Basic Principles of Medicine 1

Module: Foundations to Medicine

Lecture No: 17

Lecture Title:
Structure and Functions
of Proteins

Name of Lecturers: Andrew Sobering, PhD. and Felicia Ikolo PhD.

St Georges University ©
Copyright

All year 1 courses materials, whether in print or online, are protected by

copyright. The work, or parts of it, may not be copied, distributed or published in
any form, printed, electronic or otherwise.

As an exception, students enrolled in year 1 of St. George’s University School of

Medicine and their faculty are permitted to make electronic or print copies of all
downloadable files for personal and classroom use only, provided that no
alterations to the documents are made and that the copyright statement is
maintained in all copies.

View only files, such as lecture recordings, are explicitly excluded from download
and creating copies of these recordings by students and other users are strictly
illegal.

The author of this document has made the best effort to observe current
copyright law and the copyright policy of St George's University. Users of this
document identifying potential violations of these regulations are asked to bring
their concern to the attention of the author.
 Assigned Reading

• Lippincott’s Biochemistry: Chapter 2

• Concept map: page 23

• Questions: 2.1 – 2.3

 Lecture Objectives
SOM.1a.BPM1.1.FTM.3.BCHM.BT.0401 Describe the general structure and stereochemistry of

Video 1
amino acids.

SOM.1a.BPM1.1.FTM.3.BCHM.BT.0402 Classify amino acids based on their R groups (with

Video 1
examples for each group).

SOM.1a.BPM1.1.FTM.3.BCHM.BT.0403 Name the amino acids with a charged side chain, the amino
acids containing a hydroxyl group and the amino acids

Video 2 Video 1
containing sulphur.

SOM.1a.BPM1.1.FTM.3.BCHM.BT.0404 Discuss the acid/base properties of amino acids with the

aid of a graph (e.g. histidine).

SOM.1a.BPM1.1.FTM.3.BCHM.BT.0405 Discuss the role of histidine residues in buffering in

haemoglobin.

Video 2
SOM.1a.BPM1.1.FTM.3.BCHM.BT.0406 Describe the concept of the formation of biological active
amines

Video 3
SOM.1a.BPM1.1.FTM.3.BCHM.BT.0407 Discuss the biomedical importance of derivatives of amino
acids (GABA, histamine, serotonin and catecholamines).

Video 4 Video 3
SOM.1a.BPM1.1.FTM.3.BCHM.BT.0408 Describe the main features of the peptide bond.
4
 Lecture objectives
SOM.1a.BPM1.1.FTM.3.BCHM.BT.0501 Outline the general functions of proteins.

Lecture
SOM.1a.BPM1.1.FTM.3.BCHM.BT.0502 Discuss in general the synthesis of proteins and the concept of formation of

Lecture
peptide hormones from precursor proteins.

SOM.1a.BPM1.1.FTM.3.BCHM.BT.0503 Differentiate between the hierarchical levels of protein structure.

Lecture
SOM.1a.BPM1.1.FTM.3.BCHM.BT.0504 Discuss the significance of bond forces involved in maintenance of protein
structure (covalent bonds and hydrogen bonds, ionic bonds, hydrophobic

lecture
forces and Van der Waals forces).

SOM.1a.BPM1.1.FTM.3.BCHM.BT.0505 Describe the structure of insulin.

Lecture
SOM.1a.BPM1.1.FTM.3.BCHM.BT.0506 Define secondary structures including α-helix and β-pleated sheet.

Lecture
SOM.1a.BPM1.1.FTM.3.BCHM.BT.0507 Discuss the change of the protein secondary structure in Prion disease.

Lecture
SOM.1a.BPM1.1.FTM.3.BCHM.BT.0508 Describe the role of chaperone proteins in protein folding.

Lecture
SOM.1a.BPM1.1.FTM.3.BCHM.BT.0509 Discuss protein denaturation in vivo and in the laboratory.

Lecture
5
General Functions of Proteins
Structural (fibrous)
Regulatory:
Repressors and Collagen, Keratin, Elastin
activators

Enzymes (globular), large variety

Defense:
Antibodies, Transport (globular)
Blood clotting
Albumin, Hemoglobin

Contractile: Actin and Myosin

6
 Replication • Central dogma of the
cell:
• Proteins and peptides are
synthesized by translation
of mRNA.
Transcription • Expression of mRNA is
under genetic control of
transcription
• Many peptide hormones
Translation may be formed by specific
cleavage of a larger
precursor protein
7
In humans, proteins are built using the
20 standard amino acids
-Some aa may be modified later

Proteins are abundant and

functionally diverse molecules in living
systems

The primary sequence may provide

insight about how the protein may
fold and function 8
Structure and function of proteins is correlated

9
Polarity of the side chains play an important
role in protein folding and function

10
The amino acid sequence (primary structure) will
determine the three dimensional structure of the protein

11
Protein conformation is its three
dimensional shape

• The primary structure determines the three-

dimensional conformation.

• Every molecule of the same protein folds into the

same native conformation.

• Both non-covalent and covalent bonds are

Important

12
Bond forces found in proteins in kcal mol-1
Covalent bonds are strong > 50 kcal mol-1,
They are not meant to be broken other than during
protein degradation

• Examples:

• Peptide bonds formed by 2 amino acids

• Disulfide bonds formed by 2 cysteine residues in

proteins

13
Noncovalent bonds are weaker

• These “weak attractive forces” specify protein

folding & conformational changes

• Hydrophobic forces are about 2-3 kcal/mol

• Hydrogen bonds are about 1-7 kcal/mol
• Ionic bonds are about 1-20 kcal/mol
• Van der Waals (London) forces are <1 kcal/mol

• These forces may be additive, so in aggregate they may

provide a strong stabilizing force
14
Secondary structures of proteins are stabilized by
hydrogen bonds involving the atoms of the peptide bond

The b- pleated sheet

The b- turn
The a- helix, 15
The a-helix as
secondary structure
• A very special helix:
• Tightly packed and right-
handed helix wound around an
imaginary axis.
• There are 3.6 residues per turn.
• Hydrogen bonds are parallel to
the direction of the helix axis
• Side chains stick out from helix

16
• The amino acid side-chains
(R-groups) are directed to
the outside
• May lead to constraints on
structure
• Dependent on primary
structure

17
Interruption of the a-helix
• Electrostatic repulsion (or attraction) between
successive (or 3-4 residues apart) amino acids
with charged R-groups

• Bulkiness of adjacent R-groups

• steric hindrance

• Helix disruption by specific residues:

• Proline residues (bend, or kink)
• Glycine residues (allow rotation)
18
β-pleated sheet is a secondary structure characterized by:
1. perpendicular H-bonds between peptide bond atoms, and
2. amino acid side chains that alternate above and below the
plane of the pleated sheet

This is an anti-parallel b-sheet because

of the direction of the peptide bonds

The b-sheet may be parallel or anti-parallel 19

 Hydrogen bonds involving
atoms of the peptide bonds
stabilize the b-pleated sheet.
They are formed between two
areas of the polypeptide chain.

The inter-chain hydrogen

bonds between N-H and C=O
groups connect each amino
acid to a single amino acid
somewhere else in the protein
– repetitive.

L p. 17 20
Protein organization

• Monomeric: a single polypeptide chain

• leads to a tertiary structure description

• Multimeric: more than one polypeptide chain

• leads to a quaternary structure description

• Homomultimeric: all chains are the same

• Heteromultimeric: different chains

27
Multimeric proteins are described in
terms of quaternary Structure

• The subunits associate via noncovalent

attractive forces

• Examples of quaternary structure:

• Hemoglobin
• Some enzymes (typically allosteric)

28
Tertiary structure refers to the three dimensional
conformation of a protein

• Water-soluble proteins fold into three-dimensional

structures with nonpolar side-chains to the inside
• Termed the “hydrophobic core”.

• Side-chains of amino acids can be involved in stabilizing

tertiary structure
• Formation of non-covalent associations (weak attractive
forces)
• Formation of the covalent disulfide bond
• Ionic interactions
29
 Noncovalent bonds
• Water excludes compounds that do not form
hydrogen bonds
• This creates the Hydrophobic force

• Ionic bonds are formed between two oppositely

charged side chains

• Hydrogen bonds can be formed between polar

uncharged side chains or between one charged side
chain and one polar side chain

30
 • The Hydrophobic
interaction (“bonds”)
• Results from water
exclusion
• These are formed from
weak noncovalent forces
of attraction
• The Van der Waals force
AKA the London force
• Form between two non-
polar amino acids

L p. 19 31
• Hydrogen bonds can be formed
between a polar group (-OH) and a
charged group (side chain -carboxyl)
This may also be called the
“ion dipole attractive force”

• Hydrogen bonds can also be formed

between 2 polar uncharged groups
• Consider R-groups of Ser and Asn
• Remember: the atoms comprising
the polar peptide bonds are involved
in the hydrogen bonding that
stabilizes the a-helix and b-sheet

L p. 19 32
• Ionic bonds are formed between
negatively and positively charged side
chains of amino acid residues
• Opposite charges attract
• Negatively charged side chains are found
in aspartate and glutamate residues
• Same charges repel
• Positively charged side chains are found
in lysine, arginine and histidine residues
• Same charges repel

33
 • Covalent bonds are formed
between the side chains of two
cysteine residues
• Forms the Cystine residue
• Formation is catalyzed by specific
enzymes
• Extracellular proteins often have
several disulfide bonds
• Intracellular proteins usually lack
disulfide bonds

L p. 18 34
 Insulin: 2 polypeptide chains:
• 51 amino acids (aa)
• subunit A=21 aa
• subunit B=30 aa
• two disulphide bridges

• The two inter- chain

disulfide bonds hold
the A- and B- chains
of insulin together

• The intra-chain disulfide bond in the A- chain folds the peptide

hormone and is needed for receptor recognition
35
C-peptide
• The C-peptide is needed for the proper formation
of disulfide bonds in insulin

• The C-peptide is then cleaved from insulin and it is

released together with insulin into the blood

36
• Myoglobin is described
in terms of tertiary
structure

• Myoglobin contains
about 80% a-helix
secondary structure
• Myoglobin is devoid of
β-sheet structure

37
Quaternary structure of hemoglobin

Another enzyme… 2 polypeptides (each a

protein) associate together to form the
active enzyme. (this is an example of
quaternary structure)

If more then one polypeptide associate together to form an active

complex, we describe the protein in terms of quaternary structure
38
Quaternary structure of hemoglobin

39
Chaperones facilitate proper folding
(also known as heat shock proteins - Hsp)

mRNA ribosome
transcript
Correctly
folded
Nascent
protein
polypeptide
being
translated Chaperones
come off,
and may be
used again

A function of Hsp70 (MW 70,000) is the prevention of aggregation of

unfolded protein 40
Marks’ Basic Medical Biochem.
• Hsp60 proteins have a barrel
shape and are required for
correct folding of cellular
proteins that do not fold
spontaneously.

• HSP60 proteins are also used

to aid refolding a protein after it
has crossed a cellular
membrane

41
Misfolded or Defective Proteins

• Proteins that are misfolded, oxidized,

old, or that are generally defective
are normally tagged by the protein
ubiquitin and degraded in a complex
called the proteasome
• ATP dependent proteolysis

L. p. 247
• This is not the case in Alzheimer’s
disease or a Prion disease
• In these cases the diseased protein is
very stable
• Abnormal proteins accumulate
• Damage the brain

42
TSE: Transmissible Spongiform
Encephalopathy - Prion disease
• Three routes to acquiring the disease
• Sporadic (most cases)
• Infection (eating infected tissue; ie., brain)
• Genetic predisposition (mutations)
• Creutzfeld-Jacob disease in humans, scrapie in sheep and mad-
cow disease (outbreak 1996)

• The diseased brain develops holes (resembles sponge)

• Typical symptoms include dementia and loss of coordination,

leading to death
• Definitive diagnosis upon autopsy

43
 Prion: proteinaceous infectious
agent
• The infectious agent is a single protein
• Contains no nucleic acid
• Named PrP, prion protein.
• PrP is a normal constituent of cells in the brain
• Found on the surface of neurons in all mammals
• Its function is not well understood

44
The abnormal form of PrP is called PrPsc

• Illness occurs when the normal cellular PrP (PrPc) occurs in

the altered form PrPsc (sc from scrapie).

• PrPsc acts like a template and leads to conversion of PrP to

large aggregates of PrPsc
• Sometimes called a “catalytic” process
• The abnormal protein is highly infective and is not
destroyed by sterilization
• Resistant to any DNA damaging treatment

45
Changing the a-helix to b-pleated
sheet in PrP leads to Prion disease

Abundant b-sheet
Abundant a-helix

M p.76 46
 Denaturation of proteins means that the
three dimensional structure is changed
• Noncovalent bonds and disulfide bonds are broken but
not the peptide bond backbone
• Primary structure remains intact

• Dietary protein is denatured in the lumen of the

stomach due to the low pH
• Acidity in stomach is not low enough to cleave peptide bonds

• In most cases, denatured proteins cannot regain their

natural configuration and precipitate
• Once an egg is fried, you can’t “un-cook” it

47
Denaturating proteins in the laboratory
• Heat, 5-10 M urea, salt, to break hydrogen bonds
• Strong acids or bases to break ionic bonds
• 1-2% SDS (detergent) to break hydrophobic interactions
• Thiol containing compounds to reduce disulfide bonds
• β-mercaptoethanol or
• 2-mercaptoethanol

• In animals, the disulfide bonds of insulin are cleaved in

the liver
• part of the degradation of insulin.

48
High abundance of bME

Leads to reduction of disulfide

bonds in proteins – helps
protein to denature

49