Bio-Chemistry II

Start Studying!

Terms

undefined, object

copy deck

Donates Methyl groups in phospholipid modification: SAM 3-S-Adenosyl methionine
Phospholips containing an alpha, beta-unstaurated ether at C-1 found in lung tissue: Plasmalogens
Precursor for ether phospholipid synthesis also an intermediate in glycolysis: Dihydroxyacetone phosphate
ether phospholipid implicated in a number of allergic and inflammatory responses: PAF platelet activating factor
1st precursor of phosphatidate: Glycerol 3-phosphate
this molecule is formed via a hydration of phosphatidate and the loss of a Pi: DAG diacylglycerol
Triacylgylcerol is formed by the addition of this molecule and an acyl-CoA: DAG diacylglycerol
the nucleoside tirphosphate that activates phospholipids giving them energy for modifcation: CTP + phosphatidate ->
CDP-diacylglycerol
Enzyme: Acyl-CoA + FAD -> transenoyl CoA + FADH2: Acyl-CoA-dehyrogenase
Enzyme: trans enoyl CoA + H2O -> L-3-Hydroxyacyl CoA: enoyl-CoA hydratase
rxn catalyzed by Acyl-COA dehydrogenase: Acyl-CoA +FAD -> transenoyl CoA + FADH2
rxn catalyzed by enoyl-CoA hydratase: trans enoyl CoA +H2O ->
L-3-hydroxyacyl CoA
oxidizing agent in the following rxn: L-3-hydroxyacyl CoA -> 3-ketoacyl: NAD+ -> NADH
enzyme: 3-ketoacyl + CoA -> Acetyl CoA + Acyl CoA: Thiolase
(thiolysis rxn)
enzyme that breaks down triacylglycerols into fatty acids in the intestines: Pancreatic lipases
Fatty acid degradation occurs where?: mainly in the mitochondria
also in peroxisomes
Pancreatic lipases hydrolyze triacylglycerols at what positions: 1st: position 3
last: position 1
name a common bile acid: glycocholate
in adipose tissue and muscle cells what hormone initiats triacylglycerol lipases: epinephrine thourgh a G-protein mediated receptor system (7m receptor->Andenylate cyclase-> cAMP -> protien kinase A-> phosphorylation)
only molecule form fat break down that can be used to make glucose in net amounts in animals: Glycerol
After glycerol is trans ported to the liverit is converted into one of these two molecules: DHAP dihydorxyacetone phosphate
or
G3P D-glyceraldehyde-3-phosphate
fatty acids are activated fro degradation by conjugation with CoA in a rxn catalyzed by: acyl-CoA ligases or
THIOKINASES
Fatty acid activation occurs in the ....: cytosol
fatty acids are transported through the blood stream by ...: Serum Albumin
enzyme that transesterifizes Acyl groups for preparation of transport into the mitochondria: Carnitine acyl tranferase I
*Carnitine acyl transferase II creats free carnitine out of mitochondria
~10% of infants that have died due to SIDS or suden infant death syndorme have a deficiency in this enzyme: Medium chain Acyl-CoA Dehydrogenase
Acyl-CoA dehydrogenase has three forms....: Short (4-6 C)
medium(4-14C)
long(12-18C)
most biological fatty acids have this kind of double bond configuration: Cis configuration and are never conjugated
the break down of fatty acids is called: Beta oxidation
the two enzymes that enable the cell to oxidize unsaturated fatty acids are: enoly-CoA isomerase
2,4 dienoyl-COA reductase
what does enoyl-CoA isomerase cataylze?: the movement of double bond form 3-4 cis configuration to 2-3 trans configuration in preparation of the enzyme =>transenoyl hydratase
what does 2,4 enoyl-CoA reductase catalyze?: uses 2 reducing equivalents of NADPH to convert conjugated double bondds at 2-3 and 4-5 to a single cis double bond at position 3-4 in preparation of enoyl-CoA isomerase
what is the final product of beta oxidation of a odd chained fatty acid?: propionyl-CoA
enzyme: Propionyl-CoA -> D-methylmalonyl-CoA: propionyl-COA carboxylase
what kind of co-factor does propionyl-COA carboxylase have?: biotin
Propionyl CoA is eventually converted to this citric acid cycle intermediate: Succinyl-CoA
what is one of only two mammalian enzymes to use Cobalamin group: Methylmalonyl-CoA mutase
In peroxisomal beta-oxidation, what is the ultimate electron receptor and the product formed?: the ultimate e- receptor is oxygen and H2O2 is the product
Name a disease related to the deficient ability to metabolize very long chain fatty acids in peroxisomes: X-Adrenoleukodystrophy
Name a disease related to the deficient ability to inport enzymes for peroxisomal beta oxidation: Zellweger syndrome
Name the enzyme that is common to both ketogenesis and cholesterol metabolism: HMG-CoA synthtase
in ketogenesis the enzymethat joins two acetyl-CoAs to form acetoacetyl Co-A: Thiolase
the rxn catalyzed by HMG-CoA synthase in ketogenesis: Acetoacetyl -CoA + aecteyyl CoA +H2O -> HMG-CoA + CoA
Ketone body comonly travels in the blood: Acetoacetate
while traveling through the blood acetoacetate can break down to: Acetone
In individuals suffering from ketosis what is one likely to smell on their breath: acetone
in fatty acid biosynthesis what are two differences from beta oxidation: ACP is a carrier molecule (vs. CoA)and NADPH is a reducing agent (vs. NADH)
What is the enzyme that catalyzes the 1st step in fatty acid synthesis: Acetyl-CoA carboxylase
this is the first comitted step in fatty acid synthesis
what is the rxn catalyzed by Acetyl-CoA carboxylase?: Acetyl CoA +ATP + HCO3- -> Malonyl CoA (3 carbons)
Where in the cell does fatty acid synthesis occur?: in the cytoplasm
the enzyme that catalyzes the majority of the reactions of fatty acid synthesis: Fatty acid synthase complex (6 units)
name the types of rxns in one round of fatty acid synthesis: 1 condesation
2 reduction
3 dehydration
4 reduction
how many NADPH are oxidized in the reduction rxns in one round of fatty acid synthesis?: 2
(NADPH -> NADP+)*2 different rxns
WHat is the main regulatio point in fatty acid synthesis?: acetyl-CoA carboxylase
is activated by dephosphorylation
and partly active by allosteric activation by citrate (even in phosphorylated form)
What kinase phosphorylates acetyl-CoA caroxylase?: AMP-dependent protien kinase (AMPK)
what hormone activates fatty acid synthesis?: Insulin
what hormone deactivates fatty acid synthesis?: epinephrine, glucagon
name three allosteric regulators of Acetyl-CoA carboxylase and their overall effect on fatty acid metabolism: Citrate activates thus stimulates FAS
AMP and Palmitoly CoA inhibit FAS
Where are the elongases located: cytosolic face of the ER
what enzyme lengthens palmatoyl-CoA? what is the substrate?: elongases two carbons at a time (using malonyl CoA a three carbon molecule)
prostaglandins are formed from what fatty acid?: Arachidonate (20C, w/4 double bonds)
What enzymes catalyze the formation of prostaglandins for arachidonate?: cyclooxygenases or
prostaglandin synthase
Asprin is what type of anti inflammatory drug?: NSAID (non-sterodal anti-inflammatory drugs)
COX I inhibitors
what enzymes add double bonds to fatty acids?: Terminal desaturases
What transports Acetyl-Coa out of the mitochondria for fatty acid synthesis?: tricaboxylate transport system as citrate
broken back down into oxaloacetate and Acetyl-CoA by ATP-citrate lyase in the cytosol
Acetyl-CoA carboxylase can form polymers. Is this an active form of the enzyme?: the polymeric form is active the monomeric form is inactive
Name one essential fatty acid: linoleic acid (delta 9, 12 double bonds)
linolenic acid 9delta 9,12,15 double bonds)
Class of membrane lipids found preferntially in the CNS are the souce of second messengers: Sphingolipids
spingosine is formed form what two precursors: palmitoyl-CoA and serine
what is the product of a long chain acylCoA and asphingosine?: Ceramide
Ceramide + activated glucose (UDP-glucose)-> ?: Cerebroside
Ceramide + phosphatidyl choline ->?: Sphigomyelin + DAG (diaceylglycerol)
the imediate precursor of a Ganglioside is?: Cerebroside (+ an activated acidic sugar)
A pathological condition resulting from the failure in the biosythetic pathway for dipalmitoyl phosphatidyl choline.: Respiratory distress syndrome
prevents lunds from collapsing
disease caused by a failure to degrade gangliosides: Tay-Sachs disease
Nucleotides consist of: a) sugar, b) nitrogenous base, and c) phosphate
Nucleosides consist of a: a) sugar and b) nitrogenous base
the purines in RNA and DNA are: adenine (purine), guanine (purine)
The pyrimindines are: thymine (pyrimidine), cytosine (pyrimidine), and uracil (pyrimidine).
Ribose sugars found in RNA and DNA are synthesized in the: Pentose Phosphate pathway
Bicarbonate, ammonia, combine to form: carbamoyl phosphate
in de novo synthesis of pyrimidines PRPP is: added after the formation of the pyrimidine ring
in pyrimidine synthesis what is the common nucleotide: all pyrimindines are formed from UTP
Carbamoyl phospahte combines with _______ to form a_________: Carbamoyl phospahte combines with aspartate to form a pyrimidine ring (orotate)
enzyme: HCO3- + NH3 (from glutamate)+ 2(ATP) -> cartbamoyl phosphate: carbamoyl phosphate synthetase (CPS)
Nucleotides consist of a base and a sugar bonded to a phosphate via a ______ ______ linkage: the phospahte is bonded to the 5' carbon of the sugar in an ester linkage
carbamoyl phosphate synthetase what kind of sites to bind what?: two ATP binding sites and one site to bind a glutamate from which an NH3 is removed
An important regulatory enzyme in pyrimidine de novo synthesis is: ATCase aspartate transcabamoylase
CTP inhibits (a pyrimidine)
ATP stimulates (a purine)
E. coli transcription rates
enzyme: catalyzes formation of NTPs and dNTPs from NDPs and dNDPs respectively: NDPK nucleotide diphosphate kinase
enzyme: formation of dNDP from NDPs (except thymidine): ribonucleotide reductase
enzyme: formation of NDPs from NMPs: specific mononucleotide kinases catalyze these reactions
phosphorylated form of ribose that is joined to a pyrimidine ring after it is synthesized or used as the base for the formation of purine bases: PRPP phosphoribosylpyrophosphate
the most important enzyme for salvaging purines is: HGPRT hypoxanthine-guanine phosphoribosyltransferase
enzyme: guainine + PRPP <-> GMP + PPi purine salvage pathway: HGPRT
enzyme: Hypoxanthine + PRPP <-> IMP + PPi: HGPRT
HGPRT is inhibited by: both IMP and GMP
(its products duh!)
enzyme: Adenine + PRPP <-> Adenylate + PPi: Adenine phosphoribosyl transferase
Branch point in nucleotide synthesis: IMP -> GMP
IMP -> AMP
IMP + (? energy) -> GMP IMP + (? energy) -> AMP: ATP
GTP
thus act as a balancing mechanism
Intermediates involved in the synthesis of purine ring(S): Glycine, NH3 (glutamate), CO2 (HCO3-) THF (folate derivatives), aspartic acid
enzyme: AMP +ATP <-> 2 ADP: adenylate kinase
enzyme: GMP + ATP <-> GDP + ADP: guanylate kinase
enzyme that catalyzes conversion of all nucleoside diphophates to nucleoside triphosphates: NDPK
from where do all nitrogens of purines come: amino acids
enzyme: conversion of ribonucleosides diphosphates to deoxyribonucleotides: ribonucleotide reductase
important aspects of ribonucleotide reductase: tyrosine radical formation
R1 unit has two allosteric control sites
thymidine is formed de novo form: dUMP
(UMP-> UDP-> dUDP-> dUTP->dUMP->dTMP)
synthesis of PRPP is inhibited by?: IMP AMP and GMP
ribonucleotide reductase is regulated ....: 1. at teh active site
*dATP general inhibitor for all substrates
*ATP is an activator
2. at the specificity site
*dATP or ATP enhances formation of dUDP and dCDP
*dTTP favors formation of dGDP
note all effectors are Triphosphates whereas it products are Diphosphates
breakdown of nucleotides: nucleotidases converts nucleotides to nucleosides (removes the phosphates)
nucleoside phosphorylases catayze rxns on nucleoside to yield ribose-1-phosphate ans free bases
syndrome linked to defects inpurine metabolism HGPRT is absent: Lesch-Nyhan syndrome
How many hydrogen bonds does the base pairing of A-T: 2 H-bonds
How many hydrogen bonds does the base pairing of G-C: 3 H-bonds
How many bases per turn are there in B DNA?: 10.4-10.5 bases per turn
DNA protien interaction occur in the ______ _______ of the DNA double helix: Major groove
enzymes that snythesize DNA using a RNA template are called: reverse transcriptases
what are the four basic rules of DNA polymerases: 1.Polymerization only occurs in the 5'to 3' direction
2.requires a template
3. requires 4 dNTPs
4. requires a pre-existing primer
E. coli DNA polymerase I: has three activities: 1)5'-3' DNA polymerase
2)3'-5' exonuclease (proofreading)
3)5'-3' exonuclease (nick translation)
the fragment in E. coli DNA polymerase I that has both the 5'-3'polymerase activity and 3'-5' exonuclease activity: Klenow fragment
Unwinding of DNA ahead on the region of polymerization (ahead of the replication fork)is done by what enzyme: helicase
helicase use energy from: hydrlysis of ATP
too many base pairs per turn: over winding
too few base pairs per turn: unde winding
circular conformation of DNA that is the result of under or overwinding: supercoiling causes writhes
An equation that describes the relationship between twists and writhes: Lk = Tw + Wr
lining number = twists plus writhes
enzyme that relieves the positive twists put into DNA by helicases by putting negative twists in to compensate: Topoisomerases
act to change the linking number
act to relax DNA by cleaving a single strand of DNA allowing it to swivel around the other strand until it is relaxed: Topoisomerase I
does not require energy
uses ATP energy to create negative supercoils in DNA by a doulbe straned break; also know as a gyrase in bacteria: topoisomerase II
anitbiotics that act on gyrase: novbiocin
ciprofloxacin
Replication of DNA in starts at specific sequences called: origins or origins of replication
in E.coli oriC locus
the measure of an enzyme's tendency to remain on the DNA as replication proceeds is: processivity
low = jump off frequently
pieces of DNA on lagging strand DNA replication: Okazaki fragments
process of lagging strand replication: RNA primer
poly III synthesizes strand
poly I 5'-3' exonuclease
(removes primer and synthesizes DNA)
DNA ligase (fills in gaps)
Materials needed for PCR: DNA
thermostable DNA polymerase
Primers
dNTPs
One way in which recombination appear to occur in cells is: Holliday junction
Types of mutations: subsitutions
insertions
deletions
two types of subsitution mutations: transition mutations
transversion mutations
mutation that involves replacement of one purine for another or one pyrimindine for another: transition
mutations that involves the subsitutions of a purine for a pyrimidine or a pyrimidine for a purine: transversion mutation
the interconversion of two isomers that differ only in the position of protons: tautomerization
examples of chemical mutagens: bromide (brominaded form of uricil can readily tautomerize)
nitrous acid (adenine -> hypoxanthine) ends up pairing with cytocine
Aflatoxin B1
Acridine dyes (induce frame shift mutations large act like two bases)
Ultraviolet light produces this kind of mutation: Thymine dimer (cross links between adjacent pyrimidines)
blocks gene expression
varities of DNA repair: direct repair
Nucleotide excision repair
base excision repair
mismatch repair
direct repair pf damaged DNA that involves conversion of the altered base back to its original form: Direct repair
e.g. E. coli's DNA photolyase
repair mechanism that replaces a section of DNA using DNA poly and DNA ligase: Nulceotide excision repair
e.g. UvrABC enzyme (cuts at two distinct sites)
removes one or more nucleotides from a site of base damage: BAse excision repair
fixes Cytosines that spontaneously deaminates to form uracil
repair system: scans newly replicated DNA for ....: Mismatch repair
MutS, MutL MutH protiens
disease associated with deficient repair pathways: XP xeroderma pigmentosum
HNPCC (colorectal cancer)
Disease associated with long tandem repeats of a DNA sequence (three nucleotides CAG): Huntington's disease
a simple test for the tendency of materials to mutate: Ames test
Hold Poly III to the DNA giving it great processivity: beta clamp
beta clamp protein in eukaryotes: PCNA
DNA replication: six proteins complexed together that target the ARS: ORC origin replicating complex
recruit Licensing factors
proteins that prevent DNA from reannealing during replication: SSBP single stranded binding proteins
DNA replication initiation sites in prokaryotes: replication origins
DNA replicatio can only occur in the ______ direction: 5'-3'
A heat stable protein used in PCR: Taq DNA polymerase
What kind of enzyme is telomerase: reverse transcriptase
Junction and process: alignment of homologous sequences, cleavage of strands on each chromosome, invasion of the strands in to the opposite chromosomes, movement junction, another cleavage, reformaton of phosphodiester bonds: Holliday junction
recombination
recombinases (are similar to topoisomerases)
DNA poly I proofreading unit: 3'-5' exonuclease
origin sequences in yeast: ARS autonomously replicating seqence
A sequence DNA or RNA that directs the synthesis of a complementary sequence: template
E.coli DNA replication: recognizes teh replication origin, binds to it, casues slight unwinding for helicase to begin: DNA A protein
An RNA polymerase that makes RNA primers necessary for DNA Poly: primase
protects single stranded DNA and interacts with replication proteins: SSB single stranded binding protein
E.coli DNA replication: relieves superhelical tension created by DNA B protien and helicase: gyrase
topoisomerase II
E.coli DNA replication: removes RNA primers: DNA poly I
E.coli DNA replication: joins DNA fragments together by catalyzing synthesis of phosphodiester bonds at nick sites: DNA ligase
E.coli DNA replication: specific site of initiation: OriC
E.coli DNA replication: OriC site contains these sequences: three repeats of AT rich sequences
transcription factors that act positively: activators
transcritpion factors that act negatively: repressors
Eukaryotic cells contain three distinct RNA poly: RNA poly I-> rRNA
RNA poly II -> mRNA, snRNA
RAn poly III -> tRNA
RNA poly: the subunit that helps polymerase to identify the promoter sequence in DNA: sigma subunit
Prokaryotic cells: two promoter regions: -35 consensus sequence TTGACA
-10 TATAAT
At the intitial encounter between RNA polymerase holoenzyme and the promoter generates a: closed-promoter complex
RNA polymerase holoenzyme unwinds ~17 base pairs of DNA form a..: open-promoter complex
~18 bp of DNA are unwound to form a moving "...": transription bubble
Two kinds of transription termination: factor-independent

factor independent
protein involed in factor dependent transcription termination: rho protein a hexamer of indentical subunits
two features of factor independent termination: 1. two symetrical GC-rich segments in transcription sequence have the potential to form a sSTEM_LOOP structure
2. downstream run of 4-8 A residues
minimal transcription complex in eukaryotic cells: TATA binding protein
TFIID
TAFs
a promoter sequence that is on the same molecule as the genes they control: cis-acting element
proteins or promoter regions on different molecules: trans-acting elements
Eukaryotic transcription: promoters: -30-100 TATA box
CAAT box -40-150
GC box -40-150
function of TFIIF: helicase
order of binding of transcriptionfactors: TFIID, TFIIA, TFIIB, TFIIF, RNA POLYII, TFIIE
DABFpolyE
collectively TFIID, TFIIA, TFIIB, TFIIF, RNA POLYII, TFIIE is called the: basal transcription apparatus
what begins RNA poly transcription: phosphorylation of the carboxyl end
two features common to enhancers: *do not activate transcription
*increase transcription rates
*can be thousands of bp away form gene they regulate
processing of tRNA (yeast0: 1.cleavage of 5' leader
2.remove of intron
3.replacement of 3' UU seq. w/ CCA
4. base modification
Prokaryotes sequnce taht binds to a site on ribosomal RNA for initiation of translation: Shine-Dalgarno sequence
complex of protiens and snRNA: snRNPs small nuclear ribonucleoprotein particles
complex of snRNP--pre--mRNA: spliceosome
where splicing occurs
RNA that catalyze rxns: ribozymes
e.g ribonuclease P

Start Studying!

Deck Info

Number of cards 195