Biochemistry-Molecular

Question 1

Chromatin Structure

Answer 1

1. Negatively charged DNA wrapped around positively charged histones
2. Histone octomer with DNA= nucleosome. Rich in lysine and arginine. H2A, H2B, H3, H4
   H1- linker
3. DNA and histone synthesis in S Phase

Question 2

Heterochromatin

Answer 2

Highly condensed and transcriptionally inactive

Question 3

Euchromatin

Answer 3

Less condensed and DNA is accessible. Transcriptionally active

Question 4

DNA methylation

Answer 4

Differentiates between new and old strand. Methylation at cytosines and adenine . Allows for mismatch repair.
CpG lslands repress transcription= muted.

Question 5

Histone methylation

Answer 5

Most of the time makes DNA mute

Question 6

Histone acetylation

Answer 6

Relaxes DNA coiling and makes DNA active

Question 7

Nucleotides

Answer 7

PURines (AG)- Pur As Gold
PYrimidies (CUT)- CUT Py
Thymies are methylated

Question 8

What does deamination of cytosine create?

Answer 8

Uracil

Question 9

Which bond is stronger G-C or A-T?

Answer 9

G-C because it has three hydrogen bonds as opposed to only two in A-T. Increased G-C = increased melting temperature

Question 10

What three amino acids are necessary for purine synthesis?

Answer 10

Glycine, Aspartate, and Glutamate

Question 11

What is a nucleoside?

Answer 11

base+(deoxy)ribose Sugar

Question 12

What is a nucleotide?

Answer 12

Base+ (deoxy)ribose sugar+ Phosphate

Question 13

Describe purine synthesis.

Answer 13

Start with a sugar (ribose 5-phosphate) + Phophoribsoyl Pyrophosphate (PRPP) and then add base.

Question 14

Describe pyrimidine synthesis.

Answer 14

Make a temporary base (orotic acid). Then add sugar + phosphate (PRPP). Then modify the base

Question 15

What is the function of ribonucleotide reductase?

Answer 15

Converts ribonucleotides to deoxyribonucleotides

Question 16

What is the role of Leflunomide?

Answer 16

Inhibits the dihydroorotate dehydrogenase (important in the orotic acid production in pyrimidine synthesis)

Question 17

What is the role of mycophenolate and ribavirin?

Answer 17

They inhibit IMP dehydrogenase (important in purine synthesis pathway)

Question 18

What is the function of hydroxyurea?

Answer 18

Inhibits ribonucleotide reductase(enzyme important in pyrimidine synthesis)

Question 19

What is the function of 6-mercaptopurine and prodrug azathioprine?

Answer 19

Inhibition of de nove purine synthesis

Question 20

What is the function of 5-fluorouracil (5-FU)?

Answer 20

Inhibits thymidylate synthase which decreases deoxythymidine momophosphate which results in a decrease in dTMP

Question 21

What is the function of methotrexate, trimethoprim and pyrimethamine?

Answer 21

All inhibit the function of dihydrofolate reductase (decrease dTMP) in humans, bacteria, and protozoa, repectively.

Question 22

Describe Adenosine deaminase deficiency.

Answer 22

Creates an excess of ATP and dAT imbalances nucleotide pool via feedback inhibition of ribonucleotide reducatase and prevents DNA synthesis and thus low lymphocyte count.

Question 23

What is one major cause of autosomal recessive SCID?

Answer 23

Adenosine deaminase deficiency

Question 24

What is hypoxanthine-guanine phosphoribosyltransferase?

Answer 24

An enzyme that converts hypoxanthine to IMP and Guanine to GMP.

Question 25

What enzyme is absent in Lesch-Nyhan syndrome?

Answer 25

Hypoxanthine-guanine phosphoribosytransferse which results in an excess of uric acid production and de novo synthesis of purine production

Question 26

What is the inheritance pattern of Lesch-Nyhan syndrome?

Answer 26

X-linked recessive

Question 27

What are the symptoms of Lesch-Nyhan syndrome?

Answer 27

``` Results from HGPRT deficiency: H-Hyperuricemia G- Gout P-Pissed off (aggression and self-mutilation) R- Retardation T-dysTonia ```

Question 28

What enzyme does fluoroquinolones inhibit?

Answer 28

DNA gyrase or prokaryotic topoisomerase II

Question 29

Please define a transition mutation.

Answer 29

A transition mutation is a mutation that changes a purine to another purine (e.g. A to G) or pyrimidine to antoher pyrimidine (C to T)

Question 30

Please define a transversion mutation.

Answer 30

A mutation that results in a change of a purine to a pyrimidine or vica versa.

Question 31

Please give an example of a missense mutation

Answer 31

Sickle cell anemia

Question 32

Please give an example of a frameshift mutation

Answer 32

Duchenne muscular dystrophy

Question 33

Please describe nucleotide excision repair mechanism and what type of mutations they fix.

Answer 33

Specific endonucleases release the oligonucleotide-containing damage bases; DNA polymerase and ligase fil and reseal the gap respectively. Repairs bulky helix-distorting lesions

Question 34

Describe xeroderma pigmentosum and what mutation causes it.

Answer 34

Mutation: Nucleotide excision repair mechanism so cell cannot repair pyrimidine dimers. Cuases early melanoma, basal cell carcinoma, and squamous cell carcinoma

Question 35

Please describe base excision repair and what type of mutations they fix.

Answer 35

Base-specific glycosylase recognizes altered base and creates AP site. ONe or more nucleotides are removed by AP-endomucleases, which cleaves the 5' end. Lyase cleaves the 3' end. DNA polymerase-beta fills the gap and DNA ligase seals it. It fixes spontaneous deamination

Question 36

Please describe mismatch repair.

Answer 36

Newly synthesized strand is recognized, mismatched nucleotides are removed, and the gap is filled and resealed.

Question 37

Please name a disorder caused by a defect in mismatch repair mechanism.

Answer 37

Hereditary nonpolyposis colorectal cancer (HNPCC)

Question 38

Please describe nonhomologous end joining

Answer 38

Brings together 2 ends of DNA fragments to repair double-stranded breaks. Require no homology

Question 39

What causes ataxia telangiectasia?

Answer 39

mutation in nonhomologous end joining

Question 40

What do the start codons code for in eukaryotes and prokaryotes?

Answer 40

Eukaryotes- mthionine | Prokaryotes- formylmethionine

Question 41

Name the three stop codons

Answer 41

UGA- U Go Away UAA- U Are Away UAG- U Are Gone

Question 42

Describe a promoter.

Answer 42

Site where RNA polymerase and multiple other transcription factors bind to DNA upstream from gene locus (AT-rich upstream sequence with TATA box)

Question 43

Enhancers/ Silencer

Answer 43

Stretch of DNA that alter gene expression. Can be thousands of bp up or downstream or in introns.

Question 44

Name and describe the functions of eukaryotic RNA polymerases.

Answer 44

RNA Pol I- makes rRNA RNA Pol II- makes mRNA RNA Pol III- makes tRNA

Question 45

Name the compound found in the death cap mushroom that inhibits RNA polymerase II.

Answer 45

Alpha-amanitin. Causes severe hepatotoxicity. Symptoms appear between 1-2 weeks

Question 46

How many RNA polymerases do prokaryotes have?

Answer 46

One

Question 47

Name three modifications that occur in the maturation process of mRNA.

Answer 47

5' methylguanosine cap 3' poly A tail Splicing of introns

Question 48

What makes up the sliceosome?

Answer 48

Primary transcript + small nuclear ribonucleoproteins(snRNP)

Question 49

What causes SLE?

Answer 49

Antibodies to spiceosomal snRNPs

Question 50

Anti-U1 RNP antibodies cause...

Answer 50

mixed connective tissue disease

Question 51

Name the parts their function in tRNA

Answer 51

T Loop- recognition of ribosome D Loop- recognition of correct aminoacyl tRNA synthetase Anti-Codon- recognizes mRNA codon 3' CCA- binds amino acid

Question 52

Describes aminoacyl-tRNA synthetase

Answer 52

Enzyme that loads amino acid onto the 3' end of tRNA. If it adds the wrong amino acid it will hydrolyze and take it off

Question 53

Translation-Initiation

Answer 53

Initiated by GTP hydrolysis; initiation factors help assemble the 40S ribosomal subunit with the initiator tRNA and are released when the mRNA and the ribosomal 60S subunit assemble with the complex

Question 54

Translation- Elongation

Answer 54

1. Aminoacyl-tRNA binds to A site 2. rRNA catalyzes peptide bond formation, transfers growing polypeptide to amino acid in A site 3. Ribosome advances 3 nucleotides toward 3' end of mRNA, moving peptidyl tRNA to P site

Question 55

Translation- Termination

Answer 55

Stop codon is recognized by release factor. and completed polypeptide is released from ribosome

Question 56

Name three posttranslational modification

Answer 56

1. Trimming 2. Covalent alterations 3. Chaperone protein

Question 57

Name 7 covalent alterations that can be made on a protein.

Answer 57

1. Phosphorylation 2. Dephosphorylation 3. Carboxylation 4. Hydroxylation 5. Methylation 6. Acetylation 7. Ubiquitination