L1 Central Dogma of Molecular Biology and Genetics Flashcards
What are the functions of nucleic acids?
storage (in mostly DNA, retrovirus useRNA), expression and transmission of hereditary info
What are nucleotides?
monomeric units of DNA and RNA
what is the structure of a nucleotide (common to all)?
phosphate group linked by a phosphoester bond to a pentose sugar that is linked to an organic base
Ph –[PhE bond]–pentose—base
where is the phosphate esterified to and how?
the C5’ of pentose sugar by ester bond (phosphoester bond)
where does the N-glycosidic bond attach?
to the 1’ position of the sugar in both DNA and RNA
if the C2’ position of the pentose sugar has a hydroxyl group, what does that mean?
it is a ribonucleotide – ribose was used as sugar in this example
it would be deoxyribonucleotide is there was hydroxyl group…
what is the structure of purines and what are examples?
bicyclic
adenine and guanine
what is the structure of pyrimidine and what are examples?
6 member ring
uracil, thymine, cytosine
what bases are found in DNA?
A,T,G,C
what bases are found in RNA?
A,T,U,C - uracil replaces thymine
what catalyzes phosphodiester bonds?
DNA/RNA Polymerase … also, by DNA Ligase (+ATP)
The 5’ ____ group of one residue becomes linked to the 3’___ group of the next.
CH2, OH
what does the directionality of the phosphodiester bond tell us?
that polynucleotides have one end that is a 5’ phosphate and the other end is a 3’ OH
are sugar phosphate backbones hydrophilic or hydrophobic?
hydrophilic (water loving) - N and O atoms on the base edges may interact with surrounding water molecules!
Are the faces (flat sides) of the sugar phosphate backbones hydrophillic or hydrophobic?
hydrophobic - they interact with one another and produce base stacks which are physically and chemically stable (no free space between) = good interactions!
what is the charge of the phosphate backbone at physiological pH?
negatively charged
how many hydrogen bonds does G and C have?
3
how many hydrogen bonds does A and T have?
2
what are 2 characteristics of the two right handed helical polynucleotide chains in DNA?
complementary and anti-parallel
where do the DNA strands make contact and where?
through H bonds formed at the hydrophillic edges of bases
between what base pairs does DNA hydrogen bonding occur effeciently?
between A and T, G and C
*the bases can only pair this way if the 2 chains that contain them are anti-parallel to eachother = complementary
what is Chargaff;s Rule?
calculate the amount of bases…
35% A - then you have 35% T and 15% C and 15% G
What is the structure of mRNA and what is the function?
linear, single-stranded molecule
carried codon info for translation
ribose instead of deoxyribose - you have an 2’OH group
what does RNAse enzymes do?
they want to destroy RNA because its only meant to be a messenger… they shouldn’t be around for a long time
human mRNA - used and degraded within hours to day
bacterial mRNA - used and degraded within minutes
the DNA code of an individual is relatively ___ for the lifetime of the organism
stable
what are the post-transcriptional modifications of mRNA in Eukaryotes?
- transcription by RNA polymerase II
- addition of 5’ cap
- Addition of 3’ poly A tail
What are the steps involved with capping the 5’ mRNA in eukaryotes by the addition of a 7-methyl-guanosine?
- phosphatase removes 1 phosphate group from the 5’ end of the nascent RNA
- 5’ to 5’ triphosphate linkage (unusual to eukaryotes) - guanyl transmethyl transferase
- methylated
- methylated again
what is the function of the 7-me G-5’ mRNA cap?
- regulates export of mRNA out of the nucleus - mature mRNA is exported in complexes that contain cap binding complex (CBC) at the 5’ end and RNA binding proteins along the rest of the sequence - no capping, no export
- required for the efficient translation of the mRNA into protein – the CBC facilitates recognition by the translation initiation machinery
- CAP and the CAP binding protein slows 5’ degradation of the mRNA–blockage of the de-capping enzymes to the cap increased half life of mRNA
what are the functions of the 3’ mRNA poly A tail?
- increases the half life of the mRNA by protecting it from enzymatic degradation in the cytoplasm - poly A binding protein (PABP) binds to poly A tracts, aids in transcription termination, protects mRNAs from ribonuclease attack.
- PABP interacts with stuff at the 7-Me-G CAP - aids in export of the mRNA from nucleus, promotes the circularization of eukaryotic mRNAs which stimulates translation
protein coding sequences (exons) of eukaryotic genes are interrupted by what?
non-coding sequences (introns)
*note both introns and exons are transcribed, but introns are spliced out…
how large can introns be?
10 - 100,000 bp
when does most mRNA splicing take place?
transcription
where does mRNA splicing take place?
splice junctions located on the 5’ and 3’ end of the intron
what is a consensus sequence?
6-8 conserved nucleotides of the splice site
what does the 5’ splice donor sequence always have?
GU sequence
what does the 3’ splice acceptor always have?
AG sequence
how many introns does each splicing event remove?
1 intron per splicing event
how does intron removal begin?
cleavage at the 1st intron/exon junction (5’) = lariat structure
how does the lariat structure form?
the 5’ splice donor links to the invariant A within the intron
what holds everything together during intron removal/lariat structure etc.?
spliceosomes!
what percent of human genes are spliced in alternative ways? What does this allow?
60%
production of a different set of mRNAs - different proteins to be produced from the same gene!
- altered function, tissue-specific isoforms, alt. intracellular localization, membrane-bound and soluble isoforms
-1 gene, many proteins = alt. splicing!
what is RNA editing?
when a codon within mRNA can be edited — Change C to U etc.
Example - Apo-B100 (CAA -glutamine) and Apo-B48 (UAA - termination codon=shorter)
what does RNA Polymerase I do?
- rRNA genes (nucleoli)
- most abundant RNA in cells
- protein synthesis machinery
what does RNA Polymerase II do?
- mRNA from all protein-coding genes and some snRNAs
- inhibited by alpha-amanatin (poison deathcap mushroom)
what does RNA polymerase III do?
- tRNA genes and some snRNAs
- 2nd most abundant RNA in cells
- tRNA is the adaptor molecule between nucleic acids and peptide
what are the eukaryotic promoters?
- CAAT
- TATA (most common)
- GC Box
- they bind to transcription factors, not to RNA polymerase II directly…
what does eukaryotic RNA polymerase require?
transcription factors
- cannot bind DNA alone
what are enhancer sequences?
can also affect transcription - proteins bind to them
may be very far away but they can function by DNA looping
when are most TF released?
prior to transcription initiation
what are the roles of enhancers in increases basal levels of transcription?
- cis-acting DNA sequences on the same chromosome
- increase rate of transcription by RNA pol II
- bind to a type of TF called an activator using its sequences called ‘response elements’
- by bending/looping, the DNA activators can interact with both the enhancer sequence and TFs and RNA pol II at promoters and stim. transcription
- sequences far away can help regulate a gene
how is mature mRNA exported to the cytoplasms from the nucleus?
via nuclear pore – to be translated into a protein
