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CMB > CMB Exam 1 - All > Flashcards

CMB Exam 1 - All Flashcards

1
Q

linkage equilibrium

A

Used to describe the relationship between loci that segregate independently. If genes sort independently then we say we have linkage equilibrium, if there is an association of certain combinations of genes with a disease phenotype then we have linkage disequilibrium.

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2
Q

stearic acid

A

18:0; meat. Non-essential.

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3
Q

vitamin K

A

The only fat soluble cofactor. Helps modify key proteins including clotting factors.

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4
Q

IF-3

A

In prokaryotes, binds to the 30S subunit to prevent premature association with the 50S subunit.

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5
Q

cystic fibrosis

A

Autosomal recessive disorder with over 1000 diff pathogenic variants of CFTR gene (allelic heterogeneity)

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6
Q

Describe the orientation of microtubules in axons vs dendrites.

A

In axons, microtubules all extend with the + end projecting down the axon. In dendrites, they arrange themselves in antiparallel fashion.

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7
Q

diphtheria toxin

A

Inhibits eEF-2 and prevents translocation

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8
Q

quiescence

A

Temporary cell cycle arrest, initiated by p53.

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9
Q

linoleic acid

A

18:2 (Ω-6/2); vegetable oils, corn, soya grains, flax. Essential.

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10
Q

base analogs

A

erroneously incorporate into DNA; eg 5-Bromouracil

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11
Q

xanthelasma palpebrarum

A

Cholesterol accumulation around the eyelids, often due to familial hypercholesterolemia

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12
Q

cytochalasin B & D

A

Fungal toxin that binds to the + end of actin filaments to block elongation. Causes break up of filaments and inhibits mitosis.

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13
Q

p53

A

“Guardian of the genome”. Tumor suppressor gene activated in response to DNA damage; induces p21 (a CKI inhibitor) to inhibit G1/S-CDK and S-CDK. Mutated in more than 50% of cancers.

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14
Q

Z disc (sarcomere)

A

Marks bounds of the sarcomere. Actin projects from here.

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15
Q

intrinsic (mitochondrial) cell death pathway

A

Mitochondrial integrity is compromised causin release of cytochrome c (and stuff) to initiate apoptosis (regulated by Bcl-2 family). Cytochrome c facilitates interaction of Apaf 1 with the procaspase-9 CARD domain.

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16
Q

PKC

A

Activated by DAG. Phosphorylates lots of stuff.

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17
Q

allozygous

A

Individuals have the ancestral gene by chance, NOT by inheritance.

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18
Q

Restriction point

A

Cells that pass this point are committed to pass into S phase.

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19
Q

Cyclin E

A

Expressed late in G1. Required for passage through the restriction point into S phase.

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20
Q

PI 3-kinase

A

Turned on by IRS-1 phosphorylation in the insulin tyrosine kinase receptor pathway. Phosphorylates PIP2 to PIP3, which activates Akt. Akt activation leads to GLUT4 insertion and glycogen synthase activation.

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21
Q

snRNA

A

(small nuclear) These form part of the spliceosome, which cuts introns out of maturing mRNA molecules.

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22
Q

translation initiation in prokaryotes

A

First, amino acid activation via aminoacyl-tRNA synthtases. Then, 30S subunit binds IF-1 and IF-3 to prevent premature binding of tRNA and 50S, respectively. Binding of AUG on mRNA to P site of 30S is guided by the Shine Dalgarno sequence. IF-2*GTP+fmet-tRNA bind to 30S forming the pre-initiation complex, and fmet-tRNA binds to the RNA. The 50S subunit arrives, the GTP is hydrolyzed, and the IF’s all leave. This completes the initiation complex.

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23
Q

membrane asymmetry (apoptosis)

A

Translocation of phosphatidylserine to the outer leaflet of the membrane (membrane flips inside-out).

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24
Q

E2F

A

Transcribes genes necessary for S phase transition. Suppressed by Rb.

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25
Q

What is the effect of cholesterol in plasma membranes?

A

Increased cholesterol makes the membrane more orderly, more rigid, less fluid. We see this especially in the brain and other tissues.

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26
Q

Ink4 family

A

A CKI (Cdk inhibitor) family that inhibits Cdk4 and Cdk6, thus inhibiting G1 phase.

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27
Q

anticipation

A

With each generation, onset happens earlier and is more severe

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28
Q

isomerases

A

Enzyme that converts a molecule from one isomer to another (like changing chirality, etc)

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29
Q

“poor metabolizer”

A

Absent or greatly reduced ability to clear or activate drugs. High risk of toxic doses.

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30
Q

Explain how mitochondria import proteins.

A

First, the OM has porins that allow passage of proteins. The protein has an N-terminal signal sequence with multiple + AAs to help it find TOM (and TIM, since the IM is -). Molecular chaperones (Hsp70) losely hold the protein and prevent it from folding so it can cross. Proteins in the TIM complex drve protein import with the help of ATP.

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31
Q

function of rough ER

A

Synthesis of proteins destined for export, endosomes/lysosomes, or membrane; protein sorting; oxidizing environment allows disulfide bond formation (w/ protein disulfide isomerase); oligosaccharyl transferase starts N-linked glycosylation of Asn (with help of dolichol); attaches glycosyl phosphatidyl inositol (GPI) anchors for membrane proteins;

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32
Q

helix-loop-helix domain

A

Contain DNA-binding proteins formed by dimerization of two polypeptide chains

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33
Q

Euchromatin

A

Relaxed DNA, ready for replication

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34
Q

kuru

A

Transmittable spongiform encephalopathy (from eating dead family members’ brains). Prions.

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35
Q

vincristine

A

Binds to tubulin & selectively inhibits rapidly dividing cells. Anti-cancer drug.

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36
Q

proline

A

“imino acid” with a 5 member ring

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37
Q

Z form DNA

A

CG and 5-methyl CpG rich regions; left hand turn

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38
Q

colcemid

A

Binds tubulin & inhibits microtubule polymerization, disrupting mitosis in metaphase. Anti-cancer drug.

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39
Q

O^6 methylguanine

A

alkylated form of guanine (MNNG); repaired by O^6 methylguanine methyltransferase

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40
Q

Cdk4

A

Serine/threonine kinase that is active in G1 phase when bound to CycD. Inhibited by Ink4 CKIs.

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41
Q

profilin

A

Stimulates the exchange of ATP for ADP in actin, facilitating repolymerization.

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42
Q

nonsense mutation

A

Point mutation resulting in the errant introduction of a stop codon (truncating the protein).

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43
Q

cilia

A

Motile cytoplasmic projections made up of 9 microtubule doublets; in mammalian cells, they move mucus. Cilia are much shorter than flagella. Core “axoneme” allows bending.

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44
Q

insulin receptor process

A

When insulin binds tyrosine kinase receptors dimerize and then phosphorylate each other. Next they phosphorylate IRS-1 (scaffold protein). Phosphorylated IRS-1 scaffolding can activate GRB2/Ras pathway (alters gene expression), or it can activate PI-3 kinase (phosphorylates PIP2 to PIP3 which activates Akt, triggering the insertion of new GLUT4 channels and activation of glycogen synthase).

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45
Q

penetrance

A

The likelihood that someone with the disease genotype will manifest symptoms (it’s binary, do they have it or do they not?)

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46
Q

Edwards syndrome

A

trisomy 18

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47
Q

small amino acids

A

glycine, alanine

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48
Q

pro-apoptotic Bcl-2 family proteins

A

Bax, Bak, Bid, Bad, Bim

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49
Q

pertussis toxin

A

(bordetella pertussis) ADP-ribosylates the Gi subunit locking it in inactive conformation, resulting in increased cAMP and loss of cilia in the respiratory track. Cannot move mucus = whooping cough.

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50
Q

nonsyndromic deafness

A

Inherited deafness, can be either autosomal dominant or recessive. Locus heterogeneity.

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51
Q

rifampicin

A

Inhibits mitichondrial RNA polymerase

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52
Q

next-generation sequencing

A

“not routinely done but coming soon”??

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53
Q

MERRF

A

(myoclonic epilepsy with ragged red fibers) mtDNA disease

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54
Q

A form DNA

A

dry

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55
Q

p120

A

Stabilizes the actin/cadherin/catesin complexes in adherens junctions.

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56
Q

5-fluorodeoxyuracil

A

Nucleotide analog used to treat cancers of the colon, pancreas, stomaach, esophagus, and breast.

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57
Q

Describe the formation of the 3’ end of eukaryotic mRNA

A

There’s a U- or GU- rich sequence sequence downstream of the gene; this signals endonuclease cleavage at the polyadenylation site. Poly-A polymerase adds the tail.

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58
Q

Name the non-essential fatty acids.

A

Palmitic acid, stearic acid, oleic acid.

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59
Q

B form DNA

A

normal

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60
Q

Where are sphingolipids synthesized?

A

Ceramide from the smooth ER are processed into sphingolipids like sphingomyelin in the Golgi.

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61
Q

IF-1

A

In prokaryotes, prevents premature binding of tRNA to the A site of the 30S subunit.

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62
Q

secondary structure (protein)

A

Regular, repetetive pattern that emerges when all the phi and psi angles are the same (eg a-helix, b-sheet)

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63
Q

Gaucher’s disease

A

Lysosomal storage disorder. Deficiency in the beta-glucosidase (aka glucocerebrosidase) enzyme results in the accumulation of glucosylceramides in the lysosomes. Common in Jewish populations (1:2500)

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64
Q

Cyclin D

A

Induced by growth factors or mitogens early in G1 phase. Determinw whether a cell should divide in response to external stimuli.

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65
Q

sulfur amino acids

A

cysteine, methionine

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66
Q

beta-galactosidase

A

Cleaves lactose into glucose and galactose (lac operon)

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67
Q

microtubules: FUNCTION

A

Cell shape, mitotic spindle, intracellular transport of big stuff, axonal transport, cilia & flagella translocation of mRNA?

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68
Q

xeroderma pigmentosum (XP)

A

Results from lost ability to perform nucleotide-excision repair (mutated XPA-XPG products). Presents with cutaneous photosensitivity.

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69
Q

calnexin

A

checks that proteins are folded corectly

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70
Q

mismatch repair (prokaryotes)

A

Possible in the hemimethylated state (strand differentiation). RECOGNITION: MutS recognizes mismatch, recruits MutL which recruits MutH which identifies the daughter strand (thanks to hemimethylation). REMOVAL: MutH is an endonuclease and cleaves up methylated strand at GATC sequence; MutS and MutL work with DNA helicase and exonuclease to excise DNA between mismatch and break. DNA polymerase and DNA ligase fix hole.

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71
Q

Mendel’s Principle of Independent Assortment

A

Segregation of one pair of alleles is independent of the segregation of other pairs.

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72
Q

Review the breaking of high-energy bonds in the addition of 1 AA to a polypeptide.

A

4 bonds per AA: 2 high energy phosphate bonds are broken to activate the amino acid (ATP -> AA*AMP + 2Pi; AA*AMP -> AA-tRNA + AMP); 1 to bind the AA-tRNA in the ribosome (EF-Tu*GTP -> EF-Tu*GDP +Pi), 1 to translocate (EF-G uses GTP hydrolysis to fuel the translocation).

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73
Q

cholera toxin

A

(vibrio cholerae) toxin is endocytosed and ADP-ribosylates the Gs subunit (to inactivate its GTPase). Since it’s stuck in active mode, continuous cAMP production resulting in massive water loss through intestines.

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74
Q

PrP^Sc

A

“scrapie” abnormal, pathological refolding product of PrP^C

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75
Q

translation initiation in eukaryotes

A

eIF-2*GTP+fmet-tRNA binds with the 40S subunit. 40S recognizes the 7-methylguanosine cap on the 5’ terminus and then scans downstream until it finds an AUG initiation codon. GTP is hydrolyzed, followed by the dissociation of the eIF’s and the binding of the 60S subunit.

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76
Q

mannose-6-phosphate

A

In the Golgi, tags proteins for the lysosome

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77
Q

frameshift mutation

A

shifts the code up or down

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78
Q

amino acid activation

A

First, ATP and amino acids react to form an adenylated amino acid +2P. The AA-AMP and the tRNA are then acted on by aminoacyl-tRNA synthetase to esterify them together.

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79
Q

actin: FUNCTION

A

Cell movement, cell adhesion, mitosis, other structure and movement stuff.

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80
Q

G proteins (3 types)

A

Beta/gamma and alpha subunits anchored to membrane by 7-helix transmembrane region. When ligand binds the subunits dissociate and alpha exchanges GDP for GTP (GTPase will eventually hyprolyze it back to GDP). Gs activate adenylyl cyclase (Gi inhibit), which makes cAMP from ATP. Gq activates phospholipase C, which breaks down PIP2 to IP3 and DAG.

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81
Q

PCR: purpose

A

(Polymerase chain reaction) IF we know enough about the nucleotides around the target gene to make a primer for the right spot, target gene can be selectively amplified from complex mixtures.

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82
Q

nonhomologous end joining

A

Fixes accidental double strand break in the absence of the sister chromatid. Final product has deletion of DNA sequence due to degradation from break ends.

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83
Q

vitamin B12

A

Only vitamin that possesses a metal ion (Co++). Involved in methyl transfer reactions.

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84
Q

Pex genes

A

ER membrane proteins that enable peroxisome budding.

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85
Q

V1 receptors

A

GPCR; vasopressin acts on specific V1 receptors to increase intracellular Ca++ and stimulate contraction of smooth muscle.

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86
Q

puromycin

A

Resembles aminoacyle-tRNA and binds to A-site, causing premature release of polypeptide chain in PRO and EU

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87
Q

Describe the spliceosome process

A

The 5’ end of U1 snRNA recognizes the 5’ splice site of pre-mRNA. U2 snRNA recognizes the branch site of pre-mRNA, and binds U1, folding the RNA over. U4/U6 and U5 snRNPs joins the complex and form the intron loop at the branch point.

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88
Q

AP endonuclease

A

in base-excision repair, RECOGNIZES and EXCISES damaged base (eg deaminated cytosine (U)) leaving an AP site

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89
Q

RNA polymerase 3 (eukaryotes)

A

Synthesizes tRNA, and some snRNA and scRNA. Also synthesizes 5S rRNA. Sensitive to a-aminitin.

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90
Q

beta’ subunit of bacterial RNA polymerase

A

Helps with DNA binding

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91
Q

Describe transcription in prokaryotes

A

RNA polymerase binds the promoter (at -10 and -35 bp upstream) to initiate. Polymerase unwinds 12-14bp DNA, forming open complex. After ~10 nucleotides are added, sigma is released. Stop signal is a polyGC region (hairpin) followed by either polyA or its Rho protein.

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92
Q

initiation complex (prokaryotic translation)

A

Comprises the 30S subunit, mRNA, fmet-tRNA, and 50S subunit. The GTP was hydrolyzed and the IF’s dissociated.

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93
Q

What are the (4) morphological features of apoptosis?

A

Chromosomal condensation, cytoplasmic blebbing, apoptotic bodies, cell shrinkage.

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94
Q

doxorubicin

A

human type II topoisomerase inhibitor; chemotherapeutic

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95
Q

lac a gene

A

Codes for transacetylase, which inactivates toxic thiogalactosides that are transported into the cell along with lactose (lac operon)

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96
Q

Rb

A

Substrate of G1/S-Cdk. Rb binds/suppresses E2F, releases when Rb gets phosphorylated.

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97
Q

Rho protein (prokaryotes)

A

Termination protein that binds extended segments of ssRNA (prokaryotic transcription).

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98
Q

Variant CJD

A

“Mad cow”. Transmittable spongiform encephalopathy. Prions

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99
Q

warfarin (Coumadin)

A

Used for treatment and prevention of thromboembolic events. Narrow therapeutic window, 20% hospitalization rate for new patients.

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100
Q

Allopurinol

A

A purine analog used to treat gout

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101
Q

posttranslational translocation into the ER

A

Chaperones escort completed polypeptides to the translocon where the Sec62/63*BiP complex regulates the entrance of proteins into the lumen. BiP brings them in.

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102
Q

thymidine kinase

A

Protein that’s a target of study for transcription initiation. Has two cis-acting regulatory sequences: TATA box and GC boxes, with a CAT box in between the GC boxes.

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103
Q

hydroxyl amino acids

A

serine, threonine (and tyrosine)

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104
Q

eEF-1alpha

A

In eukaryotes, complexes with GTP and escorts the AA-tRNA to the A site of the ribosome.

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105
Q

dynein

A

Motor protein that moves towards the - end of microtubules.

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106
Q

interphase

A

Chromosome/centrosome duplication and cohesion

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107
Q

benzo[a]pyrene

A

carcinogen from cigarettes: oxidized within cells and then covalently binds to guanine, distorting helix

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108
Q

cofilin

A

(aka ADF, actin depolymerizing factor) Controls rate of actin depolymerization in 3 ways 1) Enhances rate of dissociation from - ends, 2) can sever filaments to increase degradation, and 3) binds to ADP-actin monomers to prevent exchange for ATP.

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109
Q

CAP

A

(catabolite activator protein) Is stimulated by binding cAMP (low glucose) to bind upstream of lac operon, facilitating the binding of RNA polymerase

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110
Q

neurofibromatosis

A

Condition with variable phenotype ranging from cafe au lait spots (abnormal pigmentation) to cancerous growths, ADHD, hypertension, learning disabilities, reduced stature, large head, etc. Peiotropic.

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111
Q

Where are mitochondrial proteins synthesized?

A

In the cytosol by free cytosolic ribosomes.

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112
Q

Describe transcription in eukaryotes

A

First, TFIID (includes TATA binding factor TBP and TAF’s) binds promoter, then TFIIB binds TBP and the BRE sequences. RNA pol II and TFIIF bind, and then recruit TFIIE and TFIIH (phosphorylates C terminal domain serine-5 residues), completing the preinitiation complex. The mediator complex is also necessary for initiation.

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113
Q

Wee1 kinase

A

Phosphorylates M-Cdk to inactivate it.

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114
Q

deamination of cytosine

A

Mutation that turns cytosine to uracil

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115
Q

Beriberi

A

Caused by deficiency of thiamin.

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116
Q

early endosomes

A

Where endocytosed vesicles hang out when the first come in. Once vesicles from the Golgi that have acid hydrolases fuse, they become lysosomes.

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117
Q

G2 phase

A

RNA and protein synthesis continues.

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118
Q

autophagy

A

Cytosolic membranes, damaged/sensescent stuff or mitochondria can be recycled. often an attempt to survive nutrient-deprived conditions.

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119
Q

ganglioside

A

Ceramide + carb chain (+sialic acid)

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120
Q

DOPA Decarboxylase

A

Requires pyridoxal phosphate.

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121
Q

EF-Ts

A

In prokaryotes, facilitates the regen of EF-Tu*GTP by removing the GDP after hydrolysis.

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122
Q

deaminating agents

A

eg nitrous acid (HNO2); Convert adenine, guanine, and cytosine into hypoxanthine, xanthine, and uracil, respectively

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123
Q

Palade experiment

A

Pulse & chase experiments in pancreatic acinar cells; label newly synthesized proteins with radio-labeled amino acids and watch where they go.

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124
Q

Creutzfeldt-Jacob disease

A

Non-transmittable (among humans) spongiform encephalopathy. Prions.

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125
Q

transferases

A

Enzyme that transfer a group from one molecule to another, Kinases transfer phosphate from ATP to a second substrate,

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126
Q

sphingolipids

A

Primary components of membranes in nervous tissue. Similar to phosphoglycerides, but they have sphingosine instead of glycerol. Sphingosine + fatty acid (amide bond NOT ester bond) = ceramide, + sugar = glycosphingolipid.

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127
Q

prophase

A

Chromosome condensation; breakdown of “interphase microtubule display” and their replacement with mitotic astes; mitotic aster separation.

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128
Q

Cyclin A

A

Induced at late G1 after cyclin E. Required for initiation of DNA replication.

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129
Q

basic amino acids

A

lysine, arginine, histidine

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130
Q

a-helix

A

H-bonds align parallel with helical axis. Proline is too rigid, glycine is too flexible. Appears in short segments (

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131
Q

S phase

A

After passing through the restriction point (requires cyclin E, Cdk2), DNA synthesis doubles the DNA in the cell (requires cyclin A, Cdk2/Cdk1) for initiation. RNA and protein also synthesized.

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132
Q

Cdk6

A

Serine/threonine kinase that is active in G1 phase when bound to CycD. Inhibited by Ink4 CKIs.

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133
Q

Sanger sequencing

A

Introduce tagged dideoxynucleotides to halt replication; separate via electrophoresis and see what base they ended on to get sequence.

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134
Q

alpha subunit of bacterial RNA polymerase

A

Helps with chain initiation

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135
Q

ATR

A

Checkpoint protein. Recognizes and binds single strand breaks or unrecognized DNA; activates (phosphorylates?) Chk1to inhibit Cdc25 (via phosphorylation?) and arrest cell cycle.

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136
Q

carbamino hemoglobin

A

Formed in high CO2 conditions; CO2 binds covalently and decreases O2 affinity.

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137
Q

Which are the effector caspases?

A

Caspases 3, 6, and 7.

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138
Q

imprinting

A

Different genes are expressed depending on the parental origin of the gene (methylation, gene silencing) eg Prader-Willi syndrome vs Angelman syndrome

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139
Q

CsB

A

(aka ERCC6) Recognizes stalled RNA polymerase at site of DNA damage. Recruits CsA, XPA, RPA, TFIIH.

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140
Q

nucleotide-excision RECOGNITION

A

RECOGNITION = XPC which recruits XPA, RPA and TFIIH (contains XPB and XPD); TFIIH unwinds ~25bp bubble.

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141
Q

locus heterogeneity

A

Mutations in different genes can cause the same disease

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142
Q

ataxia-telangiectasia

A

Results from defective checkpoint protein ATM (Chk2). Presents with loss of motor coordination, immune deficiency, chromosome breaks, lymphomas, leukemia.

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143
Q

tRNA structure

A

Single strand of RNA with guanylate (pG) on the 5’ end and CCA as the amino acid binding site on the 3’ end. Codon recognized by complementary base pairing at the anticodon; 1st base of anticodon pairs with 3rd of codon (5’-3’).

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144
Q

What is the most common stop signal during transcription in prokaryotes?

A

Symmetrical, inverted repeat of a GC-rich sequence followed by seven A residues (forms a stem loop and a poly U tail)

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145
Q

allelic heterogeneity

A

Different mutations in the same gene can cause the same disease

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146
Q

lac z gene

A

Codes for beta-galactosidase, which cleaves lactose into glucose and galactose (lac operon)

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147
Q

Cdk1

A

Serine/threonine kinase that is active in the G2/M transition when bound to cyclin A, or in M phase when bound to cyclin B. Inhibited by Cip/Kip family CKIs.

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148
Q

restriction endonucleases

A

Cleave DNA at specific palindromic sequences

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149
Q

22q11 deletion syndrome

A

Autosomal dominant deletion on chromosome 22 affecting 1:68 individuals with congenital heart defects (associated with truncus arteriosus and tetralogy of Fallot). Can cause cleft palate, learning disabilities, hypocalcemia, etc.

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150
Q

Intron

A

sequence of gene usually spliced out - typically serve as recognition sites for exon splicing and recombination sites, and exon shuffling. Histones do not have any introns.

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151
Q

“next generation” sequencing

A

Err:509

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152
Q

pleiotropy

A

When one gene affects more than one phenotypic trait or organ system

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153
Q

Paracrine

A

cell messenger that relies on diffusion

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154
Q

tetracycline

A

Inhibits binding of aminacyl-tRNA to A site in PROKARYOTES

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155
Q

ERCC (1 & 6)

A

excision repair cross-complementing genes; ERCC1 + XPF excise damaged bases, ERCC6 = CsB

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156
Q

lyso-phosphoglycerides

A

One of the products of phosphoglyceride hydrolysis (eg phosphatidylcholine acted on by phospholipase A2 forms lyso-phosphatidylcholine, a component of snake venom that disrupts membrane structure).

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157
Q

On which chromosomes do you find the immunoglobin chain gene clusters?

A

Kappa light chins = 2, lamda light chains = 22, heavy chains = 14

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158
Q

I-cell disease

A

Deficiency in enzyme catalyzing the first step in tagging lysosomal enzymes with M6P in the golgi. Lysosomal enzymes are erroneously secreted into the serum.

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159
Q

function of smooth ER

A

Synthesis of glycerophospholipids, cholesterol, ceramide. Glycerol-3-phosphate and fatty-acyl CoA’s get processed in the ER membrane, leading to phospholipid synthesis on the cytosolic layer of the lipid membrane (flippases even things out).

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160
Q

GRB2

A

Adaptor protein turned on by IRS-1 phosphorylation in the insulin tyrosine kinase receptor pathway. Activates the Ras pathway and gene expression.

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161
Q

intermediate filaments: STRUCTURE

A

Contain a central alpha-helical “central rod domain” that coils with another to form a dimer (C with C, N with N). Dimers form antiparallel tetramers. Tetramers stack end to end to form protofilaments, 8 protofilaments form a filament. (eg keratin). Can be phosphorylated to inhibit assembly/facilitate disassembly (eg mitosis).

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162
Q

6-methyladenine

A

In E. Coli, formed when Dam methylase methylates the N^6 position of A residues in the GATC sequence

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163
Q

depurination

A

Adenine or Guanine can spontaneously lose their nitrogenous base to become depurinated deoxyribose (apurinic sites)

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164
Q

Which are the initiator caspases?

A

Caspases 8 (extrinsic) and 9 (intrinsic).

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165
Q

apoptosome

A

Cytochrome c facilitates interation of Apaf1 with initiator procaspase-9 CARD domain. Activates caspase-9.

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166
Q

kinesin

A

Motor protein that walks towards the + end of microtubules.

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167
Q

arcus senilis cornea

A

Cholesterol accumulation within the iris, often due to familial hypercholesterolemia.

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168
Q

missence mutation

A

Point mutation that results in the incorporation of a different amino acid due to a single base change (possibly changing function of the protein).

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169
Q

H zone (sarcomere)

A

Clear space surrounding M line where only mysosin is present

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170
Q

Cyclin B

A

Appear at the beginning of G2 and accumulate through G2. Required for entry into mitosis.

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171
Q

choramphenicol

A

Inhibits peptidyl transferase activity of the 50S subunit

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172
Q

trp operon

A

Trp binds trp repressor to block polymerase to attenuate/limit expression.

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173
Q

IP3

A

Cleaved from PIP2 by phospholipase C. Results in Ca++ release into the cytoplasm.

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174
Q

cis-acting control element

A

Affect expression of genes on the same DNA molecule

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175
Q

G2/M checkpoint

A

Check for damaged or unduplicated DNA before mitosis.

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176
Q

exonucleases

A

Cleave nucleotides from one end, either 5’ or 3’

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177
Q

DNA glycosylase

A

in base-excision repair, RECOGNIZES damaged base (eg deaminated cytosine (U)) and break the N-glycosyl linkage, excising base and leaving an AP site

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178
Q

ascorbic acid (vit C)

A

Antioxidant: can react with superoxide. Deficiency causes scurvy.

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179
Q

Endocrine

A

Cell messenger travels via blood

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180
Q

What are the two types of self-splicing introns?

A

Group I: mediated by a guanosine cofactor. Group 2: attack by an adenosine nucleotide in the intron.

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181
Q

Dam methylase

A

In E. Coli, methylates the N^6 in A residues in the GATC sequence, forming 6-methyladenine

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182
Q

Cip/Kip family

A

A CKI (Cdk inhibitor) family that inhibits Cdk2, thus inhibiting eiher G1 phase or S and G2 phasese, depending on whether cyclin E or A is attached.

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183
Q

lac y gene

A

Codes for lactose permease, which transports lactose into the cell (lac operon)

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184
Q

fragile-x syndrome

A

X-linked dominant disease in individuals with over 200 CGG repeats in the FMR1 gene (too many repeats leads to inactivation by methylation). 50% penetrance in females, 90% in males. Most common form of inherited retardation in males. SSX: mental retardation and stereoypical phenotype, heart problems, enlarged testes, skin problems. Anticipation effect.

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185
Q

intermediate filaments: FUNCTION

A

8 things: Cell shape, cell adhesion, intracellular transport, protection in skin, positioning of nucleus, nuclear organization & heterochromatin, nuclear envelope assembly, and DNA replication.

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186
Q

myosin light chain kinase

A

Activated by calmodulin. Contractile rings form around the middle of two cells in mitosis: MLCK phosphorylates light chains in the cells which do two things: promote the assembly of myosin into filaments and then increase the myosin catalytic activity to allow contraction to take place.

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187
Q

Transcription-coupled repair

A

RNA polymerase is stalled by damage and is recognized by CsB at damage. CsB recruits CsA, XPA, RPA and TFIIH, which unwinds. XPG and XPF excise damaged bases. DNA polymerase and DNA ligase replace and rejoin.

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188
Q

Wobble hypothesis

A

In translation, the first two bases of a codon bind strongly, but the third (the first of the anticodon, aka Wobble base) pairs loosely. In the Wobble base position, U can pair either A or G, and I can pair A,U,or C.

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189
Q

b-sheet

A

H-bonds form side by side between the C=O and N-H. Can form parallel or antiparallel.

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190
Q

ubiquitination - degradation

A

STEPS: Ub is activated following attachment to ubiquitin-activating enzyme (E1). It’s transferred to ubiquitin-conjugating enzyme (E2). Ubiquitin ligase (E3) catalyzes the transfer of ubiquitin to amino group of a lysine residue on the target protein. Polyubiquinated proteins recognized by the 26S proteasome.

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191
Q

process of endocytosis

A

Foreign macromolecules bind to the receptors. Adaptors bind the receptor and to clathrin, which forms the coat and pinches off the vesicle.

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192
Q

IRE1

A

Receptor system in the ER’s unfolded protein response. Leads to activation of XP1 transcription factor.

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193
Q

nucleolus

A

Site for synthesis of rRNA

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194
Q

ribozyme

A

An enzyme made of RNA instead of protein

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195
Q

What does a high level of chaperones in a cell tell you?

A

That the cell has high levels of ER stress and needs excess chaperones to correct protein issues.

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196
Q

signal patches

A

In the Golgi, proteins recognize the 3D conformation of a protein (as opposed to a single sequence)

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197
Q

eicosepentenoic acid

A

20:5 (Ω3/5); fish oil. Essential.

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198
Q

tertiary structure (protein)

A

Higher-order folding induced by hydrophobic interactions. 100-400 AA’s.

199
Q

bacterial RNA polymerase: STRUCTURE

A

Has 5 types of subunits, sigma subunit identifies the correct sites for transcription. a2B’Bws

200
Q

alpha-1 receptors

A

GPCR; NE initiates contraction of vascular smooth muscle by raising intracellular free Ca++.

201
Q

fluorescence in situ hybridization (FISH)

A

Special fluorescent dyes are used to determine if specific abnormalities are present or absent

202
Q

lipoic acid

A

Acts as a cofactor for pyruvate dehydrogenase; attached to the enzyme through an amide bond with lysine. Helps transfer acyl group from TPP.

203
Q

palmitic acid

A

16:0; dairy. Non-essential.

204
Q

Describe the cleavage signal sequences of proteins being synthesized in the rough ER.

A

Stretch of hydrophobic amino acids, preceded by basic residues.

205
Q

long noncoding RNA’s

A

eg Xist gene on X chromosome, leads to X inactivation

206
Q

substitution (genetics)

A

Base change (mutation) carried within the population or species, as opposed to a base change in a single gene copy.

207
Q

nalidixic acid

A

bacterial type II topoisomerase inhibitor; antimicrobial

208
Q

senescence

A

Permanent cell cycle arrest, induced by p53.

209
Q

STAT

A

(signal transducer and activator of transcriiption) phosphorylated by JAK; dimerizes and enters nucleus to act as a transcription factor.

210
Q

KKXX sequence

A

Targeting sequence at C-terminus that sends TRANSMEMBRANE proteins back to the ER

211
Q

JAK kinase

A

Non-receptor protein kinases often act through this protein, which is activated after the receptor dimerizes and which phosphorylates STAT to alter transcription.

212
Q

X-gal

A

Substrate of beta-galactosidase used as an indicator to show that your cloning worked (beta-gal cleaves it to glucose and a blue precipitate if you haven’t inserted your gene into the promoter).

213
Q

oxidoreductases

A

Enzyme that catalyze oxidation-reduction reactions. (electron transfers, hydrogen transfers, and reactions involving molecular oxygen)

214
Q

prometaphase

A

Nuclear envelope breakdown (phosphorylation of intermediate fibers); chromosomes captured and oriented.

215
Q

MNNG

A

alkylating agent: attaches alkyl group to bases (adds CH3 to the O); converts guanine to O6-methylguanine

216
Q

phospholipase C pathway

A

Activated by Gq GPCRs. Cleaves phosphatidyl inosine 2 (PIP2) to inositol triphosphate (IP3) and diacylglycerol (DAG). DAG activates PKC, which phosphorylates other stuff. IP3 increases intracellular Ca++, which activates calmodulin. Calmodulin activates enzymes like myosin light chain kinase.

217
Q

ATM

A

Checkpoint protein. Recognizes and binds double strand breasks; activates Chk2 to inhibit Cdc25 and arrest cell cycle

218
Q

cycloheximide

A

Inhibits peptidyl transferase activity of the 60S ribosome

219
Q

Name the essential fatty acids.

A

Linoleic acid, linolenic acid, arachadonic acid, eicosopentenoic acid, docosohexanoicacid

220
Q

insertion

A

add a base pair (frameshift)

221
Q

peroxisomes

A

Bud off of ER. Detox cell, breakdown lipids (FAs) and toxins. Produce and degrade hydrogen peroxide using catalase. Also SYNTHESIZE: cholesterol, bile acids, lipids for myelin.

222
Q

methylation

A

Methylation of C5 in CpG dinucleotides leads to repression, mono- and dimethyl lysine are in enhancers, trimethyl lycine is in the promoter.

223
Q

pyridoxine

A

Participates in aminotransferase reactions. Also important for DOPA decarboxylase.

224
Q

heteroplasmy

A

When mitochondria divide there’s random deparation of cytoplasm, including mitochondria. This means some cells may have more diseased mitochondria than others, leading to variable expressivity.

225
Q

HDAC

A

(histone deacetylase)

226
Q

Zellweger syndrome

A

Most severe of the peroxisome biogenesis disorders

227
Q

sphingomyelin

A

Ceramide + phosphocoline. Sythesized in the Golgi.

228
Q

“ultra metabolizer”

A

Greatly increased metabolic activity, accelerating clearance or activation. Regular doses of drugs may be ineffective.

229
Q

caveolae

A

A kind of lipid raft that is very cholesterol-heavy.

230
Q

cholate derivatives

A

Bile acids. Important for digestion and absorption of fats. This is augmented by conjugating these acids with either glycine or taurine.

231
Q

phallotoxin (phalloidin)

A

Binds tightly to AFs and prevents their dissociation into G actin. Prohibits dynamic behavior.

232
Q

Explain sex differentiation in Drosophila.

A

mRNA splicing. Females express the SXL gene that helps splice out the UAG gene. Males don’t express the SXL gene, so UAG is included inthe mRNA.

233
Q

hexosaminidase A

A

Enzyme involved in lipid metabolism. When deficient, leads to the accumulation of Cer-Glc-Gal(NeuAc):GalNAc GM2 ganglioside, causing Tay Sachs disease.

234
Q

phosphatidyl inositols

A

Inositol has many hydroxyl groups, and up to 4 phosphates can be esterified there to form PIP, PIP2, PIP3, and PIP4.

235
Q

U5 snRNA

A

snRNA involved in spliceosome complex.

236
Q

cadherins

A

Mediates contact between cells in adherens junctions.

237
Q

M phase

A

Mitosis and cytokinesis. Require cyclin B, Cdk1 for entry into mitosis.

238
Q

Describe cytokine receptor mechanism

A

Cytokine receptors recruit “non-receptor protein kinases” which dimerize and phosphorylate JAK. JAK phosphorylates STAT, which dimerizes and then can enter the nucleus and act as a transctiption factor.

239
Q

phosphodiesterase

A

Degrades cAMP into AMP. Insulin activated.

240
Q

O^6 methylguanine methyltransferase

A

repairs O^6 methylguanine by transferring the extra methyl group to a cysteine residue in the enzyme

241
Q

niacin

A

NAD and NADP are e- and H+ acceptors (eg liver dehydrogenase reaction). Deficiency causes pellagra.

242
Q

start sequence in mRNA

A

AUC; codes for fMet

243
Q

IRS-1

A

Scaffold protein associated with the insulin receptor, is phosphorylated by tyrosine kinase; Recruits PI 3-kinase and/or GRB2.

244
Q

Neurocrine

A

cell messenger released in direct visinity of target

245
Q

Tay-Sachs disease

A

Deficiency in the hexosaminidase A enzyme leads to errant metabolism of lipids, forming the “Tay Sachs ganglioside”. Accumulated lipid: Cer-Glc-Gal(NeuAc):GalNAc GM2 ganglioside

246
Q

To what position in the ring is the N-glycosidic bond formed in purines? Pyrimidines?

A

N9 in purines, N1 in pyrimidines

247
Q

aromatic amino acids

A

phenylalanine, tyrosine, tryptophan

248
Q

Ribosome structure

A

PRO: 30S + 50S = 70S, EU: 40S + 60S = 80S. Small subunit provides framework for tRNA to be matched with mRNA. Large subunit catalyzes peptide bond formation. 4 binding sites: mRNA site, E site (exit), P site (peptidyl-tRNA), and A site (aminoacyl-tRNA).

249
Q

chromosome microarray analysis

A

“deletions and insertions are observed”

250
Q

LHON

A

(Leber’s hereditary optic neuropathy) Rare inherited disease causing optic nerve degeneration, caused by mutation in mitochondrial DNA that codes for NADH dehydrogenase. Since this reduces ATP capacity, CNS and optic nerve suffer most. Incomplete penetrance.

251
Q

protein disulfide isomerase

A

Housed in the rough ER; helps oxidize cysteine residues to form disulfide linkages in proteins;

252
Q

HNPCC (Lynch syndrome)

A

Autosomal dominant disease caused by mutations in 1 of 5 genes; causes up to 5% of all colorectal cancers.

253
Q

peroxisome targeting signals

A

PTS1: Ser-Lys-Leu, or SKL; PTS2; 9 AA sequence at N-terminus

254
Q

Ion Torrent PGM (sequencer)

A

Basically: world’s most sensitive pH meter. As polymerase replicates the DNA, it detects changes in pH as the pyrophosphates come off. Shortcoming: can only do small pieces of DNA.

255
Q

CTCF

A

Insulator; interacts with cohesin to limit enhancer activity.

256
Q

riboflavin

A

FMN and FAD help in oxidation/desaturase reactions like fatty acyl-CoA desaturase, which does biosynthesis of unsaturated fats.

257
Q

tautomeric shifts

A

change in pH shuffles the H’s around on DNA bases; eg the enol form of thymine can pair with guanine

258
Q

SCID

A

(severe combined immune disorder) X-linked recessive.

259
Q

beta-glucosidase

A

(aka glucocerebrosidase) Deficiency results in the accumulation of Cer:Glc Glucosylceramide, causing Gaucher’s disease.

260
Q

U4/U6 snRNA

A

snRNAs involved in spliceosome complex

261
Q

Name 4 classes of cell receptors

A

G-protein coupled receptors (GPCR), Receptor Tyrosine kinsase, Receptor-Associated tyrosine kinase, cytosolic/nuclear

262
Q

DNA photolyase

A

*not present in humans; uses light energy to repair thymine dimers

263
Q

Arp2/3

A

Facilitates branch splitting on growing actin filaments.

264
Q

Mitochondrial polymerase (eukaryotes)

A

Synthesizes mitochondrial RNA. NOT sensitive to a-aminitin, but inhibited by rifampicin.

265
Q

pre-initiation complex (prokaryotic translation)

A

Comprises the 30S subunit, IF-3, IF-1, mRNA, IF-2, GTP, and fmet-tRNA.

266
Q

mitochondria

A

Contain some DNA, ribosomes (more similar to PRO than EU), small granules, and protein for the citric acid cycle and electron transport chain.

267
Q

Where do proteins from rough ER ribosomes go?

A

Nuclear membrane, plasma membrane, vesicles, endosomes/lysosomes, or the peroxisome membrane. Basically, to membranes or lysosomes.

268
Q

streptomycin

A

Causes misreading of the genetic code in PROKARYOTES. Interferes with initiation.

269
Q

alpha-aminitin

A

Inhibits RNA polymerase II (and III)

270
Q

adenylyl cyclase cascade pathway

A

Turns ATP into cAMP, which acts on protein kinase A (and other stuff). The activated C portion of PKA can phosphorylate glycogen synthase (to inhibit), and phosphorylase kinase (to activate) which phosphorylates phosphorylase (to activate) which helps turn glycogen to glucose.

271
Q

pyknosis

A

Nuclear condensation in apoptosis

272
Q

NucleoSide

A

just the nitrogenous base and a 5 carbon sugar (ribose, deoxyribose)

273
Q

Sec62/63 complex

A

Regulates the entry of completed polypeptides into the ER through the translocon, with the help of BiP.

274
Q

lipid rafts

A

Contain sphingomyelin, glycolipids, and cholesterol-based clusters

275
Q

homeodomain proteins

A

Important in the regulation of gene expression during embryonic development

276
Q

What are the (4) main mechanisms for inducing apoptosis? As in, what happens in the cell to undergo apoptosis?

A

Activation of caspases, activation of endonuclease, membrane asymmetry, expression of eat-me signal on cell surface.

277
Q

ethidium bromide

A

intercalating agent: inserts between stacked DNA bases, resulting in frameshift mutations

278
Q

A band (sarcomere)

A

Region where actin and myosin overlap.

279
Q

autozygous

A

A homozygous individual with the ancestral gene as a result of consanguinity

280
Q

Steroid hormone receptors

A

Regulatory proteins that have zinc fingers as tthe DNA binding domain (DBD). Protected in the cytosol by heat shock proteins (HSP).

281
Q

intercalating agents

A

eg ethidium bromide, proflavin; insert themselves between stacked DNA bases, resulting in frameshift mutations

282
Q

competitive antagonism between O2 and CO

A

Hb binds CO 200 times more tightly than O2. 30%-50% CO saturation leads to: headache, confusion, and fainting. 80% CO saturation is fatal. Overcome by elevating pO2.

283
Q

autophagy

A

Cell recycles its own components to survive nutrient-deprived conditions. Too much can lead to cell death.

284
Q

Chk1

A

Checkpoint protein. Phosphorylates and inhibits Cdc25 to arrest cell cycle in the presence of single strand breaks or unreplicated DNA; activated by ATR

285
Q

branched-chain amino acids

A

valine, leucine, isoleucine

286
Q

paclitaxel/taxol

A

Stabilizes microtubules to arrest mitosis. Anti-cancer drug.

287
Q

albuterol

A

Relaxes smooth muscles, prevents premature labor

288
Q

Helix-turn-helix domain

A

One helix binds DNA, the other binds the other proteins

289
Q

eEF-1betagamma

A

In prokaryotes, facilitates the regen of eEF-1alpha*GTP by removing the GDP after hydrolysis.

290
Q

sarcomere

A

The structural unit of myofibrils, bounded by the Z discs. Actin projects from Z-discs, myosin projects from M line.

291
Q

transacetylase

A

Inactivates toxic thiogalactosides that are transported into the cell along with lactose (lac operon)

292
Q

Pacific Biosciences RS (sequencer)

A

Basically: big machine that can sequence big molecules. Shortcoming: big machine, lots of errors.

293
Q

clathrin

A

Forms endocytotic coats

294
Q

oxytosin

A

Contracts smooth muscle, induces labor

295
Q

ciprofloxacin

A

bacterial type II topoisomerase inhibitor; antimicrobial

296
Q

strand sequencing

A

Basically: a synthetic protein can “feel” the nucleotide motifs going through and sends back an electric signal.

297
Q

linolenic acid

A

18:3 (Ω-3/3); grains, flax. Essential.

298
Q

Cdc25 phosphatase

A

Activates M-Cdk via dephosphorylation. Inhibited at the checkpoints by Chk1 or Chk2 in the case of DNA damage.

299
Q

methotrexate

A

Anti-cancer drug that blocks the folic acid binding site on DHFR, preventing cell division.

300
Q

docosehexanoic acid

A

22:6 (Ω3/6); fish oil. Essential.

301
Q

Competitive inhibitor

A

Impacts Km (shifts curve to the right), but Vmax unaffected

302
Q

oligosaccharyl transferase

A

Housed in the rough ER; N-linked glycosylation of proteins during translation;

303
Q

myoglobin

A

Single 153 AA polypeptide. Heme is tucked between the E and F helices. It has no disulfide bonds.

304
Q

Not competitive inhibitor

A

Vmax decreased dramatically, km also decreased

305
Q

cotranslational targeting of secretory proteins to the ER

A

As soon as the “ER” signal sequence emerges from the ribosome it is bound by SRP (signal recognition particle) and escorts the ribosome to the membrane, binding the SRP receptor that is adjacent to the translocon. Once ribosome is tethered, SRP is released. Polypeptide is translated and inserted into membrane: the hydrophobic N-terminus of the protein remains in the membrane, the rest enters the ER. Signal peptidase cleaves sequence.

306
Q

N-glycosidic bonds

A

Sugars binding to acidic asparagine (and glutamine?)

307
Q

miRNA

A

Endogenous. Non-perfect pairing with mRNA to repress translation. Non-specificity allows for broader-spectrum influence.

308
Q

unfolded protein response

A

If there is consistent misfolding, receptor systems (ATF6, IRE1, PERK) activate other chaperones and lipid synthesis to expand ER and limit the number of new proteins directed to the ER.

309
Q

expressivity

A

Variable phenotype

310
Q

ricin

A

Inactivates 60S subunit of ribosome

311
Q

SUMO

A

(Small ubiquitin-related modifier) marker for nuclear targeting.

312
Q

familial hypercholesterol

A

Autosomal dominant defect in the LDLR gene (normally removes LDL from circulation). 20%-40% affected individuals present with xanthelasma palpebrarum, arcus senilis cornea, and/or tendon xanthoma, while others show no symptoms (incomplete penetrance). 85% of men have heart attack by 60, women by 70.

313
Q

gangliosides

A

The accumulated lipid of Tay Sachs disease caused by a deficiency of the hexosaminidase A enzyme.

314
Q

DNA looping

A

Contortion of DNA strand to allow distant enhancers/silencers to influence expression

315
Q

primary structure (protein)

A

Peptide and disulfide bonds (covalent bonds; the order of the string)

316
Q

phospholipases

A

Cleave phospholipids to release arachidonic acid, which is used in the biosynthesis of eicosanoids. Also the targets of anti-inflammatory steroids.

317
Q

insulators/barrier domains

A

Prevent enhancers/silencers from influencing non-target genes by dividing chromosome into distinct functional domains.

318
Q

FAP

A

(familial adenomatous polyposis) mutation in the APC (a. dominant) or MUTYH (a. recessive) genes cause colon polyps age 39-55.

319
Q

hemochromatosis

A

Autonomic recessive mutation of the HFE gene resulting in iron overload, 35%-40% penetrance

320
Q

KDEL sequence

A

Targeting sequence at C-terminus that sends proteins back to the ER

321
Q

metaphase

A

chromosomes aligned at the metaphase plate

322
Q

pK

A

Equilibrium point between ionized and non-ionized forms. Property of a specific functional group.

323
Q

RNase P

A

Ribozyme involved in cleavage of the 5’ end of pre-tRNAs

324
Q

O-glycosidic bonds

A

Sugars binding to hydroxyl AAs in glycoproteins.

325
Q

Helix-loop-helix

A

DNA binding protein that consists of alpha helix and two dimerization helices.

326
Q

What does it mean to say that amino acids are “degenerate”?

A

They may be specified by more than one codon.

327
Q

alkylating agents

A

eg MNNG; attach alkyl groups to DNA bases (eg convert guanine to O^6-methylguanine; (N-methyl-N-nitro-N-mitrosoguanidine)

328
Q

vinblastin

A

Binds to tubulin & selectively inhibits rapidly dividing cells. Anti-cancer drug.

329
Q

15q11-13 deletion

A

Causes either Prader-Willi syndrome or Angelman syndrome, depending on whether it was inherited from the father or the mother, respectively.

330
Q

HNO2

A

deaminating agent: Convert adenine, guanine, and cytosine into hypoxanthine, xanthine, and uracil, respectively

331
Q

scRNA

A

(small cytoplasmic) Involved in the targeting of proteins destined for secretion, and their sequestering into the ER.

332
Q

Chk2

A

Checkpoint protein. Phosphorylates and inhibits Cdc25 to arrest cell cycle in the presence of single strand breaks or unreplicated DNA; activated by ATR

333
Q

3 RNA polymerases in eukaryotes

A

3 types of RNA polymerases: 2 does mRNA, miRNA (and some snRNA and scRNA); 1 does most rRNA; 3 does tRNA, some snRNA and scRNA, and 5S rRNA.

334
Q

TPP

A

Metabolite of thiamin (B1). In pyruvate dehydrogenase complex, TPP has the role of transfering the acyl intermediate.

335
Q

folic acid

A

Tetrahydrofolate helps DHFR produce nucleic acid bases.

336
Q

Hardy-Weinberg equilibrium

A

Tells us how alleles should behave in a model population. Represented by the equation p^2 + 2pq +q^2 = 1.

337
Q

glucosylceramides

A

The accumulated lipid of Gaucher’s disease, caused by a deficiency of the beta-glucosidase enzyme.

338
Q

flippase

A

Flip newly synthesized phospholipids to the inner side of the ER, evening out distribution of growth.

339
Q

How does actin bind to adherens junctions?

A

Contacts between cells are mediated by cadherins and catenins, and stabilized by p120.

340
Q

biotin

A

Cofactor for enzymes that add a carboxyl group to substrate

341
Q

Exon

A

Coding sequence of gene

342
Q

comparative genomic hybridization

A

Detects “chromosomal abnormalities through competing fluorescent probes; it detects deletions, insertions and other abnormalities”

343
Q

CYP2C9

A

Responsible for matabolism of various drugs, including warfarin.

344
Q

myosin

A

Motor protein involved in muscle contraction,

345
Q

lac i gene

A

Codes for a repressor that binds the operator in the ABSENCE of lactose (upstream of lac operon)

346
Q

Turner syndrome

A

lone X chromosome

347
Q

U2 snRNA

A

Recognizes the branch site of pre-mRNA, and binds U1, folding the RNA over.

348
Q

Shine-Dalgarno sequence

A

In prokaryotes, a CT rich sequence just upstream of the 5’ side of the initiation codon used by the 16S rRNA of the 30S subunit to target the initiation codon.

349
Q

anti-apoptotic Bcl-2 family proteins

A

Bcl-2 (mutations due to chromosomal translocation at t14:18), Bcl-xl, Mcl-1

350
Q

RNA polymerase 2 (eukaryotes)

A

Synthesizes mRNA, miRNA, and some snRNA and scRNA. VERY sensitive to a-aminitin.

351
Q

oleic acid

A

18:1 (1); vegetables, olive oil. Non-essential.

352
Q

caspase 9

A

Cleaves procaspase 3 to activate it, leading to apoptosis. Activated by the formation of the apoptosome.

353
Q

sigma subunit of bacterial RNA polymerase

A

Identifies the correct sites for transcription initiation, binds both the -10 and -35 regions.

354
Q

nucleotide-excision repair

A

Involves 7 genes (XPA-XPG): RECOGNITION = XPC which recruits XPA, RPA and TFIIH (contains XPB and XPD); TFIIH unwinds ~25bp bubble. REMOVAL: XPG and XPF/ERCC1 complex are endonucleases and excise ~30 bases. DNA polymerase and DNA ligase replace and rejoin.

355
Q

aneuploidy

A

An individual has too much or too little chromosome material.

356
Q

admixture

A

Groups that were separated are now brought together, resulting in introgression. Could be good or bad.

357
Q

ligases

A

Enzyme that facilitates the joining of DNA strands

358
Q

amyloid

A

Classic amyloid cases involve misfolded proteins that accumulate in the extracellular space.

359
Q

catenins

A

Facilitate binding of actin to cadherins in adhherens juntions.

360
Q

Angelmann syndrome

A

Caused by a 15q11-13 deletion inherited from mom (imprinting). SSX: excessive smiling/laughing, speech impairment, wide mouth and wide-spaced teeth, movement disorders, crave social interaction.

361
Q

transition

A

in replication, purine –> purine, pyrimidine –> pyrimidine

362
Q

7-methylguanosine

A

The cap at the 5’ end of mRNA; target for the 40S subunit of the ribosome.

363
Q

anaphase A

A

APC/C activated and cohesins degraded. Chromosome movement to poles

364
Q

quaternary structure (protein)

A

Interactions between subunits; noncovalent interactions or disulfide bonds.

365
Q

zinc fingers

A

Finger-like protein projections that bind DNA and zinc ions. Can act as receptor for steroid and thyroid hormones

366
Q

proflavin

A

intercalating agent: inserts between stacked DNA bases, resulting in frameshift mutations

367
Q

p21

A

CKI inhibitor, inhibits G1/S-CDK and S-CDK (Cdk2/Cyclin E); induced by p53 in the presence of DNA damage.

368
Q

calreticulin

A

Folding sensor in the ER; encapsulates protein/sugar complex. If it’s correctly folding the glucose is removed and protein is released. If it’s incorrect, glucose gets added back on and goes back and it tries to fold again. If it’s severely misfolded then it gets targeted for the ubiquitin degradation pathway.

369
Q

Huntington’s disease

A

Trinucleotide repeat causes proteins to aggregate and kill brain cells. Lethal by middle age.

370
Q

actinomycin D

A

Binds tightly to dsDNA (deoxyguanosine residues) and acts as an intercalating agent at G-C pairs. This will inhibit RNA synthesis. Not PRO or EU specific.

371
Q

homologous recombination

A

Fixes accidental double strand break in the presence of the sister chromatid. Damage is repaired accurately using information from sister chromatid.

372
Q

calmodulin

A

Activated by increased intracellular Ca++. Activates lots of stuff, including myosin light chain kinase.

373
Q

actin: STRUCTURE

A

Filaments (F-actin) is composed of globular subunits (G-actin). Subunits have a + (barbed) end and a - (pointed) end. Subunits*GTP jump on the barbed end (stable) 5-10 times faster than subunits*GDP (unstable) fall off the pointed end (treadmilling). Arp2/3 facilitates braching. Cross-linking proteins facilitate either a bundle (contractile, alpha-actinin; or parallel) or a network organization of filaments.

374
Q

HbF

A

Fetal hemoglobin: major in pregnancy; two alpha chains, two gamma chains. Has higher O2 binding affinity than adult Hb so the fetus can get oxygen from maternal blood.

375
Q

aminoacyl-tRNA synthetase

A

Synthesizes aminoacyl-tRNA’s by pairing AA-AMP’s with correct tRNA’s. Specific for 1 amino acid. Can also hydrolyze the incorrect ester linkages between AA’s and the incorrect tRNA’s.

376
Q

deamination of guanine

A

Mutation that turns guanine into xanthine

377
Q

Which 3 hormone receptors are not bound by HSPs (because they are already in the nucleus)?

A

Thyroid hormone, retinoic acid, and vitamin D.

378
Q

pantothenic acid

A

Component of CoA. Important for lots of stuff, eg synthesis of acetylcholine.

379
Q

cytokinesis

A

Reformation of interphase microtubule array; contractile ring forms cleavage furrow

380
Q

retinoblastoma

A

Two hits required, one inherited and one spontaneous mutation in retinal cells.

381
Q

hemoglobin

A

4 subunits, no disulfide bonds. Deoxy in T (tense) conformation held by 8 salt bonds etc. The first subunit to bind O2 is the most difficult, then cooperative (allosteric). Oxy in R (relaxed) conformation; salt bonds break and form hydrogen bonds.

382
Q

pI

A

(isoelectric point) pH at which the number of positive charges equals the number of negative charges. Proprty of the entire molecule, not just one group.

383
Q

ATF6

A

Receptor system in the ER’s unfolded protein response. It’s a transcription factor.

384
Q

PIP2

A

Cleaved by phospholipse C into IP3 and DAG

385
Q

beta subunit of bacterial RNA polymerase

A

Helps with chain initiation and elongation

386
Q

sickle cell disease

A

Autosomal recessive condition common in black populations (1:12 allelic frequency, 1:500 disease frequency).

387
Q

Li Fraumeni syndrome

A

Results from defective checkpoint proteins Chk2 and/or p53. Presents with motor in coordination, immune deficiency, chromosome breaks, lymphomas.

388
Q

thiamin (B1)

A

Water soluble. Converted to thiamine pyrophosphate (TPP), a cofactor for decatboxylation reactions, eg pyruvate dehydrogenase. Deficiency causes Beriberi.

389
Q

G1/S checkpoint

A

Check for damaged DNA before entering S phase.

390
Q

BiP

A

Chaperones entry of proteins into lumen of ER, facilitates correct folding and assembly.

391
Q

translational elongation in eukaryotes

A

eEF-1alpha complexes with GTP and escorts the AA-tRNA to the A site of the ribosome. GTP is the hydrolyzed (rate limiting step, allowing for proofreading!) and eEF-1alpha*GDP and Pi dissociate. eEF-1alpha*GTP is regenerated with the help of eEF-1betagamma. mRNA slides 3 nucleotides downstream, and eEF-2 (aka translocase) uses GTP hydrolysis to move the P tRNA to the E site and the A tRNA to the P site. Binding of new AA-tRNA to A site releases tRNA in E site. Completion is signaled by termination codons UAG, UAA, or UGA. eRF-1 recognizes stop and hydrolyzes peptidyl-tRNA bond and initiates the release process.

392
Q

deamination of adenine

A

Mutation that turns adenine to hypoxanthine

393
Q

color blindness

A

x-linked recessive, affects 8% males of european decent, 0.5% females

394
Q

dolichol

A

Membrane-associated protein in the rough ER, carries oligosaccharides to be attached to Asn residues in newly-synthesized proteins. Oligosaccharide transferase does the switch; changes to the oligosaccharide happen later in the ER.

395
Q

telophase

A

Nuclear envelope reassembly; assembly of contractile ring

396
Q

peptidyl transferase

A

The catalytic activity of the large ribosomal subunit that moves the polypeptide from the tRNA in the P site to the tRNA in the A site.

397
Q

stress fibers

A

Large contractile bundles of actin fibers cross-linked by alpha-actinin and stabilized with tropomyosin. Interact with membrane via integrins (focal adhesions).

398
Q

PERK

A

Receptor system in the ER’s unfolded protein response. Phosphorylates eIF2 (eukaryotic initiation factor 2) leading to translation of additional proteins.

399
Q

snRNPs

A

Complexes of snRNAs and proteins, involved in spliceosome activity

400
Q

oxygen-binding prosthetic group

A

Contains protoporphyrin IX (4 5-membered pyrrole rings with lots of conjugated double bonds) and a ferrous iron (Fe2+) chelated in the center.

401
Q

M-CDK regulation

A

One phosphate turns it on, two phosphates turns it off. CAP kinase adds the first phosphate to turn it on, Wee1 kinase adds the second phosphate to turn it off, Cdc25 phosphatase removes the second phosphate to turn it back on.

402
Q

U1 snRNA

A

The 5’ end of U1 snRNA recognizes the 5’ splice site of pre-mRNA.

403
Q

M line (sarcomere)

A

Center line (middle of H zone) that myosin projects from.

404
Q

Where do proteins from cytosolic ribosomes go?

A

The nucleus, mitochondria, chloroplasts, and/or the peroxisomes.

405
Q

erythromycin

A

Binds to the 50S subunit and inhibits translocation

406
Q

Ilumina MiSeq (sequencer)

A

Basically: cloning on a microchip instead of on a plate. Shortcoming: can only do small pieces of DNA.

407
Q

IF-2

A

In prokaryotes, joins with GTP and fmet-tRNA and binds to the 30S subunit, completing the preinitiation complex.

408
Q

tendon xanthoma

A

Cholesterol accumulation in the tendons of the hands, feet, elbows or knees. Often related to familial hypercholesterolemia.

409
Q

dipalmitoyl phosphatidylcholine

A

A highly saturated glycerophospholipid; a very important ingredient in pulmonary surfactant. An important test for this compound (aka lecithin) can determine infant readiness for birth.

410
Q

extrinsic (receptor-initiated) apoptosis

A

Death ligand (eg TNF) initiates receptor oligomerization; death domain (DD) recruits adaptors that interact with caspase-8 (forming the death-inducing signaling complex, DISC) leading to autoproteolytic activation of Bcl-2 proteins, caspase-3, etc.

411
Q

nocodazole

A

Binds tubulin & inhibits microtubule polymerization, disrupting mitosis in metaphase. Anti-cancer drug.

412
Q

Describe a cross-section of a cilia.

A

9 mimcrotubule doublets: 8 outside and one inside. Inner double surrounded by protein “inner sheath”, and is linked to the outer doublets via “radial spokes”. The outer doublets are joined to each other by nexin links, and are associated with inner and outer dynein arms that help with motility.

413
Q

stop sequence in mRNA

A

UAA, UAG, UGA.

414
Q

G1 phase

A

RNA and protein synthesis. Mediated by cyclin D and Cdk6/Cdk4, which decide if the cell should divide in response to extermnal growth factors or mitogens.

415
Q

Michaelis-Menten equation

A

Vmax*[S] / Km +[S], since Km (substrate concentration at 1/2 max velocity) is in the denominator, the lower the km, the higher the affinity an enzyme has for a substrate

416
Q

treadmilling

A

Actin subunits*GTP jump on the barbed end (stable) 5-10 times faster than subunits*GDP (unstable) fall off the pointed end. Dynamic instability.

417
Q

Allosteric Binding site

A

Site other than Catalytic site, changes confirmation. Binding causes graph to shift from hyperbolic to sigmoidal…

418
Q

Rett syndrome: etiology

A

X-linked neurological disease of females involving a mutation of MeCP2 (a protein that binds methylcytosine in DNA to repress translation).

419
Q

disulfide bonds

A

Form between cysteine residues to stabilize the structure that emerges from hydrophobic interactions

420
Q

Lineweaver-Burk plot

A

1/Vmax at x=0, -1/Km at y=0, In the presence of a competitive inhibitor, the slope will increase but will still cross at x=0

421
Q

EF-Tu

A

In prokaryotes, complexes with GTP and escorts the AA-tRNA to the A site of the ribosome.

422
Q

acidic amino acids (and derivatives)

A

aspartate, glutamate, asparagine, glutamine

423
Q

Mediator complex

A

Cofactor for initiation of transcription in eukaryotes

424
Q

leucine zipper

A

Contain DNA-binding proteins formed by dimerization of two polypeptide chains. Leucine forms the “zipper” between the dimers.

425
Q

Explain coding vs anticoding vs template vs antisense strands

A

When we split DNA, we have a 5’ end and a 3’ end. Proteins match the 5’->3’ orientation of DNA, but RNA (and everything else) is synthesized 5’->3’. So, the 5’ end of DNA is the sense strand, the 3’ end is the antisense. The RNA, which is synthesized off the DNA template (antisense) strand (read 3’->5’) so that the protein will match the coding (sense) strand.

426
Q

HAT

A

(histone acetyltransferase) lysine residues in the N-terminal tail domain of histones

427
Q

Removal of RNA primer for Prokaryotes

A

Polymerase 1 (acts as exonuclease)

428
Q

RNA polymerase 1 (eukaryotes)

A

Synthesizes most rRNA (5.8S, 18S, 28S) in the nucleolus. NOT sensitive to a-aminitin.

429
Q

nitric oxide (NO)

A

Potent vasodilator that activates guanylyl cyclase, making cGMP and resulting in Ca++ efflux (and vasodilation).

430
Q

microarrays

A

Look at the expression of genes using a “gene chip”

431
Q

PrP^C

A

Normal conformation of the prion protein

432
Q

CO2 disposal

A

Dissolved in water; carbamino hemoglobin; 80% is turned into bicarbonate by carbonic anhydrase (in tissues this is in the erythrocyte, in lung capillaries it’s in the plasma. Cl- antiport channels allow CO2/HCO3- to enter/leave the cell).

433
Q

pellagra

A

Caused by deficiency of niacin. Presents with dermatitis, diarrhea, dementia.

434
Q

microtubules: STRUCTURE

A

Alpha- and beta-tubulin heterodimers stack into protofilaments (gamma-tubulin in the centrosome), 13 protofilaments make a filament. Both subunits bind GTP, which hydrolyzes after polymerization. Dynamic instability.

435
Q

NucleoTide

A

is a nucleoside + 1 or more phosphate groups

436
Q

hereditary nonpolyposis colon cancer

A

Defective proteins of post-replication mismatch repair.

437
Q

Telomeres

A

repeated sequences at the end of chromosomes that act as a buffer for exonucleases, continually synthesized by Telomerase

438
Q

Helix-turn-helix

A

Recognition of a DNA binding protein. Composed of two alpha helices seperated by Beta turn

439
Q

Removal of RNA primer for both

A

Filled with Polymerase delta, joined with ligase

440
Q

Describe the folding process in the ER

A

Calreticulin is a folding sensor, encapsulates protein/sugars. If it’s correctly folding the glucose is removed and protein is released. If it’s incorrect, glucose gets added back on and goes back and it tries to fold again. If it’s severely misfolded then it gets targeted for the ubiquitin degradation pathway.

441
Q

What is the order of protein binding in eukaryotic transcription?

A

TFIID finds spot, then TFIIB, then TFIIF and polymerase, thenn TFIIE and TFIIH.

442
Q

What are the biggest differences between peroxisomes and lysosomes?

A

Lyso- come from Golgi with their proteins inside, pero- come from ER and have proteins imported (peroxisome target signal: Ser-Lys-Leu, or SKL). Pero- does more detox.

443
Q

karyotyping

A

Chromosomes are stained and observed under a microscope

444
Q

Removal of RNA primer for Eukaryotes

A

RNase H

445
Q

“read through”

A

When a frameshift mutation postpones the stop sequence (eg abnormal hemoglobin Wayne).

446
Q

vector (genetics)

A

A DNA molecule that is capable of indeependent replication in a host cell into which a DNA fragment of interest is inserted.

447
Q

metHb

A

(methemoglobin) Nonfunctional oxidized form of hemoglobin (ferric Fe3+), loses affinity for O2

448
Q

mismatch repair (eukaryotes)

A

RECOGNITION: MLH and MSH complex binds to mismatch, identifying the daughter strand via single strand breaks. REMOVAL: The endonuclease cleaves between nick (ss break?) and mismatch, THEN helicase unwinds and exonuclease removes several nucleotides. DNA polymerase and DNA ligase replace and rejoin.

449
Q

dsRNA

A

Interferes with gene expression, and larger chunks (>28nt) elicit immune response

450
Q

“intermediate metabolizer”

A

Often heterozygotes for normal and reduced activity genes. Normal doses of genes may put them in danger of toxicity.

451
Q

HbA

A

Major adult hemoglobin: 97%, two alpha chains and two beta chains

452
Q

deletion

A

remove a base pair (frameshift)

453
Q

PCR: steps

A

Heat DNA to 95°C to separate strands (heat changes the pH). Cool to 55°C so primers can bind. Warm to 72°C and have Taq polymerase extend the DNA strands. Repeat.

454
Q

hydrolases

A

Hydrolases cleave bonds by the addition of water

455
Q

colchicine

A

Binds tubulin & inhibits microtubule polymerization, disrupting mitosis in metaphase. Anti-cancer drug.

456
Q

The CO2 effect

A

In addition to CO2’s role in the Bohr effect, CO2 can bind covealently to amino groups on Hb forming carbamino hemoglobin, reducing O2 affinity.

457
Q

Which DNA polymerase does what in eukaryotes?

A

Pol epsilon does leading strand, pol delta does lagging, pol alpha/primase lays the primase and starts laying okazaki fragments.

458
Q

transversion

A

in replication, purine –> pyrimidine, pyrimidine –> purine

459
Q

What are the components of phosphatidylcholine?

A

It’s a typical glycerophospholipid with a polar head group (choline in this case, but it could be ethanolamine, serine, inositol, etc), a phosphate, glycerol, and two fatty acids. It donates a fatty acid to cholesterol ester.

460
Q

BPG

A

(2,3-Bisphosphoglycerate) 1 molecule can bind per Hb when it’s in T conformation. Decreases O2 binding affinity (dumps oxygen). BPG increases in hypoxic conditions. Shifts the binding curve to the right and makes it more sigmoidal.

461
Q

nonsense-mediated mRNA decay

A

Eliminates mRNA that lack complete open-reading frames. When ribosomes encouter premature stops

462
Q

function of lysosomes

A

To degrade proteins, nucleic acids, oligosaccharides, and phospholipids. pH = 5.

463
Q

DAG

A

Cleaved from PIP2 by phospholipase C. Activates PKC

464
Q

translational elongation in prokaryotes

A

EF-Tu complexes with GTP and escorts the AA-tRNA to the A site of the ribosome. GTP is the hydrolyzed (rate limiting step, allowing for proofreading!) and EF-Tu*GDP and Pi dissociate. EF-Tu*GTP is regenerated with the help of EF-Ts. mRNA slides 3 nucleotides downstream, and EF-G (aka translocase) uses GTP hydrolysis to move the P tRNA to the E site and the A tRNA to the P site. Binding of new AA-tRNA to A site releases tRNA in E site. Completion is signaled by termination codons: RF1 (UAG, {UAA), or UGA} RF2. RF1 or RF2 hydrolyze peptidyl-tRNA bond, and RF3 initiates the release process.

465
Q

Describe the process of contraction in the contraction ring of mitosis.

A

Contractile rings form around the middle of two cells in mitosis: MLCK phosphorylates light chains in the cells which does two things: promotes the assembly of myosin into philaments and then increases the myosin catalytic activity to allow contraction to take place.

466
Q

etoposide

A

human type II topoisomerase inhibitor; chemotherapeutic

467
Q

lyases

A

Lyases remove a group nonhydrolytically, forming a double bond

468
Q

Prader-Willi syndrome

A

Caused by a 15q11-13 deletion inherited from dad (imprinting). SSX: obesity, insatiable appetite, hypotonia, infertility, other physical manifestations (almond eyes, downturned mouth, thin upper lip, soft light skin, small hands and feet, flattened ulnar border).

469
Q

Cockayne’s syndrome

A

Results from defective CsB protein (involved in transcription-coupled nucleotide-excision repair). Presents with poor growth, neurological degeneration, and early senility.

470
Q

Cdk2

A

Serine/threonine kinase that is active in the G1/S transition when bound to CycE, or in the S and G2 phases when bound to CycA. Inhibited by Cip/Kip family CKIs.

471
Q

lactose permease

A

Transports lactose into the cell (lac operon)

472
Q

Patau syndrome

A

trisomy 13

473
Q

thymine dimer

A

UV radiation causes covalent linkage between adjacent thymine residues; repaired by DNA photolyase in some organisms

474
Q

I band (sarcomere)

A

Clear space surrounding Z line where only actin is present.

475
Q

siRNA

A

Endogenous or exogenous. Perfect base pairing with target mRNA allow silencing of specific mRNA (via cleavage and degradation).

476
Q

Heterochromatin

A

Tightly packed DNA around Histones

477
Q

The Bohr Effect

A

Acidic environment (high CO2 or high lactic acid) reduces Hb’s O2 binding affinity. So, since Hb*O2 is more acidic than Hb + O2, the Bohr effect facilitates oxygen delivery.

478
Q

VKORC1

A

VKOR is a vitamin K reductase that is the target of warfarin. Mutation in the VKORC1 requires lower doses of warfarin.

479
Q

DHFR

A

Enzyme that converts folic acid into a cofactor (tetrahydrofolate), synthesizes nucleic acid bases.

480
Q

nucleotide-excision REMOVAL/repair

A

REMOVAL: XPG and XPF/ERCC1 complex are endonucleases and excise ~30 bases. DNA polymerase and DNA ligase replace and rejoin.

481
Q

anaphase B

A

spindle pole separation

482
Q

physical linkage (genetics)

A

The tendency of nearby markers on the same chromosome to be transmitted as a unit. Beyond ~50cM (centimorgans) can be considered unlinked and hence segregate independently.

483
Q

G0 phase

A

Terminally differentiated cells withdraw from the cell cycle indefinitely. Reentry into G1 when necessary.

484
Q

cholesterol ester

A

The more water soluble form of cholesterol (75% of blood cholesterol). Formed in a reaction in which lecithin donates a fatty acid.

485
Q

arachidonic acid

A

20:4 (Ω6/4); vegetable oils. Essential.

486
Q

cytochrome p450s

A

Key enzymes for phase I metabolism of foreign substances.

487
Q

snoRNA

A

(small nucleolar) Guides chemical modifications on RNAs (not usually mRNA) and help process rRNA.

488
Q

HbA2

A

Minor adult hemoglobin: 2%-3%, two alpha chains and two delta chains

489
Q

base-excision repair

A

RECOGNITION: DNA glycosylase excises damaged base (eg deaminated cytosine (U)) leaving an AP site; REMOVAL: AP endonuclease cuts phosphodiester bond and deoxyribose is removed; REPLACEMENT by dna polymerase, REJOINing by dna ligase.

490
Q

Rett syndrome: SSx

A

Develop normally for 1-2 years, then lose motor and cognitive skills: mental deficiency, autism, repetitive hand movements, and/or autonomic dysfunction (pleiotropic). Death between 12 and 50 years. Due to its X-linked dominant nature and x inactivation, this disease has high variability in phenotype.

491
Q

cloning (genetics)

A

Inserting DNA fragment of interest into a DNA molecule that is capable of independent replication in a host cell.

492
Q

retinitis pigmentosum

A

Disease related to incorrect folding of rhodopsin that ultimately leads to apoptosis of rods and night blindness. Protein is retained in ER/Golgi, never sent to membrane.

493
Q

The underlined word is missing.

A

CMB (8 decks)

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