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Cell and Molecular Biology > Protein Structure > Flashcards

Protein Structure Flashcards

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1
Q

Define cell differentiation

A

cells become specialised to perform a specific function (only certain genes are expressed)

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2
Q

Where is the site of protein synthesis

A

ribosomes

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3
Q

Outline the difference between SER and RER

A

SER: no ribosomes attached
RER: ribosomes attached to membrane

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4
Q

Which organelle is in charge of protein degradation

A

lysosome

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5
Q

Define lysosome

A

organelle that contains digestive enzymes

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6
Q

Why are lysosomes acidic

A

the digestive enzymes are at optimum at low pH

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7
Q

Why do white blood cells have a lot of lysosomes

A

they need digest bacteria

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8
Q

What is the central dogma

A
  • the flow of genetic information
  • DNA –> RNA –> protein
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9
Q

Define zwitterions

A

molecule that has an overall neutral charge but have a positively and negatively charged regions

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10
Q

Give an example of a zwitterion

A

amino acid

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11
Q

Why is the R’ group in amino acids so important

A
  • it determines the chemical properties of the amino acid
  • affects protein folding
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12
Q

What factors affect the R’ group

A
  • size
  • charge
  • hydrophobicity
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13
Q

Name some of the different protein functions

A
  • enzymes
  • support (ex: collagen)
  • immunity (ex: antibodies)
  • control of growth and differentiation
  • generation and transmission of nerve cells
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14
Q

What are the main functions of transmembrane proteins

A
  • cell signalling
  • cell-cell recognition
  • transport of molecules across the membrane
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15
Q

Where are transmembrane proteins found

A

across the lipid bilayer of cell membrane

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16
Q

What are examples of transmembrane proteins

A

ion channels and receptors

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17
Q

What is the structure of globular proteins

A

spherical

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18
Q

What is the structure of fibrous proteins

A

long and narrow

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19
Q

What is the function of globular proteins

A

catalysts + transport (functional properties)

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20
Q

What is the function of fibrous proteins

A

structural support and strength

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21
Q

What is an example of a fibrous protein

A

collagen

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22
Q

What is an example of a globular protein

A

hemoglobin

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23
Q

What is the function of natively unfolded protein

A

biologically inactive

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24
Q

What is the structure of a natively infolded protein

A

no well-defined 3D structure (disorded + open)

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25
Q

What is an example of a natively infolded protein

A

neurotransmitters

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26
Q

How do proteins have so many functions

A
  • 20 different amino acids allows there to be many different combinations
  • the different 3D structures determine the function
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27
Q

Outline primary structure

A
  • sequence of amino acids in a polypeptide chain
  • unique to that protein + defines structure and function
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28
Q

Outline secondary structure

A
  • folding of polypeptide chain due to H bonds
  • H bonds provide structural stability
  • alpha-helix and beta-sheets
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29
Q

Outline tertiary structure

A

folding of secondary structure to form a specific 3D shape held together by interactions btw side chains

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30
Q

Outline quaternary structure

A

the interactions between multiple polypeptide chains

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31
Q

What happens to amino acids in low pH

A
  • amino acid becomes positively charged
  • COOH gains an H+
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32
Q

What happens to amino acids in high pH

A
  • amino acid becomes negatively charged
  • NH3 loses an H+
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33
Q

What are the optical properties of amino acids

A
  • all are chiral carbons (except 1)
  • all are mirror images (stereoisomers)
  • all exist only in an L configuration
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34
Q

Outline formation and breakdown of peptide bond

A

formation: condensation + H2O removed
breakdown: hydrolysis + H2O needed

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35
Q

What is the structure of peptide bonds

A

they are planar

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36
Q

Why are peptide bonds planar

A
  • the double bond between C=N restricts rotation
  • locks atoms in planar arrangement
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37
Q

What are the different types of amino acids

A
  • non-polar & polar
  • acidic & basic
  • aliphatic & aromatic
38
Q

What is the main characteristic of non-polar amino acids

A

side chains are hydrophobic

39
Q

What is the main characteristic of polar amino acids

A

side chains are hydrophilic (ex: OH, NH2, SH)

40
Q

What is the main characteristic of acidic amino acids

A

side chains contain COOH

41
Q

What is the main characteristic of basic amino acids

A

side chains contain NH2

42
Q

What is the main characteristic of aliphatic amino acids

A

non-polar and hydrophobic

43
Q

What is the main characteristic of aromatic amino acids

A

ring-shaped + absorbs UV light

44
Q

Why are aromatic amino acids special in function

A

its ability to absorb UV light can be used to estimate protein concentration and structure

45
Q

Outline the difference between a trans and cis peptide bond

A

trans: the oxygen and hydrogen atoms face two different directions
cis: the oxygen and hydrogen atoms face same direction

46
Q

How is hydrophobicity determined

A
  • the number of carbon atoms in a hydrocarbon chain
  • greater C atoms = greater hydrophobic
47
Q

What is cytochrome c

A

protein involved in cellular respiration

48
Q

Why is cytochrome c a marker of evolutionary relationship

A

-similarity of cytochrome c across provides evidence for a common ancestor
- it has been found in all aerobic organisms

49
Q

What is sickle cell anemia

A

genetic disease which affects red blood cells due to a mutation of haemoglobin

50
Q

How is sickle cell anemia caused

A
  • codon GAG mutated to GTG
  • GTG is transcribed to GUG
  • GUG is translated to valine
51
Q

What are the consequences of sickle cell anemia

A
  • sickle-cell shape red blood cell
  • carry less o2 + clog blood vessels
  • immunity to malaria
52
Q

Outline the alpha-helix structure

A
  • helical strcuture
  • the R’ groups are on the outside
  • R’ groups are free to interact
53
Q

Outline the beta-sheet structure

A
  • multiple polypeptide chains are running side by side
  • parallel or anti-parallel
  • R’ groups extend above and below + free to interact
54
Q

Which amino acids are most likely to form alpha-helices

A

amino acids w/ small sie chains

55
Q

Which amino acids are most likely to form beta-sheets

A

amino acids w/ big side chains

56
Q

What are backbone torsion angles

A

how atoms in the backbone are rotated around specific bonds

57
Q

What is a psi angle

A

angle between the alpha carbon and C=O (carbonyl)

58
Q

What is a phi angle

A

angle between C=O and N-H

59
Q

Why are backbone torsion angles important

A

they influence the 3D structure of proteins

60
Q

What are beakers

A

side chains that disrupt the secondary structure

61
Q

How do beakers disrupt secondary structure

A

they introduce kinks/twists to prevent uniform secondary structure

62
Q

What is the function of beta-turns

A

provides flexibility, facilitating the formation of compact protein structures

63
Q

When are beta-turns needed/come into action

A

when the protein chain needs to change direction to connect 2 secondary structural elements

64
Q

What is the function of protein loops

A

interconnect secondary structural elements and change direction of polypeptide chain

65
Q

What are characteristics of protein loops

A
  • connect different secondary structural elements
  • contains binding sites
  • form active sites where catalytic reactions occur
66
Q

What is a supersecondary structure

A

an intermediate between secondary and tertiary structures

67
Q

What is the function of H bonds in protein structure

A

provides stability + enables maintenance of secondary + tertiary structures

68
Q

What are electrostatic interactions

A

arises from attraction or repulsion between charged particles

69
Q

What is salt bridge

A

electrostatic interaction between a negatively charged side chain and a positively charged side chain

70
Q

Why are salt bridges important

A
  • help stabilise 3D structure
  • pH sensitive –> can affect conformation of protein
71
Q

What is the hydrophobic effect

A

non-polar molecules aggregate in aqueous solutions

72
Q

Why is the hydrophobic effect important

A
  • formation of a hydrophobic core = stabilises protein structure
  • reduces unfavourable interactions between hydrophobic and water
  • this could disrupt protein structure
73
Q

True or False:
the polymerisation of amino acids can lead to an electrically neutral backbone

A

True

74
Q

What are multimeric proteins

A

made up of multiple polypeptide chains held together by non-covalent bonds

75
Q

What are monomeric proteins

A

consists of single polypeptide chain

76
Q

What are protein-protein interfaces

A

each protein interacts only with certain partner proteins that have complementary interfaces

77
Q

What is the function of protein-protein interfaces

A

ensures they carry out biological functions accurately

78
Q

What are characteristics of permanent protein-protein interactions

A
  • stable + long-lasting
  • part of structural integrity + play essential role in cellular processes
79
Q

What are characteristics of transient protein-protein interactions

A
  • temporary + lasts for short periods
  • involved in regulatory processes
80
Q

Outline protein-protein interaction sites

A
  • surface accessible + complementary
  • planar
81
Q

Give examples of protein-protein interaction sites

A

any type of ion channel

82
Q

What is Levinthal’s paradox

A

not enough time to sample all possible conformations for a protein to fold

83
Q

How do proteins fold

A

they follow a folding pathway guided by amino acid Side chains interactions

84
Q

True or False
All proteins fold by themselves

A

False
- some proteins cannot

85
Q

What is the role of Heat shock proteins (chaperons)

A
  • they help other proteins fold correctly
  • prevent misfolded proteins from aggregating (can be harmful)
86
Q

What is the role of chaperonins

A
  • they shield out bad influences from the folding proteins
  • reduces likelihood of misfolding or aggregation
87
Q

How does protein folding fail

A
  • mutation changes amino acid + making it difficult for a protein to find its native fold
  • proteins don’t fold correctly 100% of the time
  • proofreading mechanism fails
88
Q

What are the consequences of protein misfolds

A
  • protein is non-functional
  • protein can aggregate and accumulate
89
Q

What are amyloid plaques

A

aggregates of misfolded proteins forming in spaces between nerve cells

90
Q

What is a prion

A

type fo protein that can trigger normal proteins in the brain to fold abnormally

91
Q
A

Cell and Molecular Biology (8 decks)

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