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186 Cards in this Set

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BIOCHEMISTRY
0
Chromatin: In mitosis, the negatively charged DNA condenses by wrapping around…
nucleosomes
Chromatin: name the proteins nucleosomes are made of:
Histones: H2A, H2B, H3, H4
Chromatin: the structure that ties nucleosomes together to form chromatin:
H1 (another histone)
Chromatin: how long is a chromatin fiber?
30 nm
Chromatin: which one is transcriptionally active, heterochromatin or euchromatin?
Euchromatin = true, active, less condensed, open Heterochromatin = condensed, darker/more color, inactive (less open)
Nucleotides: the purines are
A and G -- Pure As Gold = Purines
Nucleotides: the pyrimidines are:
C, U, T -- CUT the PY -rimidines
Nucleotides: Which pair is stronger, G-C or A-T?
GC has 3 H bonds. AT has 2 bonds. (AT = 2 points in Scrabble, GC = 6 points -- GC wins!)
Nucleotides: significance of # of H bonds?
higher GC content, more H bonds, higher melting temperature
Nucleotides: guanine has this side group:
ketone
Nucleotides: thymine has this side group:
methyl -- thymine has methyl
Nucleotides: deamination of cytosine gives -->
Uracil -- remember U before C in CUT (see above)
Nucleotides: Nucleotides are held together by these bonds:
3'-5' phosphodiesterase bond
Transition vs. Transversion: substituting purine for purine, pyrimidine for pyrimidine is call:
transition - staying inside the same class
Transition vs. Transversion: substituting purine for pyrimidine, vice versa
transversion - change from 1 type to another, 1 version to another version of nucleotide
Genetic Code features: each codon specifies only 1 amino acid:
Unambiguous
Genetic Code features: more than 1 codon can code for the same amino acid:
Degenerate
Genetic Code features: all organisms have nonoverlapping, commaless nucleotides except for:
viruses (are they really organisms? …)
Genetic Code features: name 4 organisms/structures where a different genetic code is used:
mitochondria, archaeobacteria, Mycoplasma, some yeasts
Mutations in DNA: A silent mutation is…
when the base change (usually @ 3rd codon) does not change the aa, thanks to the degenerate feature of the genetic code!
Mutations in DNA: what's worse, nonsense, missense, or silent?
nonsense > missense > silent
Mutations in DNA: what is a conservative mutation?
new amino acid is similar in structure (e.g. small vs. bulky, linear side chain vs. rings)
Mutations in DNA: what is a missense mutation?
changed amino acid - e.g. Glu-->Val in sickle cell anemia
Mutations in DNA: what is a nonsense mutation?
early stop codon. Nonsense = No meaning, no aa.
Mutations in DNA: what happens if a frameshift mutation occurs?
the open reading frame is shifted so that all the nucleotides are misread --> result is usually a truncated protein
Prokaryotic DNA replication and DNA polymerases: how many origins of replications does a prokaryote (bacteria, viruses, plasmids) have?
1
Prokaryotic DNA replication and DNA polymerases: a primase makes…
RNA primer on which DNA polymerase initiate replication
Prokaryotic DNA replication and DNA polymerases: what is needed to replicate DNA on the lagging strand?
Okazaki fragments
Prokaryotic DNA replication and DNA polymerases: DNA polymerase III - action?
has 5'-->3' synthesis ability -- reaches the primer of preceding "O" fragment. Also has 3'-->5' exonuclease proofreading ability!
Prokaryotic DNA replication and DNA polymerases: RNA primers are degraded by:
DNA polymerase I
Prokaryotic DNA replication and DNA polymerases: the DNA fragments are sealed by:
DNA ligase
Prokaryotic DNA replication and DNA polymerases: proofreading of the DNA is done by:
DNA polymerase III
Prokaryotic DNA replication and DNA polymerases: What happens if there is a supercoil of the DNA, ready to snap?
DNA topoisomerases -- create nick in the helix to relieve supercoils
Eukaryoyic DNA polymerases:: DNA polymerase alpha
replicates lagging strand and synthesizes RNA primers
Eukaryoyic DNA polymerases:: DNA repair is done by:
DNA polymerase beta and epsilon
Eukaryoyic DNA polymerases:: When mitochondria divide we need this to replicate the mitochondrial DNA
DNA polymerase gamma
Eukaryoyic DNA polymerases:: This DNA polymerase replicates the leading strand:
DNA polymerase delta
DNA repair : single strand: to remove a damaged base:
single-strand, excision repair-specific glycosylase
DNA repair : single strand: Endonuclease - action?
cleaves the DNA several bases to the 5' side
DNA repair : single strand: Exonuclease - action?
remove short stretches of nucleotide
DNA repair : single strand: What can happen if both strands are damaged?
repair --> recombination!
DNA repair defects: defective uvr ABC endonuclease --> thymidine dimers seen in:
Xeroderma pigmentosum -- autosomal recessive, inability to repair thymidine dimers which form when exposure to UV light
Directions: Direction of transcription and translation?
5' --> 3' ! (please BYOPhosphate from 5 to 3)
Directions: Direction of protein synthesis?
N to C - also 5 to 3
types of RNA: what is the largest RNA?
mRNA ( m = massive)
types of RNA: what is the most abundant RNA?
rRNA -- in ribosomes! R = Rampant
types of RNA: what is the smallest RNA?
tRNA -- T = Tiny
RNA polymerases: Whose RNA is all made with one enzyme, prokaryote or eukaryote?
Prokaryote! RNA polymerase makes all 3 RNAs
RNA polymerases: RNA polymerases I, II, III (1, 2, 3) make (respectively):
RMT -- rRNA, mRNA, tRNA
RNA polymerases: RNA polymerase II has another talent with DNA:
can initiate chain by opening DNA at promoter site (AT rich upstream sequences: TATA, CAAT)
RNA polymerases: alpha-amanitin - action?
inhibit RNA polymerase II
Start and Stop Codons: start codon:
AUG -- AUG inaugurates protein synthesis!
Start and Stop Codons: What does the start codon code for?
Methionine -- removed in eukaryotes; formyl-methionine in prokaryotes
Start and Stop Codons: Stop codons - how to remember?
UGA: U Go Away; UAA = U Are Away; UAG = U Are Gone
Regulation of gene expression: What happens if a promoter is mutated?
reduction in amount of gene transcribed -- this is where RNA polymerase and other transcription factors bind to DNA upstream from gene locus
Regulation of gene expression: a stretch of DNA, far or near, that can alters gene expression by binding transcription factors is called:
Enhancer
Regulation of gene expression: AUTHOR
Sarah Goldman
Introns vs. Exons: Which part of DNA is transcribed to mRNA?
Exons
Introns vs. Exons: _______ are intervening noncoding segments of DNA
Introns (INtrons stay IN the nucleus; EXons Exit and are EXpressed
Splicing of mRNA: ________ facilitate splicing by binding to primary mRNA transcripts and forming spliceosomes
Small nuclear ribonucleoprotein particles (snRNP)
RNA processing (eukaryotes): Where does RNA processing occur?
In the nucleus
RNA processing (eukaryotes): What are the 3 steps of RNA processing, following transcription?
1) caping on 5' end (7-methyl-G); 2) Polyadenylation on 3' end (200 A's); 3) Splicing out of introns
RNA processing (eukaryotes): The initial transcript is called_________. The capped and tailed transcript is called_______.
Heterogeneous nuclear RNA (hnRNA); mRNA
tRNA structure: True or false: The anticodon end of tRNA is opposite the 5' end
False. The anticodon end is oposite the 3' aminoacyl end
tRNA structure: What codon is at the 3' end of all tRNAs?
CCA and chemically modified bases
tRNA structure: The amino acid is covalently bound to which end of the tRNA?
3' end
tRNA charging: What enzyme scrutinizes the amino acid before and after it binds to tRNA?
Aminoacyl-tRNA-sythetase (1 per amino acid, uses ATP)
tRNA charging: What happens if a tRNA is mischarged?
It reads the usual codon, but inserts the wrong amino acid.
tRNA Wobble: True or false: codons that differ in the 3rd position may code for the same tRNA/amino acid
True. Accurate base pairing is required only in the first 2 nucleotide positions of an mRNA codon; the 3rd position is the "wobble" position.
Protein synthesis: ATP vs. GTP: (a) ATP or (b) GTP is used in tRNA charging?
(a) ATP (tRNA Activation)
Protein synthesis: ATP vs. GTP: What energy form is required for binding of tRNA to the ribosome and for translocation?
GTP (tRNA Griping and Going places)
Polymerase chain reaction (PCR): What is the laboratory procedure used to synthesize many copies of a desired fragment of DNA?
PCR
Polymerase chain reaction (PCR): What are the 3 steps of PCR?
1) DNA denatured by heating into 2 separate strands; 2) Annealing of premade DNA primers to a specific seqence of each strand, during cooling; 3)Heat-stable DNA polymerase replicates the DNA sequence following each primer
Molecular biology techniques: Match the following techniques with the appropriate interaction: Techniques: a) Southern blot; b)Northern blot; c)Western blot; d)Southwestern blot Interactions: 1) DNA-RNA hybridization; 2)Antibody-protein hybridizaton; 3) DNA-protein interaction; 4)DNA-DNA hybridization
a) Southern blot---4)DNA-DNA (Southern-Same) b)Northern blot---1)DNA-RNA c)Western blot---2)Antibody-protein d)Southwestern blot---3)DNA-protein interaction
Enzyme-linked immunosorbent assay (ELISA): What interaction is tested by ELISA?
antigen-antibody reactivity
Enzyme-linked immunosorbent assay (ELISA): What indicates a positive test result?
An intense color reaction in the test solution
Modes of inheritance: What percentage of offspring from two carrier parents are affected by an autosomal recessive trait?
0.25
Modes of inheritance: Which mode of inheritance is often due to defects in structural genes, and affects many generations?
Autosomal dominant
Modes of inheritance: If a woman is heterozygous for an X-linked recessive disorder, what is the chance that her son will be affected?
0.5
Modes of inheritance: True or False: Females heterozygous for an X-linked trait may be affected by the disorder.
TRUE
Modes of inheritance: What mode of inheritance is transmitted only through the mother? What are some examples of such disorders?
Mitochondrial inheritance; examples include Leber's hereditary optic neuropathy and mitochondrial myopathies
Modes of inheritance: AUTHOR
Lee Kiang
Genetic Terms: Distinguish between variable expression and incomplete penetrance
In variable expression, NATURE and SEVERITY of PHENOTYPE VARIES amongst individuals. In incomplete penetrance not all individuals with mutant GENOTYPE show mutant PHENOTYPE
Genetic Terms: Define pleiotropy
1 gene has > 1 effect on individual's phenotype
Genetic Terms: Angelman's syndrome is an example of _______.
Maternal imprinting. In imprinting, phenotype differs based on whether mutation is maternal or paternal.
Genetic Terms: Give an example of Paternal imprinting
Prader-Willi syndrome
Genetic Terms: In Huntington's disease, severity worsens or age of onset becomes earlier with successive generations. This phenomenon is called________.
Anticipation
Genetic Terms: What is Loss of Heterozygosity, and in what situation does it not apply?
With congenital or acquired mutation of tumor supressor gene, the completement allele must be deleted/mutated before the development of Ca. NOT TRUE with ONCOGENES.
Genetic Terms: When the body cannot produce enough normal gene product with only one functional allele, there is a ______mutation. An example is the mutation COL1A1 in the disease _________.
Dominant negative mutation; Osteogenesis Imperfecta.
Genetic Terms: Define Linkage Disequilibrium
Tendency for certain alleles at 2 linked loci to occur together more often than expected by chance. Measured in a population, not within a family; varies among pops.
Genetic Terms: When cells in the body have a different genetic makeup, this is ________.
Mosaicism
Hardy-Weinberg population genetics: For a population in Hardy-Weinberg equilibrium, where p and q are separate alleles, what is the heterozygote prevalence?
Hardy-Weinberg equation for alleles p and q: p^2 + 2pq + q ^ = 1; p+q=1. The heterozygote prevalence is 2pq
Hardy-Weinberg population genetics: The Hardy-Weinberg law assumes 4 criteria. List them.
1. No mutation at the locus; 2. No selection for any genotypes at the locus; 3. Mating completely random; 4. No migration into/out of population being considered
Genetic Errors: What is a main risk factor for Trisomy 21?
Down syndrome=Trisomy 21. Prevalence 1:800, increased risk with advanced maternal age.
Genetic Errors: Name 3 genetic diseases that involve mental retardation
Down Syndrome, Fragile-X, Phenylketonuria
Genetic Errors: The mechanism of this disease involves failure to express gene-encoding RNA binding protein, due to progressive expansion of unstable DNA
Fragile X-associated mental retardation
Genetic Errors: A single missense mutation in beta globin, conferring susceptibility to infections, painful crises
Sickle Cell anemia, 1:400 African-Americans
Genetic Errors: Name 3 characteristics of the CF phenotype
Recurrent pulmonary infection, exocrine pancreatic insufficiency, infertility.
Genetic Errors: Characterized by café-au-lait spots, neurofibromas, increased tumor susceptibility- what is this, and what is the inheritance?
Neurofibromatosis, prevalence 1:3000. AD, with 50% new mutations
Genetic Errors: Name two X-linked genetic errors
Fragile X, Duchenne's muscular dystrophy
Genetic Errors: Characterized by increased susceptibility to fractures, connective tissue fragility:
Osteogenesis Imperfecta
Genetic Errors: Phenotype of Phenylketonuria
Mental and growth retardation.
Trinucleotide repeat expansion diseases: Name 4 trinucleotide repeat expansion diseases
Freidreich's ataxia, Huntington's chorea, mytotonic dystrophy, fragile X syndrome
Lysosomal Storage Diseases: What are the two categories of lysosomal storage diseases?
1. Sphingolipidoses; 2. Mucopolysaccharidoses
Lysosomal Storage Diseases: In _______disease, a deficiency of alpha-galactosidase A results in the clinical finding of _____.
Fabry's disease; Renal Failure.
Lysosomal Storage Diseases: What are the manifestations of the AR disease leading to accumulation of galactocerebroside in the brain?
Krabbe's disease. Optic Atrophy, spasticity, early death.
Lysosomal Storage Diseases: This disease leads to glucocerebroside accumulation in 4 sites, and has characteristic "crinkled paper" cells.
Gaucher's disease. Glucocerebroside accumulation in brain, liver, spleen, bone marrow. Gaucher's cells have "crinkled paper" apearance with enlarged cytoplasm.
Lysosomal Storage Diseases: Match: Galactocerebroside accumulation, Glucocerebroside accumulation to Gaucher's, Krabbe's
galaKto = Krabbe. GlUco=GaUcher's.
Lysosomal Storage Diseases: AR disease with buildup of sphingomyelin and cholesterol in reticuloendothelial and parenchymal cells and tissues
Niemann-Pick disease. "NoMAN PICKs his nose with his sphinger"
Lysosomal Storage Diseases: In _______disease, a deficiency of the enzyme _______results in a cherry-red spot on the macula and death by age 3.
Tay-Sachs disease. "Tay-saX lacks heXoaminidase"
Lysosomal Storage Diseases: Carrier rate for Tay-Sachs in Jews of European Descent
1 in 30
Lysosomal Storage Diseases: What is Metachromatic Leukodystrophy?
Deficiency of arylsulfatase A results in accumulation of sulfatide in brain, kidney, liver and peripheral nerves.
Lysosomal Storage Diseases: What are the two mucopolysaccharidoses?
Hurler's and Hunter's syndromes
Lysosomal Storage Diseases: Inheritance of Hurler's syndrome, clinical manifestation:
AR, alpha-L-iduronidase results in corneal clouding, mental retardation.
Lysosomal Storage Diseases: Inheritance of Hunter's, clinical manifestation:
X-linked Recessive. "Hunters aim for the X" Deficiency of iduronate sulfatase- a milder form of Hurler's with no corneal clouding and with MILD mental retardation.
Lysosomal Storage Diseases: AUTHOR
Ronnie Gurevich
Enzyme kinetics: Km = ___ at 1/2 Vmax
[S]
Enzyme kinetics: what is the relationship between affinity and Km?
inverse correlation (lower Km = higher affinity)
Enzyme kinetics: when adding a competitive inhibitor: what happens to Vmax and Km
Vmax is unchanged; Km is increased
Enzyme kinetics: when adding a non-competitive inhibitor: what happens to Vmax and Km
Vmax is decreased; Km is unchanged
Enzyme regulation methods: name 5 methods by which enzyme activity is regulated
1. concentration alteration; 2. covalent modification; 3. proteolytic modification; 4. allosteric regulation; 5. transcriptional regulation
Cell cycle phases: name the 5 phases of the cell cycle
G1= growth, S = DNA synthesis, G2 = growth, Go = quiescent G1 stage, M= mitosis "G stands for Gap/Growth, S stands for synthesis"
Cell cycle phases: which parts of the cell cycle are considered INTERPHASE
G1, S, G2
Cell cycle phases: what phase is usually the shortest? what phase is shortened in rapidly dividing cells?
M; G1 (duration varies)
Cell cycle phases: what phase are most cells in
G0
Plasma membrane composition: what is the percentage of cholesterol in the cell membrane? Phospholipids?
~ 50% each
Plasma membrane composition: which side of the membrane are glycosylated lipids on?
the noncytoplasmic
Phosphatidylcholine function: phosphatidylcholine (lecithin) is a major component of___ (list 4)
RBC membranes, myelin, bile, surfactant (DpC).
Phosphatidylcholine function: what does phosphatidylcholine esterify
cholesterol
Na-K-ATP pump: on what side of the cell membrane is the ATP pump phosphorylated (by ATP)
the cytoplasmic
Na-K-ATP pump: what is the ion exchange that goes on?
3 Na out; 2 K in
Na-K-ATP pump: what is a pump inhibitor that binds to the K site?
Ouabain
Na-K-ATP pump: how do cardiac glycosides work?
(digoxin, digitoxin). They bind to the Na-K-ATP pump and increase cardiac contractility
G protein linked 2nd messengers : what is the G protein class and main function of the alpha1 receptor
class q; increase smooth muscle contraction
G protein linked 2nd messengers : what is the G protein class and main function of the alpha 2 receptor
class i; decrease sympathetic outflow, decrease insulin release
G protein linked 2nd messengers : what is the G protein class and main function of the beta1 receptor
class s; increase: heart rate, contractility, renin release, lipolysis, aqueous humor production
G protein linked 2nd messengers : what is the G protein class and main function of the beta 2 receptor
class s; vasodilation, bronchodilation, increase glucagon release
G protein linked 2nd messengers : what is the G protein class and main function of the M1 receptor
class q; CNS
G protein linked 2nd messengers : what is the G protein class and main function of the M2 receptor
class i; decrease heart rate
G protein linked 2nd messengers : what is the G protein class and main function of the M3 receptor
class q; increase exocrine gland production
G protein linked 2nd messengers : what is the G protein class and main function of the D1 receptor
class s; relax renal vascular smooth muscle
G protein linked 2nd messengers : what is the G protein class and main function of the D2 receptor
class i; modulates transmitter release, especially in the brain
G protein linked 2nd messengers : what is the G protein class and main function of the H1 receptor
class q; increase nasal and bronchial mucous production, contraction of bronchioles, pruritis, pain
G protein linked 2nd messengers : what is the G protein class and main function of the H2 receptor
class s; increase gastric acid secretion
G protein linked 2nd messengers : what is the G protein class and main function of the V1 receptor
class q; increase vascular smooth muscle contraction
G protein linked 2nd messengers : what is the G protein class and main function of the V2 receptor
class s; increase water permeability and reabsorption in the collecting tubules
G protein linked 2nd messengers : how does Gq work?
stimulates phospholipase C which causes cleavage of PIp 2.
G protein linked 2nd messengers : how does Gs work?
binds to adenylcyclase which converts ATP--> cAMP
G protein linked 2nd messengers : how does Gi work?
by inhibiting adenylcyclase
G protein linked 2nd messengers : what do the 2 products of PIp 2 do?
Ip 3 increases intracellular [Ca] DAG activates protein kinase C
arachadonic acid products: name the enzyme that liberates AA from the cell membrane
phospholipase A2
arachadonic acid products: what does the lipoxygenase pathway yield
leukotrienes (L for Lipoxygenase and Leukotrienes)
arachadonic acid products: LTB4 is a____
neutrophil chemotactic agent
arachadonic acid products: which leukotrienes are involved in bronchoconstriction, vasoconstriction, smooth muscle contraction, and increased vascular permeability
LT C4, D4, E4 (SRS-A)
arachadonic acid products: what are the 3 products of the cyclooxygenase pathway?
thromboxane, prostacyclin, prostaglandin
arachadonic acid products: what are the 2 functions of TxA2
platelet aggregation, vasoconstricion
arachadonic acid products: what are the 2 functions of PGI2
inhibition of platelet aggregation; vasodilation (Platelet Gathering Inhibitor)
microtubule: what are the shape and dimensions of a microtubule?
cylindrical, 24 nm in diameter, variable length.
microtubule: what are the components of a microtubule
polymerized dimers of alpha and beta tubulin (+2 GTPs per dimer)
microtubule: where are microtubules found
cilia, flagella, mitotic spindles, neuronal axons (slow axoplasmic transport)
microtubule: antihelminthic drug that acts on microtubules
mebendazole/thiabendazole
microtubule: anti breast cancer drug that acts on microtubules (prevent disassembly)
taxol
microtubule: antifungal drug that acts on microtubules
griseofluvin
microtubule: anti cancer drug that acts on microtubules (prevent assembly)
vincristine/vinblastine
microtubule: anti gout drug that acts on microtubules
cholchicine
collagen synthesis and structure: hydroxylation of specific prolyl and lysyl residues in the ER requires ____
vitamin C
collagen synthesis and structure: how is collagen synthesized form procollagen
procollagen is exocytosed into the EC space, and cleaved by procollagen peptidase to make tropocollagen which aggregates to form collagen fibrils.
collagen synthesis and structure: what is the function of lysine-hydroxylysine in collagen
it cross links tropocollagen and reinforces the fibrillar structure of collagen
collagen synthesis and structure: a collagen fibril is made of many stagggered collagen molecules. What is a collagen molecule made of?
3 collagen alpha chains, usually Gly-X-Y. X and Y- proline, hydroxyproline, hydroxylysine)
Ehlers-Danlos syndrome: in this disease, faulty collagen synthesis causes what 3 things
1. Hyperextensible skin; 2, tendency to bleed; 3. Hypermobile joints
Ehlers-Danlos syndrome: what is the genetic inheritance of type IV EDS
autosomal dominant
Ehlers-Danlos syndrome: what is the genetic inheritance of type VI EDS
autosomal recessive
Ehlers-Danlos syndrome: what is the genetic inheritance of type IX EDS
x linked
Ehlers-Danlos syndrome: what type of cerebral vascular disorder is EDS associated with
berry aneurysms
Osteogenesis imperfecta: brittle bone disease causes____
multiple fractures w/ minimal trauma
Osteogenesis imperfecta: blue sclera is due to ______
translucency of the connective tissue over the choroid
Osteogenesis imperfecta: what is the main pathology in OI
genetic defect in collagen synthesis
Osteogenesis imperfecta: what is the most common form of OI
autosomal dominant with abnormal type I collagen
Osteogenesis imperfecta: the presentation of a child with OI may be confused with_____
child abuse
ATP: what are the units comprising ATP
adenine base; ribose sugar; 3 phosphoryls
ATP: what type of high energy bonds does ATP have
2 phosphoanhydride bonds, 7 kcal/mol each
ATP: how many ATPs are produced in aerobic glucose metabolism?
38 via malate shuttle; 36 via G3P shuttle
ATP: how many ATPs are produced in anaerobic glycolysis?
2
activated carriers: what is the active carrier of phosphoryls
ATP
activated carriers: what is the active carrier of electrons
NADH, NADPH, FADH2