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Bio-Chemistry II


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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
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 ->
Acyl-CoA + FAD -> transenoyl CoA + FADH2
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
enzyme: 3-ketoacyl + CoA ->
Acetyl CoA + Acyl CoA
(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
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
After glycerol is trans ported to the liverit is converted into one of these two molecules
DHAP dihydorxyacetone phosphate
G3P D-glyceraldehyde-3-phosphate
fatty acids are activated fro degradation by conjugation with CoA in a rxn catalyzed by
acyl-CoA ligases or
Fatty acid activation occurs in the ....
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)
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 -> D-methylmalonyl-CoA
propionyl-COA carboxylase
what kind of co-factor does propionyl-COA carboxylase have?
Propionyl CoA is eventually converted to this citric acid cycle intermediate
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
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
the rxn catalyzed by HMG-CoA synthase in ketogenesis
Acetoacetyl -CoA + aecteyyl CoA +H2O -> HMG-CoA + CoA
Ketone body comonly travels in the blood
while traveling through the blood acetoacetate can break down to
In individuals suffering from ketosis what is one likely to smell on their breath
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?
(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?
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
spingosine is formed form what two precursors
palmitoyl-CoA and serine
what is the product of a long chain acylCoA and asphingosine?
Ceramide + activated glucose (UDP-glucose)-> ?
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)
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
guainine + PRPP <-> GMP + PPi
purine salvage pathway
Hypoxanthine + PRPP <-> IMP + PPi
HGPRT is inhibited by
both IMP and GMP
(its products duh!)
Adenine + PRPP <-> Adenylate + PPi
Adenine phosphoribosyl transferase
Branch point in nucleotide synthesis
IMP + (? energy) -> GMP
IMP + (? energy) -> AMP
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
AMP +ATP <-> 2 ADP
adenylate kinase
guanylate kinase
enzyme that catalyzes conversion of all nucleoside diphophates to nucleoside triphosphates
from where do all nitrogens of purines come
amino acids
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
(UMP-> UDP-> dUDP-> dUTP->dUMP->dTMP)
synthesis of PRPP is inhibited by?
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 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
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
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
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
thermostable DNA polymerase
One way in which recombination appear to occur in cells is
Holliday junction
Types of mutations
two types of subsitution mutations
transition mutations
transversion mutations
mutation that involves replacement of one purine for another or one pyrimindine for another
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
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
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
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
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
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
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
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
E.coli DNA replication:
OriC site contains these sequences
three repeats of AT rich sequences
transcription factors that act positively
transcritpion factors that act negatively
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
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
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
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:
-30-100 TATA box
CAAT box -40-150
GC box -40-150
function of TFIIF
order of binding of transcriptionfactors
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
where splicing occurs
RNA that catalyze rxns
e.g ribonuclease P

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