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Genetic Princeton

QuestionAnswer
Why are DNA and RNA considered nucleic acids? Because they are in the nucleus and have acidic phosphate groups
Building blocks of DNA deoxyribonucleoside triphosphate (dNTP)
Components of dNTP monosaccharide (ribose, namely, deoxyribose), aromatic base (A,G,C,or T), phosphate group
Why are the aromatics in the dNTP considered aromatic BASES? becuase the nitrogens have free electron pairs
Precursor for G and A Purine
Precursor for T and C. mnemonic Pyrimidines (mnemonic, pyrimids CUT. U for uracil)
What kind of bond is between the aromatic base and ribose? B-N-glycosidic linkage
In beta configuration, is the molecule attached to the sugar above or below? above, balloon :)
nucleotide vs nucleoside. what are the two ways to say dNTP? nucleoside: sugar + aromatic base ][ nucleotide: sugar + base + phosphate ex. deoxyribonucleoside triphosphate is also deoxyribonucleotide
What part of dNTP would enzymes interact with? think bitch. aromatic bases because they are varient
Draw a rough dNTP look at pg 60 if youre too much of a bitch to remember
What is coupled to the polymerization of nucleotides to make it favorable? pyrophosphate is hydrolyzed, driving the polymerization to a more favorable deltaG
oligonucleotide vs polynucleotide? oligo - some poly - hella
What kind of bonds are nucleotides linked by ? Phosphodiester bond
In what direction are polynucleotides written? 5'-3'
What is the charge of the phosphate group between nucleotides? How does that effect the stability of the stands? negative, causes electrostatic repulsion between P-groups, making it more likely to break than if the charges were neutralized. *remember that ds is more stable than single strand
Pyrimadines and Purines (mneumonic) pyramids CUT, Pure As Gold
Term for binding complementary DNA structure to another single strand. Term for separating? Annealing/Hybridization, Melting/Denature
How many bonds does AT have? how are they bonded? 2, hydrogen bond
How many bongs does GC Have? how are they bonded? 3, hydrogen bond
What's the complement to GCTT AAGC, it's in this order because 5' is already read first
What groups of dNTP are the backbone to the dsDNA phosphate and ribose
how many basepairs/angstroms per full turn of the double helix? 10bp, 34A
how many meters is an Angstrom? 10^(-10)
What is a genome? as in, what is it composed of? several very large DNA
How many chromosomes in prokaryotes? 1 ring shaped chromosome (10^6 vs eukaryotes 10^9bp)
Is there a correlation between evolutionary sophistication and genome size? no
How do prokaryotes store their DNA (into a more stable form)? What enzyme is used? They use DNA gyrase to "super coil" their ring chromosome since dsDNA is fragile in its unwoven state
How is eukaryote DNA packaged? double stands are wraps around histones, 8 wraps is a nucleosome, nucleosomes make chromatin, chromatin makes up chromosome
Are histones basic or acidic? why? basic, because the exterior of dsDNA is acidic
Flow chart from deoxyribose -> chromosome pg 66
What is the Central Dogma of molecular biology? DNA -> RNA -> protein (unilateral flow)
Genetic code vs. codon genetic code is language spoken by DNA and RNA, the codon is the 3 base code that translates to an amino acid
What direction is the template read? 3' -> 5' because you can only polymerize 5' -> 3'
Nonsense Codon When a mutation causes a codon to be read as a stop codon as opposed to an AA
Synonym Codon Some amino acids have multiple corresponding codons (i.e. Tyrosine can be read UAU or UAC) but there is no ambiguity in reading DNA, each code signifies 1 AA
Intercalating Mutation due to a purine/pyrimidine looking molecule slipping between BASE PAIRS
Mutagen shit that causes mutations
What kinds of mutations cause frameshift mutations? (insertion, point, and/or deletion) insertion and deletion
Missense mutations, nonsense mutations and silent mutations are what kinds of mutations. what do each of them mean? They're all point mutations. Missense: changing amino acid, Nonsense: changing AA to stop codon, Silent: changing codon to same AA
Transition (point mutation) Changing a PYR -> PYR or PUR to PUR
Transversion (point mutation) Changing PYR <-> PUR
Conservative Mutation Missense that does little to the protien structure because changed AA has similar qualities
Are all insertions and deletions frameshift? no, because you can add/delete WHOLE codons. *but frameshifts are hella dangerous
DNA is Conservative/semi conservative/dispersive Semi: because each daughter cell has 1/2 original template
DNA polymerase function. driving force? (what reaction drives it?) Elongates new ds using parent template. phosphate hydrolysis (removing a pyophosphate)
Rules for polymerization 1. always 5->3, so read 3->5 2. Needs Primer
Helicase function. Where does it begin to act? Unzips DNA, acts at specific sequence, origin of replication
Topoisomerase function Cuts DNA stands to release tension made from helicase
Single strand binding protein stabilizes DNA after being unwound by helicase (single stands are unstable)
New ssDNA is made towards what end of the template? 5' (because needs to be made 5 -> 3 in antiparallel manner
Okazaki fragments lagging strand, DNA can only be synthesized 5-3, and so when the helicase unwinds, one of the strands is unzipping 5->3, and since the DNA poly needs to be read 3->5 then it has to reprime constantly, making 'fragments' of complimentary DNA
As replication fork grows, does Helicase have to continue to unwind? YES
Eukaryotic Replication (Replication bubbles). why? because it is large and working on multiple origins of replication at once makes the new DNA much quicker
How do prokaryotes replicate? or rather, what's the mechanism called? Theta replication (because replicating the prokaryote makes it look like a theta symbol)
3 types of
DNA polymerase III Prokaryote: Primary 5->3 replication, also 3-5 proof reading
DNA polymerase II Prokaryote: Unknown
DNA Polymerase I Prokaryote: primary role is to remove RNA primer via exonuclease 5-3. also, polymerase activity for that primer portion
Difference between RNA to DNA? (Base, sugar, strand) Uracil, Ribose as opposed to deoxyribose, single stranded
Prokaryotes are polycistronic. what does that mean? It means they have mRNAs that encode for more than 1 polypeptide, unlike eukaryotes who have 1:1
tRNA function, about how many kinds are there? move AA to ribosome. there are anywhere from 20 (# of AA) to 61 (# of codons)
Does both replication and translation need a primer? NO, RNA polymerase (replication primer/ primase) is made of RNA. so RNA does not need a primer
Promoter. what is it. RNA or DNA? Starting Signal sequence of RNA polymerase
*transcription is the principle site of gene expression regulation because it determines the amount of protein in both eukaryotes and prokaryotes
DNA is to Origin as RNA is to __ start site
Is the transcribed strand of DNA the Antisense/noncoding, or sense/coding? antisense/non coding because it doesn't correspond to the mRNA, it is complement to it which does not mean the same thing
Once mRNA is transcribed, is it ready for the ribosome? only in prokaryotes, eukaryotes need continued processing
During RNA polymerization, which direction is upstream and which is downstream? and which is negative, and positive? **pg 78, shit's confusing Upstream is towards the template's 3' because thats where the 5' of the new RNA is. Upstream is also negative because it's in the opposite direction of unzipping.
Prokaryote Transcription 3 steps 1.initiation 2. elongating 3. termination
does the OAT book cover prokayotic transcription in detail? check it bc MCAT doesn't say to memorize it. watch youtube video also if so. does it talk about the lac operon?
What unwinds prokaryotic dna during transcription? RNA polymerase
Eukaryotic replication vs prokaryotic? Eukaryotes have replication bubbles, Prokaryotes use DNA Poly I,II,III and use the theta mechanism.
Differences btwn Pro and Euk transcription. location, mRNA transcription, RNA polymera
RNA polymerase I-III is to ___ as DNA polymrase I-III is to ____ Eukaryotes (RNA), Prokaryotes (DNA)
Prokaryotes vs Eukaryotic transcription location Cytoplasm, nucleus
Prokaryote transcription and translation timing consequence from being able to occur in both the cytoplasm happens simultaneously
Eukaryotic RNA polymerases (I, II, III). what types of RNA does each synthesize? mneumonic aRe eMTy I: rRNA II:mRNA III : tRNA
hnRNA. wtf is it? pre mRNA. needs to be processed (spliced) before it's mRNA
What is spliced and added to hNRNA to make transferable mRNA? where are the constituents added? splice the introns (as opposed to the EXons, EXpressed), and add CAP to 5' and poly A to 3'
What does the Cap and poly A tail function as? tRNA signal and prevents exonuclease from eating the mRNA up
Question on pg 83
Question on 84, the f?
Enhancers and Sequence specific transcription factor. Where is th enhancer located? Regulation of eukaryotic transcription. Enhancer can be upstream OR downstream.
Anti codon of tRNA function complement mRNA sequence to attach the corresponding AA.
3 letter code for amino acid binding site. constant with every AA CCA at 3' end
Reactions to get amino acid onto tRNA and then as a polypeptide ATP attatches to AA making Aminoacyl AMP (lose 2Pi). AAA is then able to load onto tRNA (unfavorable) by destruction of AMP (favorable). AA and tRNA bond is then broken to power peptide bond formation
Aminoacyl-tRNA synthetase function binds corresponding AA to tRNA. very specific
Amino acid coupling with tRNA is called Amino Acid Activation. what are the 2 functions? (1 obvious, 1 not) 1. specific AA delivery to tRNA 2. thermodynamic activation (peptide bond formation is unfavorable unless coupled with hydrolysis of tRNA and AA)
How many ATp equivilents does it cost to drive amino acid + tRNA -> peptide bond reaction? 2 ATP. (AMP + 2 high energy Pi bonds)
Euk or Pro have a bigger Ribosome? how many pieces are ribosomes in in the cytoplasm? Euk, 2 pieces
Ribosomes have 3 binding sites. names/letters and function A: tRNA deliver P: polymerize E: tRNA leaves
Do prokaryotic ribosomes need to start translating from the end? and which end is that? 5'. No, we know that because prokaryotic mRNA is polycistronic and may need to translate a particular polypeptide. in fact it never translates from the end end. see next flash card
Ribosomes have ___ instead of a promoter upstream ribosome binding site / Shine-Dalgarno sequence
Created by: nqbui