Chemical Constituents

of Organisms: Part II

Peptides and Proteins

 Peptides and Proteins
Proteins are polyamides
When formed by amino acids, each amide group
is called a peptide bond
Peptides are formed by condensation of the -
COOH group of one amino acid and the NH
group of another amino acid
The acid forming the peptide bond is named
first. Example: if a dipeptide is formed from
alanine and glycine so that the COOH group of
glycine reacts with the NH group of alanine, then
the dipeptide is called glycylalanine
In the Biuret test the solution with protein
turns purple

potassium copper
hydroxide sulphate
shake

purple = protein

chopped up
food
 TEST NEGATIVE POSITIVE
Iodine solution Starch Orangey-brown Blue-black
Benedict’s test Glucose Blue Orangey-red
Biuret test Protein Blue Purple
Ethanol test Fats Clear Cloudy white
For each food, decide on the chemicals found in them.

Food sample Test Result

Iodine solution orangey-brown
Benedict’s test blue
Biuret test purple
Ethanol test cloudy white

Protein Fats Starch Glucose

For each food, decide on the chemicals found in them.

Food sample Test Result

Iodine solution blue-black
Benedict’s test blue
Biuret test blue
Ethanol test clear

Protein Fats Starch Glucose

For each food, decide on the chemicals found in them.

Food sample Test Result

Iodine solution orangey-brown
Benedict’s test orangey-red
Biuret test blue
Ethanol test clear

Protein Fats Starch Glucose

For each food, decide on the chemicals found in them.

Food sample Test Result

Iodine solution orangey-brown
Benedict’s test orangey-red
Biuret test blue
Ethanol test clear

Protein Fats Starch Glucose

 Glycylalanine is abbreviated gly-ala or GA

Polypeptides are formed with a large number

of amino acids

Glycylalanine
Gly-Ala
Alanyltyrosylaspartylgylcine
GA AlanylTyrosylAspartylGlycine
Ala-Tyr-Asp-Gly
AYDG
 Protein Structure and Function
A functional protein consists of one or more
polypeptides twisted, folded, and coiled into
a unique shape

The sequence of amino acids determines a

protein’s three-dimensional structure

A protein’s structure determines its function

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

 Groove

(a) A ribbon model of lysozyme

 Groove

(b) A space-filling model of lysozyme

 Protein categories
Globular proteins
Fibrous proteins
 Globular proteins
Usually water soluble, compact, roughly
spherical
Hydrophobic interior, hydrophilic surface
Globular proteins include enzymes, carrier
and regulatory proteins
 Fibrous proteins
Provide mechanical support
Often assembled into large cables or threads
-Keratins: major components of hair and
nails
Collagen: major component of tendons, skin,
bones and teeth
 Protein Structure
1o : The linear sequence of amino acids and
disulfide bonds, e.g. ARDV:Ala.Arg.Asp.Val
2o : Local structures which include, folds,
turns, -helices and -sheets held in place
by hydrogen bonds
3o : 3-D arrangement of all atoms in a single
polypeptide chain
4o : Arrangement of polypeptide chains into a
functional protein, e.g. hemoglobin
Animation: Protein Structure Introduction
 Primary Protein Structure
Primary structure is the sequence of the
amino acids in the protein
Primary structure is determined by inherited
genetic information
A change in one amino acid can alter the
biochemical behavior of the protein

Animation: Primary Protein Structure

 Sickle-Cell Disease: A Change in
Primary Structure
A slight change in primary structure can affect
a protein’s structure and ability to function

Sickle-cell disease, an inherited blood

disorder, results from a single amino acid
substitution in the protein hemoglobin

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

 10 µm 10 µm

Normal red blood Fibers of abnormal

cells are full of hemoglobin deform
individual red blood cell into
hemoglobin sickle shape.
molecules, each
carrying oxygen.
 Secondary Protein Structure
Two types exist!!
-helix
-pleated sheets
The coils and folds of secondary structure
result from hydrogen bonds between
repeating constituents of the polypeptide
backbone
Typical secondary structures are a coil called
an α helix and a folded structure called a β
pleated sheet

Animation: Secondary Protein Structure

 -helix
Amino acids interact with each other

The H on the NH group is attracted to the

O on the CO group

The H is slightly positive and the O is

slightly negative

H bond forms between these two atoms

 ……..individually
weak!

Hydrogen bonds are

numerous…….

The H bonds that keep Alpha helices together are

vulnerable to fluctuations in pH & temperature
 Secondary Structure
pleated sheet

Examples of
amino acid
subunits

helix
 -pleated sheets

Hydrogen bonds hold adjacent primary chains together

-Sheets (a) parallel, (b) antiparallel
Common motifs
Common domain folds
To go above secondary structure
Tertiary Protein Structure
Proteins need more bond types

Disulphide bonds: Adjacent cysteine AA

S-S bond is a weak bond, broken by reducing
agents

Hydrophobic Interactions: Between non polar

R-groups

Ionic bonds: Forms between ionised amine &

carboxylic groups, broken by extreme pH
Tertiary structure is determined by
interactions between R groups, rather than
interactions between backbone constituents
These interactions between R groups
include hydrogen bonds, ionic bonds,
hydrophobic interactions, and van der
Waals interactions
Strong covalent bonds namely disulfide
bridges may reinforce the protein’s structure

Animation: Tertiary Protein Structure

Tertiary Structure Quaternary Structure
 Quaternary Structure
Refers to the organization of subunits in a
protein with multiple subunits (an “oligomer”)
Subunits (may be identical or different) have a
defined stoichiometry and arrangement
Subunits are held together by many weak,
noncovalent interactions (hydrophobic,
electrostatic)
Homodimer vs. heterotrimer and etc.
Quaternary structure results when two or
more polypeptide chains form one
macromolecule
Collagen is a fibrous protein consisting of
three polypeptides coiled like a rope
Hemoglobin is a globular protein consisting
of four polypeptides: two alpha and two beta
chains

Animation: Quaternary Protein Structure

Quaternary structure of multidomain proteins
 HAEMOGLOBIN

Made of 4 polypeptide chains

2 alpha chains and 2 beta chains

Hydrophobic R groups point into the molecule

Hydrophilic R groups point out of the molecule

This makes haemoglobin highly soluble

 Each of the 4 chains has a haem group

The haem group is not made of AA, but is an

integral part of the protein – prosthetic group

Each haem group contains an ion of iron (Fe2+)

Each haem binds with one molecule of O2

Haemoglobin can carry O8

 What Determines Protein Structure?
In addition to primary structure, physical and
chemical conditions can affect structure
Alterations in pH, salt concentration,
temperature, or other environmental factors
can cause a protein to unravel
This loss of a protein’s native structure is
called denaturation
A denatured protein is biologically inactive

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

 Denaturation
Denaturation- disruption of the normal 3D shape
Denaturation agents:
alcohol
weak acid or base
heat
detergents
reducing agents
 Protein Folding in the Cell
It is hard to predict a protein’s structure from
its primary structure
Most proteins probably go through several
states on their way to a stable structure
Chaperonins are protein molecules that
assist the proper folding of other proteins

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

 Scientists use X-ray crystallography to
determine a protein’s structure
Another method is nuclear magnetic
resonance (NMR) spectroscopy, which does
not require protein crystallization
Bioinformatics uses computer programs to
predict protein structure from amino acid
sequences

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

 Animation: Structural Proteins

Animation: Storage Proteins

Animation: Transport Proteins

Animation: Receptor Proteins

Animation: Contractile Proteins

Animation: Defensive Proteins

Animation: Hormonal Proteins

Animation: Sensory Proteins

Animation: Gene Regulatory Proteins

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

 Nucleic acids store and transmit
hereditary information
amino acid sequence of a polypeptide is
programmed by a unit of inheritance called
a gene
Genes are made of DNA, a nucleic acid

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

 The Roles of Nucleic Acids
There are two types of nucleic acids:
Deoxyribonucleic acid (DNA)
Ribonucleic acid (RNA)
DNA provides directions for its own
replication
DNA directs synthesis of messenger RNA
(mRNA) and, through mRNA, controls
protein synthesis
Protein synthesis occurs in ribosomes

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

 DNA

1 Synthesis of
mRNA in the
nucleus mRNA

NUCLEUS
CYTOPLASM
 DNA

1 Synthesis of
mRNA in the
nucleus mRNA

NUCLEUS
CYTOPLASM

mRNA
2 Movement of
mRNA into cytoplasm
via nuclear pore
 DNA

1 Synthesis of
mRNA in the
nucleus mRNA

NUCLEUS
CYTOPLASM

mRNA
2 Movement of
mRNA into cytoplasm Ribosome
via nuclear pore

3 Synthesis
of protein

Amino
Polypeptide acids
 Amino
Polypeptide acids

tRNA with
amino acid
attached
Ribosome

p
Tr Phe Gly

tRNA

Anticodon

5′′ Codons 3′′

mRNA
Next lesson:

DNA