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.
2
Q
stearic acid
A
18:0; meat. Non-essential.
3
Q
vitamin K
A
The only fat soluble cofactor. Helps modify key proteins including clotting factors.
4
Q
IF-3
A
In prokaryotes, binds to the 30S subunit to prevent premature association with the 50S subunit.
5
Q
cystic fibrosis
A
Autosomal recessive disorder with over 1000 diff pathogenic variants of CFTR gene (allelic heterogeneity)
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.
7
Q
diphtheria toxin
A
Inhibits eEF-2 and prevents translocation
8
Q
quiescence
A
Temporary cell cycle arrest, initiated by p53.
9
Q
linoleic acid
A
18:2 (Ω-6/2); vegetable oils, corn, soya grains, flax. Essential.
10
Q
base analogs
A
erroneously incorporate into DNA; eg 5-Bromouracil
11
Q
xanthelasma palpebrarum
A
Cholesterol accumulation around the eyelids, often due to familial hypercholesterolemia
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.
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.
14
Q
Z disc (sarcomere)
A
Marks bounds of the sarcomere. Actin projects from here.
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.
16
Q
PKC
A
Activated by DAG. Phosphorylates lots of stuff.
17
Q
allozygous
A
Individuals have the ancestral gene by chance, NOT by inheritance.
18
Q
Restriction point
A
Cells that pass this point are committed to pass into S phase.
19
Q
Cyclin E
A
Expressed late in G1. Required for passage through the restriction point into S phase.
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.
21
Q
snRNA
A
(small nuclear) These form part of the spliceosome, which cuts introns out of maturing mRNA molecules.
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.
23
Q
membrane asymmetry (apoptosis)
A
Translocation of phosphatidylserine to the outer leaflet of the membrane (membrane flips inside-out).
24
Q
E2F
A
Transcribes genes necessary for S phase transition. Suppressed by Rb.
25
What is the effect of cholesterol in plasma membranes?
Increased cholesterol makes the membrane more orderly, more rigid, less fluid. We see this especially in the brain and other tissues.
26
Ink4 family
A CKI (Cdk inhibitor) family that inhibits Cdk4 and Cdk6, thus inhibiting G1 phase.
27
anticipation
With each generation, onset happens earlier and is more severe
28
isomerases
Enzyme that converts a molecule from one isomer to another (like changing chirality, etc)
29
"poor metabolizer"
Absent or greatly reduced ability to clear or activate drugs. High risk of toxic doses.
30
Explain how mitochondria import proteins.
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.
31
function of rough ER
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;
32
helix-loop-helix domain
Contain DNA-binding proteins formed by dimerization of two polypeptide chains
33
Euchromatin
Relaxed DNA, ready for replication
34
kuru
Transmittable spongiform encephalopathy (from eating dead family members' brains). Prions.
35
vincristine
Binds to tubulin & selectively inhibits rapidly dividing cells. Anti-cancer drug.
36
proline
"imino acid" with a 5 member ring
37
Z form DNA
CG and 5-methyl CpG rich regions; left hand turn
38
colcemid
Binds tubulin & inhibits microtubule polymerization, disrupting mitosis in metaphase. Anti-cancer drug.
39
O^6 methylguanine
alkylated form of guanine (MNNG); repaired by O^6 methylguanine methyltransferase
40
Cdk4
Serine/threonine kinase that is active in G1 phase when bound to CycD. Inhibited by Ink4 CKIs.
41
profilin
Stimulates the exchange of ATP for ADP in actin, facilitating repolymerization.
42
nonsense mutation
Point mutation resulting in the errant introduction of a stop codon (truncating the protein).
43
cilia
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.
44
insulin receptor process
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).
45
penetrance
The likelihood that someone with the disease genotype will manifest symptoms (it's binary, do they have it or do they not?)
46
Edwards syndrome
trisomy 18
47
small amino acids
glycine, alanine
48
pro-apoptotic Bcl-2 family proteins
Bax, Bak, Bid, Bad, Bim
49
pertussis toxin
(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.
50
nonsyndromic deafness
Inherited deafness, can be either autosomal dominant or recessive. Locus heterogeneity.
51
rifampicin
Inhibits mitichondrial RNA polymerase
52
next-generation sequencing
"not routinely done but coming soon"??
53
MERRF
(myoclonic epilepsy with ragged red fibers) mtDNA disease
54
A form DNA
dry
55
p120
Stabilizes the actin/cadherin/catesin complexes in adherens junctions.
56
5-fluorodeoxyuracil
Nucleotide analog used to treat cancers of the colon, pancreas, stomaach, esophagus, and breast.
57
Describe the formation of the 3' end of eukaryotic mRNA
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.
58
Name the non-essential fatty acids.
Palmitic acid, stearic acid, oleic acid.
59
B form DNA
normal
60
Where are sphingolipids synthesized?
Ceramide from the smooth ER are processed into sphingolipids like sphingomyelin in the Golgi.
61
IF-1
In prokaryotes, prevents premature binding of tRNA to the A site of the 30S subunit.
62
secondary structure (protein)
Regular, repetetive pattern that emerges when all the phi and psi angles are the same (eg a-helix, b-sheet)
63
Gaucher's disease
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)
64
Cyclin D
Induced by growth factors or mitogens early in G1 phase. Determinw whether a cell should divide in response to external stimuli.
65
sulfur amino acids
cysteine, methionine
66
beta-galactosidase
Cleaves lactose into glucose and galactose (lac operon)
67
microtubules: FUNCTION
Cell shape, mitotic spindle, intracellular transport of big stuff, axonal transport, cilia & flagella translocation of mRNA?
68
xeroderma pigmentosum (XP)
Results from lost ability to perform nucleotide-excision repair (mutated XPA-XPG products). Presents with cutaneous photosensitivity.
69
calnexin
checks that proteins are folded corectly
70
mismatch repair (prokaryotes)
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.
71
Mendel's Principle of Independent Assortment
Segregation of one pair of alleles is independent of the segregation of other pairs.
72
Review the breaking of high-energy bonds in the addition of 1 AA to a polypeptide.
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).
73
cholera toxin
(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.
74
PrP^Sc
"scrapie" abnormal, pathological refolding product of PrP^C
75
translation initiation in eukaryotes
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.
76
mannose-6-phosphate
In the Golgi, tags proteins for the lysosome
77
frameshift mutation
shifts the code up or down
78
amino acid activation
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.
79
actin: FUNCTION
Cell movement, cell adhesion, mitosis, other structure and movement stuff.
80
G proteins (3 types)
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.
81
PCR: purpose
(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.
82
nonhomologous end joining
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.
83
vitamin B12
Only vitamin that possesses a metal ion (Co++). Involved in methyl transfer reactions.
84
Pex genes
ER membrane proteins that enable peroxisome budding.
85
V1 receptors
GPCR; vasopressin acts on specific V1 receptors to increase intracellular Ca++ and stimulate contraction of smooth muscle.
86
puromycin
Resembles aminoacyle-tRNA and binds to A-site, causing premature release of polypeptide chain in PRO and EU
87
Describe the spliceosome process
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.
88
AP endonuclease
in base-excision repair, RECOGNIZES and EXCISES damaged base (eg deaminated cytosine (U)) leaving an AP site
89
RNA polymerase 3 (eukaryotes)
Synthesizes tRNA, and some snRNA and scRNA. Also synthesizes 5S rRNA. Sensitive to a-aminitin.
90
beta' subunit of bacterial RNA polymerase
Helps with DNA binding
91
Describe transcription in prokaryotes
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.
92
initiation complex (prokaryotic translation)
Comprises the 30S subunit, mRNA, fmet-tRNA, and 50S subunit. The GTP was hydrolyzed and the IF's dissociated.
93
What are the (4) morphological features of apoptosis?
Chromosomal condensation, cytoplasmic blebbing, apoptotic bodies, cell shrinkage.
94
doxorubicin
human type II topoisomerase inhibitor; chemotherapeutic
95
lac a gene
Codes for transacetylase, which inactivates toxic thiogalactosides that are transported into the cell along with lactose (lac operon)
96
Rb
Substrate of G1/S-Cdk. Rb binds/suppresses E2F, releases when Rb gets phosphorylated.
97
Rho protein (prokaryotes)
Termination protein that binds extended segments of ssRNA (prokaryotic transcription).
98
Variant CJD
"Mad cow". Transmittable spongiform encephalopathy. Prions
99
warfarin (Coumadin)
Used for treatment and prevention of thromboembolic events. Narrow therapeutic window, 20% hospitalization rate for new patients.
100
Allopurinol
A purine analog used to treat gout
101
posttranslational translocation into the ER
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.
102
thymidine kinase
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.
103
hydroxyl amino acids
serine, threonine (and tyrosine)
104
eEF-1alpha
In eukaryotes, complexes with GTP and escorts the AA-tRNA to the A site of the ribosome.
105
dynein
Motor protein that moves towards the - end of microtubules.
106
interphase
Chromosome/centrosome duplication and cohesion
107
benzo[a]pyrene
carcinogen from cigarettes: oxidized within cells and then covalently binds to guanine, distorting helix
108
cofilin
(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.
109
CAP
(catabolite activator protein) Is stimulated by binding cAMP (low glucose) to bind upstream of lac operon, facilitating the binding of RNA polymerase
110
neurofibromatosis
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.
111
Where are mitochondrial proteins synthesized?
In the cytosol by free cytosolic ribosomes.
112
Describe transcription in eukaryotes
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.
113
Wee1 kinase
Phosphorylates M-Cdk to inactivate it.
114
deamination of cytosine
Mutation that turns cytosine to uracil
115
Beriberi
Caused by deficiency of thiamin.
116
early endosomes
Where endocytosed vesicles hang out when the first come in. Once vesicles from the Golgi that have acid hydrolases fuse, they become lysosomes.
117
G2 phase
RNA and protein synthesis continues.
118
autophagy
Cytosolic membranes, damaged/sensescent stuff or mitochondria can be recycled. often an attempt to survive nutrient-deprived conditions.
119
ganglioside
Ceramide + carb chain (+sialic acid)
120
DOPA Decarboxylase
Requires pyridoxal phosphate.
121
EF-Ts
In prokaryotes, facilitates the regen of EF-Tu\*GTP by removing the GDP after hydrolysis.
122
deaminating agents
eg nitrous acid (HNO2); Convert adenine, guanine, and cytosine into hypoxanthine, xanthine, and uracil, respectively
123
Palade experiment
Pulse & chase experiments in pancreatic acinar cells; label newly synthesized proteins with radio-labeled amino acids and watch where they go.
124
Creutzfeldt-Jacob disease
Non-transmittable (among humans) spongiform encephalopathy. Prions.
125
transferases
Enzyme that transfer a group from one molecule to another, Kinases transfer phosphate from ATP to a second substrate,
126
sphingolipids
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.
127
prophase
Chromosome condensation; breakdown of "interphase microtubule display" and their replacement with mitotic astes; mitotic aster separation.
128
Cyclin A
Induced at late G1 after cyclin E. Required for initiation of DNA replication.
129
basic amino acids
lysine, arginine, histidine
130
a-helix
H-bonds align parallel with helical axis. Proline is too rigid, glycine is too flexible. Appears in short segments (
131
S phase
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.
132
Cdk6
Serine/threonine kinase that is active in G1 phase when bound to CycD. Inhibited by Ink4 CKIs.
133
Sanger sequencing
Introduce tagged dideoxynucleotides to halt replication; separate via electrophoresis and see what base they ended on to get sequence.
134
alpha subunit of bacterial RNA polymerase
Helps with chain initiation
135
ATR
Checkpoint protein. Recognizes and binds single strand breaks or unrecognized DNA; activates (phosphorylates?) Chk1to inhibit Cdc25 (via phosphorylation?) and arrest cell cycle.
136
carbamino hemoglobin
Formed in high CO2 conditions; CO2 binds covalently and decreases O2 affinity.
137
Which are the effector caspases?
Caspases 3, 6, and 7.
138
imprinting
Different genes are expressed depending on the parental origin of the gene (methylation, gene silencing) eg Prader-Willi syndrome vs Angelman syndrome
139
CsB
(aka ERCC6) Recognizes stalled RNA polymerase at site of DNA damage. Recruits CsA, XPA, RPA, TFIIH.
140
nucleotide-excision RECOGNITION
RECOGNITION = XPC which recruits XPA, RPA and TFIIH (contains XPB and XPD); TFIIH unwinds ~25bp bubble.
141
locus heterogeneity
Mutations in different genes can cause the same disease
142
ataxia-telangiectasia
Results from defective checkpoint protein ATM (Chk2). Presents with loss of motor coordination, immune deficiency, chromosome breaks, lymphomas, leukemia.
143
tRNA structure
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').
144
What is the most common stop signal during transcription in prokaryotes?
Symmetrical, inverted repeat of a GC-rich sequence followed by seven A residues (forms a stem loop and a poly U tail)
145
allelic heterogeneity
Different mutations in the same gene can cause the same disease
146
lac z gene
Codes for beta-galactosidase, which cleaves lactose into glucose and galactose (lac operon)
147
Cdk1
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.
148
restriction endonucleases
Cleave DNA at specific palindromic sequences
149
22q11 deletion syndrome
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.
150
Intron
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.
151
"next generation" sequencing
Err:509
152
pleiotropy
When one gene affects more than one phenotypic trait or organ system
153
Paracrine
cell messenger that relies on diffusion
154
tetracycline
Inhibits binding of aminacyl-tRNA to A site in PROKARYOTES
155
ERCC (1 & 6)
excision repair cross-complementing genes; ERCC1 + XPF excise damaged bases, ERCC6 = CsB
156
lyso-phosphoglycerides
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).
157
On which chromosomes do you find the immunoglobin chain gene clusters?
Kappa light chins = 2, lamda light chains = 22, heavy chains = 14
158
I-cell disease
Deficiency in enzyme catalyzing the first step in tagging lysosomal enzymes with M6P in the golgi. Lysosomal enzymes are erroneously secreted into the serum.
159
function of smooth ER
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).
160
GRB2
Adaptor protein turned on by IRS-1 phosphorylation in the insulin tyrosine kinase receptor pathway. Activates the Ras pathway and gene expression.
161
intermediate filaments: STRUCTURE
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).
162
6-methyladenine
In E. Coli, formed when Dam methylase methylates the N^6 position of A residues in the GATC sequence
163
depurination
Adenine or Guanine can spontaneously lose their nitrogenous base to become depurinated deoxyribose (apurinic sites)
164
Which are the initiator caspases?
Caspases 8 (extrinsic) and 9 (intrinsic).
165
apoptosome
Cytochrome c facilitates interation of Apaf1 with initiator procaspase-9 CARD domain. Activates caspase-9.
166
kinesin
Motor protein that walks towards the + end of microtubules.
167
arcus senilis cornea
Cholesterol accumulation within the iris, often due to familial hypercholesterolemia.
168
missence mutation
Point mutation that results in the incorporation of a different amino acid due to a single base change (possibly changing function of the protein).
169
H zone (sarcomere)
Clear space surrounding M line where only mysosin is present
170
Cyclin B
Appear at the beginning of G2 and accumulate through G2. Required for entry into mitosis.
171
choramphenicol
Inhibits peptidyl transferase activity of the 50S subunit
172
trp operon
Trp binds trp repressor to block polymerase to attenuate/limit expression.
173
IP3
Cleaved from PIP2 by phospholipase C. Results in Ca++ release into the cytoplasm.
174
cis-acting control element
Affect expression of genes on the same DNA molecule
175
G2/M checkpoint
Check for damaged or unduplicated DNA before mitosis.
176
exonucleases
Cleave nucleotides from one end, either 5' or 3'
177
DNA glycosylase
in base-excision repair, RECOGNIZES damaged base (eg deaminated cytosine (U)) and break the N-glycosyl linkage, excising base and leaving an AP site
178
ascorbic acid (vit C)
Antioxidant: can react with superoxide. Deficiency causes scurvy.
179
Endocrine
Cell messenger travels via blood
180
What are the two types of self-splicing introns?
Group I: mediated by a guanosine cofactor. Group 2: attack by an adenosine nucleotide in the intron.
181
Dam methylase
In E. Coli, methylates the N^6 in A residues in the GATC sequence, forming 6-methyladenine
182
Cip/Kip family
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.
183
lac y gene
Codes for lactose permease, which transports lactose into the cell (lac operon)
184
fragile-x syndrome
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.
185
intermediate filaments: FUNCTION
8 things: Cell shape, cell adhesion, intracellular transport, protection in skin, positioning of nucleus, nuclear organization & heterochromatin, nuclear envelope assembly, and DNA replication.
186
myosin light chain kinase
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.
187
Transcription-coupled repair
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.
188
Wobble hypothesis
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.
189
b-sheet
H-bonds form side by side between the C=O and N-H. Can form parallel or antiparallel.
190
ubiquitination - degradation
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.
191
process of endocytosis
Foreign macromolecules bind to the receptors. Adaptors bind the receptor and to clathrin, which forms the coat and pinches off the vesicle.
192
IRE1
Receptor system in the ER's unfolded protein response. Leads to activation of XP1 transcription factor.
193
nucleolus
Site for synthesis of rRNA
194
ribozyme
An enzyme made of RNA instead of protein
195
What does a high level of chaperones in a cell tell you?
That the cell has high levels of ER stress and needs excess chaperones to correct protein issues.
196
signal patches
In the Golgi, proteins recognize the 3D conformation of a protein (as opposed to a single sequence)
197
eicosepentenoic acid
20:5 (Ω3/5); fish oil. Essential.
198
tertiary structure (protein)
Higher-order folding induced by hydrophobic interactions. 100-400 AA's.
199
bacterial RNA polymerase: STRUCTURE
Has 5 types of subunits, sigma subunit identifies the correct sites for transcription. a2B'Bws
200
alpha-1 receptors
GPCR; NE initiates contraction of vascular smooth muscle by raising intracellular free Ca++.
201
fluorescence in situ hybridization (FISH)
Special fluorescent dyes are used to determine if specific abnormalities are present or absent
202
lipoic acid
Acts as a cofactor for pyruvate dehydrogenase; attached to the enzyme through an amide bond with lysine. Helps transfer acyl group from TPP.
203
palmitic acid
16:0; dairy. Non-essential.
204
Describe the cleavage signal sequences of proteins being synthesized in the rough ER.
Stretch of hydrophobic amino acids, preceded by basic residues.
205
long noncoding RNA's
eg Xist gene on X chromosome, leads to X inactivation
206
substitution (genetics)
Base change (mutation) carried within the population or species, as opposed to a base change in a single gene copy.
207
nalidixic acid
bacterial type II topoisomerase inhibitor; antimicrobial
208
senescence
Permanent cell cycle arrest, induced by p53.
209
STAT
(signal transducer and activator of transcriiption) phosphorylated by JAK; dimerizes and enters nucleus to act as a transcription factor.
210
KKXX sequence
Targeting sequence at C-terminus that sends TRANSMEMBRANE proteins back to the ER
211
JAK kinase
Non-receptor protein kinases often act through this protein, which is activated after the receptor dimerizes and which phosphorylates STAT to alter transcription.
212
X-gal
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
oxidoreductases
Enzyme that catalyze oxidation-reduction reactions. (electron transfers, hydrogen transfers, and reactions involving molecular oxygen)
214
prometaphase
Nuclear envelope breakdown (phosphorylation of intermediate fibers); chromosomes captured and oriented.
215
MNNG
alkylating agent: attaches alkyl group to bases (adds CH3 to the O); converts guanine to O6-methylguanine
216
phospholipase C pathway
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
ATM
Checkpoint protein. Recognizes and binds double strand breasks; activates Chk2 to inhibit Cdc25 and arrest cell cycle
218
cycloheximide
Inhibits peptidyl transferase activity of the 60S ribosome
219
Name the essential fatty acids.
Linoleic acid, linolenic acid, arachadonic acid, eicosopentenoic acid, docosohexanoicacid
220
insertion
add a base pair (frameshift)
221
peroxisomes
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
methylation
Methylation of C5 in CpG dinucleotides leads to repression, mono- and dimethyl lysine are in enhancers, trimethyl lycine is in the promoter.
223
pyridoxine
Participates in aminotransferase reactions. Also important for DOPA decarboxylase.
224
heteroplasmy
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
HDAC
(histone deacetylase)
226
Zellweger syndrome
Most severe of the peroxisome biogenesis disorders
227
sphingomyelin
Ceramide + phosphocoline. Sythesized in the Golgi.
228
"ultra metabolizer"
Greatly increased metabolic activity, accelerating clearance or activation. Regular doses of drugs may be ineffective.
229
caveolae
A kind of lipid raft that is very cholesterol-heavy.
230
cholate derivatives
Bile acids. Important for digestion and absorption of fats. This is augmented by conjugating these acids with either glycine or taurine.
231
phallotoxin (phalloidin)
Binds tightly to AFs and prevents their dissociation into G actin. Prohibits dynamic behavior.
232
Explain sex differentiation in Drosophila.
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
hexosaminidase 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
phosphatidyl inositols
Inositol has many hydroxyl groups, and up to 4 phosphates can be esterified there to form PIP, PIP2, PIP3, and PIP4.
235
U5 snRNA
snRNA involved in spliceosome complex.
236
cadherins
Mediates contact between cells in adherens junctions.
237
M phase
Mitosis and cytokinesis. Require cyclin B, Cdk1 for entry into mitosis.
238
Describe cytokine receptor mechanism
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
phosphodiesterase
Degrades cAMP into AMP. Insulin activated.
240
O^6 methylguanine methyltransferase
repairs O^6 methylguanine by transferring the extra methyl group to a cysteine residue in the enzyme
241
niacin
NAD and NADP are e- and H+ acceptors (eg liver dehydrogenase reaction). Deficiency causes pellagra.
242
start sequence in mRNA
AUC; codes for fMet
243
IRS-1
Scaffold protein associated with the insulin receptor, is phosphorylated by tyrosine kinase; Recruits PI 3-kinase and/or GRB2.
244
Neurocrine
cell messenger released in direct visinity of target
245
Tay-Sachs disease
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
To what position in the ring is the N-glycosidic bond formed in purines? Pyrimidines?
N9 in purines, N1 in pyrimidines
247
aromatic amino acids
phenylalanine, tyrosine, tryptophan
248
Ribosome structure
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
chromosome microarray analysis
"deletions and insertions are observed"
250
LHON
(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
protein disulfide isomerase
Housed in the rough ER; helps oxidize cysteine residues to form disulfide linkages in proteins;
252
HNPCC (Lynch syndrome)
Autosomal dominant disease caused by mutations in 1 of 5 genes; causes up to 5% of all colorectal cancers.
253
peroxisome targeting signals
PTS1: Ser-Lys-Leu, or SKL; PTS2; 9 AA sequence at N-terminus
254
Ion Torrent PGM (sequencer)
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
CTCF
Insulator; interacts with cohesin to limit enhancer activity.
256
riboflavin
FMN and FAD help in oxidation/desaturase reactions like fatty acyl-CoA desaturase, which does biosynthesis of unsaturated fats.
257
tautomeric shifts
change in pH shuffles the H's around on DNA bases; eg the enol form of thymine can pair with guanine
258
SCID
(severe combined immune disorder) X-linked recessive.
259
beta-glucosidase
(aka glucocerebrosidase) Deficiency results in the accumulation of Cer:Glc Glucosylceramide, causing Gaucher's disease.
260
U4/U6 snRNA
snRNAs involved in spliceosome complex
261
Name 4 classes of cell receptors
G-protein coupled receptors (GPCR), Receptor Tyrosine kinsase, Receptor-Associated tyrosine kinase, cytosolic/nuclear
262
DNA photolyase
\*not present in humans; uses light energy to repair thymine dimers
263
Arp2/3
Facilitates branch splitting on growing actin filaments.
264
Mitochondrial polymerase (eukaryotes)
Synthesizes mitochondrial RNA. NOT sensitive to a-aminitin, but inhibited by rifampicin.
265
pre-initiation complex (prokaryotic translation)
Comprises the 30S subunit, IF-3, IF-1, mRNA, IF-2, GTP, and fmet-tRNA.
266
mitochondria
Contain some DNA, ribosomes (more similar to PRO than EU), small granules, and protein for the citric acid cycle and electron transport chain.
267
Where do proteins from rough ER ribosomes go?
Nuclear membrane, plasma membrane, vesicles, endosomes/lysosomes, or the peroxisome membrane. Basically, to membranes or lysosomes.
268
streptomycin
Causes misreading of the genetic code in PROKARYOTES. Interferes with initiation.
269
alpha-aminitin
Inhibits RNA polymerase II (and III)
270
adenylyl cyclase cascade pathway
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
pyknosis
Nuclear condensation in apoptosis
272
NucleoSide
just the nitrogenous base and a 5 carbon sugar (ribose, deoxyribose)
273
Sec62/63 complex
Regulates the entry of completed polypeptides into the ER through the translocon, with the help of BiP.
274
lipid rafts
Contain sphingomyelin, glycolipids, and cholesterol-based clusters
275
homeodomain proteins
Important in the regulation of gene expression during embryonic development
276
What are the (4) main mechanisms for inducing apoptosis? As in, what happens in the cell to undergo apoptosis?
Activation of caspases, activation of endonuclease, membrane asymmetry, expression of eat-me signal on cell surface.
277
ethidium bromide
intercalating agent: inserts between stacked DNA bases, resulting in frameshift mutations
278
A band (sarcomere)
Region where actin and myosin overlap.
279
autozygous
A homozygous individual with the ancestral gene as a result of consanguinity
280
Steroid hormone receptors
Regulatory proteins that have zinc fingers as tthe DNA binding domain (DBD). Protected in the cytosol by heat shock proteins (HSP).
281
intercalating agents
eg ethidium bromide, proflavin; insert themselves between stacked DNA bases, resulting in frameshift mutations
282
competitive antagonism between O2 and CO
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
autophagy
Cell recycles its own components to survive nutrient-deprived conditions. Too much can lead to cell death.
284
Chk1
Checkpoint protein. Phosphorylates and inhibits Cdc25 to arrest cell cycle in the presence of single strand breaks or unreplicated DNA; activated by ATR
285
branched-chain amino acids
valine, leucine, isoleucine
286
paclitaxel/taxol
Stabilizes microtubules to arrest mitosis. Anti-cancer drug.
287
albuterol
Relaxes smooth muscles, prevents premature labor
288
Helix-turn-helix domain
One helix binds DNA, the other binds the other proteins
289
eEF-1betagamma
In prokaryotes, facilitates the regen of eEF-1alpha\*GTP by removing the GDP after hydrolysis.
290
sarcomere
The structural unit of myofibrils, bounded by the Z discs. Actin projects from Z-discs, myosin projects from M line.
291
transacetylase
Inactivates toxic thiogalactosides that are transported into the cell along with lactose (lac operon)
292
Pacific Biosciences RS (sequencer)
Basically: big machine that can sequence big molecules. Shortcoming: big machine, lots of errors.
293
clathrin
Forms endocytotic coats
294
oxytosin
Contracts smooth muscle, induces labor
295
ciprofloxacin
bacterial type II topoisomerase inhibitor; antimicrobial
296
strand sequencing
Basically: a synthetic protein can "feel" the nucleotide motifs going through and sends back an electric signal.
297
linolenic acid
18:3 (Ω-3/3); grains, flax. Essential.
298
Cdc25 phosphatase
Activates M-Cdk via dephosphorylation. Inhibited at the checkpoints by Chk1 or Chk2 in the case of DNA damage.
299
methotrexate
Anti-cancer drug that blocks the folic acid binding site on DHFR, preventing cell division.
300
docosehexanoic acid
22:6 (Ω3/6); fish oil. Essential.
301
Competitive inhibitor
Impacts Km (shifts curve to the right), but Vmax unaffected
302
oligosaccharyl transferase
Housed in the rough ER; N-linked glycosylation of proteins during translation;
303
myoglobin
Single 153 AA polypeptide. Heme is tucked between the E and F helices. It has no disulfide bonds.
304
Not competitive inhibitor
Vmax decreased dramatically, km also decreased
305
cotranslational targeting of secretory proteins to the ER
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
N-glycosidic bonds
Sugars binding to acidic asparagine (and glutamine?)
307
miRNA
Endogenous. Non-perfect pairing with mRNA to repress translation. Non-specificity allows for broader-spectrum influence.
308
unfolded protein response
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
expressivity
Variable phenotype
310
ricin
Inactivates 60S subunit of ribosome
311
SUMO
(Small ubiquitin-related modifier) marker for nuclear targeting.
312
familial hypercholesterol
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
gangliosides
The accumulated lipid of Tay Sachs disease caused by a deficiency of the hexosaminidase A enzyme.
314
DNA looping
Contortion of DNA strand to allow distant enhancers/silencers to influence expression
315
primary structure (protein)
Peptide and disulfide bonds (covalent bonds; the order of the string)
316
phospholipases
Cleave phospholipids to release arachidonic acid, which is used in the biosynthesis of eicosanoids. Also the targets of anti-inflammatory steroids.
317
insulators/barrier domains
Prevent enhancers/silencers from influencing non-target genes by dividing chromosome into distinct functional domains.
318
FAP
(familial adenomatous polyposis) mutation in the APC (a. dominant) or MUTYH (a. recessive) genes cause colon polyps age 39-55.
319
hemochromatosis
Autonomic recessive mutation of the HFE gene resulting in iron overload, 35%-40% penetrance
320
KDEL sequence
Targeting sequence at C-terminus that sends proteins back to the ER
321
metaphase
chromosomes aligned at the metaphase plate
322
pK
Equilibrium point between ionized and non-ionized forms. Property of a specific functional group.
323
RNase P
Ribozyme involved in cleavage of the 5' end of pre-tRNAs
324
O-glycosidic bonds
Sugars binding to hydroxyl AAs in glycoproteins.
325
Helix-loop-helix
DNA binding protein that consists of alpha helix and two dimerization helices.
326
What does it mean to say that amino acids are "degenerate"?
They may be specified by more than one codon.
327
alkylating agents
eg MNNG; attach alkyl groups to DNA bases (eg convert guanine to O^6-methylguanine; (N-methyl-N-nitro-N-mitrosoguanidine)
328
vinblastin
Binds to tubulin & selectively inhibits rapidly dividing cells. Anti-cancer drug.
329
15q11-13 deletion
Causes either Prader-Willi syndrome or Angelman syndrome, depending on whether it was inherited from the father or the mother, respectively.
330
HNO2
deaminating agent: Convert adenine, guanine, and cytosine into hypoxanthine, xanthine, and uracil, respectively
331
scRNA
(small cytoplasmic) Involved in the targeting of proteins destined for secretion, and their sequestering into the ER.
332
Chk2
Checkpoint protein. Phosphorylates and inhibits Cdc25 to arrest cell cycle in the presence of single strand breaks or unreplicated DNA; activated by ATR
333
3 RNA polymerases in eukaryotes
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
TPP
Metabolite of thiamin (B1). In pyruvate dehydrogenase complex, TPP has the role of transfering the acyl intermediate.
335
folic acid
Tetrahydrofolate helps DHFR produce nucleic acid bases.
336
Hardy-Weinberg equilibrium
Tells us how alleles should behave in a model population. Represented by the equation p^2 + 2pq +q^2 = 1.
337
glucosylceramides
The accumulated lipid of Gaucher's disease, caused by a deficiency of the beta-glucosidase enzyme.
338
flippase
Flip newly synthesized phospholipids to the inner side of the ER, evening out distribution of growth.
339
How does actin bind to adherens junctions?
Contacts between cells are mediated by cadherins and catenins, and stabilized by p120.
340
biotin
Cofactor for enzymes that add a carboxyl group to substrate
341
Exon
Coding sequence of gene
342
comparative genomic hybridization
Detects "chromosomal abnormalities through competing fluorescent probes; it detects deletions, insertions and other abnormalities"
343
CYP2C9
Responsible for matabolism of various drugs, including warfarin.
344
myosin
Motor protein involved in muscle contraction,
345
lac i gene
Codes for a repressor that binds the operator in the ABSENCE of lactose (upstream of lac operon)
346
Turner syndrome
lone X chromosome
347
U2 snRNA
Recognizes the branch site of pre-mRNA, and binds U1, folding the RNA over.
348
Shine-Dalgarno sequence
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
anti-apoptotic Bcl-2 family proteins
Bcl-2 (mutations due to chromosomal translocation at t14:18), Bcl-xl, Mcl-1
350
RNA polymerase 2 (eukaryotes)
Synthesizes mRNA, miRNA, and some snRNA and scRNA. VERY sensitive to a-aminitin.
351
oleic acid
18:1 (1); vegetables, olive oil. Non-essential.
352
caspase 9
Cleaves procaspase 3 to activate it, leading to apoptosis. Activated by the formation of the apoptosome.
353
sigma subunit of bacterial RNA polymerase
Identifies the correct sites for transcription initiation, binds both the -10 and -35 regions.
354
nucleotide-excision repair
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
aneuploidy
An individual has too much or too little chromosome material.
356
admixture
Groups that were separated are now brought together, resulting in introgression. Could be good or bad.
357
ligases
Enzyme that facilitates the joining of DNA strands
358
amyloid
Classic amyloid cases involve misfolded proteins that accumulate in the extracellular space.
359
catenins
Facilitate binding of actin to cadherins in adhherens juntions.
360
Angelmann syndrome
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
transition
in replication, purine --\> purine, pyrimidine --\> pyrimidine
362
7-methylguanosine
The cap at the 5' end of mRNA; target for the 40S subunit of the ribosome.
363
anaphase A
APC/C activated and cohesins degraded. Chromosome movement to poles
364
quaternary structure (protein)
Interactions between subunits; noncovalent interactions or disulfide bonds.
365
zinc fingers
Finger-like protein projections that bind DNA and zinc ions. Can act as receptor for steroid and thyroid hormones
366
proflavin
intercalating agent: inserts between stacked DNA bases, resulting in frameshift mutations
367
p21
CKI inhibitor, inhibits G1/S-CDK and S-CDK (Cdk2/Cyclin E); induced by p53 in the presence of DNA damage.
368
calreticulin
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
Huntington's disease
Trinucleotide repeat causes proteins to aggregate and kill brain cells. Lethal by middle age.
370
actinomycin D
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
homologous recombination
Fixes accidental double strand break in the presence of the sister chromatid. Damage is repaired accurately using information from sister chromatid.
372
calmodulin
Activated by increased intracellular Ca++. Activates lots of stuff, including myosin light chain kinase.
373
actin: STRUCTURE
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
HbF
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
aminoacyl-tRNA synthetase
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
deamination of guanine
Mutation that turns guanine into xanthine
377
Which 3 hormone receptors are not bound by HSPs (because they are already in the nucleus)?
Thyroid hormone, retinoic acid, and vitamin D.
378
pantothenic acid
Component of CoA. Important for lots of stuff, eg synthesis of acetylcholine.
379
cytokinesis
Reformation of interphase microtubule array; contractile ring forms cleavage furrow
380
retinoblastoma
Two hits required, one inherited and one spontaneous mutation in retinal cells.
381
hemoglobin
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
pI
(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
ATF6
Receptor system in the ER's unfolded protein response. It's a transcription factor.
384
PIP2
Cleaved by phospholipse C into IP3 and DAG
385
beta subunit of bacterial RNA polymerase
Helps with chain initiation and elongation
386
sickle cell disease
Autosomal recessive condition common in black populations (1:12 allelic frequency, 1:500 disease frequency).
387
Li Fraumeni syndrome
Results from defective checkpoint proteins Chk2 and/or p53. Presents with motor in coordination, immune deficiency, chromosome breaks, lymphomas.
388
thiamin (B1)
Water soluble. Converted to thiamine pyrophosphate (TPP), a cofactor for decatboxylation reactions, eg pyruvate dehydrogenase. Deficiency causes Beriberi.
389
G1/S checkpoint
Check for damaged DNA before entering S phase.
390
BiP
Chaperones entry of proteins into lumen of ER, facilitates correct folding and assembly.
391
translational elongation in eukaryotes
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
deamination of adenine
Mutation that turns adenine to hypoxanthine
393
color blindness
x-linked recessive, affects 8% males of european decent, 0.5% females
394
dolichol
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
telophase
Nuclear envelope reassembly; assembly of contractile ring
396
peptidyl transferase
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
stress fibers
Large contractile bundles of actin fibers cross-linked by alpha-actinin and stabilized with tropomyosin. Interact with membrane via integrins (focal adhesions).
398
PERK
Receptor system in the ER's unfolded protein response. Phosphorylates eIF2 (eukaryotic initiation factor 2) leading to translation of additional proteins.
399
snRNPs
Complexes of snRNAs and proteins, involved in spliceosome activity
400
oxygen-binding prosthetic group
Contains protoporphyrin IX (4 5-membered pyrrole rings with lots of conjugated double bonds) and a ferrous iron (Fe2+) chelated in the center.
401
M-CDK regulation
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
U1 snRNA
The 5' end of U1 snRNA recognizes the 5' splice site of pre-mRNA.
403
M line (sarcomere)
Center line (middle of H zone) that myosin projects from.
404
Where do proteins from cytosolic ribosomes go?
The nucleus, mitochondria, chloroplasts, and/or the peroxisomes.
405
erythromycin
Binds to the 50S subunit and inhibits translocation
406
Ilumina MiSeq (sequencer)
Basically: cloning on a microchip instead of on a plate. Shortcoming: can only do small pieces of DNA.
407
IF-2
In prokaryotes, joins with GTP and fmet-tRNA and binds to the 30S subunit, completing the preinitiation complex.
408
tendon xanthoma
Cholesterol accumulation in the tendons of the hands, feet, elbows or knees. Often related to familial hypercholesterolemia.
409
dipalmitoyl phosphatidylcholine
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
extrinsic (receptor-initiated) apoptosis
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
nocodazole
Binds tubulin & inhibits microtubule polymerization, disrupting mitosis in metaphase. Anti-cancer drug.
412
Describe a cross-section of a cilia.
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
stop sequence in mRNA
UAA, UAG, UGA.
414
G1 phase
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
Michaelis-Menten equation
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
treadmilling
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
Allosteric Binding site
Site other than Catalytic site, changes confirmation. Binding causes graph to shift from hyperbolic to sigmoidal...
418
Rett syndrome: etiology
X-linked neurological disease of females involving a mutation of MeCP2 (a protein that binds methylcytosine in DNA to repress translation).
419
disulfide bonds
Form between cysteine residues to stabilize the structure that emerges from hydrophobic interactions
420
Lineweaver-Burk plot
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
EF-Tu
In prokaryotes, complexes with GTP and escorts the AA-tRNA to the A site of the ribosome.
422
acidic amino acids (and derivatives)
aspartate, glutamate, asparagine, glutamine
423
Mediator complex
Cofactor for initiation of transcription in eukaryotes
424
leucine zipper
Contain DNA-binding proteins formed by dimerization of two polypeptide chains. Leucine forms the "zipper" between the dimers.
425
Explain coding vs anticoding vs template vs antisense strands
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
HAT
(histone acetyltransferase) lysine residues in the N-terminal tail domain of histones
427
Removal of RNA primer for Prokaryotes
Polymerase 1 (acts as exonuclease)
428
RNA polymerase 1 (eukaryotes)
Synthesizes most rRNA (5.8S, 18S, 28S) in the nucleolus. NOT sensitive to a-aminitin.
429
nitric oxide (NO)
Potent vasodilator that activates guanylyl cyclase, making cGMP and resulting in Ca++ efflux (and vasodilation).
430
microarrays
Look at the expression of genes using a "gene chip"
431
PrP^C
Normal conformation of the prion protein
432
CO2 disposal
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
pellagra
Caused by deficiency of niacin. Presents with dermatitis, diarrhea, dementia.
434
microtubules: STRUCTURE
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
NucleoTide
is a nucleoside + 1 or more phosphate groups
436
hereditary nonpolyposis colon cancer
Defective proteins of post-replication mismatch repair.
437
Telomeres
repeated sequences at the end of chromosomes that act as a buffer for exonucleases, continually synthesized by Telomerase
438
Helix-turn-helix
Recognition of a DNA binding protein. Composed of two alpha helices seperated by Beta turn
439
Removal of RNA primer for both
Filled with Polymerase delta, joined with ligase
440
Describe the folding process in the ER
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
What is the order of protein binding in eukaryotic transcription?
TFIID finds spot, then TFIIB, then TFIIF and polymerase, thenn TFIIE and TFIIH.
442
What are the biggest differences between peroxisomes and lysosomes?
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
karyotyping
Chromosomes are stained and observed under a microscope
444
Removal of RNA primer for Eukaryotes
RNase H
445
"read through"
When a frameshift mutation postpones the stop sequence (eg abnormal hemoglobin Wayne).
446
vector (genetics)
A DNA molecule that is capable of indeependent replication in a host cell into which a DNA fragment of interest is inserted.
447
metHb
(methemoglobin) Nonfunctional oxidized form of hemoglobin (ferric Fe3+), loses affinity for O2
448
mismatch repair (eukaryotes)
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
dsRNA
Interferes with gene expression, and larger chunks (\>28nt) elicit immune response
450
"intermediate metabolizer"
Often heterozygotes for normal and reduced activity genes. Normal doses of genes may put them in danger of toxicity.
451
HbA
Major adult hemoglobin: 97%, two alpha chains and two beta chains
452
deletion
remove a base pair (frameshift)
453
PCR: steps
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
hydrolases
Hydrolases cleave bonds by the addition of water
455
colchicine
Binds tubulin & inhibits microtubule polymerization, disrupting mitosis in metaphase. Anti-cancer drug.
456
The CO2 effect
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
Which DNA polymerase does what in eukaryotes?
Pol epsilon does leading strand, pol delta does lagging, pol alpha/primase lays the primase and starts laying okazaki fragments.
458
transversion
in replication, purine --\> pyrimidine, pyrimidine --\> purine
459
What are the components of phosphatidylcholine?
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
BPG
(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
nonsense-mediated mRNA decay
Eliminates mRNA that lack complete open-reading frames. When ribosomes encouter premature stops
462
function of lysosomes
To degrade proteins, nucleic acids, oligosaccharides, and phospholipids. pH = 5.
463
DAG
Cleaved from PIP2 by phospholipase C. Activates PKC
464
translational elongation in prokaryotes
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
Describe the process of contraction in the contraction ring of mitosis.
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
etoposide
human type II topoisomerase inhibitor; chemotherapeutic
467
lyases
Lyases remove a group nonhydrolytically, forming a double bond
468
Prader-Willi syndrome
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
Cockayne's syndrome
Results from defective CsB protein (involved in transcription-coupled nucleotide-excision repair). Presents with poor growth, neurological degeneration, and early senility.
470
Cdk2
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
lactose permease
Transports lactose into the cell (lac operon)
472
Patau syndrome
trisomy 13
473
thymine dimer
UV radiation causes covalent linkage between adjacent thymine residues; repaired by DNA photolyase in some organisms
474
I band (sarcomere)
Clear space surrounding Z line where only actin is present.
475
siRNA
Endogenous or exogenous. Perfect base pairing with target mRNA allow silencing of specific mRNA (via cleavage and degradation).
476
Heterochromatin
Tightly packed DNA around Histones
477
The Bohr Effect
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
VKORC1
VKOR is a vitamin K reductase that is the target of warfarin. Mutation in the VKORC1 requires lower doses of warfarin.
479
DHFR
Enzyme that converts folic acid into a cofactor (tetrahydrofolate), synthesizes nucleic acid bases.
480
nucleotide-excision REMOVAL/repair
REMOVAL: XPG and XPF/ERCC1 complex are endonucleases and excise ~30 bases. DNA polymerase and DNA ligase replace and rejoin.
481
anaphase B
spindle pole separation
482
physical linkage (genetics)
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
G0 phase
Terminally differentiated cells withdraw from the cell cycle indefinitely. Reentry into G1 when necessary.
484
cholesterol ester
The more water soluble form of cholesterol (75% of blood cholesterol). Formed in a reaction in which lecithin donates a fatty acid.
485
arachidonic acid
20:4 (Ω6/4); vegetable oils. Essential.
486
cytochrome p450s
Key enzymes for phase I metabolism of foreign substances.
487
snoRNA
(small nucleolar) Guides chemical modifications on RNAs (not usually mRNA) and help process rRNA.
488
HbA2
Minor adult hemoglobin: 2%-3%, two alpha chains and two delta chains
489
base-excision repair
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
Rett syndrome: SSx
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
cloning (genetics)
Inserting DNA fragment of interest into a DNA molecule that is capable of independent replication in a host cell.
492
retinitis pigmentosum
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
The underlined word is _missing_.
