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Biochemistry and Genetic Flow
Gene flow and mechanisms are explored
128
Biology
Undergraduate 3
11/29/2009

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Term
Define Nucleotide
Definition
Base, Sugar & Phosphate
Term
What is the difference between RNA and DNA.
Definition
RNA is missing a 2' -OH whereas DNA has the 2' -OH
Term
Why is it important that the DNA backbone is negatively charged?
Definition
The negative charge repels nucleophiles in solution.
Term
Why is it important that DNA is missing its 2' Hydroxyl?
Definition
This makes it more stable than RNA because the hydroxyl cannot then undergo nucleophilic attack of the phosphate. If it did, it would cleave the molecule.
Term
Define Nucleoside
Definition
Base & Sugar
Term
How are bases and sugars bound?
Definition
Beta- glycosidic linkages
Term
How do you name a nucleoside?
Definition
use the prefix from the sugar and then add -sine to the end. ex: adenine+deoxyribose=adenosine
Term
What position is the phospate at?
Definition
the 5' of the ribose
Term
Primes designate position on what?
Definition
Primes designate the position on ribose whereas no prime shows position on the base.
Term
When writing DNA sequence, which direction do you write it?
Definition
5'-3'
Term
What is on the 5' end of DNA? The 3' end?
Definition
Phosphate is on 5', -OH is on 3' end.
Term
What is the significance of the 3.4 angstrom spacing in a x-ray crystallography of DNA?
Definition
The bases are located 3.4 angstrom above/below each other along the axis of the DNA molecule.
Term
How long does a DNA helix turn take?
Definition
34 angstrom which is about 10 bases
Term
Which base pairs result in 2 hydrogen bonds? 3 hydrogen bonds?
Definition
A-T is 2 hydrogen bonds, C-G is 3 hydrogen bonds.
Term
Why are the hydrogen bonding capabilities of the bases important in DNA structure?
Definition
Hydrogen bonding creates the need for specificity for duplex formation.
Term
Why is hydrogen bonding of DNA entropically favored?
Definition
Hydrogen bonding gives the release of 2 water molecules that were originally tied up in hydrogen bonding favoring entropy.
Term
A/T ratios never fluctuate, but A/G ratios do. Why?
Definition
Specificity of base paring causes a 1:1 ratio of A/T and C/G base pairs. A/G ratios are usually stable along an organism's genome unless some is introduced from somewhere else (phage, etc)...
Term
What forces add to the stability of the DNA double helix?
Definition
Hydrogen bonding of base pairs, negatively charged backbone, base stacking
Term
What is base stacking?
Definition
The hydrophobic affects between stacked bases that have beneficial van Der Waals interactions to add to DNA stability.
Term
Does DNA absorb light better as a double helix or a single strand?
Definition
A single strand so that the bases aren't blocked by the DNA backbone. DNA absorbs at approximately 260 nm.
Term
Increasing the temperature of DNA causes it to what?
Definition
Unwind
Term
Why are counterions important in solution with DNA?
Definition
The counterions help shield the repulsive effects of the negatively charged phosphates on other adjacent backbone phosphates.
Term
DNA melting temperature depends on what factors?
Definition
Counterion concentrations, strand length, number of A/T's in a row (cooperativity and base stacking) and number of C/G (higher temp) vs A/T (lower temp) residues.
Term
When DNA is less hydrated, what form does it generally take? What form is most common in humans?
Definition
Less hydrated formes A type DNA where B type is most common in life.
Term
When is a propeller twist most common?
Definition
In the A form of DNA.
Term
What is the significance of the major groove and minor grooves on DNA?
Definition
The major groove allows proteins to read interesting signals on the inside of the major groove through interactions with the bases.
Term
What is Z-DNA?
Definition
Alternating purines and pyrimidines can form left handed helices in high salt concentrations.
Term
What is a direct repeat and an Inverted repeat?
Definition
A direct repeat is a repeat of a sequence on the same strand of DNA that reads the same both times. An inverted repeat is one where the repeat reads in the reverse order of the repeated segment and often can create structures called hairpins where the inverted repeat hydrogen bonds with the same strand of DNA.
Term
What is a cruciform and why is it important?
Definition
A cruciform is part of a DNA helix where each strand forms a hairpin at the same location on the helix. This is important for regulation.
Term
How can RNA hydrogen bonding be different than DNA bonding?
Definition
RNA hydrogen bonding can bond with 3 bases at a time if needed to confer unique geometries.
Term
What is linking number? Twist? Writhe?
Definition
Lk= (Tw+Wr) or the number of times the DNA strand winds in a right handed direction around the helical axis. Tw= "apparent linking number". Wr= Number of supercoils
Term
How does a type 1 topoisomerase work?
Definition
Its tyrosine residue nucleophilic attacks one strand of DNA, it cuts that strand, lets it untwist (with it's own built up torque) then re-attaches the strand. This is all without ATP.
Term
How does a type 2 topoisomerase work?
Definition
1. The enzyme binds to the helix, 2. ATP binds to the enzyme and causes a conformational change. 3. The double helix is cut and part of the helix downstream is allowed to pass through. 4. The strand is reconnected, 5. ATP is hydrolized and the enzyme releases itself.
Term
In the Meselson and Stahl experiment, what was proven?
Definition
Semi-conservative replication was demonstrated. The parent population had all labeled DNA, the 1st offspring had 50%, then 25%... etc.
Term
What is required for DNA replication?
Definition
deoxynucleoside 5'-triphosphates (dATP, dGTP, dCTP,dTTP), Mg2+, DNA template, Primer, and DNA polymerase.
Term
Why is DNA synthesis thermodynamically favored?
Definition
The product includes the formation of pyrophosphate which is quickly degraded pushing the reaction to the right.
Term
How does DNA polymerase proofread?
Definition
The tight binding between the fingers and thumb can quickly identify a mismatched pair.
Term
Why is Mg2+ important in DNA polymerase?
Definition
The Mg2+ ions are coordinated in the palm region by Asp residues. The Mg2+ increases the partial positive charge on the alpha phosphors. It also stabilizes the pentacovalent transition state and finally it facilitates the displacement of pyrophosphate.
Term
What exactly are the two ways that DNA polymerase proofread?
Definition
1. Minor groove interactions ensure proper hydrogen bonding. 2. The binding of the incoming nucleotide causes a conformational change where the finger region moves downward to make a tight pocket. If the incorrect base is present, this pocket will not yield a site that is capable of chemistry.
Term
How is DNA replication initiated in prokaryotes?
Definition
The enzyme primase comes in and lays down a strip of RNA primer. This allows DNA polymerase to synthesisze DNA off of the RNA primer. Once the DNA has been formed, the RNA primer gets hydrolyzed and is replaced by DNA.
Term
What direction does DNA replication move?
Definition
From 5' to 3'
Term
What enzyme seals breaks in DNA?
Definition
DNA ligase. The reaction is favorable due to the release and subsequent breakdown of pyrophosphate.
Term
How does helicase work?
Definition
Helicase binds to a single strand of DNA. ATP binds and causes a conformational change. ATP is hydrolyzed causing the frontal subunit to rachet forward, undwinding more DNA. The helicase unwinds 3' to 5'.
Term
What does it mean to be processive?
Definition
It means that the enzyme can catalyze many consecutive reactions without releasing substrate.
Term
What is the purpose of the DNA clamp?
Definition
Keeps the DNA associated with DNA Polymerase 3 making the enzyme highly processive.
Term
What are the differences between DNA polymerase I, II and III?
Definition
I fills in gaps in the lagging strand and also in DNA repair. II: Exclusivey participates in DNA damage repair. III: Catalyzes replication on the leading strand.
Term
What are SSB's?
Definition
SSBs are single stranded binding proteins and they bind with single stranded DNA during replication in order to prevent against re-annealing of the helix.
Term
What is the purpose of the clamp loader?
Definition
The clamp loader: 1. Loads the polymerases, 2. Helps keep polymerases together so that the lagging strand does not get too far behind the leading strand.
Term
What is the significance of an A/T rich sequence?
Definition
The one less hydrogen bond makes it easier for that segment of DNA to be separated.
Term
What must occur for E. coli chromosomal replication to start?
Definition
1. DnaA hexamer binds at several locations on the chromosome. 2. DnaA opens single-stranded site for primase to work. 3. DNA polymerase III holoenzyme assembles and DnaA oligomer disassembles.
Term
Name some of the differences between prokaryotes and eukaryotes for DNA replication:
Definition
1. Eukaryotes have multiple origins of replication where prokaryotes only have one ori. 2. Eukaryotes have a polymerase that is used specifically to initiate replication and another polymerase that is more processive to finish the job.
Term
What are the consequences of telomeres?
Definition
Telomeres are structures at the ends of eukaryotic chromosomes in which some DNA is not replicated due to the RNA primer needed for initiation. Without the action of telomerase, the chromosome would get shorter upon each replication cycle.
Term
How does telomerase work?
Definition
Telomerase binds to the G-rich sequence at the end of chromosomes and elongates the chromosome by acting as a pseudo-template. Once a few bases have been added, the telomerase translocates by shifting down allowing more bases to be added.
Term
What is Huntington's disease?
Definition
Huntington's disease is a trinucleotide repeat that causes one strand of DNA to anneal to itself causing a structure similar to the onces found in RNA secondary structure.
Term
What is 8-Oxoguanine?
Definition
Hydroxyl radicals interact with guanine causing one of the nitrogens to be replaced by a carbonyl group. This can cause 8-Oxoguanine to form hydrogen bonds with Adenine rather than cytosine.
Term
What is hypoxanthine?
Definition
Hypoxanthine is adenine with its nitro group replaced by a carbonyl. It can cause impropper base pairing with Cytosine.
Term
What is a thymine dimer?
Definition
Adjacent thymine molecules cyclize in the presence of UV light. This cyclization is incompatible with the structure of the double helix.
Term
What is the importance of the epsilon subunit in DNA pol III?
Definition
It acts as a 3' to 5' exonuclease. Wrong base pairing causes a weak interaction with the polymerase. This causes the DNA strand to flop around freely until it gets into the exonuclease active site where it is cleaved.
Term
How does mismatch repair occur in E. coli?
Definition
Mut S binds to the mismatch on the parental DNA strand. Mut H then moves to the new (unmethylated) DNA strand more 3' of the mismatch and marks the spot. This spot exonuclease 1 recognizes and clears a strip of bases. DNA polymerase III is then free to come in and try again.
Term
How does Mut S know which strand of DNA is the new strand and which is the parental strand?
Definition
The methylation state determines this. When new DNA is made it is unmethylated until methylase has time to act upon it. The parental DNA is already methylated.
Term
How does Base-Excision repair work?
Definition
Enzyme AlkA detects 3-methyladenine, flips the base out of the helix and cleaves the glycosidic bond. 2. AP endonuclease recognizes this site and cleaves the backbone. 3. Deoxyribose phosphodiesterase removes deoxyribose phosphate unit. 4. DNA polymerase 1 inserts new nucleotide and DNA ligase seals it in.
Term
How does nucleotide-excision repair occur?
Definition
1. 12 nucleotide fragment is cut and removed. 2. DNA is formed from DNA polymerase 1. 3. DNA ligase seals the new strip in.
Term
What is spontaneous deamination?
Definition
Spontaneous deamination is when, for example, cytosine loses its amine group spontaneously and forms uracil. This is repaired by AP endonuclease removing the faulty base and DNA pol 1 inserting a new one.
Term
How is RNA added in transcription?
Definition
RNA polymerase catalyzes the 3' hydroxyl to attack the 5' alpha phosphate. It uses Mg2+ to stabilize the intermediate.
Term
What subunits make up RNA polymerase and what do they do?
Definition
sigma=initiation of polymerase, alpha, beta, beta'=RNA polymerization
Term
To which end are new bases added on mRNA during polymerization?
Definition
The 3' end.
Term
What is the promoter?
Definition
It is an untranscribed region of DNA that directs RNAP binding that is more 5' (on the coding strand) than the region being transcribed.
Term
What two experiments help determine the promotor?
Definition
DNA footprinting and isolation/purification
Term
How does the sequence of the promotor have any control over gene expression?
Definition
Changing the consensus sequence changes the affinity to which sigma can bind thereby controlling expression.
Term
What does the promotor do?
Definition
The promotor binds the DNA and the RNAP and unwinds a short piece of helix for RNAP to work.
Term
What consequences does the dissociation of the sigma subunit dissociating from RNAP?
Definition
It changes the affinity of the alpha-beta-beta' units for the DNA making it more processive.
Term
Why is there no proofreading in elongation?`
Definition
polymerase tolerates mistakes since proteins are transient species and are often quickly degraded. Since the protein code is degenerate, often times a mistake will code for the same exact protein.
Term
How is termination accomplished?
Definition
1. The end of transcription encodes a hairpin followed by mulitple U's. This hairpin pushes the strand off of the RNAP and the poly-U tail only has 2 hydrogen bonds for easy breaking. 2. Rho-dependant termination is when Rho ATPase moves along the single stranded RNA intil it hits the RNAP causing the RNA to dissociate.
Term
What is the template strand, coding strand, antisense strand, sense strand?
Definition
The template is the DNA from which mRNA is formed. The coding strand is the reverse compliment of the template strand and is the same sequence as the mRNA. The sense strand is the coding srand and the antisense strand is the template strand.
Term
What base does uracil replace?
Definition
Thymine?
Term
What is the big difference between prokaryotes and eukaryotes with respect to initiation, elongation and termination?
Definition
There is no post trascriptional modifications of mRNA and it can immediately be transcribed. This is unlike eukaryotes since transcription and translation occur in two totally separate compartments.
Term
Why isn't post transcriptional processing required in prokaryotes?
Definition
rRNAs, tRNAs, etc are transcribed simultaneously and merely need to be cleaved. Usually an array of tRNAS are produced simultaneously.
Term
What does cis/trans mean specifically dealing with a promotor?
Definition
Cis means that the promotor is on the same strand of DNA as the gene. Trans is on the opposite strand of DNA.
Term
What things affect gene transcription?
Definition
1. Promotor strength, 2. Proximity of promotor to genes transcribed, 3. presence/absence of repressors and activatos.
Term
What is transcribed when the Lac Operon is active?
Definition
Beta-galactosidase, lactose permease, acetyltransferase, lac repressor
Term
What does beta-galactosidase do? lactose permease? acetyltransferase?
Definition
Beta-galactosidase breaks the glycosidic bond of lactose, lactose permease is a transporter that brings lactose into the cell, acetyltransferase's role is currently unknown.
Term
What is the operator?
Definition
The operator is a site on the DNA that is downstream of the promotor which can have repressors (LacI) bind to regulate expression.
Term
What molecule induces the lac operon?
Definition
Allolactose
Term
What are PAI's?
Definition
Pathogenicity island sequences- sequences of DNA encoding proteins required for infection.
Term
What do the three different eukaryotic RNA polymerases do?
Definition
Pol I- transcribes 18S, 5.8S and 28S rRNA, Pol II-transcribes mRNA and snRNA, Pol III- Transcribes tRNA and 5S rRNA
Term
What are rRNAs?
Definition
Ribosomal RNAs that make up important parts of the ribosome.
Term
Why are svedbergs non-linear coefficients?
Definition
Since they are sedementation coefficients, just because 2 proteins may have unique sedementation properties, combining them does not yield a linear sedementation factor.
Term
What is the nucleolus?
Definition
The nucleolus is a cluster formed from the DNA template, RNA Pol I, and rRNA processing ribonucleoproteins. What consequences does this have on the cell?
Term
What are some of the characteristics of rRNA?
Definition
They are transcribed in tandem repeats and cleaved to form the 18S, 5.8S and 28S subunits.
Term
What 2 ways is Pol II transcription promoted?
Definition
Either a TATA box upstream of transcription start along with an enhancer unit acts as a promotor, or a downstream promotor element works along with an enhancer. Sometimes the promotors can be intragenic. What are the consequences of intragenic promotors?
Term
Describe the initiation of Pol II transcription:
Definition
1. TBP binds to the TATA box, 2. TFIID binds to TBP, recognizes the promotor and bends the DNA. 3.TFIIA stabilizes TFIID binding to the DNA, 4. TFIIB helps determine the start site, 5. TFIIF interacts with non-template strand, 6. TFIIE recruits TFIIH, 7. TFIIH opens the promotor region and phosphorylates RNAPII
Term
What consequences does phosphorylation of the C-terminal doamin of Pol II have?
Definition
This phosphorylation allows binding of capping enzymes, splicing machinery and polyadenylation enzymes. This ensures that the enzymes and substrates find themselves in solution.
Term
What is the purpose/consequences of the 5' cap?
Definition
The unusual 5'-5' triphosphate contributes to the stability of the molecule since it repels phosphatases and nucleases. This also helps increase the chance for translation because the molecule is easier to recognize. Also, tRNAs and rRNAs are not capped.
Term
What exactly is the 5' cap?
Definition
The 5' cap is a methylated guanine attached to an adenine or guanine through a triphosphate linkage.
Term
Why does alternative splicing exist and what consequences does it have?
Definition
Alternative splicing is where various introns are removed in different tissues. This causes an array of different proteins to be made and can provide different functions for specific tissues and organs.
Term
What is an intron/exon?
Definition
An intron is a non-translated strip of RNA that is removed prior to translation. An exon is a region which is removed temporarily from a strip of RNA and is inserted back into the strand after splicing.
Term
How is splicing accomplished?
Definition
snRNAs also known as spliceosomes catalyze the removal of introns by facilitating the formation of the branch site. They also help orient the mRNA so that the branching can occur and the lariat can be created.
Term
What is polyadenylation?
Definition
poly(A)polymerase adds adenosine residues on the terminal end of mRNA (3' end) by use of ATP and by reading the cleavage signal (AAUAAA).
Term
How does splicing occur?
Definition
1. The 2' hydroxyl at the branch point attacks the phosphodiester bond at the 3' end of the exon. 2. 3' hydroxyl of the exon attacks the 5' phosphate at the 5' end of the next exon.
Term
What residue is most common at the branch point in splicing?
Definition
A. It is highly conserved as well as multiple purine and pyrimidine residues in that region.
Term
What are the three lac operon genes that are expressed?
Definition
z, y, a as well as the inhibitor
Term
What is the -35 sequence associated with sigma 70? -10?
Definition
-35=5'TTGACA3' and -10=5'TATAAT3'
Term
What happens when mRNA exits the nucleus?
Definition
PABP1 (poly-adenylated binding protein 1) and elFs (Elongation factors) proteins bind the mRNA and interact with one another to form a circular structure.
Term
Poly-adenylation occurs on which end? 5' or 3'?
Definition
3' end of the mRNA
Term
What happens to tRNA after it is transcribed?
Definition
It is spliced, cleaved and modified with bases such as inosine, pseudouridine, 5-methylcytidine, dihydrouridine, N-acetylcytidine
Term
Why is tRNA modified so much?
Definition
It does 2 things: 1. It allows for a unique structure, 2. It allows for interaction with tRNA synthetases and the ribosome.
Term
What is the function of tRNA?
Definition
It acts as an adaptor molecule to bring amino acids to the mRNA to make protein.
Term
What does PNPase do?
Definition
It is an enzyme that combines NTPs to make short RNAs (used to make strips of RNA made out of only one base)
Term
How was the genetic code determined?
Definition
A tRNA binding assay was used where they manipulated 3-nucleotide long strips of RNA along with the ribosome and attached them to a filter. By washing tRNAs over them along with the amino acids, only the ones that coded for that amino acid stuck.
Term
What are the 2 most important positions in the codon?
Definition
The first two going 5' to 3'. The last position is called the wobble position because it doesn't have as strong of an interaction with the mRNA due to the structure of the tRNA.
Term
What is the genetic code with specific regards to the words degenerate and redundant?
Definition
The genetic code is NOT redundant (as in one 3 base code ONLY codes for ONE amino acid) and the genetic code is degenerate since multiple codons can code for the SAME amino acid.
Term
What are the permiscuous 5' bases of tRNA?
Definition
Inosine= U, C or A. Guanine=U or C. Uracil= A or G.
Term
What is aminoacyl tRNA synthetase and what does it do?
Definition
Aminoacyl tRNA synthetase is an enzyme that adds the correct amino acid to the correct tRNA
Term
How is the aminoacyl-tRNA formed?
Definition
1. Amino acid binds to ATP to make aminoacyl-AMP. 2. Aminoacyl-AMP binds to the 3' -OH of tRNA to form aminoacyl-tRNA and AMP
Term
How come only some aminoacyl-tRNA synthetase enzymes have editing sites?
Definition
Since you need a different aminoacyl-tRNA synthetase for each amino acid, some don't require an editing site because the amino acid that they bind is so highly unique.
Term
What does aminoacyl tRNA synthetase interact with?
Definition
The amino acid and the anticodon site.
Term
Name the functions of the ribosome:
Definition
1. Recognise tRNA, 2. Peptide bond formation, 3. Translocation of the formed protein
Term
What are svedbergs and why are they "non-linear"?
Definition
Svedbergs are units for a specific sedementation coefficient. Different molecules have different sedementation coefficients and in solution, if they interact they further change this sedementation factor in a non-linear fashon.
Term
What are the 3 sites on the ribosome and what do they do?
Definition
They are the E, P and A sites. A: aminoacyl site where tRNA enters, P: Peptidyl site (where polypeptide forms), E: Exit (tRNA exits through this site after peptide bond is formed.
Term
Name the purines and pyrimidines:
Definition
Purines: A, G. Pyrimidines: C, T.
Term
What are the steps for ribosomal initiation?
Definition
1. Initiation factors facilitate formation of the initiation complexes, 2. f-Met is the N-terminal AA and is the first to enter the ribosome, 3. Initiation factors dissociate to allow elongation.
Term
What do initiation factors I, II and III do for ribosomal initiation?
Definition
I marks the A site of the ribosome and facilitates binding of the mRNA. II recognizes f-Met tRNA. III prevents large and small subunit reassociation so that the ribosome is open.
Term
What is Ef-Tu and what does it do?
Definition
Ef-Tu binds GTP and aminoacyl-tRNAs, brings them to the A site of the ribosome and when it matches the anticodon with the codon of the mRNA, GTP is hydrolyzed and Ef-Tu dissocuates. It prevents peptide bond formation in case the tRNA does not match properly with the codon.
Term
What is EF-G and what does it do?>
Definition
Upon peptide bond formation, EF-G comes into the A site and moves eveything over to the next site in the chain. This requires ATP hydrolysis.
Term
Name the steps for elongation:
Definition
1. EF-Tu brings aminoacyl-tRNA to the A site. 2. GTP is hydrolyzed and EF-Tu releases the aminoacyl-tRNA. 3. The 23S rRNA catyalyzes the peptide bond formation. 4. EF-G facilitates translocation of the aminoacyl-tRNA to the P site. 5. tRNA exits via the E site.
Term
What do the stop codons code for?
Definition
Release factors (RFs) that mediate the termination of protein synthesis.
Term
Promotor element is on which strand?
Definition
The coding strand.
Term
What is the Shine-Delgarno sequence?
Definition
5'-GGAGG-3'
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