BIOCHEMISTRY

Atif Mehmood
Lecturer in Radiology KMU
PROTEINS
 Characteristics of Proteins

Contain carbon, hydrogen, oxygen, nitrogen, and sulfur

Serve as structural components of animals
Serve as control molecules (enzymes)
Serve as transport and messenger molecules
Basic building block is the amino acid
 WHAT IS PROTEIN?
Proteins are a sequence of amino acids
Of the 20 amino acids that exist, 9 are
essential amino acids, and 11 are non-
essential
There are also 4 amino acids that can be
considered conditionally essential:
arginine, tyrosine, glutamine, and cysteine
 Proteins are the most structurally complex
molecules known.
Each type of protein has a complex three-
dimensional shape or conformation.
All protein polymers are constructed from the
same set of 20 monomers, called amino acids.
Polymers of proteins are called polypeptides.
A protein consists of one or more
polypeptides folded and coiled into a specific
conformation
 AMINO ACIDS: Structure

Consist of a central carbon atom bonded

to: a hydrogen, a carboxylic acid, an amino
group, and an additional side group that is
unique to each amino acid
 Amino Acid

Amine group acts like a base, tends to be positive.

Carboxyl group acts like an acid, tends to be negative.
R group is variable, from 1 atom to 20.
Two amino acids join together to form a dipeptide.
Adjacent carboxyl and amino groups bond together.
Some Amino Acids
Amino Acid + Amino Acid --> Dipeptide

Amino Acid + Dipeptide --> Tripeptide

A.A. + A.A. + ..+ Tripeptide --> Polypeptide

 AMINO ACIDS: Structure

The side group creates unique

characteristics for each amino acid so they
differ in: shape, size, composition, electrical
charge, and pH.
 AMINO ACID: Sequence

Amino acids link in specific sequences to

form strands of protein
One amino acids is joined to the next by a
PEPTIDE bond
Formation of a Dipeptide

Dehydration synthesis
 AMINO ACID: Sequence

Dipeptide 2 amino acids

Tripeptide 3 amino acids
Oligopeptides 4-10 amino acids
Polypeptide more than 10 amino acids
Proteins in the body and diet are long
polypeptides (100s of amino acids)
 DENATURING of PROTEINS
Acid, alkaline, heat, alcohol, and agitation can
disrupt the chemical forces that stabilize
proteins and can cause them to lose their
shape (denature)
Denaturing of proteins happens during food
preparation (cooking, whipping, adding acids)
or digestion (in the stomach with hydrochloric
acid)
 Classification of proteins:
The following classification is based upon
pysiochemical properties of protein.
A protein may belong to one of the three
types,i.e.
Simple proteins
Compound or conjugated proteins
Derived proteins
 Simple Proteins:
On hydrolysis,these proteins yield only amino
acids or their derivates.These consist of the
following types.
Albumins
Globulins
Globins
Histones
Protamines
Albuminoids(collagen,Elastin,Keratin)
Compound or conjugated protiens:
In these molecules the protein is attached or
conjugated to some non protein groups which are
called prosthetic groups.The following types of
proteins belong to this group,
Nucleoproteins
Phosphoproteins
Lipoproteins
Carbohydrate-containg proteins
Chromoproteins
Metalloproteins
 Derived Proteins:
This class of proteins includes substances
which are derived from simple and conjugated
proteins.These proteins are subdivided into,
Primary derived proteins
secondary derived proteins
 Other classifications of Proteins:
A) Classification based upon Function:
Catalytic proteins
Regulatory or hormonal proteins
Structural proteins
Transport proteins
Immune proteins
Contractile proteins
Genetic proteins
Storage proteins
B)Classification based upon molecular
length and shape:
Fibrous proteins
Globular proteins
The Three Dimensional Structure of
Proteins:
Primary and Secondary Structure

Tertiary and Quaternary Structure

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 Primary Structure of Proteins

The particular sequence of amino acids that is

the backbone of a peptide chain or protein
CH3
CH 3 S
CH CH3 SH CH2
CH3 O
+ CH O CH2 O CH2 O
-
H3N CH C N CH C N CH C N CH C O
H H H
Ala-Leu-Cys-Met
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 Secondary Structure Alpha Helix

Three-dimensional arrangement of amino acids with

the polypeptide chain in a corkscrew shape
Held by H bonds between the H of N-H group and
the O of C=O of the fourth amino acid along the
chain
Looks like a coiled telephone cord

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 Secondary Structure Triple Helix

Three polypeptide chains woven

together
Glycine, proline, hydroxy proline
and hydroxylysine
H bonding between OH groups
gives a strong structure
Typical of collagen, connective
tissue, skin, tendons, and cartilage

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 Learning Check P1

Indicate the type of structure as

(1) primary (2) alpha helix
(3) beta pleated sheet (4) triple helix

A. Polypeptide chain held side by side by H bonds

B. Sequence of amino acids in a polypeptide chain
C. Corkscrew shape with H bonds between amino acids
D. Three peptide chains woven like a rope

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 Solution P1

Indicate the type of structure as

(1) primary (2) alpha helix
(3) beta pleated sheet (4) triple helix

A. 3 Polypeptide chain held side by side by H bonds

B. 1 Sequence of amino acids in a polypeptide chain
C. 2 Corkscrew shape with H bonds between amino acids
D. 4 Three peptide chains woven like a rope

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 Tertiary Structure
The tertiary structure of a protein means its overall
three dimensional shape or conformation.
Specific overall shape of a protein
Its molecule is folded and refolded on itself.
Cross links between R groups of amino acids in chain
Factors maintaing the tertiary structure of a Protein:,
disulfide SS +
ionic COO H3N
H bonds C=O HO
linkages between a ---COOH and ---OH group on
two different amino acids

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 Learning Check P2
Select the type of tertiary interaction as
(1) disulfide (2) ionic
(3) H bonds (4) hydrophobic

A. Leucine and valine

B. Two cysteines
C. Aspartic acid and lysine
D. Serine and threonine

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 Solution P2
Select the type of tertiary interaction as
(1) disulfide (2) ionic
(3) H bonds (4) hydrophobic
A. 4 Leucine and valine
B. 1 Two cysteines
C. 2 Aspartic acid and lysine
D. 3 Serine and threonine

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 Globular and Fibrous Proteins
Globular proteins Fibrous proteins
spherical shape long, thin fibers
Insulin Hair
Hemoglobin Wool
Enzymes Skin
Antibodies Nails

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 Quaternary Structure
Some proteins contain two or more separate
polypeptide chains or subunits. Each of these
polypeptides has its own primary,secondary,tertiary
structure. The arrangement of these subunits in three
dimensional complexes is called quaternary structure.
Proteins with two or more chains
Example is hemoglobin
Carries oxygen in blood
Four polypeptide chains
Each chain has a heme group to
bind oxygen
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 Learning Check P3

Identify the level of protein structure

1. Primary 2. Secondary
3. Tertiary 4. Quaternary

A. Beta pleated sheet

B. Order of amino acids in a protein
C. A protein with two or more peptide chains
D. The shape of a globular protein
E. Disulfide bonds between R groups
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 Solution P3

Identify the level of protein structure

1. Primary 2. Secondary
3. Tertiary 4. Quaternary

A. 2 Beta pleated sheet

B. 1 Order of amino acids in a protein
C. 4 A protein with two or more peptide
chains
D. 3 The shape of a globular protein
E. 3 Disulfide bonds between R groups
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 PROTEINS: Function
Structural Functions:
Collagen is the most abundant protein
in mammals, and gives bone and skin
their strength
Keratin provides structure to hair and
nails
 PROTEIN: Functions
ENZYMES
Enzymes are proteins that catalyze chemical
reactions without being used up or destroyed in
the process
Used in digestion, releasing of energy from
nutrients for fuel, triggering reactions that build
muscle and tissue
 PROTEIN: Functions

HORMONES
Hormones are chemical messengers that
are made on one part of the body, but act
on cells in other parts of the body
Insulin, Glucagon
Antidiuretic Hormone (ADH)
 PROTEIN: Functions

IMMUNE FUNCTION
The Immune Response is a series of steps
your body takes to mount an attack against
invaders
Antibodies are blood proteins that attack
and inactivate bacteria and viruses
Once an antibody has been made for a
certain invader, your body can more quickly
respond (Immunization)
 PROTEIN: Functions

FLUID BALANCE
Fluids in the body are intracellular or
extracellular (interstitial and intravascular)
and must remain balanced
 PROTEIN: Functions

ACID-BASE BALANCE
Proteins help to maintain a stable pH level
in our body fluid by picking up extra
hydrogen ions when conditions are acidic,
and donating hydrogen ions when
conditions are alkaline
Otherwise, the resulting conditions of
acidosis or alkalosis could lead to coma or
death
 PROTEIN: Functions

TRANSPORT
Lipoproteins (chylomicrons, LDL, HDL)
Albumin transports a variety of nutrients such
as calcium, zinc, and Vitamin B6
Transferrin transports iron (hemoglobin a
protein, contains iron, but it transports oxygen)
Proteins may also acts as channels or pumps
across the cell membrane
 PROTEIN: Functions
ENERGY SOURCE
If the diet does not provide enough energy, the
body must begin to break down its own protein
The proteins are broken down into individual
amino acids, then deaminated, and the
remaining carbon, hydrogen, and oxygen
compounds are used to make energy or glucose
If the diet contains too much protein, the excess
will be converted to glucose, or stored as fat
 DIGESTION

No digestion of protein takes place in the

mouth, it begins in the stomach
Hydrochloric acid denatures protein and
also converts pepsinogen to pepsin
Pepsin breaks the protein down into
peptides of various lengths and some
amino acids
Pepsin completes ~ 10-20% of digestion
 ABSORPTION
In the enterocyte, other peptidases
immediately digest everything into single
amino acids which are absorbed into the
bloodstream
Some amino acids share the same transport
system, so if you take in a large amount of
one particular amino acid, you may be
inhibiting the absorption of others
 How Much Protein Do We Need?
Adults:
0.8 grams of protein per kilogram of body weight
per day

Endurance Athletes:
1.2 to 1.4 g/kg/day

Heavy Weight Trainers:

1.7 to 1.8 g/kg/day