greater enzyme concentration leads to a higher
reaction rate Inhibition
Enzyme inhibitors are substances that hinder or
halt the normal catalytic function of an enzyme by
binding to it. There are two main types of enzyme
inhibitors:
1. Competitive Inhibitors:
• These inhibitors compete with the
substrate for the same active site on the
enzyme.
• They typically have a similar shape and
charge to the substrate.
• Increasing the substrate concentration can
reduce competitive inhibition by
outcompeting the inhibitor for the active
site.
2. Noncompetitive Inhibitors:
• Noncompetitive inhibitors bind to a site
on the enzyme other than the active site.
• This binding causes a change in the
enzyme's structure, which reduces or
prevents enzyme activity.
• Increasing substrate concentration does
not fully overcome noncompetitive
inhibition.
Reversible Inhibition:
• Reversible inhibitors bind to the enzyme
in a non-permanent manner.
• Includes both competitive and
noncompetitive inhibition.
• The inhibitor can dissociate from the
enzyme, allowing the enzyme to regain
activity.
Irreversible Inhibition:
• Irreversible inhibitors form strong
covalent bonds with the enzyme's active
site.
• This permanently inactivates the enzyme.
• Increasing substrate concentration cannot
reverse irreversible inhibition.
Regulation of Enzyme Activity:
• Enzyme activity needs to be regulated to
prevent excessive product formation.
• Regulation mechanisms include
proteolytic enzymes and zymogens,
covalent modification of enzymes, and
feedback control.
• 100 mg/day saturates all body tissues -
Excess vitamin is excreted
• RDA (mg/day):
• Great Britain: 30
• United States and Canada: 60
• Germany: 75
Vitamin B
• The preferred and alternative names for
the B vitamins
• Thiamin (vitamin B1)
• Riboflavin (vitamin B2)
• Niacin (nicotinic acid,
nicotinamide, vitamin B3)
• Vitamin B6 (pyridoxine,
pyridoxal, pyridoxamine)
• Folate (folic acid)
• Vitamin B12 (cobalamin)
• Pantothenic acid (vitamin B5)
• Biotin
• Exhibit structural diversity
• Major function: B Vitamins are
components of coenzymes
Fat-Soluble Vitamins
Vitamins A, D, E, K
• Involved in plasma membrane processes
• More hydrocarbon-like with fewer
functional groups
• Vitamin A
• Has a role in vision - only 1/
of vitamin A is in retina
• 3 Forms of vitamin A are active
in the body
• Derived from β-carotene
• Functions of Vitamin A
• Vision: In the eye, vitamin A
combines with opsin protein to
form the visual pigment
rhodopsin which further converts
light energy into nerve impulses
that are sent to the brain.
• Regulating Cell Differentiation:
Process in which immature cells
change to specialized cells with
function. Examples include
differentiation of bone marrow
cells, white blood cells, and red
blood cells.
• Maintenance of the health of
epithelial tissues via epithelial
tissue differentiation. Lack of
vitamin A causes such surfaces to
become drier and harder than
normal.
• Reproduction and Growth: In
men, vitamin A participates in
sperm development. In women,
normal fetal development during
pregnancy requires vitamin A.
• Vitamin D
• Two forms active in the body:
Vitamin D2 and D
• Sunshine Vitamin: Synthesized
by UV light from the sun
• It controls the correct ratio of Ca
and P for bone mineralization
(hardening)
• As a hormone, it promotes Ca and
P absorption in the intestine
• Vitamin E
• Four forms of Vitamin E: α-, β-,
γ-, and δ-Vitamin E
• Alpha-tocopherol is the most
active biological active form of
Vitamin E
• Peanut oils, green and leafy
vegetables, and whole grain
products are the sources of
vitamin E
• Primary function: Antioxidant –
protects against oxidation of other
compounds
• Vitamin K
• Two major forms; K1 and K
• K1 found in dark green, leafy
vegetables
• K2 is synthesized by bacteria that
grow in the colon
• Dietary need supply: ~1/
synthesized by bacteria and 1/
obtained from diet
• Active in the formation of
proteins involved in regulating
blood clotting
WEEK 9 DIGESTION AND ABSORPTION
- Most of the foodstuffs ingested are
unavailable to the organism, since they
cannot be absorbed by the gastrointestinal
mucosa until they are broken down into
smaller particles. The process of changing
foodstuffs into simple absorbable forms is
called digestion. This process is
accomplished with the aid of hydrolases
which catalyze the hydrolysis of proteins
to amino acids and glycerol, and nucleic
acids to nucleotides. In the course of
digestion, minerals and vitamins in the
food stuffs are also released
DIGESTIVE ENZYMES (HYDROLASES)
1. Amylolytic or carbohydrates-splitting
enzymes
salivary amylase or ptyalin from the
salivary glands
pancreatic amylase from the pancreas
invertases or disaccharides from the goblet
cells of the small intestine
2. Proteases or protein-splitting enzymes
(secreted as zymogens or inactive
enzymes)
pepsinogen from the gastric glands of the
stomach
trypsinogen and chymotrypsinogen from
the pancreas
peptidases from the goblet cells of the
small intestine
3. Lipases or fat-splitting enzymes
gastric lipase from the stomach
pancreatic lipase from the pancreas
4. Nucleases or nucleic-acid-splitting enzymes
ribonuclease and deoxyribonuclease from
the pancreas
DIGESTION
Carbohydrates
- ptyalin acts on starch in the oral cavity
changing starch to maltose
- pancreatic amylase on starch in the small
intestine changing starch to maltose
- maltase acts on maltose changing it to
glucose
- lactase acts on lactose changing it to
glucose and galactose
- sucrase acts on sucrose changing it to
glucose and fructose
Proteins
- pepsinogen in the stomach activated to
pepsin in the presence of HCl, pepsin acts
on proteins changing it to peptides
- trypsinogen activated to trypsin by
enterokinase in the small intestine and
chymotrypsinogen activated to
chymptrypsin by trypsin; trypsin and
chymotrypsin acts on proteins to change
these to peptides
- peptidases act on peptides changing these
to amino acids
Lipids
- gastric lipase in the stomach acts on
emulsified fats changing these to fatty
acids and glycerol
- bile in the small intestine emulsifies fats;
lipase acts on emulsified fats changing
these to fatty acids and glycerol
Nucleic acids
- nucleases in the small intestine acts on
nucleic acid changing these to nucleotides
ABSORPTION
Transport Mechanism Across a Membrane
Diffusion
osmosis
dialysis
free diffusion
solvent drag
filtration
Carrier-mediated transport
facilitated diffusion
active transport
Bulk transport
phagovytosis
pinocytosis
emeiocytosis
INTESTINAL ABSORPTION
1. Sugars
glucose and galactose by facilitated diffusion
requiring the presence of high concentration of
external Na ions; glucose binds to a carrier
molecule which also binds Na and Na moves
inward along its concentration gradient dragging
glucose with it
fructose does not require Na and its transported by
a passive mechanism along its own concentration
gradient
2. Amino acids
same as glucose and galactose
in the absence of a Na gradient, transport of amino
acids will be passive in nature
3. Fatty acids
triglycerides are resynthesized utilizing the partial
glycerides or acyloglycerols and the liberated free
fatty acids are activated as fatty acyl coA
resynthesized fats pass into the lacteals or
lymphatic vessels to large thoracic duct and enters
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Biochemistry- Midterms-CHEM113
Course: BIOCHEMISTRY (CHM3)
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University: Our Lady of Fatima University
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BIOCHEMISTRY MIDTERMS CHEM113
WEEK 7 PROTEINS
Characteristics of Proteins:
• A protein is a naturally-occurring,
unbranched polymer in which the
monomer units are amino acids.
• Proteins are the most abundant molecules
in cells after water, accounting for about
15% of a cell’s overall mass.
• Elemental composition: Proteins contain
Carbon (C), Hydrogen (H), Nitrogen (N),
Oxygen (O), and most also contain Sulfur
(S).
• The average nitrogen content of proteins
is 15.4% by mass.
• Also present are Iron (Fe), phosphorus
(P), and some other metals in some
specialized proteins.
Amino Acids: The Building Blocks for Proteins:
• Amino acid: An organic compound that
contains both an amino (-NH2) and
carboxyl (-COOH) groups attached to the
same carbon atom.
• The position of the carbon atom
is Alpha (α).
• The -NH2 group is attached at the
alpha (α) carbon atom.
• The -COOH group is attached at
the alpha (α) carbon atom.
• R = side chain – varying in size, shape,
charge, acidity, functional groups present,
hydrogen-bonding ability, and chemical
reactivity.
• More than 700 amino acids are
known.
• Based on common “R” groups,
there are 20 standard amino acids.
• All amino acids differ from one another
by their R-groups.
• Standard amino acids are divided into four
groups based on the properties of R-
groups:
1. Non-polar amino acids: R-groups are
non-polar.
• Such amino acids are
hydrophobic (water-
fearing) and insoluble in
water.
• Eight of the 20 standard
amino acids are non-
polar.
• When present in proteins, they
are located in the interior of the
protein where there is no polarity.
1. Polar amino acids: R-groups are polar.
• Three types: Polar
neutral, Polar acidic, and
Polar basic.
• Polar-neutral: Contains
polar but neutral side
chains – Seven amino
acids belong to this
category.
• Polar acidic: Contain a
carboxyl group as part of
the side chains – Two
amino acids belong to
this category.
• Polar basic: Contain an
amino group as part of
the side chain – Two
amino acids belong to
this category.
Nomenclature:
• Common names assigned to the amino
acids are currently used.
• Three-letter abbreviations are widely used
for naming:
• The first letter of the amino acid
name is compulsory and
capitalized, followed by the next
two letters not capitalized, except
in the case of Asparagine (Asn),
Glutamine (Gln), and Tryptophan
(Trp).
• One-letter symbols are commonly used for
comparing amino acid sequences of
proteins:
• Usually, the first letter of the
name.
• When more than one amino acid
has the same letter, the most
abundant amino acid gets the 1st
letter.
• Both types of abbreviations are given in
the following slides.
Non-polar Amino Acids:
• Glycine (Gly)
• Alanine (Ala)
• Valine (Val)
• Leucine (Leu)
• Isoleucine (Ile)
• Proline (Pro)
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