7. Biochemistry I p139-152

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Chromatin: p. 139
In mitosis, the negatively charged DNA condenses by wrapping aroundÂ…: nucleosomes
name the proteins nucleosomes are made of:: Histones: H2A, H2B, H3, H4
the structure that ties nucleosomes together to form chromatin:: H1 (another histone)
how long is a chromatin fiber?: 30 nm
which one is transcriptionally active, heterochromatin or euchromatin?: Euchromatin = true, active, less condensed, open Heterochromatin = condensed, darker/more color, inactive (less open)
Nucleotides: p. 139
the purines are: A and G -- Pure As Gold = Purines
the pyrimidines are:: C, U, T -- CUT the PY -rimidines
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!)
significance of # of H bonds?: higher GC content, more H bonds, higher melting temperature
guanine has this side group:: ketone
thymine has this side group:: methyl -- thymine has methyl
deamination of cytosine gives -->: Uracil -- remember U before C in CUT (see above)
Nucleotides are held together by these bonds:: 3'-5' phosphodiesterase bond
Transition vs. Transversion: p. 139
substituting purine for purine, pyrimidine for pyrimidine is call:: transition - staying inside the same class
substituting purine for pyrimidine, vice versa: transversion - change from 1 type to another, 1 version to another version of nucleotide
Genetic Code features: p. 139
each codon specifies only 1 amino acid:: Unambiguous
more than 1 codon can code for the same amino acid:: Degenerate
all organisms have nonoverlapping, commaless nucleotides except for:: viruses (are they really organisms? Â…)
name 4 organisms/structures where a different genetic code is used:: mitochondria, archaeobacteria, Mycoplasma, some yeasts
Mutations in DNA: p. 140
what's worse, nonsense, missense, or silent?: nonsense > missense > silent
what is a conservative mutation?: new amino acid is similar in structure (e.g. small vs. bulky, linear side chain vs. rings)
what is a missense mutation?: changed amino acid - e.g. Glu-->Val in sickle cell anemia
what is a nonsense mutation?: early stop codon. Nonsense = No meaning, no aa.
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: p. 140
how many origins of replications does a prokaryote (bacteria, viruses, plasmids) have?: 1
a primase makesÂ…: RNA primer on which DNA polymerase initiate replication
what is needed to replicate DNA on the lagging strand?: Okazaki fragments
DNA polymerase III - action?: has 5'-->3' synthesis ability -- reaches the primer of preceding "O" fragment. Also has 3'-->5' exonuclease proofreading ability!
RNA primers are degraded by:: DNA polymerase I
the DNA fragments are sealed by:: DNA ligase
proofreading of the DNA is done by:: DNA polymerase III
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:: p. 140
DNA polymerase alpha: replicates lagging strand and synthesizes RNA primers
DNA repair is done by:: DNA polymerase beta and epsilon
When mitochondria divide we need this to replicate the mitochondrial DNA: DNA polymerase gamma
This DNA polymerase replicates the leading strand:: DNA polymerase delta
DNA repair : single strand: p. 140
to remove a damaged base:: single-strand, excision repair-specific glycosylase
Endonuclease - action?: cleaves the DNA several bases to the 5' side
Exonuclease - action?: remove short stretches of nucleotide
What can happen if both strands are damaged?: repair --> recombination!
DNA repair defects: p. 141
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: p. 141
Direction of transcription and translation?: 5' --> 3' ! (please BYOPhosphate from 5 to 3)
Direction of protein synthesis?: N to C - also 5 to 3
types of RNA: p. 141
what is the largest RNA?: mRNA ( m = massive)
what is the most abundant RNA?: rRNA -- in ribosomes! R = Rampant
what is the smallest RNA?: tRNA -- T = Tiny
RNA polymerases: p. 141
Whose RNA is all made with one enzyme, prokaryote or eukaryote?: Prokaryote! RNA polymerase makes all 3 RNAs
RNA polymerases I, II, III (1, 2, 3) make (respectively):: RMT -- rRNA, mRNA, tRNA
RNA polymerase II has another talent with DNA:: can initiate chain by opening DNA at promoter site (AT rich upstream sequences: TATA, CAAT)
alpha-amanitin - action?: inhibit RNA polymerase II
Start and Stop Codons: p. 141
start codon:: AUG -- AUG inaugurates protein synthesis!
What does the start codon code for?: Methionine -- removed in eukaryotes; formyl-methionine in prokaryotes
Stop codons - how to remember?: UGA: U Go Away; UAA = U Are Away; UAG = U Are Gone
Regulation of gene expression: p. 141
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
a stretch of DNA, far or near, that can alters gene expression by binding transcription factors is called:: Enhancer
Introns vs. Exons: p. 142
Which part of DNA is transcribed to mRNA?: Exons
_______ are intervening noncoding segments of DNA: Introns (INtrons stay IN the nucleus; EXons Exit and are EXpressed
Splicing of mRNA: p.142
________ facilitate splicing by binding to primary mRNA transcripts and forming spliceosomes: Small nuclear ribonucleoprotein particles (snRNP)
RNA processing (eukaryotes): p.142
Where does RNA processing occur?: In the nucleus
What are the 3 steps of RNA processing, following transcription?: 1) capping on 5' end (7-methyl-G); 2) Polyadenylation on 3' end (200 A's); 3) Splicing out of introns
The initial transcript is called_________. The capped and tailed transcript is called_______.: Heterogeneous nuclear RNA (hnRNA); mRNA
tRNA structure: p.142
True or false: The anticodon end of tRNA is opposite the 5' end: False. The anticodon end is opposite the 3' aminoacyl end
What codon is at the 3' end of all tRNAs?: CCA and chemically modified bases
The amino acid is covalently bound to which end of the tRNA?: 3' end
tRNA charging: p.142
What enzyme scrutinizes the amino acid before and after it binds to tRNA?: Aminoacyl-tRNA-sythetase (1 per amino acid, uses ATP)
What happens if a tRNA is mischarged?: It reads the usual codon, but inserts the wrong amino acid.
tRNA Wobble: p.142
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: p.142
(a) ATP or (b) GTP is used in tRNA charging?: (a) ATP (tRNA Activation)
What energy form is required for binding of tRNA to the ribosome and for translocation?: GTP (tRNA Gripping and Going places)
Polymerase chain reaction (PCR): p.143
What is the laboratory procedure used to synthesize many copies of a desired fragment of DNA?: 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: p.143
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: 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): p.143
What interaction is tested by ELISA?: antigen-antibody reactivity
What indicates a positive test result?: An intense color reaction in the test solution
Modes of inheritance: p.144
What percentage of offspring from two carrier parents are affected by an autosomal recessive trait?: 25%
Which mode of inheritance is often due to defects in structural genes, and affects many generations?: Autosomal dominant
If a woman is heterozygous for an X-linked recessive disorder, what is the chance that her son will be affected?: 50%
True or False: Females heterozygous for an X-linked trait may be affected by the disorder.: TRUE
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
AUTHOR: Lee Kiang
Genetic Terms: p. 145
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
Define pleiotropy: 1 gene has > 1 effect on individual's phenotype
Angelman's syndrome is an example of _______.: Maternal imprinting. In imprinting, phenotype differs based on whether mutation is maternal or paternal.
Give an example of Paternal imprinting: Prader-Willi syndrome
In Huntington's disease, severity worsens or age of onset becomes earlier with successive generations. This phenomenon is called________.: Anticipation
What is Loss of Heterozygosity, and in what situation does it not apply?: With congenital or acquired mutation of tumor suppressor gene, the completement allele must be deleted/mutated before the development of Ca. NOT TRUE with ONCOGENES.
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.
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.
When cells in the body have a different genetic makeup, this is ________.: Mosaicism
Hardy-Weinberg population genetics: p. 145
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
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: p. 146
What is a main risk factor for Trisomy 21?: Down syndrome=Trisomy 21. Prevalence 1:800, increased risk with advanced maternal age.
Name 3 genetic diseases that involve mental retardation: Down Syndrome, Fragile-X, Phenylketonuria
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
A single missense mutation in beta globin, conferring susceptibility to infections, painful crises: Sickle Cell anemia, 1:400 African-Americans
Name 3 characteristics of the CF phenotype: Recurrent pulmonary infection, exocrine pancreatic insufficiency, infertility.
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
Name two X-linked genetic errors: Fragile X, Duchenne's muscular dystrophy
Characterized by increased susceptibility to fractures, connective tissue fragility:: Osteogenesis Imperfecta
Phenotype of Phenylketonuria: Mental and growth retardation.
Trinucleotide repeat expansion diseases: p. 146
Name 4 trinucleotide repeat expansion diseases: Freidreich's ataxia, Huntington's chorea, mytotonic dystrophy, fragile X syndrome
Lysosomal Storage Diseases: p.147
What are the two categories of lysosomal storage diseases?: 1. Sphingolipidoses; 2. Mucopolysaccharidoses
In _______disease, a deficiency of alpha-galactosidase A results in the clinical finding of _____.: Fabry's disease; Renal Failure.
What are the manifestations of the AR disease leading to accumulation of galactocerebroside in the brain?: Krabbe's disease. Optic Atrophy, spasticity, early death.
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" appearance with enlarged cytoplasm.
Match: Galactocerebroside accumulation, Glucocerebroside accumulation to Gaucher's, Krabbe's: galaKto = Krabbe. GlUco=GaUcher's.
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"
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"
Carrier rate for Tay-Sachs in Jews of European Descent: 1 in 30
What is Metachromatic Leukodystrophy?: Deficiency of arylsulfatase A results in accumulation of sulfatide in brain, kidney, liver and peripheral nerves.
What are the two mucopolysaccharidoses?: Hurler's and Hunter's syndromes
Inheritance of Hurler's syndrome, clinical manifestation:: AR, alpha-L-iduronidase results in corneal clouding, mental retardation.
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.
Enzyme kinetics: pg 148
Km = ___ at 1/2 Vmax: [S]
what is the relationship between affinity and Km?: inverse correlation (lower Km = higher affinity)
when adding a competitive inhibitor: what happens to Vmax and Km: Vmax is unchanged; Km is increased
when adding a non-competitive inhibitor: what happens to Vmax and Km: Vmax is decreased; Km is unchanged
Enzyme regulation methods: pg 148
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: pg 148
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"
which parts of the cell cycle are considered INTERPHASE: G1, S, G2
what phase is usually the shortest? what phase is shortened in rapidly dividing cells?: M; G1 (duration varies)
what phase are most cells in: C2
Plasma membrane composition: pg 148
what is the percentage of cholesterol in the cell membrane? Phospholipids?: ~ 50% each
which side of the membrane are glycosylated lipids on?: the noncytoplasmic
Phosphatidylcholine function: pg 149
phosphatidylcholine (lechitin) is a major component of___ (list 4): RBC membranes, myelin, bile, surfactant (DPPC).
what does phosphatidylcholine esterify: cholesterol
Na-K-ATP pump: pg 149
on what side of the cell membrane is the ATP pump phosphrylated (by ATP): the cytoplasmic
what is the ion exchange that goes on?: 3Na out; 2 K in
what is a pump inhibitor that binds to the K site?: Ouabain
how do cardiac glycosides work?: (digoxin, digitoxin). They bind to the Na-K-ATP pump and increase cardiac contractility
G protein linked 2nd messengers: pg 149
what is the G protein class and main function of the alpha1 receptor: class q; increase smooth muscle contraction
what is the G protein class and main function of the alpha 2 receptor: class i; decrease sympathetic outflow, decrease insulin release
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
what is the G protein class and main function of the beta 2 receptor: class s; vasodilation, bronchodilation, increase glucagon release
what is the G protein class and main function of the M1 receptor: class q; CNS
what is the G protein class and main function of the M2 receptor: class i; decrease heart rate
what is the G protein class and main function of the M3 receptor: class q; increase exocrine gland production
what is the G protein class and main function of the D1 receptor: class s; relax renal vascular smooth muscle
what is the G protein class and main function of the D2 receptor: class i; modulates transmitter release, especially in the brain
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
what is the G protein class and main function of the H2 receptor: class s; increase gastric acid secretion
what is the G protein class and main function of the V1 receptor: class q; increase vascular smooth muscle contraction
what is the G protein class and main function of the V2 receptor: class s; increase water permeability and reabsorption in the collecting tubules
how does Gq work?: stimulates phospholipase C which causes cleavage of PIP2.
how does Gs work?: binds to adenylcyclase which converts ATP--> cAMP
how does Gi work?: by inhibiting adenylcyclase
what do the 2 products of PIP2 do?: IP3 increases intracellular [Ca] DAG activates protein kinase C
arachadonic acid products: pg 150
name the enzyme that liberates AA from the cell membrane: phospholipase A2
what does the lipoxygenase pathway yield: leukotrienes (L for Lipoxygenase and Leukotrienes)
LTB4 is a____: netrophil chemotactic agent
which leukotrienes are involved in bronchoconstriction, vasocondstriction, smooth muscle contraction, and increased vascular permeability: LTC4, D4, E4 (SRS-A)
what are the 3 products of the cyclooxygenase pathway?: thromboxane, prostacyclin, prostaglandin
what are the 2 functions of TxA2: platelet aggregation, vasoconstricion
what are the 2 functions of PGI2: inhibition of paltelet aggregation; vasodilation (Platelet Gathering Inhibitor)
microtubule: pg 150
what are the shape and dimensions of a microtubule?: cylindrical, 24 nm in diameter, variable length.
what are the components of a microtubule: polymerized dimers of alpha and beta tubulin (+2 GTPs per dimer)
where are microtubules found: cilia, flagella, mitotic spindles, neural axons (slow axoplasmic transport)
antihelmitic drug that acts on microtubules: mebendazole/thiabendazole
anti breast cancer drug that acts on microtubules (prevent disassembly): taxol
antifungal drug that acts on microtubules: griseofluvin
anti cancer drug that acts on microtubules (prevent assembly): vincristine/vinblastine
anti gout drug that acts on microtubules: cholchicine
collagen synthesis and structure: pg 150
hydroxylation of specific prolyl and lysyl residues in the ER requires ____: vitamin C
how is collagen synthesized form procollagen: procollagen is exocytosed into the EC spase, and cleaved by procollagen peptidase to make tropocollagen which aggregates to form collagen fibrils.
what is the function of lysine-hydroxylysine in collagen: it cross links tropocollagen and reinforces the fibrillar structure of collagen
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: pg 150
in this disease, faulty collagen synthesis causes what 3 things: 1. Hyperextensible skin; 2, tendency to bleed; 3. Hypermobile joints
what is the genetic inheritance of type IV EDS: autosomal dominant
what is the genetic inheritance of type VI EDS: autosomal recessive
what is the genetic inheritance of type IX EDS: x linked
what type of cerebral vascular disorder is EDS associated with: berry aneurysms
Osteogenesis imperfecta: pg. 151
brittle bone disease causes____: multiple fractures w/ minimal trauma
blue sclera is due to ______: translucency of the connective tissue over the choriod
what is the main pathology in OI: genetic defect in collagen synthesis
what is the most common form of OI: autosomal dominant with abnormal type I collagen
the presentation of a child with OI may be confused with_____: child abuse
ATP: pg151
what are the units comprising ATP: adenine base; ribose sugar; 3 phosphoryls
what type of high energy bonds does ATP have: 2 phosphoanhydride bonds, 7 kcal/mol each
how many ATPs are produced in aerobic glucose metabolism?: 2
activated carriers: pg 151
what is the active carrier of phosphoryls: ATP
what is the active carrier of electrons: NADH, NADPH, FADH2
what is the active carrier of acyl: coenzyme A, lipoamide
what is the active carrier of CO2: biotin
what is the active carrier of 1-C units: THF
what is the active carrier of methyl groups: SAM
what is the active carrier of aldehydes: TPP
what is the active carrier of glucose: UDP-glucose
what is the active carrier of choline: CDP-choline
S-adenosyl-methionine (SAM): pg151
what are the 2 componants of SAM: ATP + methionine
what vitamin is SAM dependent on for regeneration: B-12 (regenerates met)
what is the function of SAM: transfer methyl units ("SAM, the methyl donor man")
signal molecule precursors: pg152
what enzyme converts ATP --> cAMP: adenylate cyclase
what enzyme converts GTP --> cGMP: guanylate cyclase
what enzyme converts glutamate --> GABA: glutamate decarboxylase (with vit B 6)
what enzyme converts choline --> ACh: choline acetyltransferase (ChAT)
what enzyme converts arachidonic acid --> prostaglandines, leukotrienes, thromboxanes: cyclooxygenase/lipoxygenase
what enzyme converts fructose-6-P--> Fructose-1,6-bis-P: phosphofructokinase (rate limiting step of glycolysis)
what enzyme converts 1,3-BPG --> 2,3-BPG: bisphosphoglycerate mutase

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