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ASC222 > Topic 2 - DNA to protein > Flashcards

Topic 2 - DNA to protein Flashcards

0
Q

Translation occurs where? In which direction?

A

cytoplasm - ribosomes

From the amine group (H2N) to carboxyl group (COOH)

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1
Q

Replication & transcription occur where? In which direction?

A

nucleus

5’ to 3’

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2
Q

Nigella’s analogies… Nucleus, DNA, transcription, mRNA, translation

A

nucleus = library; DNA = recipe book; transcription; mRNA = photocopy; translation

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3
Q

In an average protein, how many nucleotides/amino acids?

A

1000-2000 nucleotides of DNA

320-640 aa’s

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4
Q

T or F - all genes encode proteins

A

false - most do but some encode RNAs eg. tRNA

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5
Q

2 classes of protein? Give examples…

A

Structural
- structural -no biological reactions eg. collagen, fibrin
- enzymatic function - protein hormones & signalling molecules
Regulatory
- regulate structural genes ie. produce proteins that regulate gene expression eg. mRNA or RNA

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6
Q

What gives proteins their particular function(s)?

A

order & number of amino acid sequences

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7
Q

How many nucleotides make up a codon?
How many bases are there?
How many amino acids?
How many triplets can be made?

A

3
4
20
64 (4 x 4 x 4 = 64)

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8
Q

3 nucleotides encode what?

A

1 amino acid

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9
Q

How many possible reading frames are there for the translational machinery to make a protein?

A

3

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10
Q

Start codon & amino acid…?

A

AUG - methionine (met)

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11
Q

Stop codons

A

UAA, UAG, UGA

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12
Q

In transcription, which molecule transcribes the gene?

A

RNA polymerase

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13
Q

What are the 3 RNA molecules made from genes? Which one(s) make up the majority?

A 
messenger RNA (mRNA)
transfer RNA (tRNA)
ribosomal RNA (rRNA)
transfer RNA & ribosomal RNA (tRNA & rRNA) make up the majority of RNA
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14
Q

mRNA makes up how much of total RNA?

A

<10%

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15
Q

First nucleotide made of DNA made into RNA is called what?

A

+1

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16
Q

Sequences to the left/right of +1 are…?

A

left - upstream

right - downstream

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17
Q

RNA contains which sugar?

A

ribose

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18
Q

Watch vid of transcription…

A

youtube

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19
Q

RNA contains which base instead of which base…?

A

uracil (U) instead of thymine (T)

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20
Q

T or F - RNA is single stranded

A

true, however certain parts of RNA can base pair with each other creating hairpin loops - occurs very widely in nature (rRNA mRNA)

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21
Q

Where is RNA synthesised in eukaryotes? Prokaryotes?

A

eukaryotes - nucleus

prokaryotes - cytoplasm

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23
Q

Specific role of RNA polymerase…?

A

catalyses formation of phosphodiester bonds

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24
Q

With respect to the mRNA (not non-coding strand), which direction does synthesis occur?

A

5’ to 3’ - just as in DNA replication

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25
Q

Which direction does DNA polymerase read the non-coding (template) strand?

A

3’ to 5’

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26
Q

T or F - the coding strand, not the non-coding (template) strand, is the main strand involved in transcription 2

A

false - the coding strand has nothing to do with the transcription process. The info required by RNA polymerase to make mRNA is is the NON-CODING strand

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27
Q

How many stages of transcription are there? What are they?

A

four. ..
1. RNA polymerase binds to a promoter
2. Initiation - RNA polymerase begins synthesising RNA as DNA is unwound
3. Elongation - RNA is synthesised 5’ - 3’ and strand is read 3’ - 5’
4. Termination - end of gene is reached and RNA polymerase falls of gene

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28
Q

What are the transcription start sites in prokaryotes (bacteria)?

A

Promoters, at -35 and -10 (Pribnow box) bp relative to +1

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29
Q

What do -10 & -35 code for…?

A
  • 35 = TTGACA

- 10 = TATAAT

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30
Q

Which sequence does RNA polymerase see first? -10 (Pribnow) or -35?

A

-35 1st, then -10

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31
Q

Define a consensus sequence

A

When sequences vary between genes or organisms ie. general structure is approximately what those sequences are but may not be exact eg. -10 = TATAAT & -10 = TATAAA

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32
Q

What are the transcription start sites in eukaryotes?

A

Promoters, at -75 (CAAT box) and -25 (TATA box/ Hogness box)

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33
Q

What are the analogous promoters in prokaryotes & eukaryotes?

A

-10 (Pribnow box) & -25 (TATA/Hogness box)

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34
Q

What are the bacterial ‘terminators’ called?

A 
Termination proteins (rho)
Hairpin loop structures
35
Q

Inverted repeat occurrences are common where? When?

A

In stem loop structures where RNA synthesis is to cease

36
Q

In bacteria, what aids transcription control?

A

Only one RNA polymerase aided by sigma factors transiently binding to RNA poly. to assist in correctly assigning the position & location of the promoter to which the polymerase binds.

37
Q

In eukaryotes, what aids transcription control?

A

3 polymerases…
Pol I - transcribes some ribosomal RNA genes
Pol II - transcribes protein coding genes
Pol III - transcribes tRNA, some rRNA & small nuclear RNA’s

38
Q

A bit about transcription factors…

A

…proteins that assist & promote RNA polymerase transcription from promoters

39
Q

Where can transcription factors bind…?

A
  • Directly to sequences within promoters themselves
  • Interact with others (transcription factors)
  • To RNA polymerase directly
    USUALLY BIND TO REGIONS CLOSE TO THE PROMOTER
40
Q

A bit about enhancers…

A
  • 50-100 bp sequences which ‘enhance’ transcription
  • Can control transcription of a gene thousands of base pairs away from the gene (upstream or downstream)
  • Bind regulatory proteins which interact with RNA polymerase
  • Loop out of DNA
41
Q

T or F - All mRNA’s in eukaryotes are processed only after they are complete

A

false - most are processed before they are complete

42
Q

How many types of RNA processing are there?

A

3

43
Q

What types of RNA processing are there…?

A
  1. Addition of methylated guanine to the 5’ end (not a normal guanine nucleotide, but a modified one) - aids to protect mRNA
  2. Addition of a poly-A tail to the 3’ end (polyadenylation)
  3. Removal of introns
44
Q

What are introns?

A

Genes that often have non-coding sequences in them which are not present in the mature mRNA and are removed or ‘spliced out’ before translation.

45
Q

RNA that encode proteins are called …? (coding regions)

A

exons

46
Q

T or F - All genes have many exons & introns

A

false - genes can have many exons & introns or none at all! Some eukaryotic genes do not have introns - majority do tho.

47
Q

T or F - Bacteria contain many introns

A

false - bacteria do not contain introns (only eukaryotes do)

48
Q

T or F - Exons are joined together after mRNA leaves the nucleus

A

false - exons are joined BEFORE mRNA leaves the nucleus

49
Q

Introns are excised from primary transcripts before or after translation?

A

before

50
Q

Ribosomes are made up of …?

A

rRNA and proteins

51
Q

Ribosomal subunits in prokaryotes/eukaryotes…?

A

30S and 50S subunits in prokaryotes

40S and 80S in eukaryotes

52
Q

Which subunit sediments quicker? Why?

A

A 50S ribosomal subunit compared to a 30S subunit would sediment quicker as it is larger

53
Q

A bit about the structure of tRNA…

A

tRNA is a small (75bp) RNA with a particular anticodon & covalently-linked amino acid

54
Q

What do tRNA molecules resemble? Name the regions…

A

clover leaf structure

anticodon, acceptor stem, amino acid binding site, amino acid

55
Q

tRNA main function

A

Transfer of amino acids to ribosome for peptide bonding & correct formation of protein molecule

56
Q

Watch a video of translation…

A

youtube

57
Q

Initiation protocol…

A

initiator tRNA + 1st aa (met) binds to small subunit then binds to 5’ end of mRNA
This initiation complex moves along until it comes to initiator codon (AUG) for 1st Met.
Large subunit then binds

58
Q

Where does the 1st (AUG) codon bind?

A

…at the P-site (peptidyl site)

59
Q

Where does the 2nd tRNA carrying the 2nd amino acid bind?

A

…the A-site (Aminoacyl site)

60
Q

Where are peptide bonds synthesised? What happens after the peptide bond is formed?

A

Between the two amino acids, and then the 1st tRNA (minus Met) leaves the ribosome

61
Q

Describe translocation…

A

Ribosome track along the mRNA until the next codon comes into the A-site. The growing chain is at the P-site. The next peptide bond is formed and so on.

62
Q

What is the wobble base hypothesis?

A

The 3rd base of CODON is called the ‘wobble base’ because the corresponding anticodon does not have to precisely base-pair. eg. codon = UUU, anticodon = AA’…’

63
Q

What happens during termination?

A

Once stop codon is reached (UAA, UAG, UGA) a PROTEIN RELEASE FACTOR interacts with stop codon & terminates translation. Ribosome comes apart & mRNA reused

64
Q

Which ribosomal subunit contains the P and A sites in prokaryotes?

A

50S ribosome

65
Q

Define a mutation

A

A stable and inheritable change in nucleotide sequence

66
Q

T or F - mutations always affect phenotype but not genotype

A

False - mutations always affect genotype and sometimes affect phenotype

67
Q

if a mutation changes a single nucleotide, what is that called? Is it relatively more common in nature?

A

Point mutation - yes

68
Q

Causes of mutations may be…?

A

Spontaneous - errors in DNA replication or repair

Rate in different genes 1 in 10^3 to 1 in 10^9 cell divisions

69
Q

If a change in phenotype is the result of a mutation, what is likely to have happened?

A

Amino acid sequence affected -> premature termination of protein

70
Q

Causes of mutation…?

A

Induced

  • Chemical: ethidium bromide, ciggies, benzopyrene (burnt toast)
  • Radiation: x-rays, gamma rays, UV
71
Q

Types of point mutation…?

A

deletion, insertion, substitution

72
Q

What can a substitution mutation (point mutation) produce…?

A

Silent mutation
Nonsense mutation
Mis-sense mutation

73
Q

What is a silent mutation?

A

A mutation occurs but intended codon is produced and resulting amino acid = normal protein

74
Q

What is a nonsense mutation?

A

One that produces a termination (stop) codon = incomplete protein

75
Q

What is a mis-sense mutation?

A

One that produces a different codon than intended = faulty protein

76
Q

T or F - mitochondria and chloroplasts have DNA genomes

A

true

77
Q

Put in order from largest MITOCHONDRIAL DNA (mtDNA) to smallest. Human, plant, yeast

A
  1. Plant (186k bp)
  2. Yeast (75k bp)
  3. Human (16.5k bp)
78
Q

T or F - mitochondrial DNA is inherited only thru the female line

A

true - thanks mum

79
Q

T or F - mtDNA vary in size between organisms

A

true

80
Q

T or F - most mammalian cells have several mitochondria with multiple copies of the circular genome

A

true

81
Q

How many genes in mitochondria?

A

37
13 - encode proteins in ox. phos.
22 - tRNA’s
2 - 1 large & 1 small rRNA genes

82
Q

T or F - mitochondrial genome has a lower mutation rate than nuclear DNA

A

false - higher mutation rate (10-fold) because of different DNA polymerase

83
Q

The human mtRNA code is considered not universal because…?

A

It is a simplified code with only 22 tRNA’s compared to the universal code of 32 tRNA’s

ASC222 (8 decks)

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