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7. Biochemistry I p139-152


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p. 139
In mitosis, the negatively charged DNA condenses by wrapping aroundÂ…
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)
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:
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:
more than 1 codon can code for the same amino acid:
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?
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
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):
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:
Introns vs. Exons
p. 142
Which part of DNA is transcribed to mRNA?
_______ 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
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
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
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
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)
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)
What is the laboratory procedure used to synthesize many copies of a desired fragment of DNA?
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
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
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?
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?
True or False: Females heterozygous for an X-linked trait may be affected by the disorder.
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
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________.
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 ________.
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
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
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
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
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?
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)
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
anti breast cancer drug that acts on microtubules (prevent disassembly)
antifungal drug that acts on microtubules
anti cancer drug that acts on microtubules (prevent assembly)
anti gout drug that acts on microtubules
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
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?
activated carriers
pg 151
what is the active carrier of phosphoryls
what is the active carrier of electrons
what is the active carrier of acyl
coenzyme A, lipoamide
what is the active carrier of CO2
what is the active carrier of 1-C units
what is the active carrier of methyl groups
what is the active carrier of aldehydes
what is the active carrier of glucose
what is the active carrier of choline
S-adenosyl-methionine (SAM)
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
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
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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