Biochem midterm

conserved biochemical reactions or processes

regardless of their ranks in the food chain or their positions in the phylogenic trees, all living organisms maintain their lives through ____

1. energy metabolisms

2. synthetic metabolisms

3. control of reactions

4. self-control

life -> biochem

1. need energy ->

2. grow and develop ->

3. respond to surroundings ->

4. reproduce ->

1. catabolism for energy and small precursors (metabolisms)

2. anabolism for synthesis (metabolisms)

3. activation and restriction of enzymes (controls)

4. 1+2+3

biological reactions

catabolism

breaking down

catabolism

for energy and small precursors

anabolism

building up

anabolism

for synthesis

chemical reactions in series; >10,000

biological reactions

metabolisms and their controls involve a great number of ____(___)

specifically; catalyst proteins (enzymes)

biological reactions

these reactions are ____catalyzed by ___

proteins

decoding products of genes, DNA

differences in biological reaction -> different phenotypes

different DNA -> ___-> ____

>10,000

___different enzymes that catalyze different reactions

central dogma

protein, carb, fat, nucleic acids

majority of biomass:

carbohydrate

protein

nucleic acid

fat

90% of cell/body mass

H, C, N, O, P, S, Cl, Na, K, Mg, Ca, Fe, and Cu takes over ____

amino acids

building blocks of proteins

monosaccharides

building blocks of carbohydrates

nucleotides

building blocks of nucleic acids

fatty acids and glycerol

building blocks of lipids

-sugars

-ring-forming and condensation reactions

alcohols

-found on ___

-take part in: ___

-simple sugars

-ring-forming reactions

aldehydes

-found on ___

-participate in ___

-simple sugars

-ring-forming reactions

ketones

-found on ___

-participate in ____

-amino acid structure

-peptide bonds

carboxylic acids

-important in ___

-form ___

sugars; complex carbohydrates

ethers

-linkage in ___to form ___

-very reactive

-ATP and 1,3-bisphosphoglycerate

acid anhydrides

-____

-include ___

-alcohols

-aldehydes

-ketones

-carboxylic acids

-ethers

-acid anhydrides

carbon-oxygen functional groups

-amino groups (primary amines)

-quarternary amines

carbon-nitrogen functional groups

-amino acid structure

-peptide bonds

-neurotransmitters

amino groups (primary amines)

-important in ___

-form ____

-include many ___

antimicrobials

quaternary amines

-used as ____

-sulfhydryls (thiols)

-disulfides

carbon-sulfur functional groups

-sulfur analogs

-enzyme catalytic activity and substrate binding

-many cofactors; coenzyme A

sulfhydryls (thiols)

-___of alcohols

-contribute to ___

-part of ____including ___

-reaction of 2 sulfhydryls

-both tertiary and quarternary protein structure

disulfides

-formed by ___

-important in ___

-esters

-thioesters

-phosphoesters

-amides (peptide bonds)

ester and amide functional groups

-carboxylic acids and alcohols react

-glycerides and fats (part of scents and odors)

esters

-formed when ____

-include ___

-intermediates; biosynthetic reactions

-acetyl CoA

thioesters

-___in ___

-____is best known thioester

phosphodiester bonds linking bases together; DNA and RNA

phosphoesters

-found in ____to form ___

-amino acids in 1° protein structure

-reaction of carboxylic acids and amines

amides (peptide bonds)

-link ____

-formed by ___

1. oxidation/reduction reactions

2. condensation reactions/hydrolysis reactions

3. group transfer reactions

4. internal rearrangement of electrons

5. cleavage and formation of carbon-carbon covalent bonds

most common types of biochemical reactions

amino acids; peptide bonds (an amide bond)

proteins are ___linked with ____

glycosidic bond

bond formed by a dehydration reaction between two monosaccharides

peptide bond

the chemical bond that forms between the carboxyl group of one amino acid and the amino group of another amino acid

peptide bond

glycosidic bond

glycosidic bond

carbohydrate bond

condensation: alcohol and alcohol

glycosidic bond type of reaction

condensation reaction

peptide bond type of reaction

phosphodiester bond

nucleic acid bond

phosphodiester bond

a chemical bond of the kind joining successive sugar molecules in a polynucleotide

phosphodiester bond

condensation: phosphoric acid and alcohol

phosphodiester bond type of reaction

fatty acids; glycerol; ester bond

lipids are ____linked to ____with ___

cell membranes and energy storage

lipids

ester bond

lipid bilayer

polar; nonpolar

lipid bilayer lipids have ____head and ____tail

physical energy; biological substances; spread out; cycle; metabolisms

living organisms need energy

-___is converted to ____, which ___and ____in the rest of the food chains through ___

oxidation pathway of fat

ΔGrxn=ΔGproducts-ΔGreactants

when G= H-TΔS, the free energy changes in reaction A + B -> C + D is defined:

exergonic

endergonic

exergonic

reagents > products

endergonic

reagents < products

ΔG>0

the reaction does not go. needs external energy input

ΔG<0

the reaction does go. spontaneous

ΔG=0

equilibrium: reactions may happen but with no net changes

irreversible reaction

reversible reaction

rate ∝ [A][B]

rate and concentration of reagents relationship

rate=k[A][B]

rate law

-no net gain

-no net loss

at equilibrium of a reversible reaction:

-_____of products and/or

-____of reactants

k1[A][B]=k-1[C][D]

equilibrium of a reversible reaction

k1/k-1=[C][D]/[A][B]=Keq

equilibrium of a reversible reaction: Keq

ΔG=ΔH-TΔS

gibbs free energy

ΔG°'rxn = -RTlnKeq = -2.303RTlogKeq

at equilibrium, ΔGrxn=0, thus...

ΔG°'

standard free energy change, free energy change in standard condition (at 298K and 1 bar pressure)

1.98 x 10^-3 kcalmol^-1degree^-10

gas constant (R)

k1[R][L]=k2[R*L]

at equilibrium biochemical reaction

k1/k2=[RL]/[R][L]=Ka

at equilibrium biochemical reaction Ka

k2/k1=[R][L]/[RL]=Kd=1/Keq

at equilibrium biochemical reaction Kd

Kd

if we know the ΔG, we can calculate ____

Kd

affinity between R and L -> affinity constant

specific

high affinity/low Kd

nonspecific

low affinity/high Kd

sorting and secretion of some proteins

golgi apparatus

-citric acid cycle

-electron transport + ATP synthesis

-fatty acid degradation

mitochondria

-oxidation

-membrane

mitochondria

-place for ___

-___

degradation of proteins, lipids, etc

lysosome

-fatty acid synthesis

-glycolysis

-most gluconeogenesis reactions

-pentose phosphate pathway

cytosol

reducing

cytosol has ____conditions

nucleic acid synthesis; has a membrane

nucleus

-delivery of proteins

-synthesis of lipids for membranes

endoplasmic reticulum

-little bit different environments (pH, salt,...)

-confined

-cellular organelles and complexes with membrane

structure of cells

-all biological reactions need ____

-some reactions can be ___

-these needs are fulfilled by ___

DNA replication and transcription, oxidative phosphorylation...

some reactions can be confined:

-some

large structure, no membrane