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
