Western U Mcbm-Biochemistry

Front 1

Function of CMAH in chimps

Back 1

Converts Neu5Ac to Neu5Gc

makes them susceptible to plasmodium reichenowi

humans only have Neu5Ac b/c of a 92 bp deletion that deactivates our CMAH.

Front 2

Pharmacokinetics

Back 2

time-course of drug concentration in the body

What the drug does, how it does it, and how long that takes (i.e., kills cancer cells; is metabolized by the liver; half life is x hours,etc.)

Front 3

Pharmacodynamics

Back 3

time-course & intensity of drug effects on the patient

What the drug elicits as side effects in the patient (i.e., causes vomiting--how intense and how long)

Front 4

Pharmacogenomics

Back 4

New branch

influence of genes on drug efficacy.

How the patient's specific genome affects absorption, distribution, metabolism, etc. of the drug (i.e., high metabolic turnover=quicker excretion and requires higher dose)

Front 5

CYP

Back 5

Group of compounds called Cytochrome P450s; all inactivate active drugs by hydroxylation

~150 isoforms

Front 6

CYP impact on Coumadin (Warfarin)

Back 6

Deactivates coumadin

i.e., homozygous CYP2C9-1 allele is "typical" rate of inactivation, requiring dose of "1".

Heterozygous CYP2C9-1 & -2/-3 is a slower rate of inactivation, requiring dose of "1/2".

Homozygous CYP2C9-2, or -3 is slowest rate of inactivation, requiring smallest dose

Front 7

Mechanism of Coumadin action

Back 7

Targets VKORC1 and inhibits it, thereby impairing the clotting cascade.

Front 8

VKORC1 action

Back 8

Converts epoxide form of Vit K to a usable form. Therefore, Vit K dependent factors can work and clotting cascade can work as usual.

Front 9

Purine nucleotides

Back 9

"Pure As Gold"

Adenine & Guanine

Front 10

Pyrimidine nucleotides

Back 10

"Pyramids get CUT"

Cytosine, Uracil, Thiamine

Front 11

Nucleoside

Back 11

Nitrogenous base + sugar

Front 12

Nucleotide

Back 12

Nucleoside + Phosphate

Front 13

Difference between Deoxyribose and Ribose

Back 13

Deoxyribose is missing the OH in the 2' position.

Front 14

Chargaff's Rule

Back 14

In a double strand of DNA, the concentration of A equals T and G equals C.

Front 15

Stability of A-T vs G-C pairs

Back 15

A-T less stable b/c it only has 2 H bonds whereas G-C has 3.

Therefore, it's always a start point of transcription b/c it's easier to open.

Front 16

Types of DNA

Back 16

A, B, Z

Humans have B

Front 17

B type DNA

Back 17

10.4 bases/turn, right handed, major & minor grooves.

Major groove is 2x the size of minor.

Front 18

Denaturation process

Back 18

0th order

occurs by heat or alkylates
breaks H-bonds between nucleotides

Front 19

Renaturation process

Back 19

2nd order (concentration dependent)

Front 20

Melting Temperature (Tm)

Back 20

The point at which 1/2 of the concentration is denatured and the other 1/2 is still double stranded.

Front 21

Model of eukaryotic reproduction

Back 21

SV40 (simian virus)

Front 22

Mammal polymerases for DNA replication

Back 22

alpha=primase
delta=leading strand (some lagging)
epsilon=lagging strand

Front 23

Consquence of end replication

Back 23

shortened telomeres leading to senescence

B/c no polymerase has 3'-5' activity

Front 24

Telomere function

Back 24

"cap" of hexameric repeats in quartet formation; maintain integrity of chromosome, attach it to nuclear envelope, facilitate replication; their shortening acts as mitotic clock.

Front 25

virion

Back 25

inert virus outside of a cell

Front 26

Viral Genomes

Back 26

single/dbl DNA
single/dbl RNA

Front 27

HIV/AIDS

Back 27

genome has 2 copes of 9700 nt RNA

primes by tRNA-lys to create dbl strand DNA by reverse transcriptase (no proofread)

Front 28

Inhibition points of HIV

Back 28

replication, integrase activity, protease activity and fusion

Front 29

CCR5 Abberation

Back 29

Northern European heritage

causes resistance to HIV b/c its co-receptor on the cell surface is not present; it cannot enter cell.

Front 30

Hybridization

Back 30

basepairing of complementary strands

Front 31

Southern Hybridization

Back 31

probe pairs with DNA target

Front 32

Northern Hybridization

Back 32

probe pairs with RNA target

Front 33

Requirements of PCR

Back 33

1. Accurate primers that flank target sequence & are complementary to both strands.

2. Taq polymerase (withstands high heat)

3. Available nucleotides

Front 34

Microarray Function

Back 34

illustrate up regulated and down regulated genes.

Front 35

VNTR

Back 35

Variable Number Tandem Repeat

di-, tri-, tetra-

# & type are heritable.

Used in forensics (i.e., paternity, rape)

Front 36

Cell Doctrine

Back 36

every cell in the body arises from a current cell

Front 37

Interphase

Back 37

G1, S, G2 of cell cycle
regulated by cyclins & checkpoints

Front 38

Processivity

Back 38

length of time a polymerase will attach and add nucleotides before detaching. Pol I-III have increasing processivity.

Front 39

Positive Supercoiling

Back 39

overwinding of DNA strand
kept in check by topoisomerases

Front 40

Negative supercoiling

Back 40

underwinding of DNA strand
kept in check by topoisomerases

Front 41

Topoisomerase I

Back 41

bacterial enzyme; makes 1 cut b/c genome is single stranded & circular

Front 42

Topoisomerase II

Back 42

makes 2 cuts b/c genome is double stranded and linear. Gyrase is an example of topoisomerase II.

Front 43

Method of action for Topotecan and Fluoroquinolones

Back 43

inhibit ligation

Front 44

Method of action for levo- and cipro-flaxin

Back 44

inhibit replication enzymes via gyrase activity

Front 45

Origin sequence nucleotides

Back 45

very A-T dense

Front 46

Helicase function

Back 46

aka DNA B; unzips strand (ATP dependent)

Front 47

Function of Primase

Back 47

forms a 15 nt RNA primer with a 3' OH

Front 48

Function of Polymerase II

Back 48

adds NTs to 3' end, complementary to the sense strand

Front 49

Polymerase III function

Back 49

removes primers and extends synthesis

Front 50

Difference btw DNA A & DNA B

Back 50

DNA A locates the origin sequence, clamps on, and recruits DNA B to unzip it.

Front 51

RNA abundance (greatest to least)

Back 51

rRNA, tRNA, mRNA

Front 52

Transcription steps

Back 52

1. RNA pol binds to promoter (~60 NTs)
2. DNA opens
3. transcription proceeds (no primer/proofreading)
4. termination @ hairpin loop

Front 53

RNA sequence is a complement of which strand?

It is equivalent to which strand?

Back 53

complements template strand

equivalent to coding/sense strand

Front 54

Subunits of E. Coli Polymerase

Back 54

alpha (2): recognize promoter, assemble enzyme, bind activators

Beta & Beta': catalytic center

Sigma: promoter specificity

Front 55

How is a promoter recognized during transcription?

Back 55

by sequence's relation to consensus sequence; closer the resemblance, the faster transcription goes.

Front 56

3 parts of a promoter

Back 56

1. -35 consensus (TTGACA)
2. -10 consensus (TATAAT)
3. start point

Front 57

Difference btw Core enzyme and holoenzyme

Back 57

holoenzyme has a sigma subunit

other subunits are equal

core enzyme becomes holoenzyme when it encounters a sigma

Front 58

Terminators (transcription)

Back 58

hairpin loop: GC stem & U sequence that destabilize RNA/DNA complex

Front 59

3 different polymerases used by eukaryotes during transcription

Back 59

Pol I (rRNA), Pol II (mRNA), Pol III (tRNA)

Front 60

Method of action in Rifampin

Back 60

blocks initiation in mycobacterium

Front 61

Actinomycin D action

Back 61

unique structure; clamps on to minor groove and intercalates between G-Cs, therefore blocking RNA pol movement.

Front 62

Amanita phalloides (mushroom) action

Back 62

deactivates RNA pol II, therefore kills off intestinal mucosa, liver and kidneys.

Front 63

Consequences of processivity mistakes

Back 63

reattachment might occur in the wrong place causing replication slippage (insertions, deletions, etc.)

Front 64

Frameshift mutation

Back 64

insertion of 1 nucleotide pair

Front 65

Transition

Back 65

swapping of purine for another purine or a pyrimidine for another pyrimidine

Front 66

Transversion

Back 66

swapping of a purine for a pyrimidine or vice versa.

Front 67

1st level repair process

Back 67

exonuclease action of DNA pol fixes mismatch bases

Front 68

2nd level repair process (post-transcription)

Back 68

(prokaryotes) recognition of non-methylated A by MutS

(eukaryotes) MutS looks for mismatch, MutL looks for nick; excises the whole stretch and DNA pol recodes.

Front 69

HPCC & FAP colon cancers

Back 69

HPCC=hereditory non polyposis colon cancer

FAP=familial adenomatous polyposis

Front 70

cause of HPCC

Back 70

inherited mutation in one copy of mismatch repair gene (MutS & MutL) + spontaneous mutation of the other copy.

Front 71

Deamination

Back 71

converts C to U; can result in a U-A pair, or can get repaired to the original C-G pair.

Front 72

Pyrimidine Dimers

Back 72

caused by radiation; helicase removes section around it, DNA pol recodes, and ligase seals it.

Front 73

Depurination

Back 73

removes the purine from the NT. Causes deletion of the affected pair.

Front 74

uracil glycosylase

Back 74

cleaves the methylated C (U) out of the sequence.

Front 75

RAD genes

Back 75

DNA repair mechanism of yeasts.
RAD3 (helicase) does excision repair; part of the transcription factor.
RAD6 does post-replication repair.
RAD52 does recombination mediated repair

Front 76

Homologous End Joining (HEJ)

Back 76

repair double strand breaks by replacing the lost sequence.

Front 77

Non Homologous End Joining (NHEJ)

Back 77

repair double strand breaks by removing lost sequence; more complicated; requires many enzymes.

Front 78

Defective HEJ repair consequences

Back 78

cause nonfunction BRCA1 & BRCA2 proteins causing vulnerability to breast & ovarian cancers.

Front 79

Artemis

Back 79

endo- and exo-nuclease activity when phosphorylated.

Front 80

Most common method of gene expression regulation

Back 80

transcription

Front 81

points of control for gene expression

Back 81

transcription
mRNA (degrade or translate)
protein (active/passive & transformation between the two)

Front 82

Constitutive gene

Back 82

houskeeping gene; maintains basic metabolism and cell structure.

Front 83

inducible gene

Back 83

manages differentiated functions; responds to stress signals, growth factors, etc.

Front 84

Coordinated control of catabolites (prokaryotes)

Back 84

activate catabolic genes appropriate for substrate availability (i.e., Glc vs EtOH); lack of an appropriate end product will elicit synthetic pathway (i.e., no Trp present, make some!)

Front 85

polycistrionic

Back 85

regulated in a controlled way

Front 86

3 components of an operon

Back 86

protein coding sequence + shared promoter + regulatory site

Front 87

3 genes that contribute to utilization of Lac

Back 87

Y transports lac into cell
Z cleaves lactose into galactose & glc (?)
A removes nonmetabolites

Front 88

Regulation of Trp

Back 88

if trp is present, it creates a holopressor and binds to the repressor operon and shuts off production.

Front 89

Regulation of Lac

Back 89

lactose binds to the operon to induce Lactase production

Front 90

Catabolite Repression in E. Coli

Back 90

occurs when it changes metabolism for its preferred substrate (i.e., wants Glc in a mixture of Lac & Glc); if Glc is gone, must switch to Lac metabolism:
decr Glc increases adenylyl cyclase activity to create cAMP from ATP; cAMP activates CAP which binds to the operon to initiate Lac production.

Front 91

DNA Binding Proteins

Back 91

DBPs; regulate transcription and are themselves regulated by other molecules (i.e., CAP, cAMP); can do positive or negative control.

Front 92

Regulation of Eukaryotes

Back 92

done by 3 classes of genes, I, II, III, each with their own same-named RNA polymerase.

Front 93

3 types of promoters in eukaryotes

Back 93

1. TATA (-25 to -35)
2. Initiator (a degenerate consensus sequence near the start point.
3. TATA-less & initiator-less GC rich sequence.

Front 94

Enhancers/Silencers

Back 94

distal TF binding sites that increase or decrease transcription, regardless of their position.

Front 95

TFIID

Back 95

forms a TATA binding protein complex, which radically changes the shape of its promoter region.

Front 96

TFIIH

Back 96

helicase, ATPase (opens promoter)
CTD kinase (initiates pol II)

Front 97

Types of DBPs (4) & their function

Back 97

modulate the process of transcription; they take the following forms:
Helix-turn-helix (2 alpha helices bound together)
Helix-loop-helix
Zinc fingers
leucine zippers

Front 98

Hox genes

Back 98

homeotic genes; make homeobox proteins; a helix turn helix
Control morphology of vertebrae, segmentation and limb digitation

Front 99

TFIID-linked diseases

Back 99

Xeroderma Pigmentosum, Cockayne Syndrome, trichothiodystrophy

Front 100

Von Hippel-Lindau Disease

Back 100

rare; multiple organ system tumors;
occurs when VHL tumor suppressor gene is mutated; it cannot bind to elongin B, C, therefore does not initiate ubiquitin ligase complex; this allows the Hypoxia Inducing Factor to run rampant and angiogenesis occurs.

Front 101

Hypoxia Induced Factor (HIF)

Back 101

synthesizes more vessels; key for advancing tumor size

Front 102

Growth Hormone problems

Back 102

result from mutations in Pit-1 and PROP-1; causes short stature syndrome.

Front 103

nucleosome

Back 103

fundamental subunit of chromatin

Front 104

histone

Back 104

spool around which 142 bp DNA will wind for compression; made of a tetramer and 2 dimers.

Front 105

chromosome arms

Back 105

P=petite
Q

Front 106

dark stain bands vs light stain bands

Back 106

dark=AT rich
light=GC rich

Front 107

chromatin decompression occurs during what phase of the cell cycle

Back 107

interphase; required for normal cellular processes & for replication during S phase.

Front 108

Position Effect Variegation

Back 108

depending on a gene's location, expression can be silenced or enhanced.

i.e., "white" gene in drosophila can be moved and therefore will express white eyes; otherwise it normally expresses red.

Front 109

Epigenetics

Back 109

modifies bases, not the sequence, via methylation of C (inactivates) and acylation of histones (activates)

Front 110

Dosage compensation

Back 110

deactivation of one allele (i.e., in XX, one becomes Barr body); mediated by Xist RNA (very unstable)

Front 111

Deactivation of genes and their segregation

Back 111

Deactivation is random, but segregation is specific (every daughter cell of a given cell with a given deactivated gene will all have the same gene deactivated)

Front 112

imprinted

Back 112

inactive; not expressed; i.e., a Barr body is imprinted.

Front 113

Prader-Willi Syndrome

Back 113

mental retardation, hypotonia & poor feeding infancy leads to obesity in adulthood and short stature; due to deletion of paternal 15q11-q13 (maternal equivalent gene is imprinted, therefore disease manifests)

Front 114

Angelman Syndrome

Back 114

severe retardation, seizures, jerky gait, large mouth & tongue, excessive laughter; due to deletion of maternal 15q11-q13 (paternal equivalent gene is imprinted, therefore disease manifests)

Front 115

Rett Syndrome

Back 115

X-linked; increasing inability to speak/walk; progressive dementia leading to death; problem with methyl cytosine binding protein encoding gene (MECP2)

Front 116

ICF Syndrome

Back 116

mutation of de novo methyltransferase (DNMT3); causes immunodeficiency, facial anomalies and chromosomal instability.

Front 117

ATRX mutations

Back 117

Chromatin Remodeling Protein

causes retardation, urogenital abnormalities and alpha thallesemia.

Front 118

Differences in transcription by eukaryotes & prokaryotes

Back 118

euks uncouple transcription/translation due to nuclear envelope, RNA processing and transport; also, each protein has its own mRNA

Front 119

Modifications of euk mRNA

Back 119

100-200 residue poly A tail (poly A transferase) on poly A site (AAUAA)

5' cap on triphosphate bridge

increase stability of mRNA

neither modification is part of DNA transcript

Front 120

Splicing

Back 120

removal of introns and gluing together of exons

Front 121

Method of splicing

Back 121

A residue of intron attacks the intron/exon border at the 5' end, and forms a lariat. In turn, the 3' end of that exon attacks the intron/exon border on the 3' end, popping out the intron and sticking the exons together.

Front 122

purpose of alternative splicing

Back 122

expand the already enormous potential of a given genome by splicing transcript in ways not oulined in original code; changing the sequences will form different products.

Front 123

Silent mutation

Back 123

1. no abnormal (still functioning) phenotype results
2. mutated codon still codes for same protein and normal phenotype results.

Front 124

RNA editing

Back 124

post transcriptional changes in RNA sequence; Adenine becomes Inositol
i.e, apoplipoprotein B codes for 1 protein in the liver and another in the sm intestine.

Front 125

Start codon

Back 125

AUG (methionine)

Front 126

Stop Codons

Back 126

UAA, UAG, UGA

Front 127

what does it mean to say that DNA is "comma-less"

Back 127

changing 1 codon may alter other codons--esp in the case of a 1 nt insertion/deletion

Front 128

nonoverlapping

Back 128

codons only read in distinct triplets

Front 129

degenerate

Back 129

multiple codons will call for the same AA

Front 130

universal

Back 130

codons mean the same thing among species.

Front 131

missense mutation

Back 131

substitution of 1 AA for another

(not the same as a frameshift)

Front 132

nonsense mutation

Back 132

replace a regular codon with a stop codon

Front 133

Function of tRNA

Back 133

acts as an adaptor between mRNA and AA sequence; its sequence is anticomplementary to mRNA's (i.e., the position 1 of tRNA complements pos. 3 on mRNA, etc.)

Front 134

unique features of tRNA

Back 134

1/2 of bases are intrastrand pairs (forms cloverleaf), all bases modified (i.e., A to I); 3' end has codon CCA + AA

Front 135

Wobble

Back 135

tRNAs recognize multiple codons--alternate base pairing possible between pos 3 codon and 1 anticodon; others are standardized. Alternate pairing is especially true with inosine.

Front 136

Function of Aminoacyl-tRNA Synthetase

Back 136

proofreads on one site and edits on another

Front 137

Ribosome & its surfaces

Back 137

ribonucleoprotein with surfaces to catalyze protein synthesis; E site, P, site and A site. (A "arrival" and E "exit")

Front 138

Selenocysteine

Back 138

builds selenoproteins; mutations of Sec cause congenital muscular dystrophy w/ spinal rigidity (RSMD1) and associated myopathies.

Front 139

Steps of eukaryotic translation (12)

Back 139

1. tRNAi initiates synthesis via aminoacyl tRNA synthetase to form initiation complexes
2.IFs anchor mRNA in a loop attached by 5' cap and poly a tail
3. eIF4 unwinds 2' structure
4.initiation complex seeks out 5' cap, then the 1st AUG in the Kozak sequence.
5.Ribosome units converge
6.GTP hydrolyzed from eIFs and they depart
7. tRNAi is in P site, ready for elongation.
8. GTP binds EF1alpha
9. peptidyl transferase forms peptide bonds
10. EF2-GTP translocates tRNAs
11. stop codon recognized by RFs
12. RFs hydrolyze peptide and ribosome dissociates.

Front 140

Excess TPO

Back 140

a restructured 5' sequence eliminates AUG#7 thereby giving a clear and efficient start point at AUG #8. Consequently TONS of thrombopoietin is made.

Front 141

MDM2

Back 141

incr tumor activity b/c mechanism for degrading the tumor suppressor is enhanced.
elimination of pre start codon AUGs #1 & #2 allow for clear efficient start point; NORMAL cells show inefficient translation, and a decrease in tumor activity.

Front 142

Cyclohexamide

Back 142

binds to 60S subunit; decr peptidyl transferase (eukaryotes)

Front 143

Chloramphenicol

Back 143

binds to 50S subunit; decr peptidyl transferase (prokaryotes)

Front 144

Puromycin

Back 144

Binds to 60S and 50S subunits and causes premature chain termination

Front 145

Streptomycin

Back 145

inhibit initiation on 30S ribosome (prokaryotes)

Front 146

Erythromycin

Back 146

inhibit translocation on 50S ribosome (prokaryotes)

Front 147

Tetracycline

Back 147

binds to 30S subunit and prevents aminoacyl-tRNA binding.

Front 148

Consequences of Premature translation termination

Back 148

Duchenne & Becker muscular dystrophies
Cystic Fibrosis

Front 149

Aminoglycoside antibiotics

Back 149

enhances aminoacyl-tRNA activity to facilitate read-throughs of nonsense mutations in order to form functional proteins.

Front 150

Diptheria toxin

Back 150

decreases activity of EF-2, causing efflux of water and Cl- into gut lumen.

Front 151

Ricin

Back 151

depurinates specific A residue on 28S ribosome; works very fast.

Front 152

Steps of Prokaryotic Translation

Back 152

1. IF-1 & IF-3 keep the 30S ribosome free
2. IF-2 joins 30S, kicking IF-3 out
3. fMet tRNA binds via GTP
4. IF-1 & IF-2 dissociate and 50S ribosome joins.
5. EF-Tu & EF-G elongate polypeptide with GTP
6. peptidyl transferase translocates
7. RFs recognize stop codon and cleave polypeptide, break up ribosome.

Front 153

Role of translation in innate immunity

Back 153

N-fMet peptides are powerful chemoattractants for neutrophils. They are often found on plasma membrane.

Front 154

Signal sequence

Back 154

hydrophobic residues at the N-terminus of a protein, 13-36 AAs long; directs proteins to their target loci.

Front 155

free ribosome protein products

Back 155

intracellular

Front 156

ER ribosome protein products

Back 156

secretory

Front 157

SRP & SRP Receptor

Back 157

SRP contacts the signal sequence in the cytosol and guides it to the appropriate SRP receptor at the intended organelle; translation completes through the SRP receptor.

Front 158

Topological classes of proteins

Back 158

I: cleavable signal, COO- (insulin, LDL)
II: no cleavable signal, NH3+ (influenza, transferrin)
III: no cleavable signal, COO-
IV: multi (GPCRs, Voltage Ca2+, GLUT1), COO-

Front 159

Zellweger Syndrome

Back 159

peroxin Pex2 mutated membrane proteins impair transport into peroxisome; causes empty peroxisomes; brain, kidney, liver don't survive.

Front 160

Constitutive Secretory Pathway

Back 160

secretory vesicles bud out at will

Front 161

Regulated Secretory Pathway

Back 161

secretory vesicles at the ready but do not bud out of cell until requested by hormone or neurotransmitter signal.

Front 162

Lysosome-bound protein tags

Back 162

added at the Golgi; mannose-6P on an N-linked oligosaccharide.

Front 163

I-cell disease

Back 163

no enzymes in the lysosome due to a lack of mannose-6P tagged proteins b/c of a deficiency in the enzyme that does the tagging (GlcNAc-Phosphatase); allows for lysosomal enzymes in circulation.

Front 164

receptor mediated endocytosis

Back 164

used for uptake of soluble proteins and large molecular weight materials; ligand binding to receptor causes intake (i.e., LDL)

Front 165

Protein modifications in the ER

Back 165

glycosylation, disulfide bonds, proteolytic cleavage

Front 166

dolichol function

Back 166

carries oligosaccharides and deposits it on Asp residue; part of post-translational modification.

Front 167

alpha 1 antitrypsin

Back 167

inhibits trypsin and blood protease elastase; important in hereditary emphysema

Front 168

hereditary emphysema

Back 168

point mutation prevents proper folding of alpha 1 antitrypsin & it accumulates in the ER; w/o it, elastase runs unchecked and degrades lung tissue.

Front 169

ubiquitin tags

Back 169

damaged proteins tagged with ubiquitin and subsequently degraded by proteasome.