Biochem Exam 4 Flashcards

Terms Definitions
Gly Glycine -H
most abundant protein
what are pyridine nucleotides?
G6PDH deficiency
drug-induced hemolytic anemia
BPG up
O affinity down
antibiotic. produced by streptomycetes in soil. inhibitor of bacterial RNA polymerase
fuel use
ATP/Creatine phosphate
glucose: fast type II
fatty acids: slow type I
essential fatty acids
linolenic acidlinoleic acid
the spatial arrangement of substituent groups that are free to assume different positions in space, without breaking any bonds, because of the freedom of bond rotation
What charge does DNA have?
Synthesizes RNA primers during primer stage of DNA Replicationone of 6/7 polypeptides in the aggregragte-Primose
Made of Niacin and tryptophan
makes NAD
"about 50% of the niacin equivalents in the average diet in the usa are derived from tryptophan".  know because testing by giving niacin different diets
How many electrons can FeS carry?
Lesch-Nyhan syndrome
absent HGPRT, defective purine salvageX-linked recessivesx: unrecovered purines are degraded to uric acid -> hyperuricemia, gout, *self-mutilation*, aggression
always face cytosol except during apoptosis PS molecules flip to the outer leaflet where they are recognized by PSspecific receptors on phagocytes.
specifity constant is
Turnover # / Km
nucleoproteins bound to RNA contain the _____
viral genome
Ribosomes are mostly ________ by mass.
a small group of indispensable persons or things
Adenylyl Cyclase
Activated by phopshorylated G protein subunit alphareleases cAMP proportionately to how much glucagon is present
What is the antidote to Tylenol?
N-acetyl cysteine
how is glucose transported into the cell
Reciprocal regulation
Glucogon's has opposite effects than insulin
Prader-Willi syndrome
Deletion of normally active Paternal allele.Mental retardation, hyperphagia, obesity, hypogonadism, hypotonia.
isocitrate dehydrogenase
- oxidation of isocitrate to alphaketogluterate is accompanied by reduction of NAD and release of CO21. regulation is ATP/NADH inhibitADP and NAD stimulateoxalosuccinate is an intermediate
keratan sulfate
galactose and n-acetyl glucosamine in a beta 1-4 bond
During the charging reaction, does the Aminoacyl tRNA synthetase disassociate from the intermediate?
What is DNA ligase?
seals nicks in DNA
which favor lipid bilayer?
glycerophospholipids and sphingolipids (because of bulky tails)
what makes:
lactic acide
amino acids
lactic acid: from anaerobic resperation
amino acids: from dietary proteins
glycerol: from tryasal glyceral neutral fat.
etiology of hemophilia A
deficiency of functional factor 8
Describe pheynylalanine to tyrosine
Phenylalanine + O2 + tetrahydrobiopterin (BH4) --Phenylalanine hydroxylase→ Tyrosine + H2O + dihydrobiopterin (BH2)dihydropteridine reductase then reconverts BH2 to BH4 using NADH(BH4 made from GTP)
Primary Structure
A description of all the covalent bonds linking amino acid residues in a protein; the sequence of amino acides within a protein starting with the n-terminus and ending with the c-terminus.
Becker's muscular dystrophies
X-linked mutated dystrophin gene. Less severe than Duchenne's. Onset in adolescence or early adulthood
catalyze formation of bonds b/n C and O, S, and N
catalyze rxns in which two chemical groups are joined with the use of energy from ATP
If C1 = C2 (C=concentration) and molecules can travel across the membrane. The system is at ________ and there is _____ net flow of molecules.
equilibrium, no
role of 5alpha-reductase?
convert testosterone to DHT in E.R.
DNA Polymerase III
primary enzyme for synthesizing new DNA strand
The formaiton of a phagophore is driven by this compound associating with lipids and proteins
Beclin 1
What's the start compound of dark reactions?
C5-Ribulose?? and CO2
What two TCA conversions give off CO2?
Isocitrate to a-Ketoglutaratea-Ketoglutarate to Succinyl CoA
Where is a not wiedely used place to regulate gene expression?
G6PDH deficiency causes what
normally, no problem, bc supply exceeds needwith drugs, causes drug-induced hemolytic anemia
Orotic aciduria
In ability to convert orotic acid to UMP (de novo pyrimidine synthesis pathway) due to defect in either orotic acid phophribosytransferase or orotidine 5'-phophate decarboxylase. Autosomal recessive.incr orotic acid in urine, megalobastic anemia (does not improve with B12 or folic acid), failure to thrive. No hyperammonemia (vs. OTC def - incr orotic acid with hyperammonemia).Treatment: oral uridine admin.
what are four types of directly coupled atp-dependent pumps(primary active transport systems)
P-typeF-typeV-type ABC transportors
What is conformation? configuration? native conformation?
a. a unique shape/folding/coiling rotating arounf a single bond
b. the unique arrangments of a molecule
c. refers to the working shape of real proteins
cholesterol in the skin is exposed to UV light and undergoes electronic rearrangement to give cholecalciferol (______)
vitamin D3
LeChatelier's Principle
A system at equilibrium responds to a disturbance in a way that minimizes the effect of the disturbance.
what are proteoglycans?
proteins + carbs to make cartilage or connective tissue
what is delta G for hydrolysis of ATP forming AMP
-45 kJ/mol
what is the tight-conformation of the beta subunits
ATP is tightly bound
what is the rate determine enzyme of fatty acid synthesis?
Acetyl-CoA carboxylase (ACC)
The double-reciprocal transformation of the Michaelis-Menten equation, also called the Lineweaver-Burk plot, is given by1/V0 = Km /(Vmax[S]) + 1/Vmax.To determine Km from a double-reciprocal plot, you would:
multiply the reciprocal of the x-axis intercept by -1.
What defect exists in Gauchers disease?
problem with Glucocerebrosidase (GM2 to GM3)
What defect exists in Tay-Sachs disease?
problem with Hexosaminidase A (glucocerebroside to ceramide)
disease that presents itself in bones where you would have fractures.
death by age 5, can develop in adulthood
Gauchers disease

some gene replacement therapy and bone marrow transplant
What is going through the mitochondrion?
Electrons! Where are they coming from?-"NADH"
describe active site of HIV protease
dimer of equivalent subunits: the active site has 2 aspartates at the interface
How is blood glucose concentration maintained between meals?
-Dietary carbs can maintain blood glucose levels for a few hours (2-4)-Beyond this time, blood glucose is supplied by the liver in 2 ways-breakdown of glycogen-gluconeogenesis
What does the extra Phenylalanine combine to in Phenylketonuria pts?
Acetate and pyruvate to form Phenylacetate and Phenylpyruvate => Musty odor PEE
True/ false the first step of renaturation is first order?
false- second-order because it depends on concentration and time
What is the Reaction Coordinate?
The reaction path of lowest free energy.
5’->3’ exonuclease activity
of DNA Pol I is used to repair mutations in the DNA
What is the effect of an increase in the concentration of calcium ion on the activity of PDC phosphatase?
Activates/Increases PDC phosphatase activity
AA structures Obj 1: Describe some of the functions of your body’s proteins (8)
Cell adhesion molecules are proteinsSome hormones are proteins such as insulin and glucagonIon channels and pumps in membranesAlmost all enzymes are proteinsEssential for movement (motor proteins) such as myosinElastin, keratin, and collagens are important proteins in connective tissuesExtra and intra cellular receptorsAntibodies
pyruvate + CoA + NAD -> acetyl CoA + CO2+ NADH
pyruvate dehydrogenaserequires cofactors (thiamine, lipoic acid, CoA, FAD, NAD)
Urea is used to do what?
To break disulfide bonds and denature the protien from its native conf.
mech off PKA activation?
cAMP comes in and bind the 2 r subunits off and leaves the 2 C units to be catalytic
 Can an endothermic reaction have a negative ∆G?
Yes, if there is an "Over-Riding" entropy term
Cholesterol 11Where do LDLs get apo B-100 and apo E?
HDLs responsible for donation of both to LDLs
Glucagon. What does it do. Relation to insulin.
Controlling hormone when glucose in blood stream is low. Opposite effect of insulin
maple syrup urine is caused by defect in _ which leads to build up of
branched chain alpha keto acid decarboxylation complex - build up of toxic alpha keto acid derivatives of valine, isoleucine, and leucine
explain penetrances effect on family pedigree that has bad genotype but show no symptoms?
the penetrance of the disease must be very low so the phenotype is not what the genotype dictates
what does the second part of the TCA cycle do?
converts citrate back to oxaloacetate and CO2
Where does the amino group from catabolism of branched chain amino acides end up.
on pyruvate resulting in alanine or on alpha-ketoglutarate resulting in glutamate and then glutamine. Therefore, the catabolism of branch-chain amino acids by skeletal muscle results in a release of glutamine and alanine into the blood.
islets of langerhans are? percentage of organ constitute? main types and what secrete?
in liver have alpha, beta, D, and F cells
1-2% organ
alpha- glucagon
D- somatostatin
F- sum1 tell me
What actually causes the death of an aids patient?
Not the virus itself.The patient has a very low immune system and many opportunistic virus' and bacteria infections cause actual death
what cant be done with biopharms that sucks and keeps ppl out?
patents hold in place cuz generics are hard to tests and so is bioavailibity of them so no generics
Chlorophyll molecules have 1,2,3, & 4 is the ____.
The 4 one is phytyl- Has to do with Isopreniod side cahin that allows them to anchor in the membrane
fructokinase deficiencybenign
what activates zymogens?
Components of Genes
-examined the effectiveness of ultraviolet light for killing bacterial at 265 nm, demonstrating nucleic acid in DNA is the genetic material
Less condensed, transcriptionally active, sterically accessible
Lac operon
Promoter – Operator region
Proteins that allow the uptake and utilization of lactose
apneustic center
prolongs inspiration by effecting pre botzinger
Where does transcription begin?
+1 site
targets Ca channels in neurons
Lipid Plasma membrane
Peri-plasmic space
Gram negative bacteria
Compound C3H7Br has how many isomers?
cholesterol is transfered by
alpha-ketoglutarate can be converted to:
amino acids
light emission from excited electron as it returns to ground state
Pompe's disease
type IICardiomegaly and systemic findings leading to early deathLysosomal alpha-1,4-glucosidase defPompe's trashes the pump (heart, liver, and muscle).
what is the enzyme in saliva
Maltoporin is used to transport ________.
______ is made from isoprene units
Anterograde transport requires this as a sorting signal
Where is the ER located?
In the cytosol.
Lysosomal Storage Disease
what enzyme damaged?
what lipid buildup?
what symptoms?
most common lysosomal storage disease
damage to β-glucosidase
cant convert glucocerebroside into ceramide
buildup of glucosylceramde (glucocerebrosides)
symptoms: hepatosplenomegalt, osteoperosis of long bones
treated with cerezyme
What two things activate PFK-1?
AMP, F 2,6-BP
Water splitting complex
attached to PS2
electrons are passed from Mn to a tyr residue this makes the Mn very positive and able to pull electrons from water. The electrons on the tyr residue are given one at a time to the PS2 RC to replace lost electrons.
for every electron take from water one hydrogen is pumped
Altered Apolipoprotein C-II
Type I familial dyslipidemia- Hyperchylomicronemia
elevated blood TGs and Cholesterol
protein that acts as an infectious agent in the absence of RNA and DNA
The side chains of nonpolar amino acids are best categorized as:
role of pyridoxal phosphate (B6) in transamination reaction?
describes a structure in a molecular polymer that has a net twisting of strands about each other in some simple and regular way
BiP binds lumenal domains of these elements: an endonuclease, a kinase and a transcription factor
cytarabine (Cytosar, Tarabine)
Treats Leukemia- analogue of cytidine with arabinose. Active cytarabine tri-phosphate competes with deoxyribonuclease for DNA polymerase binding. Replication and repair blocked
FMN (stands for and function)
Flavin Mononucleotide; electron carrier in complex one gives to Fe-S then to CoQH2 then to Complex 3; synthesized by riboflavin
Cholesterol 2eMitochondrial vs cytosolic HMG-CoA
mitochondrial to make ketone bodiescytosolic used to make cholesterol or fat
block HMG CoA reductase which is the rate limiting step in cholesterol synthesis
ketogenic amino acids
leucine, lysinecan make ketone bodies in severe fasting
in collagen the plane of the peptide bond is (parallel/perpendicular) to the helix to form strong hydrogen bonds with other polyproline helical polypeptides
what are the 4 histones?
H2a, H2b, H3, H4.
What are domains?
Super-secondary structures made up of alpha helices.
bile acids act as ______ and are synthesized in the liver, released into the duodenum and act as detergents
mismatch repair
enzymes recognize that two bases are incorrectly paired, the area of mismatch is removed, and the area replicated again.
step 4 of glycolysis
fructose 1,6 bisphosphate -> glyceraldehyde 3-phosphate + dihydroxyacetone phosphate
what is hyperosmolar (non ketotic) syndrome?
severe dehydration
high blood sugar
no ketosis
observed in undiagnosed DMII
believed that some insulin inhibits lipolysis
what role does aspartic acid residues in the active site of HIV protease serve?
acid base catalysis
Role of the shuttle mechanisms?
Transport NADH across inner mitochondrial membrane, since it is impermable. NAD/FAD is also recycled allowing shuttles to continue
Tight, Open, Loose conformation of Beta Subunits?
Tight-ATP bound tightOpen-exchanges ATP for ADPLoose-ADP+P bound loosely
an immunizing vaccine may contain what?
killed bacterial cells/virus, nonvirulent form of live bacterium/virus, denatured bacterial toxin or viral protein, or recombinant protein
double helix
the helical shape of the double chain of DNA that is like a spiral staircase w/a sugar-phosphate backbone on the outside and base pairs like stair steps on the inside
name two cellular compartments where urea cycle operates?
mitochondial matrix and cytosol
Definition of secondary structure
the ordered arrangement of nucleic acid strands
amino acyl tRNA synthetase
amino acids, anticodons, and CCA end of tRNA
Describe differences in the permeabilities of the two membranes towards most small molecules
Inner membrane is highly impermeable (requires protein carrier); outer membrane permeable
What is the basis of all geneic information flow in cells?
Complimentary base pairing
Where do the oxidation reaction take place? What catalyzes them?
MitochondriaCatalyzed by TCA cycle.
name some storage polysaccharides
1. starch: mix of amylose and amylopectin2. glycogen: basically it is amylopectin3. dextran: all linkages are branched
What is the enzyme responsible for the conversion of pyruvate to lactate during anaerobic glycolysis in red blood cells and skeletal muscle?
Lactate Dehydrogenase (LDH)
Biosynthesis of histamine and its function?
Histadine -- cofactor B6--> Histadine D Carboxylase --> Histamine.
Function is imflammation, vasodialator, bronchoconstrictor, increase of HCl in the stomach.
de-repression of lac operon
Lac I protein binds inducer
and cannot bind to DNA
What two types of glucose transport mechanisms are there?
Secondary active transport with Na+-glucose carrier proteins, and facilitative glucose transporters (GLUT transporters)
Integration 7: Describe mechanisms that affect the storage of triacylglycerols in adipose tissue during the fed state. Describe how adipocytes make the glycerol 3-phosphate needed for triacylglycerol synthesis, and how adipocytes can import fatty acids f
Insulin increases glut 4 proteins in liver cells, with the glucose being then used for FA production--Adipocytes import FA's using LPLLiver can phosphorylate glycerol --glycerol kinase--> G3P and can use glucose to make DHAP and G3P (uses NADH to NAD+) adipoctyes can only use glucose to make DHAP via G3P (uses NADH to NAD+)
How can you seperate the electron carriers in the mitochondria membrane?
osmotic rupture of the inner membrane with a gentle detergent
inner membrane can be seperated with ion exchange chromatography (complex 5 will come out as its own fraction)
polypeptide chains are held together in collagen by what type of interaction?
hydrophobic with glycines on apolar edge of each of the polypeptide chains; covalent crosslinks between lysine residues
What are the two enzymes involved in the conversion of pyruvate to Phosphoenolpyruvate (PEP) Bypass-1?
Mitochondrial Pyruvate carboxylase (ATP required)
PEP carboxykinase (PEPCK)
Pkas of propionate, methylmalonate and malonate
4.9, 2.77, 13 respectively i think
pyruvate under anaerobic conditions in yeast
alcoholic fermentation where CO2 is lost and the remaining aldehyde is reduced to ethanol
what does warfarin and dicoumeral essentially do?
inhibits Vit K reductases, which keep vit K in the KO form (which is inactive)
Describe the body's production of glutamate and glutamine from glucose (6)
glucose → pyruvate → (tca) → a-KG or a-KG + NH4+ + NADPH ←GDH→ Glutamate + NADP+Glutamate + ATP --glutamine synthetase→ Glutamine + ADP + Pi
name and describe the 3 various analytical tests for antibodies
1. ELISA (enzyme linked immunoglobulin substrate assay) - can be used to read immunoglobulin + antigen
2. Immunohistochemical Staining - staining of tissue sections with primary and secondary antibody for identification of specific proteins in tissue sections
3. FACS (fluoresence activated cell scanning) - a mixed T lymphocyte suspension is mixed with primary antibodies that bind to cell surface markers on T-helper and T-killer cells; these are then incubated with fluorescent labeled secondary antibodies
What agents can break secondary protein structure and how?
a. urea and guanidinium chloride
b. by competing for hydrogen bonding sites of the protein.
Pur repressor is also known as a
corepressor. represses only when bound to a small molecule. this is different than the lac repressor, which represses when NOT bound to a small molecule
How is atp generated from fuel molecules?
Electrons lost from the fuels during oxidative reactions are transferred to O2 by a series of proteins in the ETC. The energy of e- transfer is used to convert ADP & Pi to ATP via oxidative phosphorylation.
Goals of fuel metabolism in the fasting state?
Maintain blood glucose levels, esp for tissues that depend on glucsoe for fuel (RBC's, brain)Provide alternative TAG based fuels to spare available blood glucose
what are some unique properties of elastin
1. do NOT contain the Gly-Pro-Y and Gly-X-Hyp repeats and does not fold into a poly Pro helix
2. lacks secondary structure but contains unordered coiled structure
3. contains covalent crosslinks between lysine residues
What forces hold the subunits of multimeric proteins together? In multimeric globular proteins do the peptide chains intertwine?
a. A range of non-covalent forces-- hydrophobic, hydrogen bonds, and salt bridges.
b. No, because they have a native tertiary structure. Only in fibrous proteins do they intertwine.
What is the tag that you need to be a lysosomal protein?
Mannose 6 Phosphate
What are a main storage form of energy? Why
TAG's, b/c of their highly reduced nature
What helps to ensure that origin licensing occurs only once per origin per cell cycle?
one ORC per origin

one set of Cdc6, Cdt1 per origin

MCM, Cdc6 and Cdt1 are all destroyed after one use.
Sucrose is formed by what two sugars joined by this type of linkage
Glucose linked alpha 1,2 with fructose gives rise to this disaccharide
What is the only coenzyme required for the pentose phosphate pathway, and what does it participate in?
The only coenzyme required for PPP is thiamine pyrophosphate (TTP) bytransketolase. The transketolase activity in RBCs is used to measure thiamine nutritional status and diagnose the presence of thiamine deficiency. (Remember that TTP was also required by pyruvate dehydrogenase complex and a-ketoglutarate dehydrogenase-
What RNA pol is capping associated with?
RNA pol 2, b/c form on mRNA (which is RNA pol2)
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