Biochem Flashcards

Terms Definitions
phosphate group
Hydrolyzes fructose-1,6-bp to fructose-6-Pi,
First committed step of gluconeogenesis
Allosterically regulated by:
Negative Effectors: AMP, Fructose-2,6-bisphosphate
Positive Effector: Citrate
Key enzyme for regulating the flux of intermediates through gluconeogenesis
building blocks of carbohydrates
Prokaryotes, causes mRNA misreading (30S Sub)
building blocks of proteins
amino acids
Branching Enzyme
synthesizes a(1,6) glycosidic linkages (glycogen synthase only synthesizes a(1,4)linkages.
Branching is crucial because it increases the solubility and number of reducing ends of a glycogen molecule. this increases the rate of biosynthesis and degredation.
Enzyme takes a block of ~7 Glc residues and transfers them to an interior site, creating the a(1,6) linkage. The new linkage must be at least 8 residues away from a previous branching point and the 'added onto chain' must be at least 11 residues long.
Anderson's disease--deficiency in branching enzyme. Autoimmune death by age 4.
carb: sources
plants, bread, pasta, rice, potato
What do all organic compounds contain?
Essential amino acids cannot be synthesized within the human body. TRUE/FALSE
speeds up chemical reactions without changing the product
Integral Proteins
Stop transfer sequence. Default = plasma membrane
the building of substances by the body
The beta-oxidation of fatty acids with an odd number of carbons requires conversion to pyruvate before entering the citric acid cycle. TRUE/FALSE
What is the dominant form of DNA?
a polysaccharide fiber that is tough and flexible and gives plants strength and rigidity
Irriversible inhibitors:How do transition state analogs work ?
Compounds resembling the transition state of a catalyzed reaction effectively inhibits enzymes
What is the name for a large molecule?
In the urea cycle which molecule, that is synthesized in the cytosol, meets with the carbamoyl phosphate, which is made in the mitochondrial matrix, for subsequent reactions.
a solution where the hydrogen ions are greater than hydroxide ions
Regulation of Glucose-6-Phosphatase
High Km for substrate; under substrate level control (linear relationship with concentration of substrate)
From the equations, what is ?[S]
[S] = Substrate concentration
The bond linking a fatty acid to conenzyme A is...
a thioester
4 uses of isotopes

radio isotopes used in cancer treatment
radio carbon dating of fossils
kill bacteria on food
radio isotopes used to "trace" movement throughout the body
Glycoproteins often require the ability to recognize specific molecules. Why are carbohydrates good candidates for the "recognition" role?
They are structurally complex, which allows a wide variety of forms that are needed for a high degree of specificity.
The formation of ___ , due to it being a highly favorable reaction, tends to pull the pathway of glycolysis forward.
atoms with 4 valence electrons tend to...
share their valence electrons
High energy phosphorylated compounds achieve their ^G by having products that are more stable than the reactants. ATP achieves this in part via the resonance stabilization of the released Pi. What is the major mode of stabilization of the products from hy
Tautomeric shift- goes from enol to more stable keto state.
Name the consequence of deficiency of the following:Vitamin K1Vitamin A - RetinolVitamin E - alpha TocopherolVitamin D2 - Calciferol
Deficiency of, causes:Vitamin K1*blood clotting problemsVitamin A - Retinol*lacking visionVitamin E - alpha Tocopherol*becomes deactive in lipid membranesVitamin D2 - Calciferol*no calcium Regulation
What function does DNA polymerase 3 lack?
5' to 3' exonuclease activity
A marathon runner collapses. What happened?
High levels of lactic acid= acidic blood= muscles fail
Define atom
The smallest basic unit of matter
ATP is a high energy molecule because the products of its hydrolysis (ADP and Pi)are more stable than the ATP reactant. What are 3 explanations for why this difference exists? What kind of bond is broken in the hydrolysis of ATP to ADP and Pi?
1)Greater degree of solvation in product 2)ADP ionizes 3)resonance stabilization of Pi The bond broken is a phosphoanhydride bond.
What role does fructose-2,6 bis-P play in the reciprocal reglation of glycolysis and gluconeogenesis? How is its production affected by glucagon? Does this result in raising or lowering blood glucose levels?
The role it plays is inhibiting fru-1,3 bis-P and glycolysis. An increase in glucagon results in a decrease in fru-2,6 bis-P. This raises blood glucose.
What is the difference between an ionic compound and a covalent compound?
Ionic compounds are formed by ionic bonds, where electrons are transferred between two atoms. A covalent compound is formed by a covalent bond, where electrons are shared between two atoms.
Why might a bacterial species that has gained the ability to change surface glycolipids/glycoproteins be dangerous?
Because they could invade our immune systems.
Draw a diagram (in your head) of an integral membrane protein with 5 membrane spanning domains. Indicate the hydrophobic regions. What sort of secondary structure is usually present? Does this protein require lipids for its activity?
The hydrophobic region is within the lipid bilayer. The secondary structure is the alpha helix. No lipids are not required.
Does ATP usually provide energy as the result of a single or double step reaction? Explain.
It is the result of a double step reaction. It involves a phosphorylated intermediate (Phosphate is lost in last step, only used as a good LG).
What is a compound made of?
A C I M O A O 2 O M D E B T
A compound is made of atoms of 2 or more different elements bonded together
carbohydrates: monomer
Phosphorylates glucose-1-Pi to glucose-1,6-bisphosphate
binds to a dephosphorylated Serine in phosphoglucomutase (and subsequently phosphorylates it to restore enzymatic activity)
major 4 organic compounds

nucleic acids
Prokaryotes, blocks incoming AA-tRNA, 30S Sub
joining of several amino acids
UDP-glucose pyrophosphorylase
catalyzes the acylation of Glucose-1-Pi with a UTP to create UDP-glucose
(Glc-1-Pi + UTP --> PPi + UDP-Glucose)
UDP glucose "carries" activated glucose molecules
Inorganic Pyrophosphatase is required to make this reaction irriversible, it hydrolyzes the released pyrophosphate molecule into 2Pi
carbohydrates: functions-examples
energy (emediated): starch. structural (plants walls): storage: glycogen.structural (eksoskeleton): chitin
In beta-oxidation of fatty acids, initiation occurs at the methyl end of the fatty acid...TRUE/FALSE
The conversion of glutamate to glutamine is catalyzed by glutamine synthetase requires ATP. TRUE/FALSE
joining amino acids
by covalent peptide bonds
Collagen Mutation Clinical Examples
Osteogenesis Imperfecta, Ehler-Danlos Syndrome, Scurvy
lipids: sources
butter, oil, lard, animal fat, mayo
Isomerization of the double bonds of polyunsaturated fatty acids involves both: (i) a cis-trans isomerization; and (ii) changing the position of the double bonds. TRUE/FALSE
Which base is not found in RNA?
particles found in the nucleus that have no charge
What defines the slope in the double reciprocal or lineweaver-burk plot ?
What is the name of a smaller molecule?
Which amino acid does NOT use glutamic acid as a precursor?
building blocks of lipids
glycerol and 3 fatty acid
Which hormones activate Glycogen Phosphorylase?
Glucagon and Epinephrine activate Glycogen phosphorylase by phosphorylating in (via cAMP pathway)
"A" state = PHOSPHORYLATED (locks in the R state)
Phosphorylation is by PHOPHORYLASE KINASE (covalent modification of Ser-14 residue
Dephosphorylation (caused by INSULIN) is done by PHOSPHOPROTEIN PHOSPHATASE 1
From the equations, what is ?[P]
[P] = Product concentration
The reduction of atmospheric N2 to NH3 occurs on which subunit of nitrogenase?
molybdenum-iron-sulfur complex
purpose of the octet and duet rules
to stabilize atoms
In fascilitated diffusion, molecules move down their concentration gradients until equal concentrations are present on either side (equilibrium). With this in mind explain how erythrocytes maintain a low intracellular glucose concentration such that gluco
It converts glucose into glucose-6-P to maintain a low concentration of glucose.
What effect does a noncompetitive inhibitor have on the Vmax, and Km
Noncompetitive inhibitors don't change the Km, and decrease the Vmax
protein structure is determined by 

number of AA
kind of AA
arrangement of AA
RNA can have 1*,2* and 3* structures. Explain what is meant by each.
3*-Fully folded nucleic acids- involves long range interactions
Allosteric Enzymes-Explain the sequential model.
The enzyme starts in TT form. The sequential model fills one active site with substrate switching it to RT form, and then the second one attaches as well switcing it to RR form.
Semiconservative replication implies that...
each of the new double stranded DNA molecules contains one of the original intact strands and one completely new strand.
From the equations, what is ?Km
Km = Michaelis constant - shows dissociation
Fatty acids are advantageous forms of energy storage because...
they contain more carbons than carbohydrates, their hydrophobicity allows close packing and do not require water for transport, and contain more energy than sugars
What 2 properties are responsible for providing the stability of the DNA double helix? Which one provides most of the energy for stabilization?
Hydrophobic stacking of base pairs and H-bonding btwn base pairs. Of these, hydrophobic stacking of base pairs provides the most energy.
What is the ultimate goal of the urea cycle?
To make urea for excretion
The following substances are bases or acids?
Lemon juice, vinegar, stomach acid, baking soda, milk
(If you got this wrong, I'll hurt you. Honestly. It even says "stomach ACID" in the list.)
Briefly describe how birds and mammals deal with the problem of ammonia toxicity.
They must excrete it: Birds- uric acid Mammals- urea
Show the reaction for the terminal e- acceptor of cytochrome oxidase. Are H+s pumped as e-s move through this complex to this terminal?
4cyt (red) + O2 + 8H+ (matrix)-->2H2O + 4cyt (oxid) + 4H+ (ims)Yes, H+s are pumped
Why is it that the e-s passed from FADH2 result in fewer ATPs synthesized than those from NADH?
Because e-s from FADH bypass complex I and don't get H+ pumping.
What is an Element?
a e i t o t o a
An element is the one type of Atom
percentage of tRNA
Autosomal dominantCell-signallying defect of fibroblast growth factor (FGF) receptor 3. Results in dwarfism; short limbs, but head and trunk are normal size. Asso. with advanced paternal age.
endonuclease that recognizesthe deformity and nicks the DNA. Polymerase I elongates and removes the damaged DNAand then DNA ligase covalently re-links the strand.
isopentenyl pyrophosphate
used to make isoprenoids which are attached to proteins that target them to inner surface of the plasma membrane in isoprenation. they make hormones, carotenoids, Vitamin K E A, cholesterol, rubber, phitol of chloryphyll, dolichoils, quinones, and isprene
Km is better when
distal histidine
H-bonded to bound O2
ACP stands for
acyl carrier protein
Gilbert syndrome
UDP glucuronyl transferase deficiency
nitrogen-containing base
Nitrogen-containing compounds found in DNA and RNA: adenine (A), thymine (T), cytosine (C), guanine (JG), and uracil (U)
What are genes made of?
C5 is the basic c5 unit.
ACP has what vitamin in it?
Recognize the chemical structure of tetrahydrofolate
apo B-100 and B-48 deficiencyautosomal recessivesx in the first few months of life:failure to thrive, steatorrhea, acanthocytosis, ataxia, night blindness
Enzyme involved in steroid hormone synthesis. Target for drugs that want to prevent ER+ breast cancers
Which of the following parameters remains the same for S to P, whether the reaction is enzyme-catalyzed or uncatalyzed?
signal relay and secretion aldosterone
angiotensin I --ACE-->
agiontensin II--ACE-->
angiotensin III
both II and III active and control aldosterone release
PCR Requirements
Deoxynucleotides: dATP, dCTP, dGTP, dTTP
Taq heat stable DNA polymerase
DNA template to be amplified
A primer complementary to one DNA strand of the template DNA
A primer complementary to the other DNA strand of the DNA template
What carbohydrates make up Sucrose?
Glucose and Fructose
what converts pyruvate into lactic acid?
lactate dehydrogenase
after injury whats increased/decreased?
glucagon/EP to counter insulin, breakdown of glycogen,
more glutamine->ATP by intestine,
synthesis and excretion of proteins by liver
less albunin by liver
adipose tissue->fatty acids
protein->AA for gluconeogenesis in liver
patients have hyperglycemia
anaerobic, use cori cycle lactic acid->glucose
more coagulation
fatty acid-> ketone body by liver
less Nitrogen balance
Name the amino acid precursor(s) that your body uses to make histamine (duh)
Malate Shuttle
Uses cytosolic NADH to reduce oxaloacetate to malate.Malate enters themitochondria where it is oxidized back to oxaloacetate along with NAD being reduced to NADHNet reaction is cytosolic NADH is converted to NADH inside the mitochondriaNo energy is lost, in contrast to the glycerol phosphate shuttle.
Fragile X syndrome
X-linked defect affecting the methylation and expression of the FMR1 gene. Asso. with chromosomal breakage. The 2nd most common cause of genetic mental retardation after Down syndrome).Findings:macro-orchidism(enlarged testes), long face with a large jaw, large everted ears, autism, mitral valve prolapse.Trinucleotide repeat disorder (CGG)Fragile X = extra-large testes, jaw, ears.
catalyze redox rxns
add or remove a proton
There are ____ types of integral membrane proteins.
this marks proteins to be endocytosed and destroyed
methianine (translation initiation)
enzyme for 2 (glyceraldehyde 3-phosphate +NAD + Pi -&gt; 1,3 bisphosphoglycerate + NADH + H)
glyceraldehyde 3-p dehydrogenase
CII rules
1 RX per form
quantity written and spelled out
must be written Rx (or written givin within 7 days after verbal)
pharmacist sign each Rx
What do NSAIDS like aspirin and ibuprofen inhibit?
COX>>>TXA2>>>platelet aggregation
Key regulated enzyme in FA biosynthesis?
Acetyl CoA Carboxylase
Native State
The fully folded and functional state of the protein.
Pancreatic lipase
degradation of deitary TG in small intestine
digestion stage 3
complete oxidation of nutrients and production of ATP
everything has been converted to acetyl CoA
acetyl group is taken to citric acid cycle and is converted to CO2 and ATP
chiral center
an atom with substituents arranged so that the molecule is not superimposable on its mirror image
difficulty w/ insulin production w/ recombinant DNA?
2 separate chains
Sugar in RNA
-2' carbon has -OH on it
This process tags the protein for degradation by the proteosome
POLY ubiquination
bacteriochlorophyll a and b are found where?
In photosynthetic bacteria
Methylmalonyl CoA mutase (MCM) catalyzes...
Isomerization of methylmalonyl-CoA to succinyl-CoA
Cholesterol 5eDescribe the enterohepatic circulation of bile salts.
Bile salts released from gall-bladder in small intestine, 95% of bile salts are then later reabsorbed in ileum
proton gradient dicipators effect on ETC
prevent ATP synthesis
carry hydrogen accross the membrane and ionize the negative matrix dissipating the hydrogen gradient needed for ATP synthesis
Autosomal-dominant polycystic kidney disease (ADPKD)
AKA adult polycyctic kidney disease. Always bilateral, massive enlargement of kidneys due to multiple large cycts. Pt presents with flank pain, hematuria, hypertension, progressive renal failure. mutations in APKD1. Asso. with polycyctic liver disease, berry aneurysms, mitral valve prolapse. infantile form is recessive.
Complex I
- entry point for NADH bound electrons from glycolysis and TCA
What is co-operativity?
Occuring in hemoglobin, it is the phenomenon that addition or removal of one oxygen makes subsequent additions or removals easier
RNA: acid/base chemistry
-tolerant to acid
-Base will strip 2' OH group proton
These are involved with targeting the vesicle to the appopriate organelle
v-snares / t-snares
1.  Major FA in (3)
2.  Algae fish get it from
3.  Can body make and what from?
4.  Omega 3 or 6?
1.  Sperm; brain phospholipids; retina
2.  Schizochytrium
3.  Alpha linolenic acid and yes
4.  Omega 3
Choose the INCORRECT answer. Hydrolysis of ATP to ADP and Pi releases a large amount of free energy because:a) The ADP formed in the reaction immediately ionizes, releasing a proton in to the medium, which drives the hydrolysis towards completion.b) The r
d)    The phosphoanhydride bond found in ATP is a special type of covalent bond that contains a large amount of energy
What is classical PKU?
2 mutated genes that code for phenylalanine hydroxylase; results in high levels of phenylalanine if it is consumed
what causes sorbitol accumulation?
the lack of sorbitol dehydrogenase in tissue such as schwann cells, lens, retina, and kidney
what 2 things are ribosomes made of
rRNA and ribosomal proteins
What three methods of covalent catalysis are utilized by serine proteases?
1. concerted acid/base catalysis
2. transition state stabilization (oxyanion hole)
3. covalent catalysis
our body synthesizes EPA and DHA from____.
what oil is also rich is these?
alpha linolenic acid
Fish oil
What else is important in PS II?
1.Antenna start coming into play.Antenna chlorophyllA chlorophyll group that absorbs light energy and passes it on to a photosynthetic reaction center by exciton transfer.2.These antenna chlorophylls pass the energy of absorbed photons (units of light) from molecule to molecule until it reaches a photosynthetic reaction center.The phtosynthetic units are being captured and electrons are being bounced in chlorphylls
how can Factors be regulated if they are irreversibly activated by proteolysis?
they have short lifetimes
Delta G of ATP citrate lyase?
Very positve. Requires ATPOpposite of citrate synthase (with -DetlaG)
oxidative, irreversible step in HMP shunt
glucose 6P -> NADPH and ribuloseenzyme: glucose 6P dehydrogenase
what are the four main roles of sterols
membrane structurecardiac glycoside (digitoxin, oubain)hormonesemulsifiers (bile acids)
What is actin made up of?
Repeating G-Actin subunits arranged in helical symmetry
3'-5' exonuclease activity of DNA Pol I
Corrects incorrect nucleotides during DNA synthesis, moves backwards 3'-5' and cuts out incorrect nucleotide
What are the regulators of glucagon release? (6)
Major: Glucose -Insulin -Amino Acids +Minor:Cortisol +Neural (stress) +Epinephrine +
How are AAs transported into the Hepatic Portal Vein?
Via Na+-dependent carriers into the cellThen the AA is goes into the vein via a Facilitated Transporter
True or False:
AMP is the precursor for IMP and GMP.
False -  IMP is the precursor for AMP and GMP.
- If both AMP and GMP are present in adequate amounts, the de novo pathway of purine synthesis is turned off at the amidotransferase.
- Synthesis of AMP requires GTP, whereas synthesis of GMP requires ATP
Consider an acetate buffer, initially at the same pH as its pKa (4.76). When sodium hydroxide (NaOH) is mixed with this buffer, the:
ratio of acetic acid to sodium acetate in the buffer falls.
Which side chains are polar and uncharged?
Met, Ser, Thr, Cys, Asn, Gln
gain of ATP from glycolysis
(net and total)
net = 2 molecules of ATP
total = 2 molecules of ATP
in yeast and some bacteria, what happens to pyruvate?
pyruvate is reduced to ethanol to regenerate NAD+
Transition between cyclic and non-cyclic form of PS1 and 2 organisms
1. Blue light acts on PS2 causing over activity
2. QH2 builds up and activates a protein kinase because PS1 can't oxidize it fast enough.
3. Theronine is phosphorlyated on LCH2 (state 2)
4. LCH2 goes to stromal lamellae to get hydrogens
5. LCH2 takes hydrogens to PS1 and fixes flow imbalances by speeding oxidation.
6. increased PS1 activity will cause increased quinones A and B.
7. LCH2 will become dephosphorlyated (state 1)
it always takes less energy to excite PS1 than PS2 so without regulation PS2 would never be excited
A prosthetic group of a protein is a non-protein structure that is:
permanently associated with the protein.
what is normal BUN levels (blood urea nitrogen yea i was dissapointed too)
10-20mg/dL normally about 10g urea/day excreted
Explain why it is advantageous for glycogenolysis and glycogenesis to require some enzymes that the other pathway does not require
The pathway could not be regulated and would be a product of equilibrium if it was the same both ways. One can be activated while the other is inhibited.
where silencers and enhancers are located in relation to the gene
anywhere: close to, far way or w/i a gene
advantage of glycogen breakdown by phosphorolysis compared to hydrolysis?
no ATP used and rxn goes forward by itself cuz pyrophophate to 2Pi so fast
What happens after about 3 months of being treated with HAART agents?
Over time, the amount of virus in plasma decrease and is usually at 10 at 3 months treatment. (limit of detection is decreased)
2. What is the fuel for the c.a.c.? From what metabolites is it derived?
fuel is Acetyl CoA derived from pyruvate i think
How do you assay for transport between different stacks of the golgi?
make wild type so it can add GlcNac sugar and mutant can not add GlcNac sugar. the only way you get product is movement between the stacks because wild type can make glcnac but does not express g protein and the mutant is opposite.
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