BIOCHEMISTRY (LECTURE)

3. PROTEINS
Proteins
- One of the most abundant organic molecules in
living systems
- Have the most diverse range of functions of all
macromolecules.
- May be:
o Structural
o Regulatory
o Contractile
o Protective.
- They may serve in transport, storage, or
membranes; or they may be toxins or enzymes. Proteins
- Each cell in a living system may contain
- Have different shapes and molecular weights.
thousands of proteins, each with a unique
o Some are globular in shape
function.
o Others are fibrous in nature.
- Their structures, like their functions, vary
- EXAMPLE: Hemoglobin
greatly.
o A globular protein, but collagen,
- They are all, however, amino acid polymers
located in our skin.
arranged in a linear sequence.
o A fibrous protein.
TYPES AND FUNCTIONS OF PROTEINS - Shape is critical to its function, and many
different types of chemical bonds maintain this
Enzymes shape.
- Produced by living cells. - Changes in temperature, pH, and exposure to
- Catalysts in biochemical reactions (like chemicals may lead to permanent changes in
digestion) and are usually complex or the protein's shape, leading to loss of function,
conjugated proteins. or denaturation.
- Each enzyme is specific for the substrate (a - Different arrangements of the same 20 types
reactant that binds to an enzyme) upon which of amino acids comprise all proteins.
- Two rare new amino acids were discovered
it acts.
- May help in: recently (selenocystein and pirrolysine), and
o Breakdown additional new discoveries may be added to
o Rearrangement the list.
o Synthesis reactions. Amino Acids
- Break down their substrates catabolic
enzymes. - The monomers that comprise proteins.
o Anabolic Enzymes: - Each amino acid has the same fundamental
 Build more complex molecules structure, which consists of a central carbon
from their substrates. atom, or the alpha (α) carbon, bonded to an
o Catalytic Enzymes: amino group (NH2), a carboxyl group (COOH),
 Affect the rate of reaction are and to a hydrogen atom.
catalytic enzymes. - Every amino acid also has another atom or
- NOTE: ALL ENZYMES increase the reaction rate group of atoms bonded to the central atom
and, therefore, are organic catalysts. known as the R group.
- EXAMPLE: Salivary amylase
o Hydrolyzes its substrate amylose, a
component of starch.
Hormones
- Chemical-signaling molecules, usually small
proteins or steroids, secreted by endocrine
cells that act to control or regulate specific
physiological processes, including growth,
development, metabolism, and reproduction.
- EXAMPLE: Insulin
o A protein hormone that helps regulate
the blood glucose level.
Amino Acids (cont.)
- Scientists use the name "amino acid" because
these acids contain both amino group and
carboxyl-acid-group in their basic structure.
- There are 20 common amino acids present in
proteins.
o 9 of these: Essential Amino Acids in
humans
 Human body cannot produce
them and we obtain them from
our diet.
- For each amino acid, the R group (or side
chain) is different.
20 Standards Amino Acids
- Encoded in the genes of all organisms.
- 19 of these:
o Open chain; walang ring

NOTES:
- 1 of these: - Chemical nature of the side chain determines
o May ring form = closed figure the amino acid’s nature (acidic. Basic, polar, or
nonpolar).
o Glycine: has H atom as the R group
o Valine, Methionine, and Alanine:
Nonpolar or hydrophobic in nature.
o Serine, Threonine, and Cysteine: Have
polar and hydrophilic side chains.
o Lysine and Arginine: Positively charged
side chains (basic amino acids).
o Proline: Has an R group that is linked to
the amino group, forming a ring-like
structure.
 An exception to the amino
acid’s standard structure since
its amino group is not
separated from the side chain.
- A single upper case letter or a three-letter
abbreviation represents amino acids.
- Just as some fatty acids are essential to a diet,
some amino acids also are necessary.
o Essential amino acids in humans
include:
 Isoleucine
 Leucine
 Cysteine
o Essential amino acids refer to those
necessary to build proteins in the body,
but not those that the body produces.
Which amino acids are essential varies
from organism to organism.
RECALL: Org Chem

CHIRALITY
- NOTE: ALL amino acids are chiral EXCEPT
Glycine.
Requirements:
1. Must have 4 groups attached to the Carbon.
2. These 4 groups must be different.
Examples:
1. Alanine
CHIRAL (?)
- COOH = ✖ ESSENTIAL AMINO ACID
- Cα = ✓
- Taken from the diet.
- CH₃ = ✖ - Chicken
- Fish
- Egg Source of proteins
2. Glycine - Soy (taho, tokwa, soymilk)
CHIRAL? - Cheese
- COOH = ✖
- Cα = ✖
- CH₃ = ✖
CONSEQUENCE OF BEING CHIRAL
- Handedness or Enantiomer
o Mirror images of a structure.
o Non superimposable

FISCHER PROJECTION
- Way of representing amino acids.

CLASSIFICATION BASED ON POLARITY

1. Non-Polar
 Consequence: kapag nasa structure
sila na napapalibutan ng aqueous
(water), amino acids > makikitang
nakatago sa interior ng structure.
 Hindi nakikipag-interact with water.
2. Polar
a. Uncharged/Neutral
b. Acidic AMINO ACIDS can behave as an/a ACID/BASE.
based on Bronsted-
c. Basic Lowry’s definition 1. Alanine
BASED ON Bronsted-Lowry:
- Acid: Donates/gives off H.
- Base: Receives H.
o N atom ang tatanggap ng H which will
act as the Bronsted-Lowry’s base.
 pH STRUCTURE NET CHARGE
1.00 I +1
7.00 II 0
11.00 III -1
ISOELECTRIC POINT (pI)
- pH; ISO = equal.
- Find where among the number of electron
charges are equal.
- Get the pK value immediately before and
immediately after of that structure.

2. Aspartic Acid REVIEW: Amide Bond

PEPTIDE BOND
- Essentially amide bond.
- C = O, C ---- N, N ---- H

pH STRUCTURE NET CHARGE

1.00 I +1
2.10 II 0
7.00 III -1
9.80 III -1 # of Amino Greek Name of # of
11.00 IV -2 Acids Prefix Peptide Peptide
Bonds
(# of AA – 1)
2 di- Dipeptide 1
3 tri- tripeptide 2

PEPTIDE BOND: FORMATION

FOUR LEVELS OF PROTEIN STRUCTURE
Primary Structure
- Refers to the unique sequence in a polypeptide
chain of amino acids.
o Kapag pinagdugtong-dugtong yung
amino acids, be called POLYPEPTIDE.
- EXAMPLE: Pancreatic hormone insulin
o Has two polypeptide chains
 A and B, and they are linked
together by disulfide bonds.
o The N terminal amino acid of the A
chain is glycine
o The C terminal amino acid is
asparagine.
Directionality of peptide chain: PEPTIDE BOND: FEATURES
- Left: free amino group (N-terminal end)
- Right: free carboxyl group (C-terminal end)
Parts of the Peptide chain:
- Backbone
o The repeating sequence of peptide
bonds and alpha-carbon –CH groups in
a peptide.
- Substituents on the backbone
o This refers to the R group sidechains
o The variable R group sequence
distinguishes one peptide from
another.

PEPTIDE NOMENCLATURE (naming)

- Write the free amino group of the peptide chain
(N-terminal) to the LEFT.
- Write the free carboxyl group of the peptide (C-
terminal) to the RIGHT.
- Read it from the N- to the C-terminal end.
- Replace the names of all the amino acid
residues ending in –ine or –ic acid to –yl
EXCEPT for the following: - Rigid and planar
o Tryptophan – tryptophyl o “Flat” – cannot be rotated.
o Cysteine – cysteinyl o Why? Consequence of having partial
o Glutamine – glutaminyl double bond character.
o Asparagine – asparaginyl
- Retain the name of the rightmost amino acid.
EXAMPLES:
1. Val-Cys
- Partial double bond character

o Double bonds aren’t fixed between C

atom and O atom.
o Electrons can transfer or change
position from O atom to N atom.

2. Ser-Cys-Phe
Phi and Psi Angles Secondary Structure

- Local folding
o Within the peptide chain.
o Formed because of the presence of
hydrogen bonds.
 H atom is in between 2
electronegative atoms (O, N).
Three (3) Major Types of Secondary Structure
1. α HELIX

- When rotated, can form different structures

leading to the secondary structure (higher level
than primary).
- Dihedral Angle
o Angle formed between two flat/planar
peptide bonds.
Ramachandram Diagram

- Helical – made stable by the presence of H-

bonds.
- Polypeptide chain = 1 strand
- Remember:
o R groups are on an outward position.
 REASON: to avoid crowding;
hindi dikit dikit side chains.
 Pag nasa loob > masikip.
o Type of H-Bond – kind of interaction
kasi malapit sa isa’t isa.
 Intramolecular: walang ka-
interact na ibang polypeptide
- y-axis: Psi
chain within the strand itself ng
- x-axis: Phi
protein.)
- Labelled names: Secondary structures that are
o Single-bond
possible to form.
- SIMPLEST EXAMPLE: Keratin
- It will tell you kung nasan dyan ang
combination ng mga angles na pwedeng
merong ma-form na structure.
- This is helpful para ma-determine what are the
specific angles that could form different
secondary structures.
Keratin
- Anti-Parallel
o Have opposite ends.
o (C-terminal : N-terminal)
- Parallel
o Have same ends.
o (C-terminal : C-terminal)
o (N-terminal : N-terminal)
- To represent:
C - terminal

- Subdivided into two: N - terminal

o Hard keratin (animal’s horn, tuka ng
ibon)
o Soft keratin (wool, hair, feathers)
- Found in hair (protein) - EXAMPLES:
- Can be as smooth as hair or as hard as o Silk
animal’s horn. o Spider’s web
- SOURCES:
o Protective coating organisms
o Major protein constituent of hair
o Feathers
o Fingernails, toenails
o Claw (eagles) 3. Collagen Triple Helix
o Scales, Horns, Turtle shells
2. β - Pleated Sheet

- FOUND IN:
o Bones
o Teeth
o Tendons
o Ligaments
o Blood vessels
o Skin
- Skin: laylay (interaction within became loose)
- COLLAGEN:
o Most abundant sa lahat ng proteins.
o Composed of different amino acids.
o Around 20% - Proline
 That’s why it’s helical.
- Pag mas maraming nagccrosslink within the
strand > mas nagiging matibay.
o Aging: lumalaylay skin because
nagluloose yung crosslinks.
SUPERSECONDARY STRUCTURES

- REMEMBER:
o Composed of 2 or more
strands/polypeptide chains.
o H-bonds: perpendicular to the
polypeptide chains.
o H-bonds: Intermolecular
 Pag-H-bond niya, hindi sa sarili
nya = sa katabing polypeptide
chain sya nakikipagbond.
 - Yung secondary structure may na-form pa na
shape na similar sa nakikita nilang mga
designs.
- May nakikita silang Greek key:
o Ex: 4 adjacent anti-parallel β strand (B)
- Also known as “STRUCTURAL MOTIFS”
- Combination of different secondary structures.
Tertiary Structure
MYOGLOBIN
- FUNCTION: to store oxygen.
- Consists of a SINGLE polypeptide chain.
- Includes a prosthetic group, HEME.
- Has 8 α–helical regions.
- Has 0 β–pleated sheet regions.
- Has sequence (PRIMARY STRUCTURE)
- Has folding (SECONDARY STRUCTURE)
- Highest level: Until tertiary struc
- Part of a large family named GLOBIN
- MYO: related to muscles.
- Obvious secondary structure na makikita: >1 α
helix.
HEME
- The presence of HEME group is required for
myoglobin to bind oxygen.
- The heme group consists of:
o A metal ion: Fe²⁺
o An organic part: PROTOPORPHYRIN IX
- The porphyrin part consists of 4 five-membered
rings based on the PYRROLE structure;
o These four rings are linked by bridging
METHINE (=CH-) groups to form a
SQUARE PLANAR structure.
- The Fe(II) ion has 6 coordination sites, and it
forms six metal-ion complexation bonds.
o Four of the six sites are occupied by the
NITROGEN atoms of the four pyrrole-
type rings of the porphyrin to give the
complete heme group.
Coordination Sites Atom or Groups
Attached to Fe²⁺
1-4 Nitrogen (from the
heme)
5 Nitrogen (from Histidine
F8)
6 Oxygen gas (O₂)
- Besides oxygen, CARBON MONOXIDE also
binds to heme.
- The affinity of free heme for carbon monoxide
(CO) is 25,000 times greater than its affinity for
oxygen.
Histidine E7 (top)
- Acts as a gate > lahat ng molecule (O₂, CO) na
maattach sa 6th coordination site ng Fe²⁺ ay
naka-inclined.
o WHY? Because of the presence ng side
chain na HISTIDINE.
o WHY INCLINED? Because hindi lang
oxygen pwede magbind sa iron sa
heme; pwede rin CO.
o INCLINED = mababawasan affinity
(interaction) ng CO sa heme >
consequence: medyo madali ang
pagtanggal (unload ng molecule >
madedetach sya sa heme).
FEATURES OF TERTIARY STRUCTURE
- Is what sets it apart from supersecondary and
secondary structures.
FORCES OF STABILIZING TERTIARY STRUCTURE
 - Possible Interactions:  Pag di nag-fold
o Disulfide Bonds: correctly >
 A covalent bond between 2 nagkakaroon ng sakit.
sulfurs.
 Cystein: Amino acid na may DENATURATION AND PROTEIN FOLDING
side chain na possible - Protein > nagfold: functional.
makapagform ng disulfide - Protein structure and shape can be changed if
bond. chemical interactions are broken.
 Pag natanggal H from - Protein structure/shape can change with
your sulfur, they can altering primary structure due to:
bond together to form o Changes in pH
disulfide bridge or o Changes in temperature
linkage.  Changes occur in any of the
o Hydrophobic Bonds: following, nagkakaroon ng
 Nagsama-sama mga non-polar denaturation process.
amino acids. - DENATURATION:
 Mga side chains nila will exhibit o Changes in protein structure that leads
hydrophobic bonds. to changes in function.
 Exist in interior because
aqueous ang mga nasa
external.
o Metallic Bonds:
 Prosthetic group but can
interact with your polypeptide
chain.
o Ionic Bonds:
 Side chains that have charges
depending on the pH.
 They can also interact by
forming this kind of interaction
(by means of charges) = UNFOLDING OF A GLOBULAR PROTEIN
opposite charges.
FOLDING OF GLOBULAR PROTEIN

- Unfolded: sequence lang ng primary.

- Folded: folding (process) > accompanied by - Partial or complete disorganization of a
specialized group of proteins. protein’s characteristic 3-dimentional shape.
PROTEIN PROCESSING o Unang masisira ay secondary structure
pataas.
o MATITIRA: Primary
- It does not affect the primary structure of a
protein.
- EFFECTS (consequence):
o Loss of biochemical activity
 EX: enzyme unfolds > unable to
catalyze rxn.
o Loss of water solubility
 Side chains that can interact
well with the aqueous
- A specialized group of proteins required for environment ay nasira na rin.
proper folding of many species of proteins.
- It interacts with the polypeptide at various IDEALLY:
stages during the folding process.
removes
o To keep the protein unfolded. Protein na nag- RENATURATION:
o To act as a catalyst. undergo ng
Denaturing
babalik sa dating
o To protect proteins as they fold. DENATURATION pagkaka-fold
Agent
 CHAPERONE: ginagabayan
pag-fold ng protein > to fold
correctly.
Quaternary Structure - HEME: almost flat.
- With Oxygen: pagkakakabit (attachment) ng
- Involves the interaction between your subunit. oxygen sa iron > tendency ay hatakin ang iron
HEMOGLOBIN (Hb) pataas > sumasama pati Histidine F8.

- Highest level of structure: QUATERNARY HEMOGLOBIN: POSITIVE CREATIVITY

- Can be found in red blood cells. - Pag-bind ng 4 na oxygen sa Hb (capacity is for
- Myoglobin: 1 subunit 4 oxygen atoms) hindi sabay-sabay; paisa-isa.
- Hb: x4 of myog. - Figure A:
- 4 subunits o Nag-iba itsura ng adjacent sa position
o α chain 1 = β chain 1 ng 1st oxygen (effect?) > mas mabilis
o α chain 2 = β chain 2 pag-bind ng 2nd and succeeding
 Each subunit has HEME. oxygens sa Hb.
o Pinakamahirap mag-bind: VERY FIRST
OXYGEN.
o Once may nakapag-bond nang oxygen,
magkakaron ng changes sa structures
ng other subunits.
- COOPERATIVITY:
o Binding ng oxygen na mas napapabilis
once meron nang naunang nag-bind.
- POSITIVE:
o Kasi napapabilis.
- Contains 4 globin proteins (subunit).
o Each globin is bound to 1 molecule of
the iron-containing pigment HEME.
- A single erythrocyte can contain 300M
hemoglobin molecules, and thus more than 1B
oxygen molecules.

Cooperative Binding
- The binding of an oxygen molecule at 1 heme
- Contains of four polypeptide chains: 2 α and 2 group INCREASE the oxygen affinity of the
β. remaining heme groups in the same
- Each chain is associated with a HEME group. hemoglobin molecule.
- Each heme group has a central iron atom that HEMOGLOBIN: OXYGEN BINDING CURVE (ideal)
can bind a molecule of OXYGEN (O₂).
- Hemoglobin loads with oxygen in the lungs, - mmHg:
forming OXYHEMOGLOBIN. o unit of O₂ concentration.
o w/o O₂: Deoxyhemoglobin o How O₂ is expressed.
o Gano kadami, pano sinusukat.
HEMOGLOBIN: STRUCTURE o Pressure is being measured (partial).
- MYOG: has a higher O₂ affinity.
o Can be explained by their nature of
FUNCTION.
- p50:
o Partial pressure of O₂ needed to
achieve half-saturation of the binding
sites.
# of
p50 bindi
(mmHg FUNCTION ng Graph
) sites
for O₂
Myoglobin 2 Store O₂ 1 Hyperbolic
Hemoglobin 27 Transport O₂ 4 Sigmoidal
Hb (Function): Affinity should be just enough to
carry/load oxygen in its destination. Once it arrives
there, it should be able to unload it.
 2,3-Bisphosphoglycerate (2,3-BPG)
- Second factor that affects your O₂ binding to
Hb.

- The plot of Y measured at different partial

pressure of oxygen (pO₂). - Synthesized from an intermediate of the
- p50 glycolytic pathway.
o trend: ↓ p50, ↑ oxygen affinity. - Most abundant organic phosphate in the red
- % Saturation with O₂ (Y) can vary from: blood cells.
o Zero: all oxygen binding sites are - It ↓ oxygen affinity of Hb by binding to deoxyHb
EMPTY. but not to oxyHb.
o 100%: all oxygen binding sites are
FULL. GRAPHS

HEMOGLOBIN: BOHR EFFECT

- Has something to do with the effect of the pH
sa O₂ binding sa Hb.
- pH ↓ = O₂ binding curve ay nagshishift to the
right. (consequence?) > ↓ affinity O₂.

- The pH effect is known as the Bohr shift

o Increased CO₂ in blood ↑ H+.
o Lower pH ↓ hemoglobin’s affinity for O₂.
o Facilitates oxygen unloading in the SICKLE CELL ANEMIA
tissue.
o If there is high levels of CO₂, that
means the oxygen is needed – the
hemoglobin lets go of the oxygen.
- Increase CO₂
o In the tissues, CO₂ is converted to
CARBONIC ACID (H₂CO₃) which
spontaneously loses a proton (H+) to
become BICARBONATE (HCO₃⁻).
 H+: nagpapababa ng pH
 ↓ pH = ↓ affinity of O₂.
o The deoxy form of Hb has a GREATER
affinity for H+ than does
oxyhemoglobin.