Biochemistry Flashcards
What is a pseudogene?
a section of a chromosome that is an imperfect copy of a functional gene
What are some of the functions of junk DNA?
at least 80 % of DNA serves some kind of purpose apparently
- places for proteinsto attach to that infuence gene activity
- strands of RNA with various roles, influencing gene action - non coding
- Places where chemical modification (backbone/methylation/phospharylation) silence stretches of chromosome
Which base is different in RNA?
Uracil instead of thymine
What sugars are in the backbone of DNA and RNA?
DNA - deoxyribos
RNA - ribox
What is the coding strand and the template strand?
Genetic info carried on the coding strand and not the template strand - template strand used for replication of DNA
Where does RNA polymerase attach?
Binds to one or more short sequences upstread of the start of each gene i.e. slightly closer to the 5 prime end (these are the promoter sequences of DNA)
What are the 3 types of RNA polymerase? -
Polymerase I - nucleolar region of nucleus, transcribes
large ribosomal RNA
Polymerase II - mRNA precursors (mostly producing the mRNA)
Polymerase III - small RNAs (tRNA), 5S ribosomal RNA
and other small DNA sequences
What is RNA polymerase composed of?
Several subunits and requires several accessory proteins (transcription factors).
All added to the complex in a defined order to initiate and carry out transcription.
What are basal promoters?
basal promoter contains TATA box and found in all protein-coding genes
What are enhancers?
DNA sequences which can control efficiency
and rate of transcription. Regulate expression of genes in
specific cell type and control timing of gene expression.
Effects can be powerful
Why are promotors and enhancers cis acting elements?
they are on the same molecule of DNA as the gene they regulate
What can changes in promoter strength, deleterious effects on a cell result in?
disease e.g tumours
Where can enhancers be placed?
can be 5’ or 3’ of transcription start site, in introns or even on non-coding strand
Can be thousands of nucleotides away from promoters with which they interact, brought into close proximity by looping of DNA (due to interactions between proteins bound to enhancer and those bound to promoter)
What are activators and repressors?
Protein facilitating looping are called activators and those that inhibit are repressors
How do enhancers affect Transcription factors?
Enhancers contain binding site sequences for transcription factors (TF) and enhance/upregulate transcription.
Active enhancers are bound by activating TF and brought into proximity of target promoters by looping
What are transcription factors?
Transcription factors bind to promoter and enhancer sequences
and recruit RNA polymerase
Why are TF trans acting factors?
they are encoded by a different gene to that being regulated
What does the polymerase enzyme do to the DNA?
it unwinds the double
helix over a short length and splits them apart – “bubble” of
about 10 bases
How can RNA become functional?
base-pair interactions between complementary sequences found elsewhere on same molecule allow an RNA molecule to fold into a three-dimensional structure that isdetermined by its sequence of nucleotides - similar to protein folding, this allows it to have structural and catalytic functions
How is polymerase 1 terminated?
hair pin loop which causes RNA pol to pause and release transcript.
How is polymerase 2 terminated?
Transcription of pol II genes can continue for hundreds or thousands of nucleotides beyond the end of a coding sequence.
Mature pol II mRNAs are polyadenylated at the 3’ end
= poly(A) tail (AAAAAAAAAAA).
- signifies end of RNA sequence
What does the CAP on the 5 prime end do?
stabilize the mRNA,
essential for transport of RNA out of nucleus
PROTECTS RNA FROM DEGRADATION
Serves as assembly point for proteins needed to recruit
small subunit of ribosome to begin translation
What is altenative splicing?
Different parts (introns and exons) of the same sequence can be removed to make different sequences i.e. one exon may be removed in one sequence but kept in in another so different proteins produced from the same gene by alternative splicing
- gives us diversity
alternative selection of splice sites within a pre-mRNA - leads to production of different mRNA isoforms of a gene
- alters composition and function of encoded protein
- plasticity allows for disease development –cancer
What is a spliceosome?
The enzyme that does the splicing