fundamentals of DNA, RNA and proteins Flashcards
dna structure
- double stranded helix
- complementary base pairs
- nuecleotide bases
- hydrogen and phosphodiester bonds
- antiparallel
what is a gene
- stretch of DNA that carries coded info for a sequence of amino acids to build a protein
gene structure
- introns
- exons
- promoter region
- untranslated sequences
- other regulated sequences
DNA organisation
- tightly packed, organised, accessible
- coiled around histones
- packed in chromosomes
- 46 chromosomes in 22 pairs of autosomes and 2 sex chromosomes
what are the parts of the chromosomes
centromere, p arm (at the top), q arm (at the bottom)
what does it mean if chromosomes are metacentric?
the arms are fairly equal in size
what does it mean if chromosomes are submetacentric?
the p arm is shorter than the q arm
what does it mean if chromosomes are acrocentric
there is no visible p arm
how are DNA fragments joined (okazaki fragments)
- DNA primase that uses DNA nucleotides synthesis the primers on the lagging strand
- DNA ligase joins the 3’ hydroxyl with the new strand to the 5’ phosphate of the previous fragment with a phosphodiester bond
main mechanisms in replication that reduce error
- structural differences of purine/ pyrimidines
- proof reading activity of DNA polymerase
- mismatch repair
what is transcription
making RNA from DNA
- uses RNA polymerase II complex and helicase to unwind DNA duplex to form a transcription bubble
transcription factors
- protiens that turn on or off binding to nearby DNA
- binding sites called enhancers of silencers
stages of transcription factors helping transcription
- transcription factor II D binds to the TATA box which allows adjacent binding of transcription factor II B
- TFIID causes distortion of the DNA at the TATA box
- other transcription factors bind along with RNA polymerase II forming a transcription initiation complex
- TFIIH - parts double helix at the transcription start point, exposing template strand
what does the mediator do in transcription
- physically links the transcription factors to other components of the initiation complex to RNA polymerase II
- allows activator protein to communicate with RNA polymerase II
what are the pre-mRNA modification
- 5’ end of pre-mRNA is modifies to form a cap
- 3’ end is adenylated
what are the 3 main sites involved in RNA splicing
- splice donor
- splice acceptor
- branch site
RNA splicing stages
- cut at the splice donor site at the 5’ end of the intron
- cut at the splice acceptor site at the 3’ end of the intron
- this is catalysed by spliceosomes
- matured RNA is then exported from the nucleus into the cytosol and guided through nuclear pore complex
what happens in translation?
- mRNA is translated through complementary codon on a tRNA molecule
- 4 short sections of tRNA, are double helical
- an anticodon binds to the complementary codon on the mRNA molecule
- there is a short single stranded region at the 3’ end where there is an amino acid attachment site
what are the sites of a ribosome
- A site (accepting)
- P site (processing)
- E site (exciting)
how are ribosomes used in translation
- the 2 subunits of ribosomes join together at the 5; end of the tRNA transcript
- mRNA is pulled through the ribosome 3 nucleotides at a time
- codons enter ribosome core the mRNA sequence is translated to amino acids
summary stages of translation
- tRNA binding
- peptide bond formation
- large subunit translocation
- small subunit translocation
what do elongation factors do
- make translation more efficient and accurate
- enter and leave ribosome during each facto
- hydrolyse GTP and GDP
- ensure translation occurs forwards
functions that reduce translation errors
- induce fit
- kinetic proofreading
initiation of translation
- start codon and initiator tRNA are recognised by specific initiator factors due to the unique nucleotide sequence
- loaded into the small subunit with eukaryotic initiation factors
- initiator factors bind to the p site
- small subunit binds to 5’ end of the mRNA and is recognised by the cap
- move 5’ to 3’ to find start codon
5 when found initiation factors dissociate and allow binding of the large subunit to allow protein synthesis and translation
termination of translation
- occurs at the stop codon - UAG, UAA, UGA
- not recognised by tRNA and are not specified by an amino acid
- release factor to recognise the termination codon and elongation stops
things needed in DNA replication
- DNA helicase - hydrolyse ATP
- DNA polymerase
- Sliding clamps - keep it stable and kept on by clamp loader
- RNA primer
- single stranded DNA binding proteins (SSBs) - bind to DNA strand and don’t cover bases, stabilise unwound helix and straighten out
- topoisomerase - release tension to stop coiling
- replication bubble
elongation on the lagging strand
- DNA polymerase releases itself from the clamp then associates at with the clamp at the next RNA primer
- jumps between fragments to synthesis strands
elongation of the leading strand
- RNA primer adds nucleotides one base at a time
- 5’-3’ direction
