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Biochem BLOCK 3 > Translation > Flashcards

Flashcards in Translation Deck (104):
1

What is the first step in protein synthesis?

Translation
-the code contained in a mRNA is translated into a particular series of amino acids to form a polypeptide

2

What are the mRNAs, tRNAs, and RRNAs synthesized during transcription used for?

To complete translation

3

What does the protein coding region of an mRNA contain?

A series of nucleotide triplets

4

What is each Triplett called?

Codon

5

How many possible combinations of nucleotides are there?

64

6

How are the nucleotides read?

5' to 3'

7

In what direction is the protein synthesized?

From its N-terminus to its C-terminus

8

Start codon

AUG
-for all protein synthesis and defines the reading frame

9

Reading frame

The serious of triplets that make the subsequent codons

10

WHat does AUG code for, besides being the start codon?

Methionine

11

Are all AUGs start codons?

No, but all start codons are AUG

12

How many codons does methionine have?

1

13

Internal codons containing AUG

They are methionine codons, not additional start codons

14

The first AUG encountered reading 5' to 3'

Defines the start codon and the subsequent reading frame

15

Stop codons

-do not encode an amino acid
-UAG, UAA, UGA

16

___ of the 64 codons define as amino acid

61
-AUG defines an amino acid, but 3 are stop codons and do not code for AA

17

Codon specificity

Each codon is specific to a certain amino acid

18

Codons-universal

Genetic code defines the same amino acids in almost all organisms

19

Codon redundancy

Each amino acid may have more than one codon

20

How many codons do each amino acid have?

Between 1 and 6

21

Codon: nonoverlapping and commaless

-code is defined as a continuous series of 3 basses, no overlap and no "punctuation" (no codon is read more than once and no bases are skipped or repeated)
-should start at beginning and read through to the end

22

Do stop codons code for amino acids?

Nope
START DOES!

23

What are some examples of single nucleotide changes?

1. Silent mutation
2. Messenger mutation
3. Nonsense mutation

24

Single nucleotide mutations

Point mutation

25

Silent mutation

-single nucleotide mutation
-if the DNA sequence is mutated, so that the codon is changed, but still encodes the same amino acid, it is called a silent mutation

UCA to UCU, both encode for serine

26

Missense mutation

-single nucleotide mutation
-point mutation
-if the point mutation results in a codon that defines a different amino acid, it is called a missense mutation
-can be conservative


UCA to UCU serine to proline

27

Conservative mutation

-missense mutation that results in an amino acid with similar properties (not as serious, non-polar AA to another non-polar AA)

28

Nonsense mutations

-single nucleotide mutation
-point mutation
-if the mutation results in a change from an amino acid to a STOP codon

UCA to UAA serine to stop codon

29

Frameshift mutations

-insertion/deletion is NOT a multiple of 3
-usually result in a premature stop codon and a truncated protein; the closer to the beginning of the protein, generally the more severe the mutation (similar to nonsense)

30

If the insertion/deletion is not a multiple of 3

Frameshift mutation

31

If the insertion/deletion is a multiple of 3

You will have an insertion/deletion of amino acids

32

Splice site mutations

Changes in nucleotides involved in splicing RNA

33

Splice site mutations could result in any of the following

-deletion of nucleotides from an exon
-leaving nucleotides from an intron in the final mRNA
-completely deleting an exon from the final mRNA

Can be cause by single nucleotide (point) mutations

34

Trinucleotide repeat expansion

Regions in a gene where a sequence of bases is repeated many times can undergo trinucloetide repeat expansions
-the repeat is amplified significantly

35

Trinucleotide repeat expansion in the coding region of mRNA (reading frame)

A faulty protein

36

Trinucleotide repeat expansion in the 5' or 3' UTR

Decreased production of the protein due to the effect of the UTRs on translation
-usually underexpressed

37

Effect on protein: silent mutation

None

38

Effect on protein: missense

Possible decrease in function; variable effects

39

Effect on protein: nonsense

Shorter than normal; usually nonfunctional

40

Effect on protein: frameshift

Usually nonfunctional; often shorter than normal

41

Effect on protein: splice donor or acceptor

Variable effects ranging from addition or deletion of a few AA to deletion of an entire exon

42

Effect on protein: triplet repeat expansion

Expansions in coding regions cause protein product to be longer than normal and unstable

Disease often shows anticipation in pedigree

43

Components required for translation

-amino acids
-tRNA
-aminoacyl-tRNA synthetases
-tRNA charging
-mRNA
-ribosomes
-protein factors

44

Amino acids in translation

All amino acids encoded on the mRNA must be present
-in an amino acid is absent or in limited supply, translation will stop at the codon specifying that amino acid

45

tRNA in translation

-at least one specific tRNA for each of the amino acids
-amino acids that are specified by multiple codons often have multiple tRNAs

46

What is the tRNA-amino acids attachment site?

CCA-3' terminus
-if amino acid is attached, the tRNA is charged

47

Anticodon

Specific 3 nucleotide sequence that base pairs with the mRNA

48

What is the anticodon that would bind AUG?

5'-UAC-3'
Or
3'-CAU-5'

49

Aminoacyl-tRNA synthetases

Enzymes that attach amino acids to the corresponding tRNA

50

What attaches amino acids to their corresponding tRNAs?

Aminoacyl-tRNA synthetases

51

What does each aminoacyl-tRNA synthetase recognize?

The amino acid and ALL of the tRNAs that correspond to that amino acid

52

How many different aminoacyl-tRNA synthetases in humans?

20

53

tRNA charging

Two step reaction in which the amino acid is covalently linked via its carboxyl group to the hydroxyl group on the 3' terminus of the tRNA (ester bond) using energy from ATP
-pyrophosphate generated and its subsequently cleaved to two molecules of inorganic phosphate

54

What is the energy for the amino acid attachment to tRNA?

Cleavage of two high energy phosphate bonds

55

Where does the amino acid attach to the tRNA?

CCA-3' terminus of tRNA

56

mRNA in translation

Required as a template

57

Ribosomes

-Complexes of rRNAs and many proteins
-molecular machines that translate the message on an mRNA molecule into a specific protein

58

Eukaryotes ribosome size

80s ribosome
-60s and 40s large and small subunits

59

Prokaryote ribosome size

70s ribosomes
-50s and 30s large and small subunits

60

Ribosome subunits

Exist separately until proteins synthesis is about it being

61

What are the 3 ribosome sites

A, P, E

62

A site of ribosome

Binds incoming aminoacyl-tRNA

63

P site of ribosomes

Binds peptides-tRNA (peptides-tRNA carries the chain of amino acids that have already been synthesized

64

E site of ribosomes

-only in prokaryotes
-exit site, contains empty tRNA as it is about to exit the ribosome

65

Where are ribosomes located in eukaryotes?

Cytosol or bound to ER

66

proteins translated on the ER are destined for post-translational modifications and/or subcellular compartmentalizations and are commonly referred to as

Secretory proteins

67

Any protein made on the ribosome on the ER is

A secretory protein

68

Protein factors

Accessory proteins involved in stages of peptide synthesis
-invitation factors
-elegonation factors
-termination (release) factors

69

Energy requirement total for translation

Total of 4 high energy bonds are required for each amino acid that is added

70

Energy requirement for charging the tRNA

Two high energy bonds from ATP

71

Energy requirement for binding the aminoacyl-tRNA to the A site

One GTP

72

Energy requirement for the translocation step of translation, movement of the ribosome to the next codon

One GTP

73

What kind of binding between the codon and anticodon?

Antiparallel

74

How is mRNA read?

5' to 3'

75

What would the orientation of the complementary anticodon to the mRNA be?

mRNA is read as 5' to 3' and the binding is antiparallel so the anticodon would be in the opposite orientation

76

What is the anticodon for AUG?

5'-AUG-3'
3'-UAC-5' (rewrite it not)
5'-CAU-3' or simply CAU

77

Wobble hypothesis

.tRNAs can recognize more than one codon for a specific amino acid
-the 3rd nucleotide of a codon (5' to 3') and the 1st nucleotide of an anticodon (3' to 5') can sometimes pair non-specifically
-this allows a single tRNA to recognize more than one codon

78

What is the net result of the wobble hypothesis?

61 different tRNAs are not absolutely required

79

Genetic code in wobble hypothesis

Often amino acids with multiple codons differ in the 3' nucleotide (of the codon)

80

Polycistronic

Prokaryotes sometimes have multiple coding regions on the same gene
Can also have polyribosomes

81

Polyribosome

How many ribosomes are associated with one mRNA

82

Monocistronic

Euk are always this, but can have polyribosomes, slower though

83

When can translation being in prokaryotes?

It can being before transcription is complete

84

When can eukaryotic translation being?

Transcription and translation are spatially and temporally separated

85

How is initiation of translation potentiated in prokaryotes?

By the presence of the shine dalgarno sequence
-the 16S rRNA in the small ribose all subunit contains a sequence complementary to the Shine-Delgarno sequence- this allows correct alignment of the small ribosomal subunit with the AUG start codon

86

Initiation in eukaryotes (translation)

Beings with the small ribosomal subunit recognizing the 5'-cap structure and scanning along the mRNA until the first AUG is found

87

What makes euk monocistronic?

The mechanism of the small ribosomal subunit to recognize the 5' cap structure and then the scanning along the mRNA until the first AUG is found

88

Why can prokaryotes be polycistronic?

Because the initiation process can being in the interior of the mRNA (as long as a shine-delgarno sequence and an AUG starry codon present)

89

Initiator tRNA

Binds the small ribosomal subunit

90

Initiator tRNA in prokaryotes

Bound to a formylated- methionine

91

Initiator tRNA in euk

Bound to a methionine (not formylated)

92

What is the difference in the methionine of a start codon and methionine in the polypeptide?

The start codon methionine is formylated (prok), rest are not

93

Elongation (translation)

The polypeptide chain is elongated by the addition of amino acids to the carboxyl end of the growing chain-forming peptide bonds

94

Elongation: delivery of next aminoacyl-tRNA

To the A site on the ribosome
Requires elongation factors and GTP

95

What is the P site on the ribosome?

The holding site

96

How is the formation of the peptide bond done?

By peptidyltrasnferase (a component of the large ribosomal subunit)

97

What plays a role in the formation of the peptide bond?

Peptidyltransferase

98

Where does the energy for the formation of the peptide bond come from?

Charged tRNA

99

Translocation

-ribosome moves three nucleotides to the next codon to be translated
-uncharged tRNA into E site
-peptiyl-tRNA into P site
-opens up A site for next aminoacyl-tRNA
-requires elongation factors and GTP

100

What does translocation require?

Elongation factors and GTP

101

Termination

When a stop codon appears in the A site
Requires GTP

102

Polysome/polyribsome

The mRNAs are normally much longer than the space required for a ribosome to bind, so multiple ribosomes are usually found on a single mRNA molecule
-do not confuse with polycistronic!

103

Secretory proteins

-model for translation
-the signal peptide is part of the polypeptide being translated
-translated at ER
-stop receptor on ER

104

Protein trafficking and post translational modifications

-the newly synthesized peptide emerges in the lumen of the ER and the signal peptide is cleaved
-includes secreted proteins (for exampl insulin and collagen), protein inserted into cell membranes, and others such as lysosomal enzymes