Biochem - FINAL

draw concept map for ssDNA and dsDNA

electrostatic interaction equation??

dielectric constant for polar

80

dielectric constant for nonpolar

2

Energy Diagram for H and VDW

explain cooperavity for dsDNA

explain salt’s relationship in DNA

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draw peptide bonds and other bonds that can be found

draw ramachandran plot and explain

allowed angles of phi and psi to prevent steric

protein folding concept map!

Entropy equation

S=Rln(n)

R=0.008314

5 types of catalysis

covalent

acid/base

catalysis by proximity

metal catalysis

transition state stabilization

myoglobin’s biological importance

prevent escape of lethal ROS

myoglobin’s biochemical importance

binding/releasing of O2

hemoglobin’s biological role

effectively and safely transport O2 by coopervity

Proximial His - draw it

Distal His - draw it + the equation

saturation plot of myoglobin and hemoglobin

explain fetal hemoglobin

binds together to O2. binds tightly!! this is because Ser replaces His (his in adult) and encourages the R state

reducing affinity for fetal hemoglobin

less cooperavity, binds more tightly to O2

concept map for hemoglobin

draw energy graph

michaelis - menten model write reaction

E+S==E.S=E+P

michaelis - menten equation

Kcat/Km?

how good is this enzyme

ATCase? (2)

allosteric regulation refers to proteins/enzymes whose functions is controlled by binding of signal molecules at distinct regulatory site

these proteins demonstrate cooperativity

ATCase biological role

catalyzes 1st commited step in pyrimidine synthese

ATCase reaction?

CTP?

structure of ATCase - draw and explain

R and T state

2 catalytic trimers

3 regulatory subunits

Whats binds to what?

* catalytic trimers
* regulatory subunits

* L-ASP
* CTP and ATP

ATCase concept map

ATCase: rate vs. \[S\] for ATCase DRAW

carbonic anhydrase draw

Acid/Base catalysis and Metal Ion

carbonic anhydrase biological role

hydrate CO2 to transport to lungs for exhalation

MutY biological role

help prevent DNA mutation

MutY draw

T.S

catalysis by approx

acid base catalysis

chymotrypsin biological role

breakdown proteins

chymotrypsin draw

oxyanion hole

covalent catalysis

tetrahedral t.s

metabolism

chemical rxns that support the growth + activities of the cells

ATP draw

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glycolysis purpose

convert glucose into pyruvate

glycolysis location

cytoplasm

glycolysis net products

2 ATP, 2 NADH, and 2 pyruvate molecules

draw glycolysis and reversible steps

gluconeogenesis

when the cells has enough energy, glucose will be stored in the liver

reversible reactions in glycolysis

role of biotin

used in metabolic rxn as a cofactor

CO2-biotin-enzyme + pyruvate = biotin-enzyme + oxaloacelate

fates of pyruvate

1) acetyladehyde - (nadh→nad+) - ethanal : alcohol fermentation

2) lactate: lactic acid fermentation

3) acetyl CoA: citric acid cycle

Cori cycle draw it

citric acid cycle purpose

Harvesting the reductive power stored in glucose to create \n ATP

citric acid cycle products

* Per glucose molecule, the Krebs cycle produces:  4 × CO2  ;  2 × ATP  ;  6 × NADH + H+  ;  2 × FADH2

draw citric acid cycle

Glyoxylate Cycle

bypasses decarboxylation steps \n allows some plants + other microorganisms to grow on acetate

draw Glyoxylate Cycle

isocitrate -(isocitrate iyase)-glycoxylate-(malate synthase)\[Acetyl COA+H2O → COA\] -malate

Electron transport cycle location

inner membrane of mitochondria

Electron Transport Cycle draw

ETC: cycle I

NADH Q oxidoreductase

input: NADH

output: QH2, 4H+

ETC: cycle II

succinate Q reductase

input: FADH2

output: QH2

ETC: cycle III

Q-cytochrome c oxidoreductase

input: QH2

ouput: reduced cyto c, 4H+

ETC: cycle IV

cytocrome c oxidase

reduction of O2

ATP synthase anatomy draw

ATP synthase in action draw pls

A

ATP binding change model

L,T,O

loose, tight, open

L: ADP+Pi comes in

T: coverts ADP to ATP

O: ATP leaves

DNA vs. RNA

R group: DNA (H), RNA(OH)

dna has less chemical potential

splicing

introns are removes from RNA to make mRNA bcause they do NOT encode proteins

mRNA is made of exons that do code proteins

spliceosomes

complex of 5 small nuclear ribonucleoprotein, known as SnDNPs, that combine with pre-mRNA to form the enzyme active site

spliceosome mech

intron removal requires 2 transesterification reactions. BPA 2"‘ OH acts as the 1st nucleophile while 5’ P-exon 1 acts as the 1st electrophile

exon 1 3’ OH acts as the second nucleophile while 5’ P-exon 2 acts as the second electrophile

spliceosome draw it

tRNA synthesis

a codon is a series of 3 nucleotides on mRNA that matches with an anticodon on tRNA that is bound to an amino acids to be added to a peptide chain

draw tRNA synthesis

practice reading a genetic code w dots plot

draw reaction for animo acid-tRNA synthesis

draw Thr tRNA-synthetase

peptide bond synthesis

ribosome is the main enzymes performs protein synthesis

enzymes - EF-Tu and EF-G assist

3 sites tRNA can be bound to E,P,A

moves from A to E

draw peptide bond synthesis

peptide bond making by ___

EF-Tu - comes w AA tRNA. allows time to pass to ensure correct AAtRNA

acts a molecular clock

binds to amino acyl tRNA when in GTP form

brings amino acyl tRNA to A site

translocation via ___

EF-G - help move mRNA site to site

catalyzes movement of mRNA

uses GTP hydrolysis to mRNA from site to site: mRNA + peptidyl-tRNA from A to P, deacylated-tRNA from P to E

peptide release via ___

RFs

stop codon interpreted by release factors

act as a molecular clock using GTP hydrolysis

then allows H2O to perform hydrolysis

membrane protein - where to go

mail man - signal recognition proteins. recognize signal peptides and bind to ribosome to transport to ER membrane (6 proteins)

SRP - mailbox. binds with SRP in the ER membrane where the ribosome and peptide can be delivered

verification? translocation (door) at door SRP is released. must be in open configuration to peptide inside

signee - removes the signal peptide with signal peptidase in the ER lumen.

draw a lineweaker-burk plot

vmax - y axis

km - x axis

enzyme inhibition factor equation and draw

competitive inhibition draw and explain

competes for active site/ inhibitor resembles substrate and occupies the active site

KM increase, vMax unaffected

KMapp= KM x IIF

decreases affinity for substrate needs more substrate to fill sites

uncompetitive inhibition draw and explain

inhibitor and substrate bind simutousely

binds to ES complex

KM decreases and Vmax decreases

less active enzyme

increase affinity to substrate

noncompetive inhibition draw and explain

binds allosteric sites

KM unaffected, vMax decreases

less active substrate

IC50

\[I\] to reduce response 50% of max response

EC50

\[I\] to elicit response 50% of max response

LD50

lethal does require to kill 50% of the population dosed

therapuetic index draw curve

toxicity of drugs LD50/EC50

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lipinski’s rules

good absorption

* No more than 5 hydrogen bond donors.
* No more than 10 hydrogen bond acceptors.
* Molecular mass less than 500 Da.
* Partition coefficient not greater than 5. measured as log(P)

Partition coefficient

logP measures hydrophobicity

higher logP - more hydrophobic

DNA polymerase draw reaction

O-helix

structure in active site of DNA polymerase contributing to specificity and low error rater

movement of O-helix

stabilizes T.S

dramatic, impressive, sledge hammer

light dependent reaction

thylakoid membrane in stroma

energy from light excite electrons, H2O in the thylakoid lumen to pump H+ from the stroma to be used in ATP synthesis

draw light dependent reaction

PSII

P680

e- donor: H2O

e- acceptor: plastoguinone

photons: 4

cytocrome bf complex

photons: 8

catalyses e- transer from PQH2 to plastocyanin

PSI

P700

e- donor: plastocyanin

e- acceptor: NADPH+

photons: 4

Calvin cycle

light rxn in stroma

carbon fixation, CO2 + ribulose 1,5 biphosphate= RnBP via rubisco

draw calvin

RuBisCo

facilitates carbon fixiation

uses metal catalysis with a Mg2+ ion that is coordinated with carbamate (CO2 and lysine)

puts CO2 in proximityto ribulose 1,5 biphosphate

input: ribulose 1,5 biphospahte, CO2

output: 3-phosphoglycerate (2x)