Theme 1 Flashcards
(31 cards)
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.
