Old Exam Practice Questions Flashcards
Draw Hydrogen bond of adenine and thymine without sugar phosphate backbone.
At which two spots can ATP and glycolysis be generated? (weird wording, probably a translation error)
ATP can be generated in:
1) the cytoplasm by glycolysis
2) the mitochondrion by the citric acid cycle and oxidative phosphorylation
What is a palindrome? Draw a sequence of 6 bases as a double strand.
A palindrom is a sequence of DNA where the bases at the beginning of the sequence are complementary to those in the other half of the sequence.
Example:
CCGCGG
GGCGCC
Name 3 second messengers by their full names:
1) cyclic AMP (cAMP)
2) cyclic GMP (cGMP)
3) Calcium Ion (Ca2+)
4) inositol 1,4,5-trisphosphate (IP3)
5) Diacylglycerol (DAG)
How many genetic codes exist and how many of them are stop codons? How many are start codons?
3 base codons, 4 bases total = 4^3 codons = 64 codons
3 stop codons
1 start codon
Describe the wobble position
The base on the anticodon of tRNA that corresponds to the 3’ codon on the mRNA can sometimes be a flexible I (inosine) base that can match with more than one base.
Name 4 RNAs and their functions
1) mRNA - is translated by the ribosome to make protein
2) rRNA - makes up the structure of the ribosome and catalyzes some reactions having to do with translation
3) tRNA - transfer RNA that brings the amino acids to the ribosome to be assembled into polypeptides.
4) snRNA - small nuclear RNA. Makes up the spliceosome
Draw and label a lineweaver burk diagram
Name 3 Epitope tags that can be used in affinity chromatography.
- His tag - a string of histidine residues
- MBP
- GlutathionS
Name 3 small molecule electron carriers as they can be found in oxidative phosphorylation.
1) NADH
2) FADH2
3) QH2
Why does SDS-PAGE contain SDS and Beta-mercaptoethanol?
Contains SDS (sodium dodecyl sulfate) to disrupt all non-covalent interactions
Contains beta-mercaptoethanol to reduce disulfide bonds
What are northern, western, southern blot and what molecules can be identified with it?
Electrophoresis and then transfer to a membrane and stained or tagged to see where specific molecules are and how far they have travelled - which corresponds to size.
1) Southern - DNA
2) Northern - RNA
3) Western - Protein
What is an Operon and ORF and what are the differences?
1) an operon is a sequence on DNA that is transcribed depending on if certain conditions are met. It will have a promotor site, a operator site, and then structural genes which code for the mRNA to be translated. They are mostly associated with prokaryotes, but they will sometimes show up in eukaryotes. They can be turned on or off, meaning allow transcription of the structural genes up on the release or binding of a represor to the oporator site.
2) ORF, or open reading frame, is a stretch of bases starting at a start codon and ending at a stop codon that has the potential to be translated.
3) the difference between an operon and an ORF is that the operon can be within an ORF potentially, but is regulated by repressor proteins to stop or allow transcription. An ORF is just a potentially translatable region due to the presence of bases between a start and stop codon.
What is a ribozyme? Name 2 examples.
A ribozyme is RNA that demonstrated catalytic acitivity.
1) the rRNA in the ribosome
2) the snRNA in the spliceosome
Name 3 organic coenzymes and the most important cosubstrates
1) Coenzyme A
2) Coenzyme Q
3) SAM
Cosubstrates:
ATP
GTP
NAD+
H2O
What are okizaki fragments?
The lagging strand during DNA replication still has to be assembled by adding to the 3’ end, but cannot simply start from the 3’ end of the template strand since it has not been unzipped by helicase yet.
It is assembled in small pieces called Okizaki fragments , with an RNA primer being placed in a point on the template strand that has been opened up.
Small pieces of DNA (the okizaki fragments) are created by DNA polymerase and ligated together by DNA ligase. This is how the lagging strand is assmebled.
Name and describe 3 methods to detect protein-protein interaction.
- Co-immunoprecipitation
- yeast 2 hybrid assay
- tandem affinity chromatography
Which 3 amino acids can become phosphates?
1) Tyrosine
2) Serine
3) Threonine
basically the 3 with hydroxyl groups.
Which 2 alpha-keto acids from the citric acid cycle can be transformed into which amino acids?
1) Oxaloacetate - can be used as a precurser for:
- Aspartate, which is used as a precurser for:
- Asparagine, Methionine, Threonine, Lysine, Isoleucine
2) Alpha-ketoglutarate - Can be used as a precurser for:
- Glutamate, which is used as a precurser for:
- Glutamine, Proline, Arginine
Describe cooperative binding and allostery
1) Cooperative binding - as one substrate binds to the enzyme, more active sites open up allowing more substrates to bind.
2) Allostery - the binding of a molecule to a site other than the active site regulates the enzyme, either enhancing or limiting its activity.
Allosterically regulated enzymes will exhibit non-Michaelis Menton kinetics.
Describe the structure of 5-methyl-cytosine. Where can it be found in a mammal?
Is basically a standard Cytosine base, but it has a methyl group at the 5’ carbon (where it would be found in Thymine).
It is found that the CpG junctions in mammals.
Describe and draw the structure of ATP
Adenosine Triphosphate.
Is 3 phosphoryl groups attached to a ribose sugar attached to an adenine.
Process steps of pre-mRNA in Eukaryotes.
1) capping the 5’ end
2) addition of the polya(A) tail to the 3’ end
3) splicing out introns and connecting exons
Main differences between prokaryotes and eukaryotes in cell division.
- Eukaryotes: Mitosis and cytokinesis
- Prokaryotes: Binary fission
Name 3 prokaryotic proteins that are important for homologous recombination. Describe also their function.
- RecA
- Promotes strand invasion
- Cre-Recombinase
- Works through Holliday junction intermediates
- Helicase
- RuvA
How do you divide proteins according to size, charge, weight?
1) Size - gel filtration chromatography (or molecular exclusion chromatography)
2) Charge - ion exchange chromatography
3) Weight - SDS-PAGE (electrophoresis)
Name 2 methods for identifying protein 3D structure.
1) X-ray crystallography
2) NMR spectroscopy
What do U1 and U2 snRNA do at splicing?
U1 recognizes 5’ splice site by base- pairing with 5’ region of intron; U2 recognizes branch point and loops out adenosine for nucleophilic attack of 5’ splice site
Describe the RNA hydrolysis mechanism. Why is RNA more sensitive than DNA?
The OH group that is present at the 2’ carbon on the ribose sugar in RNA (not present in DNA) does a nucleophilic attack on the phosphate group in the backbone, breaking it. The fact that DNA does not have this hydroxyl group is why it is more stable than RNA.
What is apoptosis? What do caspases do?
Apoptosis is programmed cell death.
Caspases are protease enzymes that play key roles in apoptosis, including initiation, execution and inflamation.
(I should probably get a better answer for this one)
What is the restriction point?
Point in the cell cycle after which the cell cycle will go ahead without external stimulus. Is in later G1 phase.
What is the karyotype, autosome, genome?
1) Karyotype - number and appearance of chromsomes in a eukaryotic cell nucleus.
2) Autosome - chromosome that is not a sex chromosome
3) Genome - the complete genetic information in a cell or organism. Including DNA and RNA.
Which RNA polymerase for which RNA?
1) RNA polymerase I - 18S, 5.8S, 28S rRNA
2) RNA polymerase II - mRNA precursors and snRNA
3) RNA polymerase III - tRNA and 5S rRNA
Molecular machine for ATP-synthesis, mRNA processing and protein synthesis
1) ATP Synthesis - ATP synthase
2) mRNA processing - spliceosome
3) Protein synthesis - ribosome
What is a methyl donar and what are its pre-stages?
S-adenosylmethionine is formed from the transfer of an adenosyl group from ATP to the sulfur atom of methionine.
What are the different types of reversible enzyme inhibitors and what do they do?
(A) Enzyme–substrate complex;
(B) a competitive inhibitor binds at the active site and thus prevents the substrate from binding;
(C) an uncompetitive inhibitor binds only to the enzyme–substrate complex;
(D) a noncompetitive inhibitor does not prevent the substrate from binding.
What are the effects of the different inhibitors types on Michaelis-Menton diagrams?
Competative: As the concentration of a competitive inhibitor increases, higher concentrations of substrate are required to attain a particular reaction velocity.
Uncompetative: The reaction pathway shows that the inhibitor binds only to the enzyme–substrate complex. Consequently, Vmax cannot be attained, even at high substrate concentrations. The apparent value for KM is lowered, becoming smaller as more inhibitor is added.
Noncompetative: The reaction pathway shows that the inhibitor binds both to free enzyme and to an enzyme–substrate complex. Consequently, as with uncompetitive competition, Vmax cannot be attained. In pure noncompetitive inhibition, KM remains unchanged, and so the reaction rate increases more slowly at low substrate concentrations than is the case for uncompetitive competition.
What are the effects of the different inhibitors types on Lineweaver-Burke diagrams?
Competative: A double-reciprocal plot of enzyme kinetics in the presence and absence of a competitive inhibitor illustrates that the inhibitor has no effect on Vmaxbut increases KM.
Uncompetative: An uncompetitive inhibitor does not affect the slope of the double-reciprocal plot. Vmax and KM are reduced by equivalent amounts.
Noncompetative: A double-reciprocal plot of enzyme kinetics in the presence and absence of a pure noncompetitive inhibitor shows that KM is unaltered and Vmax is decreased.
Describe the Key-Lock model
The active site of an enzyme can only fit substrates that specifically fit the exact shape of the active site.
Catalytic triad in chymostrypsin and specifications, what bonds does it break?
The Ser-His-Asp catalytic triad in chymotrypsin hydrolyzes the peptide bonds on the carboxyl side of aromatic or large hydrophobic amino acids.
UV damage and repair
UV light covalently links adjacent pyrimidine residues.
DNA photolyase uses light energy to break this covalent bond, an example of a direct repair system.
DNA replication adn RNA translation, proof reading and repair.
DNA polymerase proof reads as it creates new strands, if there are mismatched bases, they are excised into the exonuclease site of the polymerase.
During RNA translation, the aminoacyl-tRNA synthetases actual do a certain amount of proof reading. If a tRNA is linked to the wrong amino acid, it will be excised by the aminoacyle-tRNA synthetase immedietly.
Fidelity is basically the accuracy of this stuff. How well it is replicated or translated etc. High fidelity is very very important in replication. Less important in translation.
Degenerated code: Start and stop genetic codes, how to get from 5’ to 3’
The genetic code is degenerate. This means that some amino acids can be encoded by more than one codon.
Start codon is the one that codes for methionine.
3 stop codons
What methods of DNA mending and modification?
DNA repair mechanisms:
1) Proofreading
2) Mismatch repair
3) Direct repair (photolyase is an example of this)
4) nonhomologous end joining - repairs breaks on both strands that separate DNA into 2 separate strands.
DNA can be methylated to prevent restriction enzymes from cleaving it.
draw tripept Met-Pro-His and its formylation reaction
look at curve thing to it.
Difference between biological membrane and triacylglyceride. Draw phosphatidylserine
1) Membrane lipids: are amphipathic molecules (meaning they contain both a hydrophilic and a hydrophobic moiety.) With 2 hydrophobic fatty acid chains parallel to each other.
2) Triacylglyceride: Highly concentrated energy storage. 3 fatty acid tails and a glycerol.
Describe cysteine biosynthesis
1) 3-Glyceraldehyde is the precursor to serine
2) serine is the precursor to cysteine (and glycine)
3) homocysteine is created through the activated methyl cycle (using s-adenosyl methionine)
4) Homocysteine + serine <—> cysteine + alpha-ketobutyrate + NH4
Draw oxaloacetate. Into what amino acid can it get transaminated?
It can be transaminated into Aspartic Acid/Aspartate
