Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

IMS Y1 v2 > Topic 3 - Proteins > Flashcards

Topic 3 - Proteins Flashcards

1
Q

Which amino acids have non-polar side chains?

A
  • Glycine
  • Alanine
  • Valine
  • Leucine
  • Isoleucine
  • Methionine
  • Phenylalanine
  • Tryptophan
  • Proline
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Which amino acids have polar side chains?

A
  • Serine
  • Threonine
  • Cysteine
  • Tyrosine
  • Asparagine
  • Glutamine
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Which amino acids have electrically charged side chains?

A

ACIDIC - Aspartate, Glutamate

BASIC - Lysine, Arginine, Histidine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Which amino acids are acidic?

A

Aspartate

Glutamate

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Which amino acids are basic?

A

Lysine
Arginine
Histidine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What is the charge of a histidine molecule at pH 7?

A

Mainly uncharged

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What is the pKa?

A

the pH at which a group is 50% ionised

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What happens to histidines group when pH is below pKa?

A

Group will have H attached

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What happens to histidines group when pH is above pKa?

A

Group will lose H+

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What are the levels of structure in a polypeptide chain?

A
  • Amino acid sequence (primary)
  • Local spatial arrangements of amino acids in the peptide chain (secondary)
  • Organisation of the primary and secondary structures into the 3D protein shape (tertiary)
  • Arrangement of different subunits in a protein (quaternary)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What is the primary structure of a ppt chain?

A

Amino acid sequence as coded my mRNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What is the secondary structure of a ppt chain?

A

Local spatial arrangements of amino acids in the peptide chain
(Alpha helix or beta pleated sheet)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What is the tertiary structure of a ppt chain?

A

Organisation of the primary and secondary structures into the 3D protein shape
(Di-sulfide bridges, Hydrophobic interactions, Hydrogen bonding, Ionic bonding)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What is the quaternary structure of a ppt chain?

A

Arrangement of different subunits in a protein (2+ ppt chains in one protein)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What is an alpha helix?

A

In an α helix, the carbonyl (C=O) of one amino acid is hydrogen bonded to the amino H (N-H) of an amino acid that is four down the chain. (E.g., the carbonyl of amino acid 1 would form a hydrogen bond to the N-H of amino acid 5.) This pattern of bonding pulls the polypeptide chain into a helical structure that resembles a curled ribbon, with each turn of the helix containing 3.6 amino acids. The R groups of the amino acids stick outward from the α helix, where they are free to interact.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What is a beta pleated sheet?

A

In a β pleated sheet, two or more segments of a polypeptide chain line up next to each other, forming a sheet-like structure held together by hydrogen bonds. The hydrogen bonds form between carbonyl and amino groups of backbone, while the R groups extend above and below the plane of the sheet. The strands of a β pleated sheet may be parallel, pointing in the same direction (meaning that their N- and C-termini match up), or antiparallel, pointing in opposite directions.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Which forces stabilise tertiary and quaternary protein structure?

A
  • Electrostatic interactions
  • Van der Waals forces (dipoles)
  • H-bonds
  • Burial of hydrophobic residues (hydrophobic interactions)
  • Disulphide bonds
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What does the charge of a protein depend on?

A

pI and pH

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

What is pI?

A

The isoelectric point (pI) is the pH of a solution at which the net charge of a protein becomes zero. At solution pH that is above the pI, the surface of the protein is predominantly negatively charged, and therefore like-charged molecules will exhibit repulsive forces.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

Low pH?

A

High H+ (as acidic), positive overall charge

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

High pH?

A

Low H+ (basic), negative overall charge

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

Physiological pH?

A

Overall charge of ppt chain depends on pI of protein

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

What is tetany?

A

A condition marked by intermittent muscular spasms, caused by malfunction of the parathyroid glands and a consequent deficiency of calcium

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

Which equilibrium controls blood pH?

A

CO2 + H2O <> H2CO3 <> H+ + HCO3-

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

How is calcium transported in the blood?

A

Ca2+

Half in solution half bound to proteins

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

What is alkalosis?

A

High pH.

Increased calcium binding to protein – decreased availability of free calcium.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

What is Acidosis?

A

Low pH.

Decreased calcium binding to protein – increased availability of free calcium.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

Why would an increase in blood pH reduce the availability of free Ca++?

A
  • Hyperventilation leads to increased CO2 loss.
  • This causes plasma pH to rise as H+ is combined with bicarbonate to create additional CO2 to help maintain equilibrium.
  • As plasma pH rises, proteins become more negatively charged, as they release H+ from ionisable groups such as COOH and NH3+.
  • Calcium ions, being positively charged, bind more effectively to the negatively charged proteins, decreasing the availability of free calcium.
  • Decreased free calcium in extracellular fluid causes increased excitability of sensory nerves (causing numbness/pins and needles) and motor nerves (causing prolonged muscular contraction).
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

What are two examples of globular proteins?

A

Enzymes

Haemoglobin

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

What are the features of globular proteins?

A
  • Compact
  • Soluble
  • Hydrophobic residues on the inside
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

What are two examples of fibrous proteins?

A

Keratin

Collagen

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

What are the features of fibrous proteins?

A
  • Elongated
  • Often have repeating amino acid sequences
  • Insoluble
  • Hydrophobic residues on the outside
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

What are the 3 types of proteins?

A

Globular
Fibrous
Membrane

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

How many mutant Hb are there?

A

> 400 known

95% due to single amino acid change

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

Why do we need oxygen binding proteins (Hb)?

A
  • Cells require O2 for oxidation of foodstuffs.

- O2 only sparingly soluble in blood, therefore we need a transport and storage system.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

What is the function of Hb?

A

O2 transport and CO2 transport

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

What is the function of myoglobin?

A

O2 storage in tissues

38
Q

Where are the highest concentrations of myoglobin?

A

Skeletal and cardiac muscle

39
Q

What are the features of myoglobin?

A
  • Small protein
  • Very compact
  • Contains haem prosthetic group
  • 8 alpha-helices
  • Hydrophobic residues on the inside, hence soluble
40
Q

What is the haem prosthetic group?

A
  • Haem - Fe2+ + protoporphyrin IX
  • Tightly bound, nonpolypeptide unit essential for biological activity of protein
  • Non-covalently bound in a hydrophobic crevice in protein
41
Q

How many ligands can Fe2+ coordinate with?

A

6 ligands:

  • 4N from porphyrin ring
  • N from proximal His (F8)
  • Oxygen atom
42
Q

What is the effect of O2 binding?

A 
First O2 to bind to Fe changes the position
Distal His (E7) also involved in O2 binding
43
Q

What are the advantages of associating haem unit with a protein molecule?

A
  • Fe atoms are kept in Fe2+ form

- Binding of other small molecules e.g. carbon monoxide is inhibited

44
Q

What are the symptoms of CO poisoning?

A

Dizziness
Nausea
Confusion

45
Q

What is the structure of haemoglobin?

A
  • Four polypeptide chains held together by non-covalent interactions
  • Adult haemoglobin has 2 alpha, 2β chains
  • Each chain contains a haem group, therefore Hb can bind four O2
  • Four chains packed tightly together in a tetrahedral array with overall spherical shape.
  • Hb tetramer may be considered as 2 pairs of subunits - a1β1, a2β2
46
Q

How is Hb an allosteric protein?

A

The binding of O2 to one subunit affects interactions with the other subunits

47
Q

What type of binding between O2 and Hb?

A

Cooperative and therefore binding curve is sigmoidal

Mb non cooperative

48
Q

What is Hb O2 affinity dependent on?

A

pH and CO2

Mb is independent

49
Q

What is Hb regulated by?

A

BPG

Mb not regulated by this

50
Q

What does a sigmoidal binding curve mean for Hb?

A

Cooperative binding between O2 and Hb

Binding of one O2 makes binding of next easier

51
Q

What does cooperative binding mean for Hb?

A

The change in shape caused by the first O2 binding also causes a change in affinity to oxygen; the more oxygen is bound, the higher the molecule’s affinity for oxygen becomes.

52
Q

What are the exact effects of an O2 binding to one Hb subunit?

A
  • Proximal His F8 is pulled in
  • Shifts helix F, EF and FG corners
  • Altered shape transmitted to subunit surfaces
  • Some interchain salt bridges rupture
  • These structural changes increase the affinity of the remaining subunits for O2
53
Q

What is the T state of Hb?

A
  • ‘Tense state’ – more salt bridges between subunits

- Low affinity for O2

54
Q

What is the R state of Hb?

A
  • ‘Relaxed state’ – fewer salt bridges

- High affinity for O2

55
Q

What is the Bohr effect?

A
  • Increase in [H+] (lowering of pH) decreases affinity of Hb for O2
  • Increased CO2 in blood or increased lactic acid will lower pH
  • Increased release of O2 to respiring rapidly tissues or muscle releasing lactic acid
56
Q

How so H+ ions affect O2 binding?

A
  • pH affects protonation state of amino acid residues
  • When H+ is high, additional residues are protonated (esp Histidine residues)
  • Additional positively charged residues can form new salt bridges – these stabilise the T-state and decrease affinity for O2
57
Q

What can cause BPG levels to increase?

A
  • High altitude

- Hypoxia

58
Q

What is hypoxia?

A

poor oxygenation of peripheral tissues

59
Q

What does BPG do?

A

Decreases affinity of Hb for O2 so causing more oxygen release under certain conditions

60
Q

Where does BPG bind?

A

The space between the β subunits – in the T-state only

61
Q

How does BPG decrease Hb affinity for O2?

A
  • Negative charges on BPG interact with positive amino acid residues lining the space between β subunits
  • CO2 binds to amino groups on the globin protein, forming carbaminohaemoglobin
  • H+, CO2 and BPG interact at different sites, therefore their effects are additive
62
Q

How does foetal Hb have a higher affinity for O2?

A

It binds BPG less effectively

Allows efficient transfer of O2 across placenta

63
Q

What can mutations in Hb affect?

A
  • Amount of Hb synthesised
  • Structure, e.g. subunit interfaces
  • Stability of Hb – leading to haemolytic anaemia
  • Affinity for O2
  • Affinity for regulators e.g. BPG
64
Q

What is a conservative substitution in Hb mutations?

A
  • Maintains hydrophobic interior of molecule

- Interior of Hb often see change of one non-polar residue for another, e.g.Ala → Ile

65
Q

What is a non-conservative substitution in Hb mutations?

A

e.g. Leu → Lys

will have a major effect on protein structure and function.

66
Q

What is collagen?

A
  • Family of fibrous proteins
  • Forms insoluble fibres, high tensile strength
  • Most abundant protein in mammals
  • Major fibrous element of skin, bone, tendon, cartilage, blood vessels, teeth
  • Present in most organs
  • Holds cells together in discrete units – basement membranes
  • Also a directive role in developing tissue
67
Q

What are the fibril-forming collagens?

A

Type I, II, and III

Form long fibrils

68
Q

What are the network-forming collagens?

A

Types IV and VII
Form a 2D matrix
Important in basal lamina

69
Q

What are fibril-associated collagens?

A

eg. Types V, IX, XII
Mainly associated with major forms
May be involved in crosslinking

70
Q

How many ppt chains do collagens consist of?

A

3

71
Q

What are the steps to biosynthesis of collagen?

A
  • Polypeptide synthesis
  • Post-translational modifications
  • Procollagen triple helical cable
  • Secretion
  • Removal of extension peptides
  • Tropocollogen
  • Aggregation into microfibril
  • Cross-linking to form collagen fibre
72
Q

What is the primary structure of collagen?

A

-Gly every third residue (33%)
-Covalently modified amino acids (4-Hydroxyproline (Hyp),
5-hydroxylysine (HyL),
Allysine)

73
Q

When and what by does the hydroxylation of proline and lysine residues occur in collagen?

A
  • Occurs before the ppt chain forms helix

- Enzymes involved: propyl hydroxylase and lysyl hydroxylase

74
Q

What is the function of hydroxyproline in collagen?

A

It is involved in H-bond formation, which helps to stabilise the triple helix

75
Q

What is the function of hydroxyplysine in collagen?

A

The residues are attachment sites for sugar residues, and are involved in cross-linking between collagen chains

76
Q

What is the 2,3 and 4 structure of collagen?

A

-Each polypeptide chain forms LEFT handed helix, 3.3 residues per turn
-triple helix formed
(tropocollagen)
RIGHT handed twist
-Gly residues pack into centre
-Pro and Hyp residues on the outside
-The three ppt chains folded together form a triple-helical cable

77
Q

What are the steps to assembly of collagen?

A
  • Collagen chains are synthesised with additional amino acids at each end – extension peptides
  • Assembly begins with disulphide bond formation between C-terminal extensions – facilitates triple helix assembly
  • Peptidase enzymes remove extension peptides after secretion into extracellular space
  • Tropocollagen spontaneously forms fibrils – stabilised by covalent cross-links
78
Q

What gives tropocollagen its strength and rigidity?

A

-Covalent cross links
-Lysyl oxidase deaminates some lysine and hydroxylysine residues to form allysine
-Cross-links form between Lys and allysine
or allysine and allysine

79
Q

How does collagen aid bone formation?

A

Holes between tropocollagen fibres are nucleation sites for calcium deposition.

80
Q

What is the structure of a tendon?

A 
Tendon
↓
Tertiary fibre bundle
↓
Secondary fibre bundle
↓
Primary fibre bundle
↓
Collagen fibre
↓
Collagen fibril
-Endotenon is contiguous with epitenon, the fine layer of connective tissue that sheaths the tendon unit
81
Q

When is collagen breakdown necessary?

A
  • Growth/tissue remodeling (eg pregnancy/after birth)

- Tissue repair

82
Q

Which family do collagenase enzymes belong to?

A

metalloproteinases

83
Q

What is Dupuytren’s contracture?

A

A potentially disabling condition caused by excess collagen production affecting the connective tissue of the hand. Recent report from clinical usage study shows successful treatment by injection of collagenase.

84
Q

What causes osteogenesis imperfecta?

A

Mutation in collagen chains - Type I collagen

85
Q

What is osteogenesis imperfecta?

A

Brittle bone disease

86
Q

What causes Ehlers-Danlos syndrome type VI?

A

Lysyl oxidase deficiency

87
Q

What causes scurvy?

A

Vitamin C defiency.
Vitamin C is a cofactor required for the functioning of the enzymes prolyl hydroxylase and lysyl hydroxylase, so collagen synthesis is abnormal in patients with scurvy

88
Q

What is Ehlers-Danlos syndrome?

A

Inherited disorders resulting from poorly formed/weak collagen in connective tissue

89
Q

What can Ehlers-Danlos syndrome cause?

A
  • Joint hypermobility/dislocations
  • Extreme fatigue
  • Stretchy skin
  • Digestive problems
  • Organ prolapse/hernias
  • Postural hypotension (POTS)
  • Fragile blood vessels
90
Q

What are the symptoms associated with scurvy?

A
  • fatigue
  • joint pain
  • muscle weakness
  • poor healing
  • skin hemorrhages
  • gum disease

IMS Y1 v2 (14 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2025 Bold Learning Solutions. Terms and Conditions