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Flashcards in MGD - Proteins Deck (97)
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0

What is a motif?

A polypeptide with o folding pattern that contains one or more elements of secondary structure
e.g. Beta barrel or beta-alpha-beta loop.

1

What is a domain?

Part of a polypeptide chain folding into a specific shape.

2

What are the 5 types of interactions possible in a protein?

H bonds
Van der waals
Ionic bonds
Hydrophobic interactions
Disulphide bonds

3

What decides a molecules solubility?

It's ability to form H bonds.

4

What are the essential amino acids?

Tryptophan, valine, leucine, lysine, isoleucine, phenylalanine, methionine, threonine.

5

Describe a beta pleated sheet.

0.35nm between amino acids.
Variable groups alternate on each side.
Strands arrange parallel and form H bonds.

6

Describe an alpha helix.

3.6 amino acids per turn
0.54nm pitch
Right handed helix
H binds parallel to helix
R groups on outside of helix.

7

What amino acids are helix breakers and why?

Proline - has a ring structure therefore lacks rotation around the N-C bond

Glycine - R group supports other conformations.

8

What amino acid is a helix former?

Alanine - it has a small hydrophobic side chain

9

What are the structures of proteins?

Primary - linear amino acid sequence
Secondary - local spatial arrangement of polypeptide backbone
Tertiary - 3D arrangement of atoms in the polypeptide
Quaternary - 3D arrangement of protein subunits.

10

What are amyloidoses?

Aggregations of misfolded proteins that therefore become insoluble.
They have a degree of beta pleated sheet and are stabilised by hydrophobic interactions between hydrophobic residues.

11

What drives folding?

Mostly the hydrophobic effect.

12

How are some proteins aided with folding?

By chaperones.

13

What are the features of peptide bonds?

Trans conformation
No rotation
All atoms of the bond are in the same plane

14

What are globular proteins?

They're involved in catalysis and regulation.
Compact.
Have several types of secondary structure.
e.g. Hb

15

What are fibrous proteins?

For support, shape and protection.
Form strands or sheets.
Have one type of repeating secondary structure.
e.g. collagen

16

What are the features of Hb?

Found in the blood.
Carries O2 and CO2.
Has 4 haem groups.
Is tetrametric.

17

What are the features of myoglobin?

Stored in muscle for periods of high metabolic activity
Has 1 haem group
Formed from one subunit.

18

How does foetal Hb differ from normal Hb?

It has a higher affinity (so curve is further left)
Is formed from 2 alpha and 2 gamma chains.

19

What states do Hb exist in and how does the binding of O2 affect these?

T state - tense = low affinity
R state - relaxed = high affinity

Binding of O2 stabilises the R state

20

What gives the sigmoidal curve for Hb?

Transition between the R and T states (= cooperativity of oxygen)

21

What is myoglobin s affinity for O2?

Very high, so will only release at very low pO2.

22

How does cooperativity work in Hb?

When an oxygen binds to the haem group, it pulls the iron atom into the plane of the ring, changing Hb conformation and making it easier for O2 to bind.

23

What is the Bohr effect?

The binding of H+ or CO2 lowers Hb affinity for O2 and shifts the curve to the right.

More H+/CO2 = more resp = more O2 needs releasing more readily.

24

What effect does CO have on Hb?

It binds 250x more readily than O2 = fatal when >50%

Increases the oxygen affinity of Hb left

25

What effect does 2,3-bisphosphoglycerate have on Hb and why is this good?

It decreases Hb affinity and shifts the curve right.

2,3BPG produced in metabolism so more 2,3BPG = more resp = O2 needs releasing more readily.

2,3BPG increases in concentration at high altitudes where pO2 is less = promotes O2 release.

26

What is sickle cell disease!

In the beta chain of Hb, negative glutamate is substituted for a neutral valine
= valine residues form a hydrophobic pocket and deform RBCs, causing them to struggle to hold O2 and to lyse easier.

27

What is alpha chain thalassaemia?

It is a lack of alpha subunits.
Onset before birth.
Less severe as the excess beta chains form stable tetramers with an increased affinity for Hb.

28

What is beta chain thalassaemia?

Lack of beta chain subunits.
Onset after birth.
More severe as the alpha chains don't form stable tetramers and instead precipitate = make RBC fragile, leading to premature death of cells.

29

What are the classifications of amino acids and what are the main amino acids in?

1). Negatively charged - glutamate
2). Non polar aliphatic - valine, leucine, methionine, isoleucine.
3). Aromatic R group - tryptophan, phenylalanine
4). Positively charged - lysine
5). Polar neutral - threonine