Amino Acids & Proteins

Question 0

What four types of weak bonds are present between biological molecules?

Answer 0

H bonds, ionic interactions, hydrophobic/philic interactions and van Der Waals forces

Question 1

Which isomers of proteins are found in nature?

Answer 1

L-isomers

Question 2

What is the general structure of an amino acid?

Answer 2

Carboxyl group, amino group and a side chain which are all covalently bound to a central C atom

Question 3

How are aa classified?

Answer 3

Chemical nature of R group

Question 4

State 3 features of a peptide bond

Answer 4

Linear, no orientation about the peptide bond due to double bond characteristics and the carbonyl O and amide H are in the trans orientation

Question 5

Describe a basic protein (e.g. charges, pI etc)

Answer 5

Contain many positively charged aa and have a high pI (if pH < pK value then group will be protonated and therefore have a positive charge, if pH < pI then the protein is protonated)

Question 6

Describe acidic proteins (e.g. charge, pI values etc)

Answer 6

Acidic proteins contain many negatively charged aa and have a low pI (ph of a solution > pK value gives a negative charge due to deprotonation, if pH > pI deprotonation occurs)

Question 7

Bonds involved in primary structure of proteins?

Answer 7

Covalent (peptide) bonds

Question 8

Bonds involved in secondary structure of proteins?

Answer 8

H bonds

Question 9

Bonds involved in tertiary structure of proteins?

Answer 9

H bonds, vdw, hydrophobic/hydrophilic interactions, covalent bonds, ionic interactions

Question 10

Bonds involved in quaternary structure of proteins?

Answer 10

H bonds, vdw, hydrophobic/hydrophilic interactions, covalent (disulphide) bonds, ionic interactions

Question 11

Function of globular proteins?

Answer 11

Most enzymes and regulatory proteins

Question 12

Function of fibrous proteins?

Answer 12

Provide structure, support and protection

Question 13

What are molecular chaperones?

Answer 13

Molecules that aid with protein folding

Question 14

What is a haem group?

Answer 14

Haem groups are prosthetic groups which consist of a protoporphyrin ring and an Fe atom bound to 4 N atoms of the rings. Fe2+ can make an additional bond to an oxygen molecule, one on either side of the plane

Question 15

Describe how the haem group is bonded to Hb

Answer 15

Fe atom is bound to the protein via a histidine residue (proximal histidine). Haem is covalently bonded to the Hb. This structure is planar and can make 2 bonds; one above the plane and one below the plane

Question 17

Describe the composition of myoglobin

Answer 17

153 aa
Compact
75% alpha helices in its structure
One haem group

Question 17

What is the graph for Hb like?

Answer 17

Sigmoidal curve on a graph of fractional saturation vs pO2

Question 18

What is the oxygen binding curve for myoglobin like?

Answer 18

Hyperbolic on a graph of fractional saturation against partial pressure of oxygen. High affinity for oxygen and thus will only release it when pO2 is extremely low

Question 19

Describe the composition of Hb

Answer 19

2 polypeptide chains with A2 B2 tetramer

Each chain has an essential haem prosthetic group

Question 20

Describe the two types of Hb

Answer 20

T state - tense state in which there is nothing bound to the Hb
R state - relaxed state when one or more oxygen molecules are bound to the Hb (subsequent oxygen molecules can bind more easily - co operative binding)

Question 21

What is BPG?

Answer 21

2,3-bisphosphoglycerate. Decreases the affinity of Hb for oxygen. BPG binds to positively charged lysine/histidines because P groups on BPG are negatively charged.

Question 22

Describe the Bohr effect

Answer 22

H+ and CO2 bind to Hb molecules, thus lowering their affinity for oxygen. Graph shifts to the right

Question 23

How does CO poisoning occur?

Answer 23

CO combines with ferromyoglobin and ferrohaemoglobin and blocks oxygen transport. Fatal when COHb > 50%.

Question 24

Why does foetal Hb have a higher affinity for oxygen then HbA?

Answer 24

Allows transfer of oxygen to foetus allowing the foetus to respire.

Question 25

How do beta thalasseamias occur?

Answer 25

Decreased or absent beta globin chain production, alpha chains are unable to form stable tetramers therefore symptoms appear after birth

Question 26

How do alpha thalaessaemias arise?

Answer 26

Decreased or absent alpha globin chain production, differing levels of severity, beta chains can form stable tetramers with increased affinity of oxygen therefore the onset before birth. Lack of alpha chain has a severe effect on the Hb molecule

Question 27

List the polar uncharged amino acids

Answer 27

Serine, threonine, cysteine, asparagine and glutamine

Question 28

List the non-polar, aliphatic amino acids

Answer 28

Glycine, alanine, proline, valine, leucine, isoleucine and methionine

Question 29

List the negatively charged amino acids

Answer 29

Aspartate and glutamate

Question 31

List the positively charged amino acids

Answer 31

Lysine, arginine and histidine

Question 32

Describe the key features of alpha helices

Answer 32

Right-handed helix, 3.6 amino acids per turn, 0.54 nm pitch. Small hydrophobic amino acids such as Ala + Leu are strong helix formers

Question 33

Which amino acids act as alpha-helix breakers?

Answer 33

Proline - rotation about the N-C bond is impossible

Glycine - tiny R group supports other conformations

Question 34

Describe the key features of a beta-sheet

Answer 34

Extended conformation, parallel or antiparallel, multiple inner-strand H bonds