Theme 1 Flashcards
What are the functions of DNA
carry info for: RNA and protein synthesis DNA replication and repair recombination transmission to progeny
What are 3 of chargaffs rules
A=#T and #G=#C.
base composition is constant within a species and animal
does not change with age, nutrition or environment
Explain the side chains of alpha helices and beta sheets
Alpha helices N-H and C=O point up and down. side chains point sideways
beta sheets N-H and C=O point up and down, respectively. side chains point perpendicular to sheet
Define a coding sequence
A stretch of DNA that encodes a protein
What is the initiation codon
ATG = methionine
What are the 3 termination codons
TAA, TAG or TGA
What are synonymous codons
codons that code the same amino acid, usually 3rd nucleotide varies.
Some species have preferential use of a specific synonymous codon.
Define an open reading frame
Run of codons between 2 stop codons. Becomes a coding sequence from the methionine start point.
How long does an ORF have to be for it to likely be part f a coding sequence
> 60 codons
What is a DNA sequence motif
a short, recurring pattern in DNA that usually has a biological function
Can be used to determine the definite start of a coding sequence (e.g. just cause something starts with a met doesn’t mean it is a coding sequence)
What are the 2 main sequence motifs we look for
repeats and palindromes
consensus sequences
What do repeats and palindromes do
Provide binding sites for proteins
Indicate the presence of mobile genetic elements
Contribute to single-stranded nucleic acid 2º structure.
What are consensus sequences
A virtual sequence of DNA with similar structure & function in different organisms.
a combination of gene promoters showing the most likely nucleotide at each point in the sequence.
Thought of as the optimal sequence for binding RNA polymerase.
What are the RNA base pairing rules
A pairs with U
G pairs with C (stronger)
G pairs with U (weaker)
What are the reasons why RNA needs to have a structure
transcription: (in termination, splicing, transport)
regulation of RNA stability
translation: (in initiation, elongation termination regulation)
catalysis
What is a 2º and a 3º RNA interaction
2º = local 3º = joins distant parts of the RNA (or different strands)
How do we predict the most stable RNA structure
Calculate the most negative delta G measured in kcal/mol
Describe hairpin formation
Form between complimentary RNA base pairing
Can be imperfect but each mismatch reduces stability
Optimum loop size is 7 bases, becomes less stable if loop part is quite small or large.
What are the types of RNA present in both prokaryotes and eukaryotes
mRNA
rRNA = ribosomal
tRNA
antisense RNA = regulates translation
What are the types of RNA present in eukaryotes only
microRNA: dicer dependent translational regulation
snRNA: small nuclear RNA, function in splicing
snoRNA: small nucleolar RNA, process and modify RNA
siRNA: small interfering RNA, dicer dependent, RNA degradation
Describe tRNA
Has anti-codon arm to recognises codon in mRNA
Attaches to amino acid by aminoacyl synthetase. Called an aminoacyl or charged tRNA
function depends on sequence and 3º structure.
Explain the difference between the coding and template strand
Coding: same as mRNA transcript. If not specified, a sequence is assumed to be a coding strand
Template (non-coding): what is used to produce the mRNA transcript
Outline transcription
template is read 3’ to 5’ and RNA is synthesized 5’ to 3’.
Unwound into 2 strands in RNA polymerase and template strand goes into active site (transcription bubble) and coding strand bypasses.
RNA polymerase adds ribonucleotide triphosphate and a phosphodiester bond is formed.
Outline translation
carried out by ribosomes.
5’ cap binds translational initiation factors (proteins) and the small ribosomal subunit.
small ribosomal subunit moves along mRNA to find the first methionine. rest of the ribosome joins and commences translation.
Activated tRNA enter the E (eject), P (polypeptide) and A (attach) sites.
Outline splicing
takes out introns
Carboxy tail domain (CTD) on RNA polymerase recruits splicing machinery (form splicesome).
Recognises an A considered the branch point of the intron. A forms a bond to 5’ site breaking bond at 5’ site of the intron to exon.
Exon forms bond with next exon at 3’ site of intron breaking the bond and removing the intron.
How is mRNA used efficiently
only necessary genes being active (energy saving)
Controlling the amount of gene product (protein)
modifying mRNA (splicing) to make distinct proteins.
What is an untranslated region (UTR)
Commonly fold into 2º structures and provide binding sites for proteins that stabilise, destabilise or transport mRNA.
What is the function of microRNA
regulate mRNA stability and translation.
Each miRNA forms from a double-stranded precursor that is processed into a short ssRNA that base pairs with a specific target mRNA.
A protein complex (RISC) bound to the miRNA degrades the target mRNA or impedes translation.
One miRNA can control mRNAs encoded by several different genes.
Outline prokaryotic mRNA
Used once by multiple ribosomes then degraded,
5’ and 3’ ends are unmodified and it is not spliced (unstable but polycistronic).
Start codon preceded by binding site called Shine-Dalgano sequence (AGGAGGU).
Outline distinct features of eukaryotic mRNA
Undergoes splicing to remove introns from pre-cursor RNA and create single gene mRNAs (monocistronic).
Exported from nucleus to cytoplasm and used more than once due to stability.
What processes occur on eukaryotic mRNA to ensure stability
7-methylguanosine cap added to 5’ end which is recognized by nuclear export and translational machinery.
As transcription ends, the precursor mRNA is cleaved downstream of the sequence AAUAAA, and a “tail” of As is added to the 3’end (called polyadenylation).
