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Cells, organisms and systems > 3.2 - Protein structure and function > Flashcards

3.2 - Protein structure and function Flashcards

1
Q

what does a proteins sequence always start with and what is it coded by?

A

Met, coded for by AUG

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2
Q

N-terminus (2)

A
  1. start of polypeptide chain
  2. amino group (NH2)
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3
Q

C-terminus (2)

A
  1. end of protein chain
  2. carboxyl group (COOH)
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4
Q

what does the 5’-3’ of the mRNA sequence correspond to

A

the N-terminal to C-terminal of the polypeptide q

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5
Q

what do all amino acids contain (apart from proline) (3)

A
  1. acidic carboxyl group
  2. basic amino group
  3. hydrogen
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6
Q

what are the 2 ionisable protons in amino acids? (2)

A
  1. carboxylic acid
  2. amino group
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7
Q

what does ionisation of amino acids depend on?

A

pH (usually have 0 charge at physiological pH)

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8
Q

structure of amino acids

A

chiral (L isomer)

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9
Q

what has a different chemical property in amino acids?

A

each ‘R’ group

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10
Q

which amino acids are hydrophobic?

A

non-polar

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11
Q

where are hydrophobic amino acids found?

A

inside of cytosolic globular proteins

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12
Q

which amino acids are hydrophillic?

A

polar (able to form H-bonds)

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13
Q

which amino acids can form electrostatic interactions and are basic (+ve charge) or acidic (-ve charge)?

A

polar amino acids with charged side groups

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14
Q

which amino acid can form disulfide bonds?

A

cysteine

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15
Q

describe peptide bond formation

A

carboxyl group of one amino acid bonds to amino group of another amino acid, with elimination of a molecule of water (condensation reaction)

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16
Q

what is the structure of a protein dictated by? (2)

A
  1. properties of amino acid side chains
  2. partly by properties of the peptide bond
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17
Q

where are hydrophilic/hydrophobic amino acid residues found? (2)

A
  1. hydrophilic - predominantly on surface of protein
  2. hydrophobic - predominantly found in interior of protein (cystolic)
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18
Q

primary structure

A

linear sequence of amino acids linked by peptide bonds

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19
Q

secondary structure (2)

A
  1. 3D structure formed by H-bonds between peptide NH and CO groups
  2. folding of polypeptide chain into a-helices or B-sheets
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20
Q

tertiary structure (2)

A
  1. adopt specific 3D conformation, able to fulfil specific biological function
  2. achieved by numerous weak interactions between amino acid side chains
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21
Q

quaternary structure

A

some functional proteins composed of more than one polypeptide (association through non-covalent interactions)

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22
Q

a-helix (2)

A
  1. tightly coiled, rodlike structure
  2. R groups projecting out from axis of helix
23
Q

B-sheet (3)

A
  1. formed by adjacent B-strands which have fully extended polypeptide (linked by H-bonds)
  2. strands may be parallel, antiparallel or mixed
  3. may be flat or twisted conformation
24
Q

disulfide bonds

A

oxidation reaction can generate a cystine unite with a disulfide bond (comes from thiol SH)

25
Q

globular protein domains

A

distinct 3D structural motifs

26
Q

what is a domain

A

part of polypeptide chain that is independently stable or could undergo movement as single entity

27
Q

example of a globular protein domain

A

kinase domain

28
Q

how is modular construction of proteins possible?

A

through different domain combinations

29
Q

what % of eukaryotic proteins have multiple structural domains

A

75%

30
Q

how many domains do small proteins usually have

A

1

31
Q

what are the 2 types of protein? (2)

A
  1. fibrous
  2. globular
32
Q

what are the 2 solubilities of proteins? (2)

A
  1. water soluble
  2. lipid soluble
33
Q

what is the role of fibrous proteins in nature?

A

structural

34
Q

superfamily of structural (fibrous) proteins

A

coiled-coil proteins

35
Q

give an example of a coiled-coil protein

A

a-keratin

36
Q

properties of coiled-coil proteins and why (2)

A
  1. strong/flexible
  2. because of intertwining design
37
Q

structure of fibrous proteins (2)

A
  1. two right-handed a-helices intertwining to form left-handed super helix
  2. further coiling into protofilaments and fibrils makes hair shaft
38
Q

how is the structure of fibrous proteins stabilised?

A

ionic and van der waals interactions

39
Q

globular protein structure

A

complicated and very compact 3D structure

40
Q

what do the interior/exterior of globular proteins consist of? (2)

A
  1. interior - mainly hydrophobic amino acids (little/no space)
  2. exterior - charged/polar amino acids
41
Q

how does hydrophobic amino acid distribution differ between fibrous/globular proteins? (2)

A
  1. fibrous - hydrophobic amino acids on outside of protein
  2. globular - hydrophobic amino acids inside protein
42
Q

what is the role of membrane proteins?

A

interact with lipid bilayer, have specific sequences and structures

43
Q

what type of protein are membrane proteins?

A

usually ‘inside out’ globular proteins (hydrophobic amino acids facing aqueous solution)

44
Q

what proteins are targeted by majority of drugs?

A

membrane proteins - particularly receptors and enzymes, but also membrane transport proteins

45
Q

GPCRs

A

G-protein-coupled receptors

46
Q

structure of GBCRs

A

seven transmembrane a-helical domains, form huge protein family

47
Q

examples of crucial protein-protein interactions (3)

A
  1. antibody-antigen recognition
  2. signals binding to receptors
  3. enzyme/substrate reactions
48
Q

molecule (typically small) that binds to protein

A

ligand

49
Q

how does ligand bind to protein (2)

A
  1. same non-covalent interactions that dictate protein structure
  2. induced fit model
50
Q

enzyme role

A

catalyse making/breakdown of covalent bonds (facilitates formation of transition state)

51
Q

2 fates of misfolded proteins (2)

A
  1. degraded by cellular quality control machinery
  2. form aggregates
52
Q

what are various neurodegenerative diseases associated with?

A

accumulation of tau and a-Syn aggregates (taupathies and synucleinopathies)

53
Q

what could be responsible for different neurodegenerative diseases?

A

aggregates adopting different structures

Cells, organisms and systems (26 decks)

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