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Biology 1B > Proteins & DNA > Flashcards

Proteins & DNA Flashcards

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1
Q

What are proteins?

A

Proteins are polymers of amino acids linked by peptide bonds.
They contain 20 different side chains/R-groups

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2
Q

How are peptide bonds formed?

A

Formed by condensation reaction between the amino group of one amino acid, and the carboxyl group of another

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3
Q

What are the properties of peptide bonds?

A
  • Planar shape
  • Very stable
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4
Q

What is the structural properties of polypeptides?

A
  • Linear and unbranched
  • The two ends are always distinct
  • Each polypeptide chain folds into a specific 3D structure (conformation)
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5
Q

How are polypeptide chains draw and numbered?

A

The chains are always drawn and numbered from the N-terminal (amino-terminus) end to the C-terminal (carboxy-terminus) end

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6
Q

What are the non-polar amino acids?

A

Gly
Ala
Val
Lei
Ile
Met
Phe
Trp
Pro

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7
Q

What are the polar amino acids?

A

Ser
Thr
Cys
Tyr
Asn
Gln

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8
Q

What are the electrically charged amino acids?

A

Asp (-)
Glu (-)
Lys (+)
Arg (+)
His (+)

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9
Q

What are the four terms used to describe protein folding?

A
  • Primary structure
  • Secondary structure
  • Tertiary structure
  • Quaternary structure
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10
Q

What is primary structure?

A

The amino acid sequence, as dictated by the mRNA

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11
Q

What is secondary structure?

A

The way in which the backbone of the protein folds (in a regular manner)

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12
Q

What are the two possible forms of secondary structure in proteins?

A
  • Alpha helix
  • Beta pleated sheets
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13
Q

What is the structure of alpha helices?

A

Forms a spiral structure, with the C=O of n hydrogen bonded to the N-H of residue n+4 (i.e the 4th amino acid down the chain.

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14
Q

What is the structure of beta pleated sheets?

A

Forms a flat surface that can be twisted into a cylinder. The chains in the sheet can be either parallel (running in the same direction) or anti-parallel

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15
Q

Where are the side-chains positioned on a-helices?

A

Around the outside

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16
Q

Where are the side-chains positioned on b-pleated sheets?

A

Alternatively above and below the plane of the sheet

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17
Q

What is tertiary structure?

A

The way in which the polypeptide chain folds into a compact 3-dimensional shape

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18
Q

What is quaternary structure?

A

The arrangement of subunits (chains) in proteins containing two or more polypeptide chains

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19
Q

What bonds are involved in primary structure?

A

Peptide bonds

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20
Q

What bonds are involved in secondary structure?

A

Hydrogen bonds

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21
Q

What bonds are involved in tertiary structure?

A
  • Hydrogen bonds
  • Ionic bonds
  • Hydrophobic interactions
  • Disulphide bonds
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22
Q

What bonds are involved in quaternary structure?

A
  • Hydrogen bonds
  • Ionic bonds
  • Hydrophobic interactions
  • Disulphide bonds
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23
Q

What are hydrophobic interactions?

A

Clustering of hydrophobic groups away from water

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24
Q

Where do disulphide bonds occur?

A

Between amino acids with a cysteine side-chain

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25
Q

How are proteins held together?

A

By a large number of mainly weak interactions

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26
Q

What are the 3 implications of proteins being held together by many weak interactions?

A

Protein conformation is flexible
Protein conformation can easily be destroyed
The functioning of many proteins can be regulated by events that cause a change in conformation (e.g. binding to another molecule)

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27
Q

When do proteins fold?

A

Many proteins fold spontaneously during/after translation, however some proteins require the help of other proteins to fold properly

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28
Q

What is the name given to proteins that help protein folding?

A

Chaperonins

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29
Q

What is the general structure of amino acids?

A

A carbon with an amino group (NH2), carboxyl group (COOH), a side chain (R) and a hydrogen attached

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30
Q

What is the structure of antibodies?

A

2 heavy chains and 2 light chains joined by disulphide bridges.
Both types of chains have variable and constant regions

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31
Q

What is antigen specificity determined by?

A

The variable regions of the chains

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32
Q

What is the small part of the antigen the antibody recognises?

A

The epitope

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33
Q

What protein structure are antibodies?

A

Quaternary structure

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34
Q

Where is hexokinase expressed?

A

In muscle

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35
Q

What is the role of hexokinase?

A

In glycolysis, it converts glucose into glucose 6-phosphate

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36
Q

How is hexokinase inhibited, and how does this affect function?

A

Hexokinase has a high affinity for glucose, however its activity is inhibited by glucose 6-phosphate.
Despite this, hexokinase will convert glucose no matter how high/low the concentration

37
Q

What are the differences between hexokinase and glucokinase?

A

Hexokinase and glucokinase have similar functions, however glucokinase:
- Is found in the liver instead of muscle
- Has a lower affinity for glucose
- Is not inhibited by glucose 6-phosphate

38
Q

How does glucokinase function under different concentrations of glucose?

A

If there is a high concentration of glucose in the liver, glucokinase will convert it, however at lower concentrations, little conversion will occur

39
Q

What is collagen?

A

A fibrous protein found in connective tissue

40
Q

What is the structure and properties of collagen?

A

It is made up of three collagen helices coiled, held together by hydrogen bonds.
It has a high tensile strength

41
Q

What are the 4 differences between RNA and DNA?

A
  • RNA has ribose, instead of deoxyribose
  • RNA has uracil bases, instead of thymine
  • RNA tends to be single stranded
  • RNA leaves the nucleus, DNA does not
42
Q

What are the three processes within protein transcription?

A
  • Initiation
  • Elongation
  • Termination
43
Q

Where does initiation of transcription occur?

A

At a site called a promoter, which contains a particular sequences of bases

44
Q

How is transcription initiated in prokaryotes?

A

RNA polymerase itself recognises and binds to the promoter site

45
Q

How is transcription initiated in eukaryotes?

A

A set of proteins (transcription factors) are involved in the binding of RNA polymerase to the promoter site

46
Q

What is elongation in transcription?

A

The process in which an RNA chain complementary to the template DNA strand is synthesised as RNA polymerase moves along the DNA chain

47
Q

What did Archibald Garrod mean by an inborn error of metabolism?

A

Inherited disorders such as albinism result from reduced activity or complete absence of enzymes involved in certain biochemical pathways

48
Q

What was the hypothesis of the Beadle and Tatum experiment on one gene, one enzyme?

A

The idea that each gene is responsible for the production of one (and only one) enzyme

49
Q

How does termination occur during transcription?

A

A terminator sequence will be transcribed, and proteins bind to the growing transcript, cutting it free from the polymerase.
Consequently, the transcript is released and the RNA polymerase detaches from DNA

50
Q

What is the terminator sequence in eukaryotes?

A

AAUAAA

51
Q

What happens in eukaryotes before RNA leaves the nucleus?

A

The primary RNA transcript is modified before it leaves the nucleus

52
Q

What 2 alterations are made to the primary RNA transcript (pre-mRNA) before it leaves the nucleus?

A
  • A cap is added to the 5’ end
  • A polyA tail is added to the 3’ end
53
Q

What are the 3 affects of the alterations made to pre-mRNA?

A
  • Protect mRNA from degradation
  • Aid export from nucleus
  • Help the mRNA to anchor to the ribosomes
54
Q

What is the purpose of mRNA splicing?

A

To remove non-coding regions, so as to leave the coding regions

55
Q

What is the name for the non-coding regions of mRNA?

A

Introns

56
Q

What is the name for the coding regions of mRNA?

A

Exons

57
Q

What is the name of the protein that carries out splicing?

A

Small nuclear ribonucleoproteins (snRNPs)

58
Q

What is the structure of ribosomes?

A

Ribosomes consist of two subunits, the large (50S) and small (30S).
These subunits only join together when mRNA is present

59
Q

What are the 3 phases of translation?

A
  • Initiation
  • Elongation
  • Termination
60
Q

What is translation?

A

mRNA codons are deciphered by the anti-codons in tRNA.
The tRNA adds amino acids to the polypeptide chain when the appropriate anticodon recognises its codon

61
Q

Which subunit of the ribosome binds to the start codon of mRNA during initiation of translation?

A

The small 30S subunit binds to the start codon of mRNA

62
Q

What amino acid does the initiator tRNA carry, and where does this bind?

A

The special initiator tRNA carrying the amino acid methionine binds to the start codon

63
Q

What are the three phases of elongation during translation?

A
  • Codon recognition
  • Peptide bond formation
  • Translocation
64
Q

What are the 3 sites of the ribosomes involved in translation?

A

A, P and E binding sites

65
Q

What happens during codon recognition of elongation?

A

The correct aminoacyl-tRNA is brought into the A site of the ribosome

66
Q

What happens during peptide bond formation of elongation?

A

The newly arrived amino acid is joined to the growing polypeptide chain

67
Q

What catalyses peptide bond formation during elongation?

A

rRNA (ribosomal RNA)

68
Q

What happens during translocation of elongation?

A

The ribosomes moves the tRNA in the A site to the P site; the discharged tRNA in the P site is moved to the E site to leave the ribosome

69
Q

Which steps of elongation require energy?

A

Codon recognition
Translocation

70
Q

What is the energy molecule used in elongation of translation?

A

GTP

71
Q

What direction does the ribosome move along the mRNA?

A

5’ to 3’

72
Q

What rate are amino acids added to the chain?

A

10-20 per second

73
Q

What happens during termination of translation?

A

Elongation continues until a STOP codon appears the A site.
Instead of tRNA, a release factor protein binds and the completed peptide chain is freed

74
Q

What is a missense mutation?

A

A mutation that alters the genetic code in a way that produces an amino acid that is different from the intended amino acid

75
Q

What is a nonsense mutation?

A

A mutation that causes the premature termination of a protein

76
Q

What can base pair substitution mutation cause?

A
  • No affect
  • Missense mutation
  • Nonsense mutation (if stop codon coded for)
77
Q

What can base pair insertion or deletion mutation cause?

A
  • Extensive missence mutation (as many incorrect amino acids are coded for)
  • Nonsense mutation (if stop codon coded for)
78
Q

What is the function of enzyme topoisomerase?

A

Relaxes the DNA from its super-coiled nature

79
Q

What is the function of enzyme DNA helicase?

A

Separates the two strands of DNA at the replication fork

80
Q

What is the function of enzyme single-strand DNA binding protein?

A

Binds to the single stranded DNA to prevent the separated strands from re-forming a double helix (maintains strand separation)

81
Q

What is the function of enzyme DNA polymerase?

A

Catalyses the addition of nucleotides to the growing DNA.
Also perform proof-reading and error correction roles

82
Q

What is the function of enzyme primase?

A

Provides a starting point of the RNA for DNA polymerase to begin synthesising the new DNA strand

83
Q

What is the function of enzyme DNA ligase?

A

Responsible for joining the Okazaki fragments of the lagging strand, forming a continuous strand

84
Q

What are replication bubbles/forks?

A

Where parental strands separate to allow for replication

85
Q

Why is there both continuous and discontinuous replication?

A

The strands are anti parallel (opposite orientations), and DNA polymerase can only work from 5’ to 3’, so as a result there is one leading strand of DNA (continuous), and one lagging strand (discontinuous)

86
Q

How does continuous replication of the leading strand work?

A

After a single primer is added, DNA polymerase continuously adds nucleotides to the exposed chain 5’-3’

87
Q

How does discontinuous replication of the lagging strand work?

A

The lagging strand is made in fragments because, as the fork moves forward, the DNA polymerase (which is moving in the opposite direction to the extending fork), must come of and reattach on the newly exposed DNA

88
Q

What are the DNA fragments made from discontinuous replication called?

A

Okazaki fragments

89
Q

How many primers does discontinuous replication require?

A

Multiple; whenever DNA polymerase releases and reattaches at a new point on the lagging strand, a new primer is required

Biology 1B (6 decks)

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