5 From Gene to Phenotype Flashcards
TF AT has 3 H bonds and CG has 2 H bonds
F, AT has 2 bonds and CG has 3
what is the diff between a nucleotide and a nucleoside
Side= no phosphate
Tide= phosphates
TF DNA stores data very well
T
What is the difference between Ribose (RNA) and Deoxyribose (DNA)
RNA molec has an OH in part of the 5 membered ring, in DNA its just a H
TF RNA uses Uracil not Thymine
T
what are the coding and non coding RNAs
Coding
- mRNA
Non-Coding
- snRNA
- tRNA
- rRNA
- miRNA
what are the details of transcription DNA–>RNA
○ Happens in RNA polymerase
○ Unwinds DNA
○ Creates DNA polymer
○ DNA rewinds
○ mRNA released
what are the details of RNA synthesis
○ Uses ribonucleotide triphosphates
○ U instead of T
○ Only 1 strand of DNA is used as template
○ RNA strands can be initiated de novo (no primer req)
TF RNA is complimentary to the template strand
T
the template strand is read ___to___ and is made __to__
3’ to 5’
5’ to 3’
TF in prokaryotes transcription and translation can happen at the same time
T
why can transcription and translation happen at the same time in proks
Don’t have nucleus so rna doesnt need to leave into the cytoplasm to get translated
○Ribosomes jump on rna strand as it being made
what are the steps to transcription in proks
§ Initiation
□ 2 part
® Rna polymerase binds to promoter (cis regulatory element)
® Then unwinds DNA
§ Elgogation
□ Rna chain grows copying from 3’ to 5’
□ Produces RNA dowm middle while rewinding at the end
§ Termiantion
□ 2 ways
the start of transcription in proks begins with the ___(RNA polymerase binding site)
promoter sequence (TATA Box)
what comes at the end of the promoter sequence in prok transcription
+1 site (the process of transcribing starts here)
what is the start codon
ATG
TF there is a 5’ and 3’ UTR at the beginning and end of the transcription sequence
T
what does UTR mean
untranslated region
what is after the 3’ UTR in prok transcription
3’ Poly A tail
what is intrinsic termination
- GC rich area creates hairpin structure
- Large poly A region created on hairpin
- the As not strong enough to hold on
- Pulls RNA polymerase off
what is factor dependant termination
® Rho protein (trans) binds to Rho utilization site
® Creates ball like structure (same idea as hairpin)
® Disassembles RNA polymerase
what is a cis and a trans element
- Cis element = same side rna sequences, not moving anywhere
- Trans element = across sides, can move anywhere in genome
what is the main role of RNA polymerase 2 in euks
rna transcription
how many rna polymerases are in euks
5 different ones
RNA polymerase 2 is aided by what in transcription
TF (transcription factors)
what are transcription factors + what do they do
□ Proteins that bind dna and help initiate transcription
TF Most promoters contain a TATA box (which is the promoter)
T
what happens in initiation in euk transcription
○ Transcription initition complex made by transcription factors
§ Uses general TFs
what happens in elongation in euk transcription
- polymerase starts synthesis
- CTD (C-terminal domain) recruits mRNA processing proteins
what is CTD made of
phosphorus chain
what are the 3 jobs of CTD
Capping
Splicing
Polyadenylation
what is CTD capping
□ Protect mRNA from nucleases
□ 5’-5’ cap defends the bond that the nucleases want to break (more stability)
□ Prevents degredation
what is CTD splicing
- Introns are removed prior to their transport to the cytoplasm
- the “mature gene” is the final product with the introns removed
what is an intron
non coding sequence
what does splicing allow for
gene variations from a single gene
what are 2 ways splicing happens
- self splice
- RNA/protein complex splicing
what is self splicing
- no protein involved
- no energy req
- Enzyme “ribosime” folds itself and chops
what is RNA/protein complex splicing
◊ Splisosome (Enzymes +snRNAs) recognize introns and splice them
◊ Req energy
a fault in splicing may cause
diseases and mutations
What can splicing do ?
- make multiple proteins froma single gene
what are proteins from the same gene but are spliced differently called
isoforms
what is Polyadenylation
□ Adds poly A tail to end of transcript
□ Happens during elongation
□ Protects mrna with all the As = more stability
what is the final product of transcription in euks (front-mid-back)
5’ cap - only coding sequences - 3’ Poly(A) tail
TF eukaryotes synthesise RNA faster than proks
F, Proks r faster bc theyre a lot simpler
what are the mmain differences between prok and euk transcription
prok
- 1 polymerase
- sigma TFs
- simple transcript
- Final = DNA (almost naked)
euk
- 3 polymerases
- multisubunit general TFs
- Processed transcription (cap,introns,etc)
- Final = chromatin
what are some challenges of euk transcription
□ Hard to located promoters
□ Decoupling makes it harder bc theres more mechanisms
□ Polymerase has more subunits
□ TFs needed
□ Several RNA ploymerases
how do we bind amino acids to tRNAs
- Use enzyme “aminoacyl-tRNA synthetase” (ATS)
□ Binds specific acid to specific tRNA
which ribosome is bigger a prok or a euk
prok
what are the 3 sites of ribosomes
A) Aminacyl binding site
P) Peptidyl binding site
E) Exit site
what is the starting unit of initiation in proks
shine-delgarno sequence
where is the shine delgarno sequence
in the 5’ UTR
in initiation in in euks, the small subunit binds to the _____ in P site and also bind to ________ with help of initiation factors
Met-tRNA
mRNA 5’ cap
what is elongation of translation like in proks (APE sites)
1) Aminoacyl tRNA binds to A site with help if Elongation fators (A site only used in elongation not initiation)
2) Peptide bonds form between AAs with enzyme peptidyl transferase
3) tRNAs translocate (move sites) with help of Tfs
4) tRNAs leave, cycle repeats
what are the steps to termination of translation in proks
○ Release factors bind into A site (Stop codons don’t have tRNA associated with)
○ Polypeptide chain release from ribsome
○ Everything releases and if waiting to be used again
what are the best and worst possibilities for mutations
Silent>3bp>frameshift
what are some traits of the genetic code
○ Nucleuotide triplets code for certain aminoacids
○ Non overlapping
○ Comma free
○ Start and stop codon
○ 64 permutations
○ 20 amino acids
○ Wobble rules
what is the wobble rule
the 3rd spot is less strict on what must be there in a base triplet
what is an antisense RNA (ssRNA)
- single stranded RNA t
○ Template for RNA protein synthesis as template to replicate genome (multiply virus)
○ Accomplished without DNA
○ Can create DNA from RNA (sense + antisense) - Can integrate DNA into hosts genome
□ Uses enzymes called reverse transcriptase
what is a PRION
Protein + Infection
What are some traits of Prions
○ Transmissable
○ Turns brain into dried sponge and u die (mad cow disease)
- Misfolded protein
- Resistant to proteolysis (reshaping of protein)
what is abiogenesis
○ RNA world hypothesis
§ Life may have started as RNA
§ RNA can act like DNA
§ Ribozymes
□ Like proteins but not as efficient
