Protein Structure

Question 1

Properties of peptide bonds

Answer 1

Very stable

Cleaved/broken by PROTEOLYTIC enzymes- proteases or peptidases

Partial double bond (slide 4)

Flexibility around C atoms not involved in bond, allows multiple conformations/shapes

Usually one preferred native conformation, determines mainly by the type of side chains and their sequence in the polypeptide

Question 2

Protein is…

Answer 2

Large polypeptide, usually from a few 10s to 1000s amino acids

Large variety of functions because of the large number of different 3D shapes

Function of protein is completely dependant on structure

Question 3

Representing polypeptides as a Backbone

Answer 3

A line following the peptide bonds

Question 4

Cartoon

Answer 4

A representation showing the fundamental secondary structures (helix/sheet)

Question 5

Forces that hold proteins together

Answer 5

Van der Walls forces
Hydrogen bonds
Hydrophobic forces
Ionic bonds
Disulphide bonds

Question 6

Van der Waals forces

Answer 6

Weak attractive interactions between atoms due to fluctuating electrical charges.

Only important when two macromolecular surfaces fit closely in shape.

Can also be repulsive at very short distance

Question 7

Hydrogen Bonds

Answer 7

Interaction between dipoles, involving an hydrogen and an oxygen/nitrogen

Partial negative charges on negative atoms e.g. O and N bound to H, which then has a partial positive charge.

These partial charges allow weak attractive interactions between some amino acid side chains, main-chain O and N and water.

Question 8

Hydrophobic forces

Answer 8

Uncharged and non-polar side chains are poorly soluble in water and are effectively “repelled” by water.

These hydrophobic side chains tend to form tightly packed cores in the interior of proteins, excluding water molecules.
This attraction is the “hydrophobic force”

Question 9

Ionic Bonds

Answer 9

Occur between fully or partially charged groups.

Weakened in aqueous systems by shielding by water
molecules and other ions in solution.

Question 10

Disulphide bonds

Answer 10

very strong covalent bonds between sulphur atoms

In extracellular domains of proteins.

Conditions can be harsher so extra stability is conferred by covalent bonding between side chains of cysteine residues

Cysteine (slide 11)

Question 11

Primary structure

Answer 11

Linear sequence of aa linked by peptide bonds (covalent bonds)

• While in itself does not tell very much about fuction, fuctionally and evolutionarily related proteins may have similarity - and identify motifs

• The primary structure of a protein determines its 3D conformation, i.e. dictates the way in which the chain will fold to form its native structure.

Question 12

Chaperones

Answer 12

Proteins that assist other proteins in reaching their conformation after translation themselves

Question 13

Secondary structure The a - Helix

Answer 13

H-bonds between each carbonyl group and the H attached to the N which is 4 aa along the chain

Side chains look outwards

Proline breaks the helix (ring + no H)

Question 14

Secondary structure. The b - sheet

Answer 14

• Formed by H-bonds between linear regions of polypeptide chains.
• Chains from two proteins, or same protein. Parallel or antiparallel chains, pleated or not .

If the chain is folding back, structure is usually a 4 aa turn, called hairpin loop or b-turn.

Question 15

Tertiary Structure

Answer 15

This is the overall 3D conformation of the protein.

Forces involved include electrostatic, hydrophobicity, H-bonds, and covalent bonds.

Some conformational domains occur repeatedly, and include barrels, bundles and saddle.

Folding of the secondary structure into a globular structure due to bonds such as ionic bonds, disulphide bridges and Van der Waal forces.

Conformations can change with pH, T etc.

Question 16

Quaternary structure

Answer 16

Three dimensional structure of a protein composed of multiple subunits.

Same non- covalent interactions as tertiary structures.

2 or more tertiary structures joined together to form a protein e.g. haemoglobin

Question 17

Enzymes (slides 22-28)

Answer 17

Proteins that work as catalysts, enable reactions to occurs that otherwise would not be able to occur at physiological (body) temperatures and conditions

Enzymes bind the reactants (substrates) and convert them to products. Then they release the products and return to their original form

Not only they speed-up the reactions, but provide a way to regulate the rate of reactions

Enzymes provide an alternative reaction pathway with a lower activation energy

Can be used as: disease markers, drug targets

Question 18

Porphyrin Ring (slide 32-35)

Answer 18

• At the core of the molecule is porphyrin ring which holds an iron atom.

• An iron containing porphyrin is termed a heme.

• This iron atom is the site of oxygen binding.

• The name hemoglobin is the concatenation of heme and globin

Question 19

Factors Influencing Hemoglobin Saturation

Answer 19

Temperature, H+, PCO2 :
All Modify the structure of hemoglobin and alter its
affinity for oxygen
– Increase:
• Decrease hemoglobin’s affinity for oxygen • Enhance oxygen unloading from the blood
– Decrease act in the opposite manner.

All these parameters are high in peripheral capillaries where Oxygen unloading is the target.

Question 20

Sickle Cell anemia

Answer 20

Sickle Cell Anemia is a genetic disorder that is characterized by the formation of hard, sticky, sickle-shaped red blood cells, in contrast to the biconcave-shaped red blood cells (RBCs) found in “normal” individuals.

Question 21

Cause of sickle cell anemia

Answer 21

This disease is caused by a mutation in hemoglobin.

Question 22

Immunoglobulins (Antibodies)

Answer 22

Antibodies are produced to bind antigens, typically toxins or proteins on the surface of microbial agents.

These targets are consequently labelled for destruction by cells of the immune system or by lysis or through the complement system

Diagram on slide 45

Question 23

Immunoglobulin Structure (slide 46-47)

Answer 23

The immunoglobulin fold structure of antibodies comprises a supporting scaffold (framework regions) that serves to display highly variable loops of complementarity determining regions – (CDRs)

The diverse nature of CDR regions enables a range of reversible bonding effects (hydrogen bonds, Van der Waal forces) to act between antibody and antigen

Question 24

Antigen Recognition

Answer 24

The essence of antibody/antigen interaction is the very close proximity of the antibody CDR regions and the antigen surface

Intimate contact allows the combination of relatively weak interactions to produce a strong binding surface

The CDR loops have a sequence of amino acids that “complement” the surface of the antigen

Question 25

epitope

Answer 25

The portion of antigen bound is known as the

Question 26

20 different Amino Acids in proteins

Have diverse properties

Proteins are a patchwork of charge, bulk, and hydrophobicity

Answer 26

– Charge +ve or –ve -COO- ; -NH2+
– Hydrophobicity Aliphatic, Aromatic
– Polarity
– Bulk

Question 27

Charge

Answer 27

Charged amino acids can be acidic or basic

Question 28

Bulk

Answer 28

Bulky amino acid groups can project from the antigen surface

Question 29

Hydrophocity

Answer 29

Hydrophobic groups resist exposure to surrounding
aqueous solvent (H2O)

The CDRs can form a compatible hydrophobic surface
Energetically favouring interaction

Question 30

Peptide bonds are formed by

Answer 30

condensation reaction (water released) between carboxyl group and amino group

• Amino group first and then carboxyl group at end
• Proteins are formed by linked amino acids which are bonded together by peptide bonds
• These linear chain fold in different shapes to form 3D structures
• Folding is determined by; charged interactions, flexibility and physical dimensions
• Identity of protein is determined by the sequence of amino acids, sequence also determines folding and structure

Question 31

Super-secondary structures

Answer 31

Combination of secondary structures. Structures and functional units of folded proteins often consist of combinations of alpha and beta structures.

Question 32

Factors influencing the rate of reaction

Answer 32

temperature
pH
concentration of reactants
catalyst
surface area of a solid reactant
pressure of gaseous reactants or products.

Question 33

Uses of enzymes

Answer 33

Can be used for diagnostic purposes because since they control metabolism they can be used as disease markers

e.g when released in bloodstream, when they should be present. A lot of drugs work by inhibiting the actions of enzymes

Question 34

Regulation of enzymes

Answer 34

Enzymes can be regulated by altering the concentration of substrates, products, inhibitors or activators

they can also be regulated by modifying the enzyme itself by phosphorylation.

Question 35

Haemoglobin

Answer 35

found in red blood cells, oxygen carrier in the blood

Question 36

Myoglobin

Answer 36

found in the muscle, serves as a reserve supply of oxygen and also facilitates the movement of O2 in muscles.

Question 37

What is common between myoglobin and haemoglobin?

Answer 37

Both haemoglobin and myoglobin are structurally related proteins with some common elements - have the same tertiary structure

At the core of both molecules is the PORPHYRIN RING which holds an iron atom

Question 38

Heme

Answer 38

An iron containing porphyrin

This iron atom is the site of oxygen binding - the name haemoglobin in the combination go heme and globin

Question 39

Why can haemoglobin be regarded as an enzyme?

Answer 39

Haemoglobin can be regarded as an enzyme that binds and releases O2 thus Fe can be seen as a coenzyme since its the site of O2 binding (when O2 binds, haemoglobin molecule changes shape slightly)

Question 40

Properties of immunoglobulins

Answer 40

Many different types: IgG, IgM, IgA etc

Antibody-antigen binding is very specific - one antibody only matches one antigen.

Question 41

Variable domain

Answer 41

Portion of the antibody where the antigens can bind

(THUS SPECIFICITY OF ANTIBODIES DETERMINED BY THE VARIABLE REGION). Amino acid in the variable domain can be varied to produce a potentially infinite variety of 3D shapes to recognise an infinite variety of foreign antigens

Question 42

Structure of antibodies

Answer 42

Disulphide bonds define loop characteristics of Ig.

This makes structure of antibodies complex

Variable regions have light chains (VL) and heavy chains (VH) as do the constant regions CL and CH respectively