Term
| What are the three steps of elongation of a polypeptide chain? |
|
Definition
1-charged RNA binds to ribosome
2-a peptide bond forms
3-translocation of one codon at a time |
|
|
Term
| Describe the binding of Aminoacyl-tRNA |
|
Definition
1-the anticodon of fMET-tRNA is H bonded to the initiation codon in the P site of the ribosome. The next codon is the A site.
2-the appropriate aminoacyl-tRNA binds to the codon in the A site. This aminoacyl-tRNA is brought to the ribosome with GTP and a protien elongation factor.
3-Screw this i quit |
|
|
Term
| What are the two steps in peptide bond formation? |
|
Definition
1- cleavage of Amino Acid and tRNA at P site.
2-formation of peptide bond b/w freed Amino Acid and acid still held at A site. Catalyzed by peptidyl transferase..how classic. Note one AA is still attached to a t-RNA in the A site. |
|
|
Term
|
Definition
the ribosome moves one codon along the mRNA to the 3' end. The uncharge tRNA moves away from the P site and binds to the E site, blocking the A site until translocation is complete. After translation an Aminoacyl-tRNA with the correct anticodon binds to the A site.
Rinse and repeat till stop sequence. |
|
|
Term
| Describe termination of translation events |
|
Definition
| the ribosome recognizes a stop codon with helper protiens called termination factors (RF factors) events include -release of polypeptide from tRNA at P site -release of tRNA from Ribosome -dissasociation of Ribosomal subunits and RF from the mRNA. The initiating AA (Met) is also cleaved. |
|
|
Term
|
Definition
|
|
Term
| What are the stop codons? |
|
Definition
|
|
Term
| what direction is mRNA translated? |
|
Definition
|
|
Term
| What direction are protiens made in |
|
Definition
|
|
Term
| What does aminoacyl-tRNA synthetase do? |
|
Definition
| Catalyze the attachment of tRNA to AA, yeilding a charged tRNA (aminoacyl tRNA) and a huge headache |
|
|
Term
| What are the three stages of protein synthesis or translation? |
|
Definition
1- Initiation
2-Elongation
3- Termination |
|
|
Term
| Describe Initiation of translation |
|
Definition
| 1-30S subunit binds to mRNA w/ start codon 2- binding of initiator tRNA to start codon |
|
|
Term
| Describe the Shine-Dalgrano sequence |
|
Definition
| a mRNA ribosomal binding site (RBS) 8-12 nucleotides upstream of AUG (5') that tells the ribosomal subunit (30S) where to bind |
|
|
Term
| What are the difference b/w initiation in Eukaryotic and Prokaryotic cells? |
|
Definition
1- Methionine is unmodified in Euk.
2-no Shiner sequences in Euk.
3-Euk has Kozak sequence |
|
|
Term
| What is the Kozak sequence? |
|
Definition
| a short nucleotide sequence that embeds AUG in eukaryotes |
|
|
Term
|
Definition
| macromolecular subunits that make up protiens. Polypeptides are comprised of Amino Acids |
|
|
Term
|
Definition
|
|
Term
|
Definition
| a high weight, nitrogen containing, organic compound of complex shape |
|
|
Term
|
Definition
| a covalent bond b/w the carboxyl group of one AA and the amino group of another AA |
|
|
Term
|
Definition
| NH3+ of AA group, adjacent to alpha carbon |
|
|
Term
|
Definition
|
|
Term
|
Definition
| a set of 3 nucleotides that code for one AA |
|
|
Term
|
Definition
| The set of codons within mRNA that carries the info for a specific AA sequence of a protien |
|
|
Term
|
Definition
| a phenomenom that explains how one anticodon can pair with more than one codon |
|
|
Term
| Define charged tRNA (aminoacyl-tRNA) |
|
Definition
| a tRNA molecule covalently bound to an amino acid |
|
|
Term
|
Definition
| any of the various protiens involved in initiation of translation |
|
|
Term
| Define ribosome binding site |
|
Definition
| the nucleotide sequence in mRNA on which the ribosome becomes oriented in the correct reading frame for initiantion of translation |
|
|
Term
| Define peptidyl transferase |
|
Definition
| Catalytic activity of an RNA component of the Ribosome that forms the peptide bond b/w amino acids during translation |
|
|
Term
| Define termination factor (RF) |
|
Definition
| one of several protiens that recognize stop codons in mRNA and initiate termination |
|
|
Term
| Define polycistronic mRNA |
|
Definition
| mRNA that codes for more than one polypeptide |
|
|
Term
|
Definition
| initiating AA in prokaryotes |
|
|
Term
|
Definition
| The exit site of uncharged tRNA |
|
|
Term
|
Definition
| one of two sites that make peptide bonds b/w AA in elongation, receives AA from the P site |
|
|
Term
| What are the original 4 teenage mutant ninja turtles |
|
Definition
| Leo, Ralph, Donny, and mikey |
|
|
Term
| What did the Meselson-Stahl experiment prove? |
|
Definition
| DNA replicatiion is semiconservative on prokaryotes. |
|
|
Term
| What experiment proved DNA replication was conservative in Eukaryotes? |
|
Definition
| the staining of harlequin chromosomes...(for those of you who dont know, Harlequin was the Jokers shrink, but he drove her nuts and she became psychotic as well, what a wonderful world) |
|
|
Term
| What is semiconservative replication? |
|
Definition
| Replication in which a parental strand of DNA is coupled with a new strand. Thus, one strand of DNA make 2 strands, both strands have a parental and a new strand |
|
|
Term
| What are characteristics of DNA replication? |
|
Definition
| DNA replication is semiconservative, semidiscontinuous, and bidirectional |
|
|
Term
| What are the 4 components of DNA polymerase? |
|
Definition
magnesium ion
a DNA template
DNA polymerase
the 4 dinucleotide triphosphates |
|
|
Term
| Which direction is the new strand synthesized in? |
|
Definition
|
|
Term
| What does DNA polymerase do? |
|
Definition
| catalyzes the formation of phosphodiester bonds b/w the 3'OH group of the last nucleotide added and the 5' phosphate of the next dNTP precursor |
|
|
Term
| What does DNA Pol 1 and 3 do? |
|
Definition
| DNA replication in 5'-3' direction of Parental strand, has exonuclease activity in 3'-5- direction, 1 has exonuclease activity in the 5'-3' direction |
|
|
Term
| What does DNA Pol 2,4 and 5 do? |
|
Definition
|
|
Term
| What are the enzymes responsible for DNA synthesis in order used to replicate DNA? |
|
Definition
1-DNA Helicase unwinds DNA at origin of replication
2-DNA primase binds to helicase and makes short RNA primer
3-RNA primer is extended by DNA Polymerase
4-removal of primer |
|
|
Term
| What enzyme lengthens RNA primers? |
|
Definition
|
|
Term
| What do single strand binding protiens do? |
|
Definition
| stabalizes strands, prevents reanneling, keeps strans seperate |
|
|
Term
| What is the leading strand? |
|
Definition
| Strand of parental DNA that is in the 3'-5' direction thats complement in sythesized continuously. It only requires one primer |
|
|
Term
| what is the lagging strand? |
|
Definition
| strand of parental DNA in the 5'-3' direction thats complement is synthesized disomtinuously, requires multiple primers |
|
|
Term
|
Definition
| helps join okazaki fragments along with DNA Pol1 that removes the Primer |
|
|
Term
|
Definition
| relives tension in DNA produced by replication fork |
|
|
Term
| Unwinding DNA that is circular induces negative supercoils, how is this problem solved? |
|
Definition
| Topoisomerases induce negative supercoils |
|
|
Term
| How many origins of replication do prokayotes and eukaryotes have? |
|
Definition
|
|
Term
| Describe initiation of replication in Eukaryotes |
|
Definition
-in G1 phase, protiens assemble on the replicator to form Pre-RC
-Origin recognition complex (ORC binds to replicator)
-cdk's activate pre rc's but inhibit formation or new pre rc's.
-nonactive cdk's present in G1 allow formation of pre rc's, active all other times
-pre rc's are activated to initiate replication when S cycle hits |
|
|
Term
| What is the 3 DNA Pol's and funcions in euakaryotic cells? |
|
Definition
α: primase plus low processivity polymerase
δ: both leading and lagging strand synthesis
ε: may be used in lagging strand synthesis |
|
|
Term
| When does transcription and translation of synthesis of histones take place |
|
Definition
transcription-G1
translation-S |
|
|
Term
| What are the subunits of DNA Pol 3 |
|
Definition
Minimal core_ with catalytic activity – 3 subunits α,ε, θ (alpha, epsilon , theta)
τ (tau) subunit – dimerization of the catalytic core, increased activity
Hexamer – can synthesize short DNA sequences, tend to fall off DNA, dissociate
β subunit – _dimeric clamp_, keeps it attached to DNA but allow to move easily, slide |
|
|
Term
| What are the 3 stages of DNA replication? |
|
Definition
_Inititaion_– unwinding of DNA helix and stabilization
_Elongation_– synthesis of new DNA strands
_Termination__– formation of a newly synthesized strand |
|
|
Term
|
Definition
| Replisome – replication apparatus moving along DNA molecule _@ replication fork |
|
|
Term
| What is a replication bubble? |
|
Definition
| a locally unwound region of DNA bound by replication forks at which DNA synthesis proceeds in opposite directions |
|
|
Term
| What is an initiator protien? |
|
Definition
| protien that binds to the replicator, stimulates unwinding of DNA, recruits other protiens for initiation of replication |
|
|
Term
| What is an initiator protien? |
|
Definition
| protien that binds to the replicator, stimulates unwinding of DNA, recruits other protiens for initiation of replication |
|
|
Term
|
Definition
| the protion of RNA polymerase that is the active Enzyme |
|
|
Term
| What is the central dogma? |
|
Definition
| DNA--> RNA via transcription-->protien via translation |
|
|
Term
| What is required for RNA synthesis? |
|
Definition
| magnesium,Ribonucleotides are used instead of deoxyribonucleotides, no primer |
|
|
Term
|
Definition
| codes for the AA sequence in a polypeptide |
|
|
Term
|
Definition
|
|
Term
|
Definition
| RNA molecules along with protiens tht make up ribosomes |
|
|
Term
|
Definition
| only in eukaryotes, that associate with certain proteins to for small nuclear ribonucleoprotein particles |
|
|
Term
|
Definition
|
|
Term
| What direction is mRNA synthesized in in? |
|
Definition
|
|
Term
| What are some similarities of RNA polymerase and DNA polymerase? |
|
Definition
Uses nucleoside 5'-triphosphates (NTPs) as precursors
Catalyzes phosphodiester bond between NTPs
Uses DNA _as template_
Base pairing determines correct base
Growth of nucleic acid chain only in _5’-3’_direction
Growing strand _antiparalell and complimantary_ to template strand |
|
|
Term
| What are some differences of RNA polymerase and DNA polymerase? |
|
Definition
uses ribonucleoside 5'-triphosphates instead of deoxyribonucleoside 5'-triphosphates (ATP, GTP, CTP, UTP)
can initiate the start of a new strand de novo _no primer needed_
a single strand of RNA is produced (only one strand of DNA used for RNA synthesis: the __DNA template strand__with complementary base sequence)
only short stretches of DNA are transcribed
Only one RNA polymerase to make all RNA, i.e., mRNA, rRNA, and tRNA |
|
|
Term
| What consists of RNA Polymerase holoenzyme? |
|
Definition
2 identical _alpha subunits_ and 1 each of _beta, beta’, and sigma_.
The sigma subunit dissociates from the enzyme easily - leaves shortly following initiation, critical for recognition of start of gene. |
|
|
Term
What consists of RNA Polymerase core enzyme?
Prokaryotic |
|
Definition
| core enzyme: 2 alpha, 1 beta and 1 beta' |
|
|
Term
|
Definition
| The regions of DNA that bind RNA polymerase , consensus sequnces,Control the efficiency of transcription |
|
|
Term
|
Definition
| The regions of DNA that bind regulatory proteins,are short inverted repeats,bind such that they prevent RNA polymerase binding or movement |
|
|
Term
Were are the 2 promoters and what makes them?
Prokaryotic |
|
Definition
| TATAAT, 10 nucleotides upstream if initiation site ( - 10 region), _”Pribnow Box” TTGACA, - 35 region cis-acting elements (next to or on the same side |
|
|
Term
| what are the sequences of transcription? |
|
Definition
Initiation
Elongation
Termination |
|
|
Term
|
Definition
| Positive regulator proteins_often interact with the RNA polymerase and stabilize it at poor promoters that do not closely match the consensus sequence |
|
|
Term
| What are the steps in mRNA synthesis initiation? |
|
Definition
1-template binding
2- DNA unwinding
3-dissociation of subunit after 10 bp are made
4-core E complets transcrition |
|
|
Term
| What happens in Elongation? |
|
Definition
the thing is elongated-duh
RNA Polymerase untwists DNA as it goes
has 2 proofreading mechanisms..exonuclease activity and excision |
|
|
Term
|
Definition
The core enzyme encounters _a termination signal_
_RNA_ is released from DNA template and from the enzyme
_RNA polymerase_dissociates from DNA
Enzyme reaches specific nucleotided sec (termination signal ~40bp in length)
Sequence transcribed into RNA
Newly formed transcript folds back on itself forming hairpin secondary structure |
|
|
Term
| what are some differences in prokaryotic and eukaryotic mRNA |
|
Definition
euk mRNA is capped, tailed, and spliced,
also euk has pre-mRNA and Require assistance of other proteins – _transcription factors_– to initiate transcription
.. as if this wasnt hard enough |
|
|
Term
| What are the three RNA Pol's in Eukaryotes? |
|
Definition
RNAP I – synthesis of all _rRNA’s_ except 5S RNA
RNAP II – main enzyme
RNAP III – synthesis of _tRNAs, 5S RNA and snRNAs_ |
|
|
Term
What and where are the promoters in RNA Pol
(eukaryotic) |
|
Definition
Promoter is upstream of the start of the RNA coding sequence, ensures that initiation occurs at same site
TATA box – TATAAAA _at -10_ GC box GGGCGG _at -35_ CAAT box (cat box) GGCCAATCT at -80 Another GC box GGGCGG at -100 |
|
|
Term
| What regulates promoters in Euk transcription? |
|
Definition
|
|
Term
| What is the greatest beer in the world? |
|
Definition
| Shiner Bock, been drinking that for 11 years |
|
|
Term
| Describe initiation in Eukaryote transcription |
|
Definition
Basal transcription factors:
TFIID, contains a TATA-box-binding protein, binds _to TATA box_
TFIIA joins the complex
TFIIB associates _with RNAP II_first, then together they bind to initiation complex
TFIIF has two subunits, one with _helicase activity_, binds to DNA downstream from the transcription start
Two other factors, TFIIJ and TFIIH join the complex
TFIIH has helicase activity and travels with RNAP Ii during elongation creating the _”transcription bubble”_
_Pre-initiation complex_(PIC) is formed |
|
|
Term
| What is the purpose of the 5'-5' linkage of guanine? |
|
Definition
Protection_ of RNA from degradation by nucleases
_Recognition_ by protein factors in translation initiation |
|
|
Term
|
Definition
| filler BS that doesnt code for any AA, usually has 5'-GU-AG-3' |
|
|
Term
|
Definition
| bp that actually code for something like AA |
|
|
Term
| Describe elongation in eukaryotes |
|
Definition
| Once RNAP II is released from initiation complex, it catalyzes _RNA Chain elongation |
|
|
Term
| Describe termination of mRNA synth in eukaryotes |
|
Definition
| After cleavage, poly(A)polymerase adds poly(A) tails – tracts of adenosine monophosphate about 200nt long –polyadenylation The poly(A) tails play an important role in _transport to the cytoplasm and translation |
|
|
Term
| What do poly a tails require? |
|
Definition
a specificity component that recognizes and binds to the AAUAAA sequence
A stimulatory factor that binds to GU-rich region
An endonuclease
A poly(A) polymerase |
|
|
Term
| What do mature mRNA's have? |
|
Definition
5’ cap
A leader sequence or 5’ untranslated region ( 5’-UTR)
The coding sequence
3’-UTR, A trailer sequence
Poly (A) tail. |
|
|
Term
|
Definition
| removal of exons by spliceosomes...how original |
|
|
Term
|
Definition
| a change in one or a few base pairs |
|
|
Term
|
Definition
| the process by which the sequence of base pairs in a DNA molecule is altered. A change in DNA or a Chromosome. |
|
|
Term
| Define Mutation frequency |
|
Definition
| the number of occurences of a paricular kind of mutation,expressed as a proportion of cells or # of individuals in the population |
|
|
Term
| What are the two types of point mutations? |
|
Definition
| base pair substitution and base pair insertions/deletions |
|
|
Term
| What are the two types of base pair substitution mutations? |
|
Definition
|
|
Term
| Explain transition mutation |
|
Definition
exchange of one purine-pyrimidine base pair for another, 4 types
example TA to GC |
|
|
Term
| Explain transversion mutation |
|
Definition
exchange of a purine-pyrimidine base pair to pyrimidine-purine base pair, 8 types
example AT to TA |
|
|
Term
| Explain Missense Mutation |
|
Definition
| mutation in which a base pair change in DNA causes a change in mRNA so that a differnt AA is inserted into a polypetide |
|
|
Term
Define nonsense mutation
( i love this one..nonsense, lol) |
|
Definition
| mutation in which a base pair change in DNA causes the mRNA to code for STOP |
|
|
Term
|
Definition
| bp change that changes a codon in mRNA such that the resulting AA substitution produces no detectable change in function |
|
|
Term
|
Definition
| change in bp that alters codon, but still codes for same AA |
|
|
Term
| Explain frameshift mutation |
|
Definition
| bp are not changed, but added or deleted so that incorrect AA are coded |
|
|
Term
|
Definition
| changes wild type to mutant |
|
|
Term
|
Definition
| changes mutant type to wild type |
|
|
Term
| Define Spontaneous Mutations |
|
Definition
| mutations that occur naturally |
|
|
Term
|
Definition
|
|
Term
| When can spontaneous mutations occur? |
|
Definition
| DNA replication as well as G1 and G2 |
|
|
Term
| What can cause spontaneous mutations |
|
Definition
-tautomerization leading to incorrect base pairing
-depurination, loss of a purine
-deamination, removal of amino group from a base |
|
|
Term
| What causes induced mutations? |
|
Definition
|
|
Term
|
Definition
| typically carcinogens induce bp subtitutions that produce missense or nonsense mutations, or bp additions or deletions that produce frameshift mutations |
|
|
Term
|
Definition
| a test that assays the ability of chemicals to revert mutant strains back to the wild type in salmonella |
|
|
Term
| How does the Ames test work? |
|
Definition
| a His- strain of bacteria is added to a minimal medium plate with liver enzymes. The potential carcinogen is then added. If it is a carcinogen, bacteria will grow, and we'll have a new reason to freak out. |
|
|
Term
| What are the two types of DNA repair? |
|
Definition
1-reversal of damage, termes direct correction or direct reversal
2- my favorite, excision and then new DNA is made |
|
|
Term
|
Definition
| a mutant that affects DNA Pol's proofreading ability |
|
|
Term
| Examples of Direct repair |
|
Definition
-DNA Pol proofreading
-photoreactivation
-ada gene,transfers alkyl groups. |
|
|
Term
| What does DNA Pol have that allows it to proofread? |
|
Definition
| 3'-5' exonuclease activity |
|
|
Term
|
Definition
| a uvr mutant needs light to repair UV damaged thymine. Wild type does not need light |
|
|
Term
| What are the subunits in the NER system> |
|
Definition
|
|
Term
| What do the subunits in the NER system do? |
|
Definition
-UVRA, two of these along w/ UVRB slides along DNA, UVR subunits dissociate if there is aproblem found.
-UVRC binds to UVRB
-UVRB cuts 4 nucleotides to 3' of damaged side
-UVRC cuts about 7 bp to the 5' side.
-UVRB is then released and UVRD binds to the 5' cut
-UVRD unwinds DNA segment freeing damaged DNA
-DNA Pol1 fills the gap
-DNA ligase seals the deal |
|
|
Term
| What are the types of excision repair? |
|
Definition
-NER
-Methyl Directed mismatch repair |
|
|
Term
| Explain Methyl Directed mismatch repair |
|
Definition
1. MutS binds to the mismatch
2. correct base is then determined, the parental strand is methylated, new strand is not
3. MusS forms a complex with MutL and MutH tp bring unmethylated sequence close to mismatch
4. Mut H knicks the unmethylated strand.
5. Excision by exonuclease
6. DNA pol3 and ligase finisher up |
|
|
Term
| how is xeroderma pigmentosum caused? |
|
Definition
homozygosticity (what a word) for a recessive mutation in a repair gene.
people with this cannot repair damage by UV rays. autosomal recessive |
|
|
Term
| What is cockayne syndrome? |
|
Definition
| autosomal recessive, Dwarfism, senile appearance, sensitivity to light, caused by defect in repair mechanisms |
|
|
