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Flashcards in Proteins_Molecules Deck (65):
1

What are the 4 level of architecture of proteins?

- Primary (AA sequence)
- Secondary (Alpha helix & Beta sheet)
- Tertiary (3D structure)
- Quaternary (subunit, if > 1 chain, interactions between different polypeptides)

2

What are quaternary structures?

proteins with 2 or more polypeptide

3

What are the two types of protein structure?

- Fibrous
- Gobular (can be structural)

4

What are secondary structures?

local folding of the primary chain
functional because it sticks out of the main chain

5

What type of structures do most proteins have?

Gobular

6

How are subunits arranged in quartenary structures?

Different subunits are arranged relative to each other

7

What are the properties of secondary structure?

- Local folding of chain

8

What are the three common kinds of secondary structure?

1) Alpha helix
2) Beta strand
3) Loop or coil - no specific conformation therefore no structure

9

What are secondary structure protein cores made of?

Hydrophobic

10

Which part of the secondary structure protein is hydrophilic?

-NH and -C=O (Both polar)
- need to be able to react with aqueous environment

11

How was secondary structure found?

X ray diffraction of wool and hair

12

Who predicted Alpha helix?

Linus Pauling - 1951
Confirmed (1953) by myoglobin structure

13

What type of helix is the alpha helix?

Right handed helix

14

Name the properties of the right handed alpha helix

1) 3.6 residues per turn
2) 5.4 Angstrom per turn
3) Hydrogen bond each -NH to a -C=O 4 residues later
4) Side chains point outwards
5) Very compact

15

What is the alpha helix maintained by?

Hydrogen bonds

16

Where do the AA side chains face?

Face outwards, away form the helix axis

17

What is an amphipathic helix?

One side is hydrophobic, one side is hydrophilic
- Hydrophobic edge contacts the surrounding water, hydrophilic edge faces inward to the center of the molecule
- Periodicity
- Polar or hydrophobic every 3 - 4 residues

18

What is the hydrophobic helix use for?

Transmembrane

19

Give an example of proteins that has all alpha (and loops)

- Insulin = A: 2 helixes; B: 1 helix
- Globin = 7 helices
- Cytochrome C = 4 helices

20

Name the two AA that can't fit in the alpha helix conformation?

- Proline: Too rigid to fit into the alpha helix
- Glycine: Too flexible (can assume too many alternative conformation that is more favourable than alpha helix)

21

What does beta strands look like?

Zig zag backbone

22

Name the two types of alpha helix

1) Amphiphatic helix
2) Hydrophobic helix

23

What do beta strands contain?

H bonds are formed between the peptide bond C-O and N-H groups of polypeptides that lie side by side

24

How are beta sheets formed?

H bond between 2 or more polypeptide strands

25

Name the property to beta strands

- Interacting chains can be parallel or anti parallel
- Interacting chains can belong either to different polypeptides or to different sections of the same polypeptide

26

What occurs in both fibrous and globular proteins?

Alpha helix and Beta pleated sheet

27

What is the structure of immunoglobulin?

- Beta strands and loop
- No alpha
- 2 beta sheets
- 4 strands each

28

What type of core does globular proteins have?

Hydrophobic core

29

What do fibrous proteins contain?

Long threads of alpha helix or beta pleated sheet

30

What do globular proteins fold themelves into?

Compact tertiary structure

31

How are tertiary structures formed?

Formed mainly by hydrophobic interactions between AA side chains

32

What do gobular proteins contain?

Alpha, beta and coil/loop regions

33

Are most gobular protein soluble in water?

Yes

34

What can be used to look at tertiary structure?

- X ray crystallography or NMR
- salt crystal defract X rays (wavelength is different, arrangement of dots able to figure out difference in interference pattern)

35

How was tertiary structure discovered?

Myoglobin in 1953
- Purify protein - needs to be very pure to do this
- Make crystals
- Shine X-rays
- Measure diffraction
- Reconstruct structure

36

What is the function of myoglobin?

Short term storage of oxygen for muscle contraction.
- when oxygen levels get depleted, myoglobin gives up oxygen

37

What does myoglobin contain?

- Single polypeptide with Heme group
- about 7.5% of the AA residues participate in alpha helical structures

38

What is the major stabilising force in myoglobin's tertiary structure?

Filled with tightly packed non polar chains, and hydrophobic interactions are the major stabilising force in its tertiary structure
- NO DISULPHIDE BONDS
- Maintained only by non covalent forces

39

What do haemoglobin do?

Transports oxygen in blood

40

What is the structure of haemoglobin?

Tetramer
- 2 alpha chains + 2 beta chains
- Each with its own heme
- Each like myoglobin
- Each subunit has Hydrophobic core, hydrophilic surface, subunits interact mainly through hydrogen bonds and salt bonds (no disulphide bonds)

41

What is the difference in structure between myoglobin and haemoglobin?

Myoglobin does not have any quaternary structure
Haemoglobin does (arrangement of subunits)

42

Where is haemoglobin found?

In erythrocytes/RBC

43

What is haemoglobin lacking?

- NO nucleus
- Lack mitochondria (don't consume O2 transported)

44

The heme iron in haemoglobin and myoglobin is always in what state?

Ferrous state (even during oxygen binding)

45

Where is myoglobin found?

Occurs only in muscle tissue

46

What is the conformation of deoxyhaemoglobin called?

T conformation

47

What is the conformation of oxyhaemoglobin called?

R conformation

48

Subunit of haemoglobin interactions are weaker in which type of haemoglobin?

weaker in oxyhaemoglobin than in deoxyhaemoglobin

49

Why does the conformation of haemoglobin change with oxygenation?

Because the bond distances between the heme iron and the 5 nitrogen atoms with which it is complexed shorten when oxygen binds. The distorts the shape of the heme group and pulls on the F helix to which proximal histidine belongs. The interactions with other subunits destabilised, and the shape of the whole molecule shifts towards R conformation

50

What is the difference in oxygen affinity between the two conformation of haemoglobin

R conformation has higher affinity and binds more tightly than T conformation

51

What are allosteric protein?

- Proteins that can assume alternate higher order structure
- change in conformation on binding ligand

52

On binding with oxygen what happens to the T conformation?

- "pure" T conformation destabilised and shift towards "pure" R conformation. This repeats itself after binding of the second and third oxygen molecules.
- Changes conformation of the subunits
- oxygen affinity rises steeply on binding

53

What is proximal histidine F8?

eight AA in the F helix, counting from the amino ned

54

What is a ligand?

Any small molecule that binds reversibly to a protein

55

What does the oxygen binding curve describe?

Fractional saturation of the heme groups at varying oxygen partial pressures

56

Myoglobin VS haemoglobin: which binds oxygen far tighter than the other

Myoglobin
- Myoglobin is half saturated with oxygen at 1 torr whereas haemoglobin needs 26 torr

57

What does the difference in oxygen affinity between myoglobin and haemoglobin facilitate?

Facilitates the transfer of oxygen from the blood to the tissue

58

What type of curve in the myoglobin curve?

Hyperbolic (Mb + O2 <=> Mb.O2 )

59

What type of binding curve does haemoglobin have?

Sigmoidal

60

Why is the binding curve of haemoglobin sigmoidal?

Completely deoxygenated haemoglobin is mainly in the T confirmation (low affinity). This accounts for the flat part of the curve before 10 torr. However, with increasing oxygen partial pressure, the first heme becomes oxygenated.

61

What is positive cooperativity?

Oxygen binding to a heme group in hemoglobin increase the oxygen affinities of the remaining heme group.

62

Why monomer vs tetramer?

Myoglobin and haemoglobin have different responses to O2 levels.

63

What are the different globin disease?

- Carbon monoxide poisoning
- Thalassaemia
- Sickle cell anaemia

64

What happens during sickle cell anaemia?

- Beta globin residue 6 (beta subunit has valine at position 6)
- Glutamine -> Valine (beta globin chain stick together)
- Heterozygotes resistant to malaria

65

Why can't myoglobin be used in tissue?

Myoglobin saturate at very low O2 levels, hold to O2 too strongly. Need something else that can saturate at high levels and release slowly therefore haemoglobin i used instead.