BIOC 3021 exam 1

ATP pyrophosphate cleavage

ATP -->(hydrolysis) AMP + PPi (P₂O₇⁴⁻)

Hydrophobic amino acids (nonpolar)

Ala, Val, Leu, Ile, Met, Pro, Phe, Trp

alkanes

(CH₂)n + 2H - all single bonds - nonpolar, insoluble in water - functional groups change the identity of alkane

turnover number

(kcat) max number of molecules of substrate that an enzyme can convert to product per catalytic site per unit of time (does not change as enzyme is purified - intrinsic property)

best buffering range:

+/- 1 pH unit of the pKa

amines

- RNH₂ - solubility in water depends on R chain length (10+ C's = bad) - reacts with acids, aldehydes, acyl halides, acid anhydrides

carboxylic acid

- acidity neutralized by bases - reacts with alcohols (forms ester), amines (forms amides), acids - acid= -ic - base = -ate (negative charge) - dissolves readily in water

aldehydes

-RCHO - reacts with alcohols, amines

alcohols

-ROH - solubility depends on length of alkane (10+ C's = insoluble) - reacts with aldehydes, ketones, acids

beta sheet

-pleated sheets - antiparallel= adjacent peptide strands have opposite directionality (parallel is the same directionality and is lower energy)

organic cofactors

-redox reactions - transfer of various organic functional groups - often vitamins that must be present in diet

Strength of VDW depends on...

-the size of molecule and distance from one another -bigger e- clouds = stronger interactions -strength inversely proportional to 10⁶ distance - atoms need to be 0.2nm apart

native formation

3D protein structure created by spontaneous process of protein folding into thermodynamically low energy form that requires no external catalyst

In hydrogen bonding, each H2O can form...

4 hydrogen bonds (2 on O to H's, each H on an oxygen)

pk of terminal alpha amino group

8.0

major components in organic chemistry

99% of mass of O components in living cells: H, C, N, O, P, S cannot be synthesized

alkenes

C(n)H₂(n) - double bond carbons - planar - unsaturated, can have cis and trans isomers

trace elements (abundance)

Zn, Cu, Fe 0.3%

buffers

a mixture of a weak acid and it's conjugate base in equilibrium wherein the addition of a strong acid or base has limited effect on pH concentration

peptides

covalent link between amino acid residues in proteins -bonds my hydrolysis of amino acids to get amides <--- - condensation --->

disulfide bond

cytesine's thiol group undergoes oxidation with with another thiol group (s)

Kw constant

kw= 1x10¹⁴ M²

apoenzyme

lacks an essential coenzyme

enzyme kinetics

lowers activation energy of a reaction, but the enzyme itself is not permanently changed (rate becomes REALLY fast) mild conditions are best

pK

measure of a group's tendency to ionize

domains

multiple motifs together (saddle forms, beta barrels, quadruple helixes)

essential amino acids

must be present in diet because they are not synthesized by humans

Aspartic acid, Asp, D

negatively charged, acidic, pk=3.9

Glutamic acid, Glu, E

negatively charged, acidic, pk=4.3

zwitterion

neutral molecule with both a positive and negative electrical charge

Alanine, Ala, A

non-polar, aliphatic

Glycine, Gly, G

non-polar, aliphatic

Isoleucine, Ile, I

non-polar, aliphatic

Valine, Val, V

non-polar, aliphatic

hydrophobic interactions

nonpolar molecules clump together because of exclusion from water - no attraction between them, water just herds them together)

Proline, Pro, P

nonpolar, aliphatic, Imino acid

ATP

nucleotide cofactor with adenine base, ribose sugar, and 3 phosphate groups Pi group breaks off to form phosphate groups upon hydrolysis (add water)

vitamin (coenzyme)

nutritional requirement since organism cannot biosynthesize enough on own

alpha helix

one period = 3.6 amino acid units or .56 nm (planar)

condensation reaction

one water molecule is eliminated

formula for pH

pH = -log[H+]

reaction rates are affected by...

pH, temperature, substrate concentration, presences of cofactors/ionic environments

Henderson-Hasselbach formula

pH=pKa+log([A-]/[HA])

inorganic cofactors

participate in redox reactions , substrate binding, and sometimes needed to facilitate the correct active conformation of a protein (also must be in diet)

alkyl groups

phenyl = ring with every other double bond

Asparagine, Asn, N

polar, uncharged

Glutamine, Gln, Q

polar, uncharged

Serine, Ser, S

polar, uncharged

Threonine, Thr, T

polar, uncharged

Histidine, His, H

positively charged, Basic, pk=6.0

Lysine, Lys, K

positively charged, basic, pk=10.5

Arginine, Arg, R

positively charged, basic, pk=12.5

protein crystallization

proteins can become crystals when the solution in which they are dissolved becomes supersaturated

Bronsted-Lowry Base

proton acceptor

Bronsted-Lowry Acid

proton donor

salting out

purification -add salt to aqueous solution of proteins - compete for water, some proteins aggregate and precipitate - protein redissolves if salt is removed USE: ammonium sulfate (pure, soluble, gentle)

ion exchange chromatography

purification based on attraction between charged groups in protein and column medium -selective absorption accomplished by change in pH or by change in salt concentration - negative carboxyl's attract positive proteins (Lysine, arginine, histidine)

affinity chromatography

purification based on selective binding of ligand by binding protein -ligand linked to insoluble column medium -pass protein solution over column - only binding protein is absorbed -elute high concentration of unbound ligand -exceptionally high rate of success

zonal centrifugation

purification density gradient is employed, highest density at bottom (tubes are spun horizontally)

centrifugation

purification rapidly separates proteins by size, shape, density (bottom of the tube)

dialysis

purification separates molecules in solution based on differences in diffusion rates through semipermeable membrane - removes salt from from protein solution - use buffered solution - salts move into less concentrated zone - molecules larger than the diameter of the pores retained in dialysis bag

gel filtration chromatography

purification separates proteins by SIZE - gel beads with pores of known size -molecules smaller than pore enter bead and flow retarded - molecules larger than pore flow around the bead, flow faster - larger molecules migrate faster than smaller ones

specific activity of enzyme

ratio of enzyme activity to amount of protein U/mg protein (SA increases as enzyme is purified)

ketone

reacts with alcohols, amines

oxidoreductases

redox reactions

native + heat + thiol (R-SH)

reduced and denatured (disulfides cleaved)

energy is stored in food as...

reduced carbon compounds

oxidation reactions ______ energy

release

catabolism

release energy by oxidizing reduced carbon atoms

beta turn

reverse turn (carbonyl oxygen) of the 1st amino acid h bonds to amide H atom of the 4th amino acid stabilizes

Ordering sequence with Edman's

sequence overlaps - use two methods to fragment protein, separate peptides and determine sequence of each one by edman's

ramachadran plots

show the frequency with which certain combinations of phi or psi bonds occur and is most compatible with helixes

pKa increases

strength of acid decreases

primary structure proteins

structure of a protein molecule based on covalent bonding (sequence of amino acid residues)

special features of cytesine

sulfur atoms in two cytesines react to form covalent, disulfide linkages (locks protein into particular conformation)

Methionine, Met, M

sulfur containing

Cysteine, Cys, C

sulfur containing pk=8.3

C-H bonds are _____ and _____ in nature

tetrahedral, equidistant

molecular chaperones

the occasional helpers of protein folding

amino acids are defined by..

their R group (all have an amine and a carboxylic acid)

tertiary structure

total 3D form, poly peptide chain

transferases

transfer group from one substrate to another

anabolism

uses stored energy to reduce carbon atoms

# of different proteins in bacteria, yeast, mammals

~2000 ~3000 >20,000

Leucine

Leu, L

functional group isomers

different arrangements of atoms to form different functional groups (defines properties)

Isomers

different forms of a compound with same empirical formula - enzymes recognize these as isomers

pk of terminal alpha carboxyl group

3.1

Properties of water

1. cohesive/adhesiveness 2. high heat capacity 3. high heat of vaporization: lots of E to change states 4. expansion upon freezing: fish can live in winter, ice floats 5. versatility as a solvent: good for polar and ionic solutes, not nonpolar biomolecules (our insides don't dissolve)

cleaving disulfides

1. convert disulfides to sulfhydryl form by reaction with excess sulfhydryl (another thiol) then stabilize with iodacetate to prevent further reaction or 2. oxidize disulfides with performic acid (HCOOH) to get cysteic acid

types of chemical bonds

1. covelent bonds: shared e- 2. ionic bonds: e- donated (cations and anions) 3. Hydrogen bonds: partial charge attraction 4. VanDerWaals: electrical interactions between close atoms

naming peptides

1. drawn with amino terminal end of the peptide to left, carbonyl terminal end to the right 2. named left to right (amino -> carboxyl) 3. except for carboxyl end, name every amino acid in a peptide bond with its root name + ending -yl 4. carboxyl end keeps its name

Functions of hydrogen bonding...

1. essential for protein structure 2. binding enzymes to substrates 3. holds together DNA 4. individual h bonds are weak, together they are strong 5. is what makes water so cohesive

Special features of carbon:

1. four outer electrons 2. readily donates and accepts electrons 3. forms single, double, or triple bonds 4. many different kinds of chains possible 5. carbon chains form basic molecules 6. variety of oxidation states 7. versatility of covalent bonds

secondary structure determined by

1. hydrogen bonding (between peptide carbonyl and amino acid hydrogen groups) 2. amino acid R-groups: different R groups favor different types of secondary structure 3. planar peptide bonds: limit range of no rotation and secondary structures that can be achieved 4. steric exclusion: certain bond angles not possible

forces that contribute to tertiary structure

1. hydrogen bonding: amino acid and water 2. hydrogen bonding: 2 amino acids 3. hydrogen bonding: carbonyl oxygen and amino hydrogen 4. stacking of aromatic amino acids 5. VDW of nonpolar amino acids 6. ionic forces between charged amino acids 7. disulfide bridges 8. disruption of secondary structure by proline

Classifications of enzymes

1. oxidoreductases 2. transferases 3. hydrolases 4. lyases 5. isomerases 6. ligases

Strategy of purification

1. source: high concentration of desired protein 2. analysis: assay for desired and total protein (number present) 3. separation: based on different properties of protein

# essential minerals (bonding)

17 ionic

absorbance max of peptide backbone

220 nm

Buffer in blood formula

CO₂ + H₂O ↔ H₂CO₃ ↔ HCO₃⁻ + H⁺

buffers in humans

CO₂ produced by metabolism is eliminated from the body through respiration by lungs and provides buffer for blood @ 7.4 pH

major elements in organisms (bonding and abundance)

H, O, C, N 99% Covalent

minor elements in living organisms (bonding and abundance)

P, Na, K, Ca, Mg, S, Cl 0.7% Ionic

phosphate

PO₄²⁻

Numbering unique peptide sequences

Rⁿ (R= kinds of residues and n= sequence positions)

Edman Degradation

Sequential subtractive sequencing where amino acids are released from the sequence one at a time with the reagent: phenylisothiocyanate in alkali then Triflouracetic acid to remove PTH-derivative -need bead to hold protein -not 100% yield (need to do this to short chains) then do liquid chromatography

Hydrophilic amino acids (polar)

Ser, Thr, Asp, Glu, Asn, Gln, His, Lys, Arg, Cys, Tyr

activity of an enzyme

catalytic ability to convert substrate to product -units of activity: 1U=1 micromole product / min

polypeptides

chains of polymerized amino acids

special features of Aromatic R groups

absorb UV light (@ 280 nm)

hydrolases

add water across bond to effect hydrolysis of bond

lyases

addition of group across double bond or loss of group to leave double bond (TCA cycle)

secondary structure

alpha helix, beta sheets

x-ray crystallography

analytical -determine the 3D character of proteins -proteins alone are too small to be seen with visible or UV light (need protein CRYSTALS)

mass spectroscopy

analytical -fragments (ionic) to determine mass, type, and connection -mass/charge ratio / time spent flying towards sample

NMR spectroscopy

analytical exploits magnetic properties of certain nuclei -info on # and type of chemical entities in molecule - resonate between spin states on spectra

polyacrylamide gel electrophoresis (PAGE)

analytical USE: acrylimide to stain -negative charge towards cathode and vice versa -rate at which move based off characteristics -small move faster (higher charge) -bridging: with PERSULFATE catalyst - product: highly cross-linked polymer - sodium dodecyl sulfate: used to determine molecular weight of protein subunits (denatures and coats with negative charge)

Phenylalanine, Phe, F

aromatic, non-polar

Tryptophan, Try, W

aromatic, polar

Tyrosine, Tyr, Y

aromatic, polar, pk=10.1

NAD+

common coenzyme redox reactions: accept 2 electrons or donate 2 electrons (and 1 p+) when reacting

two main functions of active site:

binding and catalysis -specificity depends upon the geometric and chemical complementarity of substrate surface and surface of the active site

enzymes

biological catalysts - are proteins or nucleic acid -enhances reaction rate without being altered - unique high degree of specificity

protein

biological molecule that consists of one or more polypeptides

active site of enzyme

compromised of amino acid chains

as pH changes by one unit...

concentration of H+ inversely changes ten fold

native + heat

denatured, but disulfides remain intact

stereoisomers

difference in spatial organization (need a stereogenic center)

What creates water stabilization?

electronegative oxygen interaction with cation and +H interaction with anion to stabilize ionic solution and increase solubility in water

haloenzyme

enzyme with cofactor bound

ligases

formation of new bond between two substrates with participation of ATP (lagging strands of DNA)

achiral amino acid

glysine

coenzyme (cofactor)

if needed in catalytic reation, cofactors help enzyme and substrate (sometimes appears as substrate and/or product) can be inorganic ion or organic molecules

motifs

interactions between two-four units of secondary structure (for example, two alpha helixes or two beta sheets)

quaternary structure

interactions of polypeptides (non covalent)

isomerases

interconversion of isomers and glycolysis

amphoteric substances

intermediates serve as acids or bases ex: H2CO3 and H3PO4