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BMS2062 > PART I: THE CENTRAL DOGMA OF MOLECULAR BIOLOGY > Flashcards

PART I: THE CENTRAL DOGMA OF MOLECULAR BIOLOGY Flashcards

1
Q

What is a coding sequence?

A
  • A stretch of DNA that encodes a protein
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2
Q

How many possible reading frames are there in double stranded DNA?

A
  • 6
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3
Q

Which strand of DNA is reading frame 4?

A
  • On the second strand of DNA read backwards (from right to left)
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4
Q

How many possible reading frames are there in any DNA sequence?

A
  • 3
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5
Q

What is the initiation codon in many DNA sequences?

A
  • ATG (AUG)
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6
Q

What are the 3 termination codons?

A
  • TAA
  • TAG
  • TGA
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7
Q

How many codons are available to encode 20 amino acids without the termination codons?

A
  • 61
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8
Q

How does redundancy commonly occur?

A
  • By varying the THIRD base of a codon
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9
Q

How do DNA accents arise?

A
  • By EITHER variations in codon usage OR preference

e. g. Arg codon in yeast is biased towards AGA

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10
Q

What effect can deletion or insertion of 1 or 2 nucleotides have on the DNA?

A
  • It can alter the reading frame
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11
Q

What effect can deleting 3 nucleotides or adding one codon have on the reading frame?

A
  • Maintains the reading frame

- NO change

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12
Q

What is an open reading frame?

A
  • DNA or RNA sequence that contains a run of codons UNINTERRUPTED by a STOP codon
  • OR a stretch of codons BETWEEN TWO STOP CODONS
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13
Q

All coding sequences are ORFs BUT…..

A
  • NOT all ORFs are coding sequences
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14
Q

Can a coding sequence fall within a longer ORF?

A
  • YES!
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15
Q

By chance, when will a STOP codon occur?

A
  • ONCE every 21 codons
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16
Q

In the SIMPLEST case (and not in all cases) in what 3 ways can we tell if an ORF is part of a protein coding sequence?

A
  • It needs a START codon (Met)
  • Should consist of codons commonly observed in authenticated genes from organism (codon usage)
  • Needs a STOP codon
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17
Q

If a sequence has multiple ATGs (Met-START) residues, what additional information do we need to tell us where a genes coding sequence starts?

A
  • LOOK AROUND FOR SEQUENCE MOTIFS
  • such as PROMOTER
  • or RIBOSOME BINDING SITE
18
Q

What is a consensus sequence?

A
  • A virtual sequence which shows the most COMMONLY found base at each particular position in a motif.
  • e.g. In PROMOTERS, this is the optimal sequence for binding RNA pol.
19
Q

What are examples of Consensus sequences (DNA sequence motifs) ?

A
  • Transcription Initiation and control sites (promoters and enhancers)
  • transcription termination sites
  • RNA splicing signals
  • Ribosome binding
20
Q

What is an example of Repeats and palindromes (Motifs)?

A
  • Restriction endonuclease recognition sites
21
Q

What are 3 reasons for repeats and palindromes having biological significance? *******

A
  1. Provide binding sites for proteins
  2. Indicate the presence of mobile genetic elements
  3. Contribute to single stranded nucleic acid secondary structure
22
Q

What are the specific steps for gene annotation?

A
  • IDENTIFY GENES–> Presence of ORFs, codon usage, transcriptional + translational control regions (promoters, terminators, ribosome binding sites)
  • Work out the AMINO ACID sequence of encoded PROTEIN
  • Identify structural elements (intron/exon boundaries or stem loops)
  • Identify MARKERS (Cleavage points for restriction endonucleases)
  • Identify ALLELES and MUTATIONS
23
Q

What is transcription carried out by in prokaryotes (which polymerase)?

A
  • DNA- dependent RNA polymerase
24
Q

What are two sections of a DNA sequence that allow transcription to start and stop respectively?

A
  • Promoter and terminator
25
Q

What are 4 things RNA is useful for?

A
  1. Transcription–> termination, splicing, transport
  2. Regulation of RNA stability
  3. Translation–> initiation, elongation, termination, regulation
  4. Catalysis
26
Q

What are two types of structures RNA can adopt?

A
  • Secondary interactions (local regions of duplex RNA)

- Tertiary interactions (Joining DISTANT elements of the SAME chain + BRING TWO CHAINS TOGETHER)

27
Q

How do we identify the most stable structure that RNA will form?

A
  • THERMODYNAMICS delta G–> the more energy released (-ve) the more stable the strucutre
28
Q

What is the optimum loop size and why?

A
  • 7bp because it isn’t too large or too small
29
Q

What are 4 RNAs that are common to BOTH prokaryotes and Eukaryotes?

A
  • mRNA
  • rRNA
  • tRNA
  • Antisense RNA
30
Q

What are 3 RNAs that are ONLY PRESENT IN EUKARYOTES?

A
  • MiRNA
  • snoRNA
  • siRNA
31
Q

How does mRNA ensure that genetic information is used efficiently? (3)

A
  1. Only the NECESSARY genes are ACTIVE thus saves energy
  2. Amount of gene product (protein) EASILY CONTROLLED and varies from gene-gene
  3. DISTINCT proteins can be synthesized from single gene via mRNA modification (SPLICING)
32
Q

What is Kozak’s sequence?

A
  • A consensus sequence important for initiation of transcription GCC(A/G)CCAUGG
33
Q

What is the distribution of miRNAs?

A
  • 50% are from non protein coding genes and the others are in the INTRONS of coding genes
34
Q

Is eukaryote mRNA and prokaryote mRNA from precursor RNA respectively?

A
  • Yes and No
35
Q

Does eukaryote mRNA and prokaryote mRNA adopt a secondary strucutre?

A

Yes and yes

36
Q

Do eukaryote mRNA and prokaryote mRNA have 5’UTRs?

A

Yes and Yes

37
Q

Do eukaryote mRNA and prokaryote mRNA have 3’ UTRs?

A

Yes and Yes

38
Q

Do eukaryote mRNA and prokaryote mRNA have multiple ORFs?

A

Yes and Yes

39
Q

Are eukaryote mRNA and prokaryote mRNA regulated by miRNA?

A
  • Yes and No
40
Q

Do eukaryote mRNA and prokaryote mRNA have a single initiation codon only?

A
  • Yes and No
41
Q

Do eukaryote mRNA and prokaryote mRNA have an operon?

A
  • No and Yes
42
Q

Is eukaryotic RNA and prokaryotic mRNA unstable?

A
  • No and Yes

BMS2062 (7 decks)

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