exam 2 flash cards (8,9,10,11,12,13,14 combined)

biochemistry

the study of the chemistry of life

looks at all chemical processes/reactions in a living organism

ammonium ion and amine group

ion= -NH₃⁺

group= -NH₂

hydroxyl group

-OH

Carboxyl group, carboxylate ion, carboxylic acid

carboxyl= -COOH

carboxylic ion= -COO^-

carbonyl group

C double bonded to O

Amide

amine connected to a carbonyl group

thiol, sulfide, disulfide

thiol= -SH

sulfide= -S-

disulfide= -S-S-

enzymes

catalyze biochemical reactions

called biological catalyst

hormones

messengers that regulate bodily functions

storage protein

stores essential substances for immediate availability

transport proteins

carry substances through blood and cell membranes

structural proteins

support and maintain shape of the cell

protective proteins

provide defense against invaders, protect from injury

contractile proteins

do mechanical work

(like muscle actin and myosin)

amino acid

-protein building block

-20 different kinds, 9 essential

-amine group, carboxylic acid group, alpha carbon, and side chain

constitutional isomer

isomers that differ from bonding order of atoms

stereoisomer

isomer with same order but different arrangements

enantiomers

mirror images of each other

would fold on top of one another

diastereoisomers

not mirror images

only small part/element is mirrored, rest are not

amino acid is classified by the properties of the….

side chain

non polar

-alkane and arene side chain→ AA as side chain

-hydrophobic, van der Waals interaction

MAPPLIG TV

Methionine, Alanine, Phenylalanine, Proline, Leucine, Isoleucine, Glycine, Tryptophan, Valine

!WATCH! tryptophan is non polar but has NH

neutral polar

-hydroxyl, thiol, or amide group side chain → HAT side chain

-hydrophillic, H-bonding

C STYNQ (see stink) with proper letters

STAT CG with actual starting letters

Cysteine, Serine, Threonine, Tyrosine (Y), Asparagine(N), Glutamine(Q)

acidic

-carboxylic acid group as side chain AC acidic=carboxylic

-NEGATIVE charge

-hydrophilic

-electrostatic (ionic), and hydrogen bonds

AGA

Acidic= Glutamate and Aspartate

basic

-amine group as side chain. BA basic=amine

-POSITIVE charge

-hydrophilic

-electrostatic (ionic), and hydrogen bonds

BLAH

Basic= Lysine, Arginine, Histidine

zwitterion

-(amine)positive and (carboxylic acid)negative charge DIPOLAR

-all amino acids are zwitterionic at pH~7

-pH less than 2→ fully protonated, positive

-pH greater than 9→ deprotonated, negative

peptide bond

two amino acids are covalently linked together by an peptide/amide bond to form a dipeptide

basically the bond between two amino acids

shape determining interactions

-covalent bonds→ IM bonds, amino acids, peptides, disulfides

-electrostatic interactions(salt bridges)→ ionic bond btwn acidic and basic side chain, btwn amino and carboxyl termini

-H bonds→ btwn donors and acceptors

-van der Waals forces→ btwn all atoms

hydrophobic effect

hydrophobic groups cause the protein to fold so they are on the inside away from the water

structural amino acids

cysteine→ thiol groups form disulfide bonds in extracellular proteins

glycine→ flexible, no organic side chain

proline→ secondary amine forms tertiary amide upon formation of peptide bond

primary structure

-protein sequence

-IM covalent bonds btwn atoms of amino acids through peptide and disulfide bonds

secondary structure

-a helix and B sheet

-noncovalent interactions where h-bonds occur btwn backbone peptide/amide groups

tertiary structure

-1 folded protein chain

-folding due to hydrophobic effect

-R group/side chain interactions

-covalent forces stabilizing protein sequence(primary structure)

-electrostatic interactions/ salt bridges

-H bonds

-Van der Waals forces

disulfide bonds form covalent bonds that stabilizes protein structure once it is folded into a tertiary structure

quaternary structure

-multiple folded protein chains

-hydrophobic effect

-electrostatic interactions

-H bonds

-Van der Waals

-can have disulfide bonds if structure is outside of the cell like blood or hair because it is an oxidizing environment (ex: hair, nails, teeth

L-chirality

Amine group on left side

amino acid type of chirality

L-chirality

L amino acids are found in nature

D-chirality

Amine on right side

alpha helix

stabilized by amide groups

L-chirality of aa produces right hander alpha helix

peptide bonds form btwn adjacent residues

H-bonds from btwn amide groups 4 residues away

helical secondary structures are stabilized by H-bonds forming btwn peptide bonds

B-pleated

stabilized by amide groups

made of B strands

form peptide bonds btwn adjacent residues and H bond btwn amide groups on adjacent strands

globular

forms globe like structure, typically water soluble as hydrophilic residues are on the surface

ex: enzymes

fibrous

forms fibers or sheets, insoluble containing small hydrophobic residues that pack tightly together in layers

glycoproteins

-covalently bound to carbohydrates

-form receptors on cell surface

lipoproteins

-covalently bound to lipids

-transport cholesterol through the blood

metalloproteins

metal ions for structure stabilization or catalytic function

phosphoproteins

-covalently bound to phosphate groups

-used to deactivate or activate a protein

-provide binding sites for protein attachment

hemoproteins

-contain heme groups or porphyrin rings

-oxygen transporters, drug metabolizing enzymes, E producing enzymes

nucleoproteins

-contain ribonucleic acids

-ribosomes used in protein synthesis

myoglobin

-found in the muscle

transports oxygen

-tertiary structure

-has higher affinity for oxygen than hemoglobin

(to remember think how many letters before “global” myo=3 so tertiary)

hemoglobin

-found in RBC

-transports oxygen

-quaternary structure

(to remember think how many letters before “global” hemo=4 so quaternary)

sickle cell anemia

-acidic residue is changed to a hydrophobic residue

-residue # 6 changes from glutamate to valine

-sickled RBC only last 10-20 days vs normal 90-120 days so there is lack go hemoglobin to carry oxygen

electrophoresis helps with determining what regarding proteins

protein charge and size(molecular weight)

collagen

-tropocollagen (3 strands)

-quaternary structure stabilized by H-bonds

in amino acid

-every 3rd residue is glycine (interior coil is all glycine for close packing of strands)

-predominant residues are proline and hydroxylated proline

in connective tissue

-covalent disulfide bonds occur btwn strands

bones and teeth

-Ca5(PO4)3OH calcium hydroxyapatite deposit in gaps

collagen related diseases

Scurvy

-vitamin C deficiency

-vitamin C is needed to created hydroxylated proline

-curable with diet

-symptoms: skin lesions, bruising, joint pain, swelling, gum or nasal bleed

Brittle bone disease:

-Type 1: normal collagen, insufficient amounts (bone fractures, brittle teeth, loose joints)

-Type 2: poor amounts and quality of collagen (fracture before birth, severe respiratory problems)

a and B keratin=fibrous protein in hair which is stabilized by what bond

disulfide bonds

chaperones

proteins and protein complexes that assist in folding of other proteins and protein assemblies; keeps proteins from forming nonfunctional units

prions

-proteins in the CNS→ brain

-Converts a helices to B sheets

-infections agents because they induce other normally folded prions to change shape

-converted proteins then also become infectious agents

transmissible spongiform encephalopathies(TSEs)

-result of prion malformation

-rare degenerative brain disorder

-brain has spongy appearance bc of tiny holes

-rapidly progressive, always fatal

-cant sterilize materials to prevent transmission of TSEs

-can be transmitted through infected tissue, bodily fluids, or medical instruments.

protein degradation/digestion/proteolysis

cellular process that breaks down unneeded, damaged, or short lived proteins into peptides and amino acids for recycling

autophagy

-self eating

-important for balancing sources of energy in critical times in development and response to nutrient stress

-housekeeper that removes misfiled or aggregated proteins, clear damaged organelles, eliminate intracellular pathogens

lysosomes

-recycle center

-degrades unwanted/unneeded material within cell and release nutrients

proteosomes

degrade unfolded or unneeded protein by proteolysis

protein denaturation methods

-heat→ disrupts non-covalent interactions

-mechanical agitation→ foam/air bubbles cause lack of water

-detergents→ can interact with hydrophobic sidechains and unfold the protein

-organic compounds→ polar solvents can disrupt H-bonds

-pH change→ basic and acidic side chains change charge disrupting salt bridges

-inorganic salts→ at high concentrations and disrupt salt bridges

denaturation: heat

disrupts non-covalent interactions

basic and acidic side chains change charge disrupting salt bridges

denaturation: mechanical agitation

foam/air bubbles cause lack of water

denaturation: detergents

can interact with hydrophobic sidechains and unfold the protein

denaturation: organic compounds

polar solvents can disrupt H-bonds

denaturation: pH change

disrupts non-covalent interactionsbasic and acidic side chains change charge disrupting salt bridges

denaturation: inorganic salts

at high concentrations and disrupt salt bridges

enzyme

biological catalyst(protein or RNA)

enzyme ends in ‘-ase”

substrate

reactant of an enzyme catalyzed reaction

turnover number

the number of substrate molecules converted to product in a given time period

cofactor

nonprotein substance that binds to protein and is needed for catalysis to happen (usually trace metals)

coenzyme

organic cofactor usually used in redox enzymes

apoenzyme

enzyme without the cofactor/enzyme

holoenzyme

enzyme with the cofactor/enzyme

catalytically active

active site

site where substrate binds and where catalysis takes place

proximity effect

brings reactants together

orientation effect

holds the reactions at required distance and orientation for the reaction

energy effect

lowers activation energy by putting a strain on the substrate bonds

catalytic effect

provides acidic, basic, and other types of functional groups that are required for catalysis

oxidoreductases

catalyze redox reactions

need coenzyme

transferases

transfer functional group (amino or phosphoryl) btwn substrates

hydrolases

catalyze hydrolysis of substrates

isomerases

catalyze isomerization of substrates (bond rearrangement)

lyases

catalyze elimination of functional groups by adding or removing double bond

ligases

catalyze bond formation coupling with ATP hydrolysis

subclass of oxidoreductases

dehydrogenases→ remove 2 H from substrate to form double bond (need FAD or NAD coenzyme)

(OD)

subclasses of transferases

kinase→ transfer phosphoryl group btwn substrates

transaminase→ transfer amino group btwn substrates

subclasses of hydrolase

lipases→ hydrolyze ester bonds in lipids

proteases→ hydrolyze peptide bonds in backbone amides

nucleases→ hydrolyze phosphate ester bonds in DNA/RNA

amylases→ hydrolyze 1,4 glycosidic bonds in amylose

(LANP)

subclasses of ligases

syntheses→ bond two substrate molecules together

carboxylase→ add CO2 to form carboxylate group

competitive inhibition

inhibitor resembles substrate and competes for same binding site on enzyme

noncompetitive inhibition

inhibitor does not resemble substrate and bind on separate site causing change in active site configuration thus preventing substrate from binding

uncompetitive inhibition

inhibitor does not resemble substrate and binds to enzyme-substrate complex (after substrate binds) to prevent enzyme from working

irreversible inhibition

covalent modification of enzyme, making it inactive

allosteric regulation

active site is changed by binding of molecule at allosteric site

positive→ binding makes active site more fit for substrate

negative→ binding makes active site change so substrate can’t fit

feedback control

product in metabolic pathway is allosteric regulator of enzyme that catalyzes a critical step

positive→product enhances activity of first enzyme

negative→ product inhibits first enzyme to save E

covalent modification

addition of phosphate group to tyrosine, serine, or threonine triggers conformational change in enzyme structure that activates or deactivates the enzyme

zymogens

enzyme synthesized in inactive from. Long protein segment needs to be removed before enzyme is active

genetic control

gene for enzyme is turned on or off to regulate amount of enzyme available in cell

water soluble vitamins

-hydrophilic

-have OH and COOH groups

-not stored in body

-form coenzymes

Vitamins C, B1, B2, B3, B5, B6, B7, B9, B12

fat soluble vitamins

-hydrophobic

-C and H atoms

-stored in liver

Vitamins D, E, A, K