CHEM113 – BIOCHEMISTRY

1ST SEMESTER – MIDTERM – A.Y. 2023-2024

LESSON: PROTEINS

Proteins 4. Polar Basic Amino Acid

→ naturally occurring, unbranched polymer in which the → amino acid that contains two amino groups (NH2 or
monomer units are amino acid. N2) and one carboxyl group, the second amino group
→ casein – main protein of milk; contains phosphorus. being part of the side chain.
→ hemoglobin – oxygen-transporting protein of blood;
contains iron.
→ accounts for about 15% of the cell’s overall mass.
→ contains the elements: carbon, hydrogen, oxygen,
nitrogen, and some also contains sulfur.

Amino Acid
→ organic compound that contains both an amino
group or nitrogen group ( − NH2 ), and a carboxyl
group (−COOH).
→ also contains a hydrogen atom and C is always the
center bond.
→ backbone – peptide bond
→ amino acids in proteins are always α-amino acids.
→ 𝛂-amino acid – amino acid in which the amino
group and the carboxyl group are attached to the α-
carbon atom.

Side Chain

R  -Carbon Atom

H2N C COOH
-Carboxyl
-Amino H
Group
Group
→ R is called the amino acid side chain.
→ standard amino acid – one the 20 α-amino acids
normally found in proteins.
Essential Amino Acids
→ four types: nonpolar, polar acidic, polar neutral, and
→ essential amino acid – standard amino acid
polar basic.
needed for protein synthesis that must be obtained
from dietary source because the human body cannot
Types of Amino Acids
synthesize it in adequate amount from other
1. Nonpolar Amino Acid
substances.
→ contains one amino group, one carboxyl group, and
→ includes: arginine, histidine, isoleucine, leucine,
a nonpolar side chain
lysine, methionine, phenylalanine, threonine,
→ hydrophobic; insoluble in water.
tryptophan, and valine.
→ tryptophan – weakly interact through hydrogen
→ arginine – only needed for growth in children.
bonding with the NH ring location.
→ complete dietary protein – contains all of the
essential amino acids in the same relative amounts
2. Polar Acidic Amino Acid
in which the body needs them; may or may not
→ amino acid that contains one amino group and two
contain all of the nonessential amino acids.
carboxyl groups, the second carboxyl group being
→ incompletely dietary protein – does not contain
part of the side chain.
adequate amounts, relative to the body’s needs, of
one or more of the essential amino acids.
3. Polar Neutral Amino Group
→ limiting amino acid – essential amino acid that is
→ amino acid that contains one amino group (amide –
missing, or present in inadequate amounts, in an
NH), one carboxyl group (alcohol – OH), and a side
incomplete dietary protein.
chain that is polar but neutral.
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 CHEM113 – BIOCHEMISTRY
1ST SEMESTER – MIDTERM – A.Y. 2023-2024
LESSON: PROTEINS

→ animal protein – complete dietary protein; meat, a. −COOH → −COO− + H +

fish, and eggs.
→ plant protein – incomplete dietary protein; limiting
amino acids – lysine (wheat, rice, oats, and corn),
methionine (beans and peas), and tryptophan (corn
and beans).
→ soy – complete dietary protein
→ complementary dietary proteins – two or more
incomplete dietary proteins that, when combines,
provide an adequate amount of all essential amino
acids relative to the body’s needs.
Chirality and Amino Acids
→ 19 out of the 20 standard amino acids possess a
chiral center.
→ each of the 19 amino acids exist in left and right-
handed forms.
→ in neutral solution, amino groups have a tendency to
accept protons (H+); produces a positive charge.
b. −NH2 + H + → N + H3
→ zwitterion – “double ion”; molecule that has a
positive charge on one atom and a negative charge
on another atom, but which has no net charge:
a. basic solution – the N + H3 of the zwitterion
loses a proton, and a negatively charge species
is formed.
b. acidic solution – the zwitterion accepts a
proton to form a positively charged ion.
→ carboxyl groups give-up a proton to get negative
charge.
→ amino groups accept a proton to become positive.
→ amino acids in solution exist in three different
species (zwitterions, positive ion, and negative ion);
equilibrium shifts with change in pH

COOH COO- COO-

+ +
H3N C H H3N C H H2N C H

CH3 CH3 CH3

Low pH High pH
Zwitter Ion
(net + charge) (net neutral charge) (net - charge)

Isoelectric Point
→ rules for drawing Fischer Projection Formula for → neutral form – no net charge; exists primarily in
amino acid: zwitterion form; important pH value, relative to the
a. the carboxyl (-COOH) group is put at the top of various form an amino acid can have in a solution.
the projection formula, the R group at the → isoelectric point – pH at which an amino acid exists
bottom. This positions the carbon chain primarily in a zwitterion form; pH at which the
vertically. concentration of Zwitterion is maximum; net charge
b. the nitrogen or amino group (-NH2) is in a is zero
horizontal position.
→ L – NH2 on the left. Isoelectric Isoelectric
Name Name
→ D – NH2 on the right. Point Point
alanine 6.01 leucine 5.98
arginine 10.76 lysine 9.74
asparagine 5.41 methionine 5.74
aspartic
2.77 phenylalanine 5.48
acid
cysteine 5.07 proline 6.48
glutamic
3.22 serine 5.68
acid
glutamine 5.65 threonine 5.87
glycine 5.97 tryptophan 5.88
histidine 7.59 tyrosine 5.66
isoleucine 6.02 valine 5.97
Acid-Base Properties of Amino Acids Cysteine: A Chemically Unique Amino Acid
→ in pure form amino acids are white crystalline solids; → the only standard amino acid with a sulfhydryl group
most amino acids decompose before they melt. (— SH group).
→ not very soluble in water due to strong intermolecular → cystine – two cysteine residues linked via a covalent
forces within their crystal structures. disulfide bond.
→ in neutral solution, carboxyl groups have a tendency → the sulfhydryl group imparts cysteine a chemical
to lose protons (H+): produces negative charge. property unique among the standard amino acids.
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 CHEM113 – BIOCHEMISTRY
1ST SEMESTER – MIDTERM – A.Y. 2023-2024
LESSON: PROTEINS

→ cysteine in the presence of mild oxidizing agents an amino acid participates in peptide bond formation
dimerizes to form a cystine molecule. as it becomes part of a peptide chain.

Peptides Peptide Nomenclature

→ peptide – unbranched chain of amino acids.
→ dipeptide – bond between two amino acids.
→ tripeptide – bond between three amino acids.
→ oligopeptide – bond between ~ 10 - 20 amino acids.
→ polypeptide – bond between large numbers of
amino acids; long unbranched chain of amino acids.
Nature of the Peptide Bond
→ amino acid is linked by amide bond/group (CONH).
→ peptide bond – covalent bond between the carboxyl
group of one amino acid and the amino group of
another amino acid.
→ water – byproduct of peptide bond.
1. The C-terminal amino acid residue (located at the far right
of the structure keeps its full amino acid name).
2. All of the other amino acid residues have names that end
in -yl. The -yl suffix replaces the -ine or -ic acid ending of
the amino acid name, except for tryptophan (tryptophyl),
cysteine (cysteinyl), glutamine (glutaminyl), and
asparagine (asparaginyl).
3. The amino acid naming sequence begins at the N-
terminal amino acid residue.
Isomeric Peptides
→ peptides that contain the same amino acids but
present in different order are different molecules
(constitutional isomers) with different properties
→ for example, two different dipeptides can be formed
between alanine and glycine
→ the number of isomeric peptides possible increases
rapidly as the length of the peptide chain increases

Biochemically Important Small Peptides

→ many relatively small peptides are biochemically
active:
→ reaction between carboxylic acid and an amine to a. hormones
produce an amide was also considered. b. neurotransmitters
c. antioxidants

Small Peptide Hormones

→ oxytocin and vasopressin (antidiuretic hormone)
– best-known peptide hormones; produced by the
→ free group – every peptide has an N-terminal (H3N) hypothalamus stored in the posterior pituitary gland.
end and a C-terminal (COO-) end. → nonapeptide (nine amino acid residues) with six of
→ N-terminal – left; C-terminal right. the residues held in the form of a loop by a disulfide
bond formed between two cysteine residues.
OH
N-terminal end
O O CH2 O

+H
H H
3N CH C N CH C N CH C O-

CH3 CH2 C-terminal end

Small Peptide Neurotransmitters

Alanine Phenylalanine Serine
→ enkephalins – reduces pain.
→ amino acid residue – portion of an amino acid → met-enkephalin and leu-enkephalin – best known
structure that remain after the release of H2O, when enkephalins.

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 CHEM113 – BIOCHEMISTRY
1ST SEMESTER – MIDTERM – A.Y. 2023-2024
LESSON: PROTEINS
→ met-enkephalin – tyr-gly-gly-phe-met
→ leu-enkephalin – tyr-gly-gly-phe-met
Small Peptide Antioxidants
→ glutathione (glu–cys–gly) – a tripeptide – is present
is in high levels in most cells.
→ regulator of oxidation – reduction reactions.
→ glutathione is an antioxidant and protects cellular
contents from oxidizing agents such as peroxides
and superoxides.
→ highly reactive forms of oxygen often generated
within the cell in response to bacterial invasion.
→ unusual structural feature – Glu is bonded to Cys
through the side-chain carboxyl group.
General Structural Characteristics of Proteins
→ protein – peptide in which at least 40 amino acid
residues are presents.
→ more than one peptide chain may be present in a
protein.
→ several proteins – contains more than 10000 amino
acid residues.
→ common proteins – contains 400-500 amino acid
residues.
→ small proteins – contain 40-100 amino acid
residues.
→ number of peptide chain – protein may be classified
as monomeric or multimeric:
a. monomeric protein – protein in which only one
peptide chain is present.
b. multimeric protein – protein in which more
than one peptide chain is present; protein
subunits – peptide chains present in multimeric
proteins.
→ chemical composition – proteins may be classified
as simple or complex:
a. simple protein – protein in which only amino
acid residue is present.
b. conjugated / complex proteins – has one or
more non-amino-acid entities present in its
structure in addition to one or more peptide
chains; prosthetic group – non-amino-acid
group present in a conjugated protein; may be
organic or inorganic.
→ conjugated proteins may be further classified
according to the nature of prosthetic groups present:
a. lipoproteins – lipid groups
b. glycoproteins – carbohydrate groups
c. hemoproteins – heme groups
d. phosphoproteins – phosphate group
TRANSCRIBED BY: BUCYOT (BSN 1 – Y1 – 37)
e. nucleoproteins – nucleic acid group
f. metalloproteins – metal ion groups
Level of Structure of Proteins
Primary Structure of Proteins
→ 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
→ “peptide bond”.
Secondary Structure of Proteins
→ arrangement in space adopted by the backbone
portion of a protein.
→ alpha-helix and beta-pleated sheet – two most
common types.
→ the peptide linkages are essentially planar thus
allows only two possible arrangements for the
peptide backbone for the following reasons:
a. for two amino acids linked through a peptide
bond six atoms lie in the same plane
b. the planar peptide linkage structure has
considerable rigidity, therefore rotation of
groups about the C–N bond is hindered
c. cis–trans isomerism is possible about C–N
bond.
d. the trans isomer is the preferred orientation
The Alpha Helix
→ protein secondary structure in which a single protein
chain adopts a shape that resembles a coiled spring
(helix), with the coil configuration maintained by
hydrogen bonds.
→ H-bonding between same amino acid chains – intra
molecular.
→ coiled helical spring
→ R-group outside of the helix – not enough room for
them to stay inside.
The Beta Pleated Sheet
→ protein secondary structure in which two fully
extended protein chain segments in the or different
molecules are held together by hydrogen bonds.
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 CHEM113 – BIOCHEMISTRY
1ST SEMESTER – MIDTERM – A.Y. 2023-2024
LESSON: PROTEINS
→ completely extended amino acid chains
→ H-bonding between two different chains – inter
and/or intramolecular
→ side chains below or above the axis
→ “backbone”
Unstructured Segments
→ protein secondary structure that is neither an alpha-
helix nor a beta-pleated sheet.
Tertiary Structure of Proteins
→ overall three-dimensional shape of a protein that
results from the interaction between amino acid side
chain (R groups) that are widely separated from each
other within a peptide chain.
→ “complex structure”
Interactions Responsible for Tertiary Structure
1. Disulfide Bond – covalent, strong, between two cysteine
groups.
2. Electrostatic Interactions – salt bridge; between
charged side chains of acidic and basic amino acids.
3. H-Bonding – between polar, acidic and/or basic R
groups; for H-bonding to occur, the H must be attached
on O, N or F.
4. Hydrophobic Interactions – between non-polar side
chains.
Quaternary Structure of Proteins
→ highest level of protein organization.
→ “multiple sub-units”.
→ dimer – two subunits
→ tetramer – four subunits
→ the subunits are held together mainly by hydrophobic
interactions between amino acid R groups.
Protein Hydrolysis
→ hydrolysis – reaction with water in which water
breaks the chemical bond present at a substance.
→ hydrolysis reaction – reverse of the formation
reaction for a peptide bond.
→ complete hydrolysis – all peptide bonds are broken
freeing up all of the constituent amino acids.
→ partial hydrolysis – some, but not all; peptide bonds
are broken producing a product mixture that contains
both free amino acids and small peptides.
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Protein Denaturation
→ partial or complete disorganization of a protein’s
characteristic three-dimensional shape as a result of
disruption of its secondary, tertiary, and quaternary
structural interaction.
→ denaturing agents: heat, microwave radiation,
ultraviolet radiation, violent whipping or shaking,
detergent, organic solvents (alcohol), strong acids
and bases, salts of heavy metals, and reducing
agents.
Protein Classification Based on Shape
→ molecular shaped is determined by tertiary and
quaternary structural features.
→ three main types of proteins:
a. fibrous proteins – molecules have an
elongated shape with one dimension much
longer than the others; tends to have simple,
regular, linear structure.
b. globular proteins – molecules have peptide
chains that are folded into spherical or globular
shapes; water-soluble substances.
c. membrane protein – associated with a
membrane system of a cell.
Alpha Keratin
→ abundant in nature
→ protective coating for organisms
→ major protein constituent of hair, feathers, wool,
fingernails and toenails, claws, scales, horns, turtle
shell, quills, and hooves.
Collagen
→ fibrous
→ most abundant proteins in humans (30% of total
body protein).
→ major structural material in tendons, ligaments,
blood vessels, and skin.
→ organic component of bones and teeth.
→ predominant structure - triple helix
→ rich in proline (up to 20%) – important to maintain
structure.
Hemoglobin
→ globular
→ an oxygen carrier molecule in blood
→ transports oxygen from lungs to tissues
→ tetramer (four peptide chains) - each subunit has a
heme group
→ can transport up to 4 oxygen molecules at time
→ iron atom in heme interacts with oxygen
Myoglobin
→ globular
→ an oxygen storage molecule in muscles.
→ monomer - single peptide chain with one heme unit
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 CHEM113 – BIOCHEMISTRY
1ST SEMESTER – MIDTERM – A.Y. 2023-2024
LESSON: PROTEINS
→ binds one O2 molecule
→ has a higher affinity for oxygen than hemoglobin.
→ oxygen stored in myoglobin molecules serves as a
reserve oxygen source for working muscles
Protein Classification Based on Functions
→ stems from:
a. their ability to bind small molecules specifically
and strongly to themselves;
b. their ability to bind other proteins, often other like
proteins, to form fiber-like structures and;
c. their ability to bind to, and often become
integrated into cell membranes.
→ has twelve different kinds:
Catalytic Proteins
→ proteins are known for their role as catalyst.
→ enzymes – proteins with the role of biochemical
catalyst.
→ almost every chemical reaction in the body is driven
by an enzyme.
→ enzymes participate in almost all of metabolic
reactions that occur in cells.
Defense Proteins
→ immunoglobins / antibodies – central to the
functioning of the body’s immune system.
→ bind to foreign substances, such as bacteria and
viruses, to help combat invasion of the body by
foreign particles.
Transport Proteins
→ bind to particular small biomolecules and transport
them to other locations in the body.
→ hemoglobin – carries oxygen from the lungs to other
organs and tissues.
→ transferrin – carries iron from the liver to the bone
marrow.
→ high and low-density lipoproteins – carriers of
cholesterol in the blood stream.
Messenger Proteins
→ transmit signals to coordinate biochemical
processes between different cells, tissues, and
organs.
→ insulin and glucagon – regulate carbohydrate
metabolism.
→ human growth hormone – regulates human body
growth.
Contractile Proteins
→ necessary for all forms of movement.
→ composed of filament-like contractile proteins that, in
response to nerve stimuli, undergo conformation
changes that involves contraction and extension.
→ actin and myosin
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Structural Proteins
→ confer stiffness and rigidity.
→ collagen – component of cartilage.
→ a-keratin – mechanical strength as well as
protective covering.
Transmembrane Proteins
→ control the movement of small molecules and ions
through the cell membrane.
Storage Proteins
→ bind (and store) small molecules for future use.
→ ferritin – iron-storage protein
→ myoglobin – oxygen-storage present in muscles.
Regulatory Proteins
→ found embedded in the exterior surface of cell
membranes.
→ often the molecules that bind to enzymes (catalytic
proteins), thereby turning them “on” and “off,” and
thus controlling enzymatic action.
Nutrient Proteins
→ particularly important in the early stages of life – from
embryo to infant.
→ casein – found in milk
→ ovalbumin – found in egg white
Buffer Proteins
→ maintains the acid-base balance within body fluids.
→ hemoglobin – buffering role
Fluid-Balance Protein
→ maintains fluid balance between blood and
surrounding tissue.
→ albumin and globulin.
Glycoproteins
Immunoglobulins
→ glycoprotein produced by an organism as a
protective response to the invasion of microorganism
of foreign molecules.
→ serves as an antibody to combat invasion of the body
by antigens.
→ antigen – foreign substance, such as bacterium or
virus, that invades the human body.
→ antibody – biochemical molecule that counteracts a
specific antigen.
Lipoproteins
→ conjugated protein that contains lipids in addition to
amino acids.
→ help suspend lipids and transport them through the
bloodstream.
→ plasma lipoprotein – involved in the transport
system for lipids in the bloodstream.
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 CHEM113 – BIOCHEMISTRY
1ST SEMESTER – MIDTERM – A.Y. 2023-2024
LESSON: PROTEINS

→ has four major classes

a. chylomicrons – transport dietary
triacylglycerols from the intestine to the liver and
to adipose tissue.
b. very-low-density lipoproteins (VLDLs) –
transport triacylglycerols synthesized in the liver
to cells throughout the body.
c. low-density-lipoproteins (LDLs) – transport
cholesterol synthesized in the liver to cells
throughout the body.
d. high-density lipoproteins (HDLs) – collect
excess cholesterol from body tissues and
transport it back to the liver for degradation to
bile acids.

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