Molecular

Question 1

Chromatin structure

Answer 1

Nucleosomes have H2A, H2B, H3, H4 – H1 histone is outside of nucleosome and binds to linker DNA to package it into a more compact form — DNA and histone synthesis occur during S phase

Question 2

Heterochromatin

Answer 2

Highly Condensed and heavily methylated (inactive) – example is Barr bodies

Question 3

Euchromatin

Answer 3

Less condense, active

Question 4

DNA methylation

Answer 4

Cytosine and adenine are methylated to distinguish between old and new strands — represses transcription at CpG islands

Question 5

Histone methylation

Answer 5

(Methylation = mute) Reversibly represses DNA transcription

Question 6

Histone acetlyation

Answer 6

(Acetylation = active) – relaxes DNA coiling to allow transcription

Question 7

Nucleotides

Answer 7

PURe As Gold (Purines, A, G, 2 rings) — CUT the PY (Pyrimidines, CUT, 1 ring) — Thymine has a meTHYl — Uracil in RNA, thymine in DNA — GC bond is stronger than AT bond so more GC means higher melting temperature

Question 8

Purine synthesis

Answer 8

Requires GAG (Glycine, Aspartate, Glutamine) — start with sugar + PRPP and add a base

Question 9

Pyrmidine synthesis

Answer 9

Requires Aspartate — Make temporary base (orotic acid), add sugar and phosphate, modify base — involves carbamoyl phosphate synthetase II (rate limiting) — thymidylate synthase requires folate so deficiency leads to decreased dTMP (thymidine supplementation can moderately increase it)

Question 10

Adenosine deaminase deficiency

Answer 10

Excess ATP and dATP prevents DNA synthesis and decreases lymphocyte count – autosomal recessive cause of SCID

Question 11

Lesch Nyhan syndrome

Answer 11

Defective purine salvage due to abscent HGPRT (converts hypoxanthine to IMP and guanine to GMP) — HGPRT (Hyperuricemia, Gout, Pissed off (self mutilation), Retardation, dysTonia) — X linked recessive – Tx: allopurinol

Question 12

DNA helicase

Answer 12

Unwinds DNA template at replication fork

Question 13

DNA topoisomerases

Answer 13

Create a single or double strand break in helix to add or remove supercoils (Fluoroquinolones inhibit topoisomerase II)

Question 14

Primase

Answer 14

Makes an RNA primer on which DNA polymerase III can initiate replication

Question 15

DNA polymerase III

Answer 15

Prokaryotic only – elongates leading strand by adding to 3’ end, elongates lagging strand until it reaches primer of preceding fragment – 3’ -> 5’ exonuclease activity proofreads

Question 16

DNA polymerase I

Answer 16

Prokaryotic only - degrades RNA primer and replaces it with DNA – 5’ to 3’ synthesis, proofreads with 3’ to 5’ exonuclease, and excises RNA primer with 5’ to 3’ exonuclease

Question 17

DNA ligase

Answer 17

Forms phosphodiester bond to join strands

Question 18

Telomerase

Answer 18

RNA dependent DNA polymerase (has reverse transcriptase activity) that adds DNA (TTAGGG) to 3’ ends of chromosomes (eukaryotes only) - found on stem cells and cancer cells

Question 19

Silent mutation

Answer 19

Nucleotide substition but codes for same amino acid (tRNA wobble)

Question 20

Missense mutation

Answer 20

Changed amino acid (Sickle cell disease)

Question 21

Nonsense mutation

Answer 21

Early stop codon

Question 22

Frameshift mutation

Answer 22

Deletion or insertion of nucleotides not divisible by 3 (Duchenne muscular dystrophy)

Question 23

Lac operon

Answer 23

Low glucose: increases adenylyl cyclase (glucose normally inhibits), increase cAMP, activate CAP protein and induce transcription — High lactose: unbinds represor protein from repressor/operator site and induces transcription

Question 24

Nucleotide excision repair

Answer 24

Endonucleases releasing damaged bases, DNA polymerase and ligase fill and reseal gap (G1 phase) — defective in xeroderma pigmentosum (UV damage prevents repair of pyrimidine dimers)

Question 25

Base excision repair

Answer 25

Enzymes involved: glycosylase (removes bad base) – endonuclease (AP, cleaves 5’ end) – lyase (cleaves 3’ end) – DNA polymerase (fills gap) – DNA ligase (seals it)

Question 26

Mismatch repair

Answer 26

Mismatched nucleotides removed, gap is filled and sealed (G2 phase) – defective in HNPCC

Question 27

Nonhomologous end joining

Answer 27

Brings together 2 ends of DNA fragments to repair double stranded breaks — mutated in ataxia telangiecctasia (ATM gene - cerebellar ataxia, increased sinopulmonary infections) and Fanconi anemia

Question 28

mRNA start codons

Answer 28

AUG - codes for methionine in eukaryotes and N-formylmethionien in prokaryotes

Question 29

mRNA stop codons

Answer 29

UGA, UAA, UAG - U Go Away, U Are Away, U Are Gone — codes for release factor

Question 30

Promoter region

Answer 30

Site wehre RNA polymerase II bind upstream from gene locus (TATA boxes)

Question 31

Enhancer region

Answer 31

Alters gene expression by binding transcription factors — can be anywhere in the gene

Question 32

Silencer region

Answer 32

Negative regulators (repressors bind) — can be anywhere in the gene

Question 33

Eukaryote RNA polymerases

Answer 33

I (rRNA - most numerous RNA, rampant, functions only in nucleus) — II (mRNA, largest RNA, massive, inhibited by a-amanitin in death cap mushrooms) — III (tRNA, smallest RNA, tiny)

Question 34

RNA processing (eukaryotes)

Answer 34

Processing IN NUCLEUS - capping of 5’ end (adding 7-methylguanosine cap), polyadenylation of 3’ end (polyadenylation signal so not transcribed from DNA), and splicing of introns — quality control occurs at CYTOPLASMIC p bodies

Question 35

Splicing of pre-mRNA

Answer 35

Transcript combines with snRNPs (rmeove introns) and other proteins to form spliceosome (cleave 5’ end of intron and joint to branch point) – Lariat shaped intermediate is generated — Lariat is released to remove intron and join 2 extons — Anti-smith antibodies (Lupus) are against spliceosomal snRNPs

Question 36

Introns vs. exons

Answer 36

Exons have genetic information – introns are noncoding

Question 37

tRNA structure

Answer 37

Cloverleaf structure (75-90 nucleotides), a lot of chemically modified bases, anticodon end is opposite 3’ aminoacyl end, CCA at 3’ end (Can Carry Amino acids) — T arm (thymine, pseudouracil, and cytosine sequence for tRNA-ribosome binding) — D arm (dihydrouracil residues for tRNA recognition by aminoacyl tRNA synthetase)

Question 38

tRNA charging

Answer 38

Aminoacyl-tRNA synthetase is matchmaker — mischarged tRNA reads usual codon but inserts wrong amino acid

Question 39

Wobble

Answer 39

Accurate base pairing is only required in first 2 nucleotide positions so codons differing in 3rd (wobble) position may code for same tRNA/amino acid sequence

Question 40

Kozak sequence

Answer 40

Initiation of translation - when AUG is near beginning of mRNA molecule and surrounded by Kozak it initiates mRNA binding to ribosomes

Question 41

Protein synthesis

Answer 41

Initiation (GTP hydrolysis, help assemble 40S ribosomal subunit with initiator tRNA) — elongation (aminoacyl tRNA binds to A site (except initatior methionine), rRNA catalyzes peptide bond formation, ribosome advances 3 nucleotides toward 3’ end of mRNA and moves to P site) —- termination (stop codon recognized by release factor)

Question 42

Protein structures

Answer 42

Eukaryotes (Even - 40S and 60S) — Prokaryotes (Odd - 30S and 50S - 16S in 30S has complementary sequence to bind Shine Delgarno mRNA sequence) — signal sequence for protein extrusion into RER is N-terminal hydrophobic

Question 43

Posttranslational modifications

Answer 43

Trimming (removing N or C terminal propeptides) — Covalent alterations, secondary structures formed by hydrogen bonds

Question 44

Chaperone protein

Answer 44

Intracellular protein involved in facilitating/maintaining protein folding (Hsp60)