PART I: THE CENTRAL DOGMA OF MOLECULAR BIOLOGY Flashcards
What is a coding sequence?
- A stretch of DNA that encodes a protein
How many possible reading frames are there in double stranded DNA?
- 6
Which strand of DNA is reading frame 4?
- On the second strand of DNA read backwards (from right to left)
How many possible reading frames are there in any DNA sequence?
- 3
What is the initiation codon in many DNA sequences?
- ATG (AUG)
What are the 3 termination codons?
- TAA
- TAG
- TGA
How many codons are available to encode 20 amino acids without the termination codons?
- 61
How does redundancy commonly occur?
- By varying the THIRD base of a codon
How do DNA accents arise?
- By EITHER variations in codon usage OR preference
e. g. Arg codon in yeast is biased towards AGA
What effect can deletion or insertion of 1 or 2 nucleotides have on the DNA?
- It can alter the reading frame
What effect can deleting 3 nucleotides or adding one codon have on the reading frame?
- Maintains the reading frame
- NO change
What is an open reading frame?
- DNA or RNA sequence that contains a run of codons UNINTERRUPTED by a STOP codon
- OR a stretch of codons BETWEEN TWO STOP CODONS
All coding sequences are ORFs BUT…..
- NOT all ORFs are coding sequences
Can a coding sequence fall within a longer ORF?
- YES!
By chance, when will a STOP codon occur?
- ONCE every 21 codons
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?
- It needs a START codon (Met)
- Should consist of codons commonly observed in authenticated genes from organism (codon usage)
- Needs a STOP codon
If a sequence has multiple ATGs (Met-START) residues, what additional information do we need to tell us where a genes coding sequence starts?
- LOOK AROUND FOR SEQUENCE MOTIFS
- such as PROMOTER
- or RIBOSOME BINDING SITE
What is a consensus sequence?
- 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.
What are examples of Consensus sequences (DNA sequence motifs) ?
- Transcription Initiation and control sites (promoters and enhancers)
- transcription termination sites
- RNA splicing signals
- Ribosome binding
What is an example of Repeats and palindromes (Motifs)?
- Restriction endonuclease recognition sites
What are 3 reasons for repeats and palindromes having biological significance? *******
- Provide binding sites for proteins
- Indicate the presence of mobile genetic elements
- Contribute to single stranded nucleic acid secondary structure
What are the specific steps for gene annotation?
- 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
What is transcription carried out by in prokaryotes (which polymerase)?
- DNA- dependent RNA polymerase
What are two sections of a DNA sequence that allow transcription to start and stop respectively?
- Promoter and terminator
What are 4 things RNA is useful for?
- Transcription–> termination, splicing, transport
- Regulation of RNA stability
- Translation–> initiation, elongation, termination, regulation
- Catalysis
What are two types of structures RNA can adopt?
- Secondary interactions (local regions of duplex RNA)
- Tertiary interactions (Joining DISTANT elements of the SAME chain + BRING TWO CHAINS TOGETHER)
How do we identify the most stable structure that RNA will form?
- THERMODYNAMICS delta G–> the more energy released (-ve) the more stable the strucutre
What is the optimum loop size and why?
- 7bp because it isn’t too large or too small
What are 4 RNAs that are common to BOTH prokaryotes and Eukaryotes?
- mRNA
- rRNA
- tRNA
- Antisense RNA
What are 3 RNAs that are ONLY PRESENT IN EUKARYOTES?
- MiRNA
- snoRNA
- siRNA
How does mRNA ensure that genetic information is used efficiently? (3)
- Only the NECESSARY genes are ACTIVE thus saves energy
- Amount of gene product (protein) EASILY CONTROLLED and varies from gene-gene
- DISTINCT proteins can be synthesized from single gene via mRNA modification (SPLICING)
What is Kozak’s sequence?
- A consensus sequence important for initiation of transcription GCC(A/G)CCAUGG
What is the distribution of miRNAs?
- 50% are from non protein coding genes and the others are in the INTRONS of coding genes
Is eukaryote mRNA and prokaryote mRNA from precursor RNA respectively?
- Yes and No
Does eukaryote mRNA and prokaryote mRNA adopt a secondary strucutre?
Yes and yes
Do eukaryote mRNA and prokaryote mRNA have 5’UTRs?
Yes and Yes
Do eukaryote mRNA and prokaryote mRNA have 3’ UTRs?
Yes and Yes
Do eukaryote mRNA and prokaryote mRNA have multiple ORFs?
Yes and Yes
Are eukaryote mRNA and prokaryote mRNA regulated by miRNA?
- Yes and No
Do eukaryote mRNA and prokaryote mRNA have a single initiation codon only?
- Yes and No
Do eukaryote mRNA and prokaryote mRNA have an operon?
- No and Yes
Is eukaryotic RNA and prokaryotic mRNA unstable?
- No and Yes
