Biochemistry

Question 1

2 major histone modifications

Answer 1

Acetylation: relaxes DNA coiling
Methylation: increases DNA coiling

Question 2

Which base has a methyl group?

Answer 2

Thymine

THYmine has meTHYl

Question 3

Which base de-aminates to uracil?

Answer 3

Cytosine

Question 4

3 amino acids necessary for purine synthesis?

Answer 4

Glycine
Aspartate
Glutamine
(GAG)

Question 5

2 Purine Salvage Deficiencies

Answer 5

Adenosine Deaminase Deficiency (SCID)
Lesch-Nyhan Syndrome (loss of HGPRT)
- Hyperuricemia, gout, pissed off, retardation, dysTonia

Question 6

Nucleotide Excision Repair

Answer 6

Endonuclease –> polymerase/ligase
Removes bulky lesions (ex thymine dimers)
G1 phase only
Defective in Xeroderma Pigmentosum (can’t fix pyrimidine dimers)

Question 7

Base Excision Repair

Answer 7

Glycosylase creates AP site –> endonuclease (5’) & Lyase (3’) –> polymerase beta & ligase
Throughout cell cycle
Important for spontaneous or toxic deamination

Question 8

Mismatch Repair

Answer 8

Mostly in G2 phase

Defective in hereditary nonpolyposis colorectal cancer

Question 9

Start codon

Answer 9

AUG (Methionine)

Question 10

Stop Codons

Answer 10

UGA, UAG, UAA

U Go Away, U Are Away, U Are Gone

Question 11

4 Types of DNA mutations

Answer 11

Silent (same AA)
Missense (different AA)
Nonsense (early stop)
Frameshift

Question 12

Lac Operon

Answer 12

Genetic response to environmental change, ex w/o glucose, increased AC activity and abundant lactose causes gene expression changes

Question 13

DNA is synthesized in the ___ direction

Answer 13

5’ to 3’ w/ 3’ hydroxyl attacking 5’ phosphate

Question 14

mRNA is read in the __ direction

Answer 14

5’ to 3’

Question 15

Eukaryotic RNA polymerases

Answer 15

RNA polymerase I (rRNA)
RNA polymerase II (mRNA)
RNA polymerase III (tRNA)

Question 16

RNA polymerase inhibitors

Answer 16

alpha-amanitin (death cap): RNA polymerase II
Rifampin: prokaryotic RNA polymerase inhibitor
Actinomycin D: generic RNA polymerase inhibitor

Question 17

Alpha-Amanitin

Answer 17

RNA polymerase II inhibitor, causes severe hepatotoxicity

Question 18

Rifampin

Answer 18

Prokaryotic RNA polymerase inhibitor

Question 19

Actinomycin D

Answer 19

generic RNA polymerase inhibitor, Euks and Pros

Question 20

Prokaryotic RNA polymerases

Answer 20

Single RNA polymerase

Question 21

mRNA processing steps

Answer 21

5’ Cap (7-methylguanosine)
splicing of introns
3’ polyadenylation

Question 22

2 major amino acids in histones

Answer 22

lysine

arginine

Question 23

Which bases get methylated for repression?

Answer 23

cytosine and adenine

Question 24

Which base synthesis is more complicated? Purine or Pyrimidine? Which uses an intermediary base? Where do most drugs act?

Answer 24

Pyrimidine is more complicated and involves orotic acid intermediary. Most drugs act on pyrimidine synthesis.

Question 25

Adenosine Deaminase Deficiency

Answer 25

too much ATP and dATP imbalances the nucleotide pool and prevents DNA synthesis This generally causes SCID

Question 26

Lesch-Nyhan Syndrome

Answer 26

Defective purine salvage from lack of HGPRT (creates IMP and GMP) Symptoms: Hyperuricemia, Gout, Aggression (pissed off), Retardation, and DysTonia

Question 27

Nonhomologous End Joining

Answer 27

No need for homology. Some DNA might be lost. | Mutated in Ataxia telangiectasia and Fanconi Anemia

Question 28

Splicing

Answer 28

mediated by snRNPs, form lariat that is cut out Anti-sliceosome ABs highly specific for SLE Anti-U1 ABs associated with mixed connective tissue disease

Question 29

Anti-Spliceosome Antibodies

Answer 29

Associated with SLE

Question 30

Anti-U1 Antibodies

Answer 30

Associated with mixed connective tissue disease

Question 31

4 arms of a tRNA

Answer 31

Acceptor stem (3' CCA sequence) T-arm (binds ribosome) D-arm (associates w/ tRNA synthetase) Anti-codon loop

Question 32

Energy source for tRNA charging (adding amino acid)

Answer 32

ATP

Question 33

Energy source for protein synthesis initiation

Answer 33

GTP

Question 34

Cell cycle regulated by 3 major types of proteins

Answer 34

Cyclins, Cyclin-dependent kinases, and tumor suppressors

Question 35

Which cell cycle regulator is constitutively expressed?

Answer 35

Cyclin-dependent kinases

Question 36

Which amino acids are N-glycosylated?

Answer 36

asparagine

Question 37

Which amino acids are O-glycosylated?

Answer 37

serine and threonine

Question 38

What is added in Golgi to traffic proteins to lysosomes?

Answer 38

Mannose-6-phosphate | This process is defective in I-cell disease

Question 39

Types of vesicular trafficking proteins

Answer 39

COPI (Golgi to ER, retrograde) COPII (ER to Golgi, anterograde) Clathrin (Golgi to other locations)

Question 40

3 types of filaments

Answer 40

Mcirofilaments (ex actin) Intermediate Filaments (ex vimentin, desmin) Microtubules (ex cilia, flagella)

Question 41

Vimentin stains positive in.....

Answer 41

Connective Tissue

Question 42

Desmin stains positive in.....

Answer 42

Muscle

Question 43

Cytokeratin stains positive in.....

Answer 43

Epithelial Cells

Question 44

GFAP stains positive in.....

Answer 44

Neuroglia

Question 45

Neurofilaments stain positive in.....

Answer 45

Neurons

Question 46

2 Molecular Motor proteins for microtubules

Answer 46

Dynein and Kinesin

Question 47

Which motor protein moves retrograde

Answer 47

Dynein

Question 48

Which motor protein moves anterograde?

Answer 48

Kinesin

Question 49

Pneumonic for drugs that act on microtubules

Answer 49

Microtubules Get Constructed Very Poorly | Mebendazole, Griseofulvin, Colchicine, Vincristine/Vinblastine, Paclitaxel

Question 50

Disease with immotile cilia from dynein defect

Answer 50

Kartagener syndrome

Question 51

Symptoms of Kartagener syndrome

Answer 51

infertility (males and females), increased ectopic pregnancy risk, bronchiectasis, recurrent sinusitis, and situs inversus

Question 52

Types of Collagen and uses in body

Answer 52

``` Type I: Bone, Skin, Tendons Type II: Cartilage Type III: Reticulin (blood vessels) Type IV: Basement Membrane Be (So Totally) Cool, Read Books ```

Question 53

3 main amino acids that make up collagen

Answer 53

Glycine, Lysine, Proline

Question 54

Hydroxylation of Collagen

Answer 54

Occurs in RER, requires vitamin C (scurvy)

Question 55

Osteogenesis Imperfecta

Answer 55

AD, reduced type I collagen synthesis | Broken bones, blue sclerae, hearing loss, dental issues

Question 56

Ehlers Danlos Syndrome

Answer 56

AD or AR, poor collagen synthesis - Type V mutation is classic - Type III mutation is less common vascular form

Question 57

Menkes disease

Answer 57

XR, impaired copper absorption, causes low lysyl oxidase activity symptoms: kinky hair, growth retardation, hypotonia

Question 58

Marfan Syndrome

Answer 58

defect in fibrillin (forms elastin sheath)

Question 59

Blotting Techniques

Answer 59

SNoW DRoP Southern=DNA Northern=RNA Western=Protein