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BIOL-119-01 > Chapter 4 - Translation & Protein Structure > Flashcards

Chapter 4 - Translation & Protein Structure Flashcards

1
Q

What is different between amino acids?

A

their side chains

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2
Q

What is the structure of an amino acid?

A

central alpha carbon atom, connected by covalent bond to an amino group (NH2) a carboxyl group (COOH), a hydrogen atom (H) and a variable side chain denoted by R.

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3
Q

What happens to the amino group in a cellular environment?

A

it gains a proton to become NH3^+ and carboxyl group loses a proton to become COO^-

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4
Q

how many different amino acids are most commonly found in proteins?

A

20

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5
Q

What are hydrophobic amino acids?

A

they do not readily interact with water or form hydrogen bonds
most have a non polar R group of hydrocarbon chain or uncharged carbon rings

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6
Q

How does the bonding work in hydrophobic amino acids?

A

water molecules in cell hydrogen bond with each other
hydrophobic R groups aggregate each other but stabilised by weak Van der Waals forces

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7
Q

Where do hydrophobic amino acids tend to reside?

A

buried within interior folds of proteins

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8
Q

how does bonding work in hydrophilic amino acids?

A

form hydrogen bonds with water
R group gains proton becomes positively charged

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9
Q

Where are hydrophilic amino acids usually found?

A

in surface of folded protein molecules
can bind to other charged particles - allows for association with macromolecules like DNA

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10
Q

What are the 3 amino acids with special properties?

A

glycine, proline, cysteine

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11
Q

What is the R group of glycine?

A

H

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12
Q

What does glycine’s R group allow for?

A

small size allows for freer rotation around C-N bond

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13
Q

What does freer rotation enabled by glycine enable?

A

increases the flexibility of the polypeptide backbone, can be important in the folding of protein

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14
Q

What is special about the R group of proline?

A

is linked back to the amine group linkage creates a kink or bend in the polypeptide chain and restricts rotation of C-N bond

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15
Q

What does the linkage of amine group in proline cause?

A

constraints on protein folding in its vicinity

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16
Q

What is the R group of Cysteine?

A

SH

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17
Q

What can happen when 2 cysteine molecules come close together? what does it allow/mean?

A

they can react to form a disulfide bond, which covalently joins the side chains = stronger than ionic interactions and form cross bridges that can connect different parts of the same protein or even different proteins

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18
Q

What bonds connect successive amino acids?

A

peptide bonds

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19
Q

where do peptide bonds form in amino acids? and what is released when they form?

A

forms between carboxyl group and amino group of amino acid
a molecule of water is released

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20
Q

What is the C=O group in amino acid chain bond?

A

Carbonyl

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21
Q

What is the N-H group in amino acid chain bond?

A

amide

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22
Q

how do electrons behave in peptide bond?

A

they are more attracted to C=O group because of greater electronegativity of oxygen atom.

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23
Q

What are some characteristics of a double bond?

A

shorter
not free to rotate

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24
Q

What is a polymer of amino acids called?

A

polypeptide

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25
Q

What is the longest polypeptide?

A

muscle protein titin at 34,350 amino acids

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26
Q

what are amino acid residues?

A

amino acids incorporated into proteins

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27
Q

What is primary structure?

A

sequence of amino acids

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28
Q

What is secondary structure?

A

interaction between stretches of amino acids

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29
Q

What is tertiary structure?

A

longer range interactions between secondary structures

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30
Q

What is quaternary structure?

A

several individual polypeptides that interact with each other

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31
Q

how do secondary structures form?

A

result from hydrogen bonding in the polypeptide backbone

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32
Q

Who conducted the X -ray crystallography experiment?

A

Liam Pawling & Robert Corey in 1950s

33
Q

What was the X-Ray crystallography experiment?

A

x rays through crystal forms a series of spots = position of arrangement of atoms in a molecule

34
Q

What are alpha helices?

A

twisted tightly with right handed coil - 3.6 amino acids per complete turn

35
Q

What are beta pleated sheets?

A

folds back and forth with hydrogen bonds
forms chains that are antiparallel = more stable

36
Q

What are tertiary structures formed by?

A

interactions between R groups and spatial distribution of hydrophobic or hydrophilic amino acids
loops or turns in the backbone allow R groups to sit near each other

37
Q

Who experimented with ribonuclease?

A

Christian Anfinsen in 1961

38
Q

What did Christian Anfinsen prove?

A

that the sequence of amino acids, in itself, determines the way the chain folds itself and that no additional genetic information is required in the process

39
Q

What are quaternary structures formed from?

A

polypeptide subunits can come together and bind
they can be identical or different polypeptides

40
Q

How can the subunits affect each other?

A

they can influence each other’s behaviour
e.g. in haemoglobin when binds with oxygen, other subunits change and increase affinity for oxygen

41
Q

What are Chaperones?

A

they help protect slow-folding or denatures proteins until they can attain their proper 3D structure

42
Q

How do Chaperones work?

A

they bind with non polar R groups to shield them from inappropriate aggregation. in repeated cycles of bind and release give polypeptides time to find shape

43
Q

What are ribosomes?

A

complex structures of rRNA and protein that bind with mRNA and are the site of translation

44
Q

What do ribosomes consist of?

A

a small subunit and a large subunit each composed of 1 to 3 types of rRNA and 20 t0 50 types of ribosomal protein

45
Q

What does the large subunit have to allow for translation?

A

3 binding sites for molecules of tRNA called the A (aminoacyl) site, the P (peptidyl) site, and the E (exit) site.

46
Q

What is the role of the ribosome?

A

making sure mRNA is read in successive, non-overlapping groups of 3 nucleotides

47
Q

What is each non-overlapping trio of nucleotides called?

A

a codon

48
Q

What does each codon code for?

A

an amino acid

49
Q

What are reading frames?

A

different places to start, synthesis of the mRNA nucleotide sequencing (only correct if translated into the proper reading frame

50
Q

What is tRNA?

A

small RNA molecules of 70-90 nucleotides. Each has a self-pairing structure can be drawn as a clover leaf

51
Q

What is an anticodon?

A

3 nucleotides that undergo base pairing with the corresponding codon. each tRNA has the nucleotide sequence CCA at its 3’ end and the 3’ hydroxyl of the A is the attachment site for the amino acid corresponding to the anticodon

52
Q

What connects specific amino acids to specific tRNA molecules?

A

enzyme aminoacyl tRNA synthetase

53
Q

What is a tRNA with no attached amino acids called?

A

uncharged

54
Q

What is a tRNA with attached amino acids called?

A

charged

55
Q

What do codons specify for?

A

an amino acid according to genetic code

56
Q

What is the codon at which translation occurs called?

A

initiation codon

57
Q

What amino acid does the codon AUG specify?

A

Met (methionine)

58
Q

When initiated what does met form?

A

amino end of polypeptide, in many cases is cleaved off, also AUG codon specifies the incorporation of met at internal sites within polypeptide chain

59
Q

What does the position of the codon establish?

A

the reading frame that determines how the downstream codons are to be read (non-overlapping bases of groups of 3 after AUG codon)

60
Q

When does the process of translation stop?

A

when a stoop codon is reached - polypeptide is finished and released into cytosol

61
Q

How many amino acids in humans? specified by how many codons?

A

20 amino acids specified by 61 codons

62
Q

When an amino acid is coded by more than 1 codon what is it considered?

A

redundant

63
Q

What are the patterns of redundancy?

A

results almost exclusively from the 3rd codon position
When an amino acid is specified by 2 codons, they differ either whether the 3rd position is a U or C, or an A or G
When an amino acid is specified by 4 codons the identity of the 3rd codon does not matter

64
Q

Who conducted experiment to decipher the genetic code?

A

Har Gobind Khornana

65
Q

What did Har Gobind Khornana do?

A

constructed synthetic RNAs with predetermined sequences, added to solution for translation - manipulated the repeating sequences to determine the reading frames and identify what bases produced which amino acids

66
Q

What are the 3 stages of translation?

A

initiation, elongation, termination

67
Q

what is initiation?

A

initiator AUG codon recognised, met = first amino acid. translation starts

68
Q

What is elongation?

A

successive amino acids added

69
Q

what is termination?

A

addition of amino acids stops and completed polypeptide chain released from ribosome

70
Q

why do we need elongation factors?

A

ribosome movement along mRNA and peptide bonds require energy

71
Q

What are the 3 stop codons?

A

UAA, UAG, or UGA

72
Q

In prokaryotes what does translation start at?

A

Shine-Dalgarno sequence

73
Q

What is a operon?

A

when functionally related genes located in a line along the DNA are transcribed in a single unit from one promoter

74
Q

What does a operon result in?

A

formation of polycistronic mRNA

75
Q

What is a protein family?

A

a group of proteins that are structurally and functionally related as a result of their shared evolutionary history

76
Q

what is a folding domain? (proteins)

A

region of a protein that folds in a similar way relatively independently of the rest of the protein

77
Q

What can amino acid evolution through mutations and selection allow for?

A

allows for complex proteins to evolve against seemingly long odds

78
Q

What is a mutation?

A

a change in sequence of the gene (can affect function)

79
Q

What is selection? (mutations)

A

in a population of organisms, random mutations are retained or eliminated through the process.
based on individuals ability to survive and reproduce (most are eliminated)

BIOL-119-01 (8 decks)

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