Proteins: French Alfred M. Maaño Marinduque State College

Proteins
French Alfred M. Maaño

Marinduque State College
Diversity of Proteins
Signaling (Insulin)
Contractile (Actin & Myosin)

Transport (Hemoglobin) Structural (Collagen)
Enzymatic (Amylase)
Protective (Antibody)
Biochemistry Lec | FMMaaño | FS AY2020-2021

Structure of Proteins
Smith, C., Marks, A. & Leiberman, M. (2012). Marks’ Basic Medical Biochemistry:
Biochemistry Lec | FMMaaño | FS AY2020-2021 A Basic Clinical Approach 2ed
Amino Acids
• Amino acids are the monomers (building blocks) of proteins.
• Almost all proteins have L-amino acids (most are chiral except
glycine)
• Amino acids are subdivided based on their polarity, aromaticity

and electronegativity.
Amino Acids
• The stereoisomer of amino acids seen in humans is L-handed.
• The properties of amino acids are based on the presence of
their amino group, carboxylic group and R group.
• It is important to note that the charge of amino acids change
with pH.
Biochemistry Lec | FMMaaño | FS AY2020-2021 Brown T. L., et al. (2015). Chemistry: The Central Science
Amino Acids
Amino Acids
Amino Acids
Amino Acids
• pKa is the pH wherein the functional group
of an amino acid will release its H+. As A
general rule the acidic carboxylic group has
the lowest pKa next is the pKa of the R
group and lastly, the one with the pKa
highest is the basic amino group.
• Hydropathy Index is the measure of

hydrophobicity of an AA. The higher
number, the more hydrophobic.
Biochemistry Lec | FMMaaño | FS AY2020-2021 From Koolman, J. & Roehm, K. H. (2003). Color Atlas in Biochemistry.
Amino Acids
• Amino acids are polyionic

• At pH=7.0, amino acids are zwitterionic.
• Amino acids are weak acid and bases, thus
they display buffer zones in their pH curve.
Amino Acids
Amino Acids
Take note:
The pH wherein the net charge of the molecule is zero is the
isoelectric point (pI).
At pI, amino acid will not migrate when subjected to pH-
gradient electrophoresis.
Computation for pI:
For Neutral Side Chains: pI= ½ (pKa1 + pKa2)
For Acidic Side Chains: pI= ½ (pKa1 + pKa3)
For Basic Side Chains: pI= ½ (pKa2 + pKa3)
Amino Acids
• 2D Electrophoresis
Biochemistry Lec | FMMaaño | FS AY2020-2021 Campbell, M. & Farell, S. (2009). Biochemistry 6ed
Functions of Amino Acids
Some amino acids could not be produced by the body:
essential AAs.
Amino acids participate in the biosynthesis of porphyrin,

purines, pyrimidines and urea.
A string of amino acids, called peptides are medically

important as some functions in neurosignalling, antibiotics or
toxins.
Protein Structure
Biochemistry Lec | FMMaaño | FS AY2020-2021 Nelson, D., & Cox, M. (2012). Lehninger’s Principles of Biochemistry 6ed
Some terminologies
Amino acid sequence- refers to the sequence of amino acids
Polypeptide chain- refers to a string of amino acid
Peptide- a small protein or a string of amino acid

Primary Structure
• Refers to how the amino acids are strung to each other.
• The sequence of amino acids are commonly important to

determine the shape, and therefore function of a protein.
• Similarity in amino acid sequence may mean similarity in

function.

Primary Structure
• How are amino acids linked into
peptide chains?
• Two AAs are linked in a condensation

reaction which results to a bond called
peptide bond.
• A polypeptide chain grows by addition
to its carboxylic end.
Primary Structure
• How do we name a peptide?
• Peptides are named from the amino-

terminal end to the carboxyl terminal
end. The base of the amino acid is
used with the suffix –yl and the last
amino acid retains its name. No
spaces between the amino acid
residues.
• e.g. Serylglycyltyrosylalanylleucine
Primary Structure
• There is restricted movement in the peptide.

• Alpha carbon to another alpha carbon produces are planar
structure. Rotation along the chain only happens in the alpha
carbons which acts like joints between the planar structure.
Primary Structure
Determination of
Amino Acid sequence
Primary Structure
Determination of
Amino Acid sequence
S protein subunit of SARS-CoV-2
1,255 aa long!
Biochemistry Lec | FMMaaño | FS AY2020-2021 https://www.uniprot.org/uniprot/P59594

Sequence Alignment of
S proteins in CoVs
Walls, A.C., Xiong, X., Park, Y.J., Tortorici, M.A., Snijder, J., Quispe, J., Cameroni,
E., Gopal, R., Dai, M., Lanzavecchia, A., et al. (2020). Structure, Function and Antigenicity of SARS-
Biochemistry Lec | FMMaaño | FS AY2020-2021 CoV-2 Spike Glycoprotein. Cell 180, 281–292
Origin: SARS-CoV-19
BioVIA Blog. (2020, 04 April). Decoding the SARS-CoV-2 Genomes – Origin.

Biochemistry Lec | FMMaaño | FS AY2020-2021 Accessed 02 September 2021
Mutations in variants of concern of
SARS-CoV-19
American Microbiological Society. (2021, July). How Dangerous is the Delta Variant (B.1.617.2)?
Biochemistry Lec | FMMaaño | FS AY2020-2021 Accessed on 02 September, 2021
What’s about the SARS-CoV-2 (δ)
variant?
• 1000x higher viral
load compared to
other variants.
• No sufficient data
that Delta variant
causes more severe
illness.
Li, B., Deng, A., Li, K. et al. (2021 July). Viral Infection and Transmission in a Large Well-Traced
Biochemistry Lec | FMMaaño | FS AY2020-2021 Outbreak Caused by Delta SARS-CoV-2 Variant. medRxiv. (Preprint)
What’s about the SARS-CoV-2 (δ)
variant?
• “Delta spike has
accumulated mutations
among which P681R is
located at a furin
cleavage site that is
absent in other group 2B
coronaviruses.”
Liu Y et al. (2021). Delta spike P681R mutation enhances SARS-

Biochemistry Lec | FMMaaño | FS AY2020-2021 CoV-2 fitness over Alpha variant, bioRxiv (Preprint)
SARS-CoV-2 (δ) variant



https://ourworldindata.org/search?q=Covid+variants+
Biochemistry Lec | FMMaaño | FS AY2020-2021 Accessed 18 September, 2021
https://news.abs-cbn.com/news/08/16/21/delta-overtaking-other-covid-variants-genome-center.
Biochemistry Lec | FMMaaño | FS AY2020-2021 Accessed 18 September, 2021
Secondary Structure
• the local spatial arrangement of a segment of a polypeptide.
Secondary Structure
• Folding or arrangement of peptides are governed by their
tendency towards stability or a conformation of lower energy
level.
• Weak interactions guides the formation of stable conformation.
• Small, hydrophobic side chains of AAs tends to hide within the
molecule while large, hydrophilic side chains tends to be
outside interacting with water molecules.
• Always remember, spatial conformations are restricted in
movement by peptide bonds.

Secondary Structure
• Weak interactions governs stable
conformation.
Secondary Structure
Common conformations of the secondary structures
• α helix
• β sheets
• Motifs
• turns

Secondary Structure
• α helix
Secondary Structure
• α helix
• An α helix is a single-stranded helix with right-handed direction.

• One complete turn has a height of 5.4 angstroms with about 3-4
AAs residues.
• An α helix also have the R groups always protruding outside of
the helix.

Secondary Structure
• What makes an α helix a stable conformation?
• The propensity towards α helix is stabilized by hydrogen

bonding from the hydrogen bonding between the hydrogen
attached to the nitrogen and the oxygen in the carbonyl of the
fourth amino acid residue.
• High presence of Ala makes formation of α helix probable.

Secondary Structure
• β sheets
Secondary Structure
• β sheets
• β sheets have a pleated structure or forming a zigzag line

wherein R groups alternate in being above or below. This
alternation of R groups allow hydrogen bonding between
hydrogen attached to nitrogen and oxygen of the carbonyl.
Secondary Structure
• What makes an β sheets a stable conformation?
• Antiparallel β sheets have a more stable hydrogen bonding and

adjacent polypeptides run antiparallel with each other.
• Parallel β sheets have less stable hydrogen bonding as the
molecules participating in hydrogen bonding are not aligned.
Adjacent polypeptides also run parallel with each other.

Secondary Structure
• Motifs
Secondary Structure
Secondary Structure: TCR
Biochemistry Lec | FMMaaño | FS AY2020-2021 Murphy, K. & Weaver, C. (2017). Janeman’s Immunobiology 2ed
Tertiary Structure
• The overall spatial structure
of the whole polypeptide.
• Examines protein structure
as affected by interaction of
side chains with each other
or electrostatic forces.
Tertiary Structure: Myoglobin
• Myoglobin contains a
prosthetic heme group
which allows the overall
structure to fold tighter.
Quaternary Structure
• The collective spatial
arrangement of a
polypeptide chains refers to
the quaternary structure.
• Each folded polypeptide
chain composing the whole
protein assembly is called
a subunit.
• Subunits are held by
noncovalent interactions.
• Adult hemoglobin is a
ternary protein (α2β 2)
• Oxygen binding changes
the quaternary structure of
hemoglobin.
A=Deoxygenated; B=Oxygenated
Disorders in Protein Structures
• Sickle-Cell Anemia
Due to G6V mutation in β
globin, resulting to HbS (α2β
s
2 ). HbS is prone to sickling at
deoxygenation, and
prolonged deoxygenation
promotes irreversible sickling
causing a crescentic-shaped
red blood cell. This sickled
cell promotes chronic
hemolysis and microvascular
occlusions.
Smith, C., Marks, A. & Leiberman, M. (2012). Marks’ Basic Medical Biochemistry: A Basic Clinical
Biochemistry Lec | FMMaaño | FS AY2020-2021 Approach 2ed; Kumar, V., Abbas, A. & Aster, J. (2013). Robbins Basic Pathology 9ed
• Alzheimer’s Disease
(Amyloidosis)
• Due to inappropriate cleavage of
amyloid precursor protein (APP)
leading to extracellular aggregation
of Aβ and neuronal Tau protein.
Biochemistry Lec | FMMaaño | FS AY2020-2021 Kumar, V., Abbas, A. & Aster, J. (2013). Robbins Basic Pathology 9ed
• Prions (bovine spongiform
encephalopathy &
Creutzfeldt-Jacob disease)
Kumar, V., Abbas, A. & Aster, J. (2013). Robbins Basic Pathology 9ed;
S protein of
SARS-CoV-2
• S2 subunit contains the
highly-flexible stalk that
allow wide movements for
attachment
• S1 subunit highly
glycosylated that stabilizes
RBD
Structural image from Lorenzo Casalino, Univ. California, San Diego (Ref. 1);
Biochemistry Lec | FMMaaño | FS AY2020-2021 Graphic: Nik Spencer/Nature
Sisyphus by Titian
“This universe henceforth

without a master seems to him
neither sterile nor futile... The
struggle itself toward the
heights is enough to fill a man's
heart. One must imagine
Sisyphus happy.”
Albert Camus
(Le Mythe de Sisyphe)

Enzymes
French Alfred M. Maaño
Marinduque State College
Enzymes
• Enzymes are protein catalysts that increase the rate of
biochemical reactions.
Biochemistry Lec | FMMaaño | FS AY2020-2021 From Koolman, J. & Roehm, K. H. (2003). Color Atlas in Biochemistry.
Enzymes
• Why do we need enzymes?
• Biochemical reactions takes time and must be regulated. If

there are no enzymes, no reaction will ever happen and if it
ever happen it will release substantial energy that will exhaust
the biochemical system.
• Metabolic reactions can only happen in the presence of
enzymes!

Enzymes
• Enzymes are mostly proteins, though nucleic acid enzymes also
exists.
• Enzymes have metallic chemical component which is termed
cofactor or if a complex metalloorganic molecule, it is called
coenzyme.
• The full and functional enzyme, ready to assist in reactions, are
termed holoenzyme. If only a part of the enzyme, it is called
apoenzyme.
• Enzymes are also produced as an inactivated form termed
zymogen.

Enzymes
• Coenzymes
Enzymes
Enzymes
• An enzyme contains an active site
where the substrate(s) must fit in
order for enzyme catalysis to occur
• Enzyme-substrate binding is a key
process in enzyme catalysis.
Enzymes
• Models of Enzyme-Substrate Binding
Enzymes
• Enzyme-Substrate Binding is specific
Enzymes
• Free energy profile during enzyme catalysis
Enzyme Kinetics
• The rate of enzyme catalysis is a function of [S].
Enzyme Kinetics
Nelson, D., & Cox, M. (2012). Lehninger’s Principles of Biochemistry 6ed;

Enzyme Kinetics
Enzyme Kinetics
Michaelis-Menten
Equation
Enzyme Kinetics
Enzyme Kinetics
Lineweaver-Burke
Equation
Enzyme Kinetics
Lineweaver-Burke
Equation
Enzyme Kinetics
• How can we determine the catalytic efficiency of an enzyme?
• Michaelis constant(Km) –[S] where 50% of enzyme is bound.

• Turnover rate (kcat) –rate of product produced per mole of
enzyme per second.
• Specificity constant (kcat / Km) –rate constant for the

conversion enzyme-substrate to enzyme-product.

Enzyme Kinetics
• From the measures of

catalytic efficiency, we can
conclude the a lower Km
and/or higher Vmax, increases
catalytic efficiency.
Enzyme Inhibition
• Inhibition could be irreversible or
reversible
• There are three main types of
noncovalent enzyme inhibition:
competitive, uncompetitive and mixed
inhibition. Noncompetitive inhibition is
a subtype of mixed inhibition.
• Some inhibitors bind with a part of the
enzyme called allosteric site which
prevents the enzyme’s function.
Enzyme Inhibition
Competitive inhibition acts by
competing with the substrate for the
active site. This kind of inhibition
increases Km -termed apparent Km.
Enzyme Inhibition
Uncompetitive inhibition acts on
an allosteric site of the enzyme-
substrate complex.
Enzyme Inhibition
Mixed inhibition acts on allosteric
site of free enzymes and enzyme-
substrate complexes.
Enzyme Inhibition
where in α=α’
Noncompetitive mixed inhibition
acts on allosteric site of free
enzymes and enzyme-substrate
complexes, affecting the Vmax alone.
Nelson, D., & Cox, M. (2012). Lehninger’s Principles of Biochemistry 6ed;

Enzyme Regulation
How is enzyme activity regulated?
• Phosphorylation
• Allosteric effectors (inhibitors/activators)
• Zymogen
• Regulation of coenzyme
• Regulation of protein synthesis
• Regulation of protein degradation
Biochemistry Lec | FMMaaño | FS AY2020-2021 Alberts, B. et al. (2008). Molecular Biology of the Cell 5ed.
Enzyme Regulation
• Regulation of Insulin
Production
• Insulin synthesized by β
pancreatic cells.
• Rise in blood glucose leads
to PKC activation,
activation of Ca2+ channels.
Fu, Z., Gilbert, E. R., & Liu, D. (2013). Regulation of insulin synthesis and secretion and pancreatic
Biochemistry Lec | FMMaaño | FS AY2020-2021 Beta-cell dysfunction in diabetes. Current diabetes reviews, 9(1), 25–53.
Kinetics of Alcohol Metabolism
• Alcohol clearance in the blood is
15mg/dL per hr.
• Mainly by liver ADH (liver alcohol
dehydrogenase) and P450-2E1.
• ADH displays wide variation in
kinetics (at pH=7.5):
• β1β1: Km (0.048mM) Vmax (9 min-1)
• βIndβInd: Km (64mM) Vmax (560 min-1) Human ADH1B
Bosron, W. F., Crabb, D. W., & Ting-Kai Li. (1983). Relationship between kinetics of liver alcohol
dehydrogenase and alcohol metabolism. Pharmacology Biochemistry and Behavior, 18, 223–227.
doi:10.1016/0091-3057(83)90175-2
Biochemistry Lec | FMMaaño | FS AY2020-2021 https://www.uniprot.org/uniprot/P00325
“We all want progress. But progress
means getting nearer to the place where
you want to be. And if you have taken a
wrong turning then to go forward does not
get you any nearer. If you are on the
wrong road progress means doing an
about-turn and walking back to the right
road and in that case the man who turns
back soonest is the most progressive
man. There is nothing progressive
about being pig-headed and refusing
to admit a mistake.”
C.S. Lewis
(Mere Christianity)

Proteins: French Alfred M. Maaño Marinduque State College

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Proteins

French Alfred M. Maaño

Contractile (Actin & Myosin)

Biochemistry Lec | FMMaaño | FS AY2020-2021

• Amino acids are subdivided based on their polarity, aromaticity

• Hydropathy Index is the measure of

• Amino acids are polyionic

Amino acids participate in the biosynthesis of porphyrin,

A string of amino acids, called peptides are medically

Biochemistry Lec | FMMaaño | FS AY2020-2021

• The sequence of amino acids are commonly important to

• Similarity in amino acid sequence may mean similarity in

Biochemistry Lec | FMMaaño | FS AY2020-2021

• Two AAs are linked in a condensation

• Peptides are named from the amino-

• There is restricted movement in the peptide.

Biochemistry Lec | FMMaaño | FS AY2020-2021 https://www.uniprot.org/uniprot/P59594

BioVIA Blog. (2020, 04 April). Decoding the SARS-CoV-2 Genomes – Origin.

Liu Y et al. (2021). Delta spike P681R mutation enhances SARS-

Liu Y et al. (2021). Delta spike P681R mutation enhances SARS-

Liu Y et al. (2021). Delta spike P681R mutation enhances SARS-

Liu Y et al. (2021). Delta spike P681R mutation enhances SARS-

Biochemistry Lec | FMMaaño | FS AY2020-2021

Biochemistry Lec | FMMaaño | FS AY2020-2021

• An α helix is a single-stranded helix with right-handed direction.

Biochemistry Lec | FMMaaño | FS AY2020-2021

• The propensity towards α helix is stabilized by hydrogen

Biochemistry Lec | FMMaaño | FS AY2020-2021

• β sheets have a pleated structure or forming a zigzag line

• Antiparallel β sheets have a more stable hydrogen bonding and

Biochemistry Lec | FMMaaño | FS AY2020-2021

“This universe henceforth

Biochemistry Lec | FMMaaño | FS AY2020-2021

• Biochemical reactions takes time and must be regulated. If

Biochemistry Lec | FMMaaño | FS AY2020-2021

Biochemistry Lec | FMMaaño | FS AY2020-2021

Nelson, D., & Cox, M. (2012). Lehninger’s Principles of Biochemistry 6ed;

• Michaelis constant(Km) –[S] where 50% of enzyme is bound.

• Specificity constant (kcat / Km) –rate constant for the

Biochemistry Lec | FMMaaño | FS AY2020-2021

• From the measures of

Nelson, D., & Cox, M. (2012). Lehninger’s Principles of Biochemistry 6ed;

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