uoft bch210 midterm

bio chemical molecules of life

- proteins

- lipids

- sugars

- nucleic acids

- small molecules

- ions

- water

why is structure so important in biochemistry

structure is important for function

examples of proteins in the cell

- enzymes

- transporters

- lipoproteins

- hormones

- signaling molecules

- receptors

- recognition molecules

- glycoproteins

- structural proteins

- motility proteins

what kinds of bonds hold together amino acids

covalent bonds

what are covalent bonds

a chemical bond that involves the sharing of electron pairs between atoms

what are non covalent bonds/interactions

- ionic/electrostatic

- h bonds

- van der waals

what kinds of bonds helps chains fold into structures

- non covalent bonds

what are cofactors

- non protein/metal ion that helps a protein with structure and/or function

how do transporters bind to molecules

non covalently

how are cofactors bound

- covalently or non covalently

what are prosthetic groups

- subset of cofactors

- tightly bound by covalent or non covalent forces

how may metal ion cofactors interact with proteins

- involvement in enzyme catalysis

- charges of ions may be important

What are coenzymes?

organic compounds that help enzymes

chain bow convention of protein colouring

blue to red

backwards through the rainbow

which elements participate in h bonding

O, Br, F, N Cl

these electronegative atoms are h bond acceptors

why can carboxylic acids act as h bond donors and acceptors

- hydroxyl group can be a donor

- double bonded oxygen can be acceptor

alcohol/hydroxyl

R-OH

carbonyl/ketone

C=O in the middle

carboxyl

COOH

amine

R-NH2

sulfhydryl/thiol

R-SH

aldehyde

CHO

amide

=O NH2

ether

C-O-C

Ester

RCOOR

phosphate

PO4 3-

phenyl

C6H5

imidazole

how many h bonds can water form

- up to 4 transient h bonds due to unequal sharing of electrons

what kind of molecules can solubilize in water

- molecules that have polar and hydrophilic functional groups

what are amphipathic molecules

molecules that contain hydrophobic and hydrophilic regions

what is the hydrophobic effect

- non polar molecules will aggregate in an aqueous solution, excluding water molecules

- main driving force behind formation of macromolecular structure

nucleophile

electron pair donor

electrophile

electron pair acceptor

why is water an excellent nucleophile

can donate the lone pairs on the oxygen

hydrolysis vs condensation reactions

hydrolysis: larger molecule forms two smaller ones and consumes water

condensation: two molecules combine to form one molecule and a water molecule

why might macromolecules fold to exclude water

- prevents reactions from occurring

- maximizes number of interactions of hydrophilic groups w water for solubility

what links AAs in polypeptide chains

peptide/amide bonds

carboxyl and amino group bond and release water (condensation rxn)

what is the alpha carbon

central carbon

what are essential amino acids

Amino acids that must be consumed because they cannot be created by the body

amino acid structure

carboxyl carbon is carbon 1 and covalently bonded to alpha carbon (carbon 2)

chirality

- non superimposable

- mirror images are called enantiomers

- isomers exhibit optical activity

- L AAs are physiologically relevant in plant & animal proteins

how to know if an amino acid is the L or Disomer

put H at back

L isomer:

- get RCN clockwise

- get RNC counterclockwise

what is a zwitterion

- a zwitterion is a species with both a positive and a negative charge, gives a net neutral charge

- when the side chain is uncharged, amino acids can be zwitterions

which letters are not used in the amino acid alphabet

JUZBOX

which amino acid is not chiral

Glycine

which amino acids are beta branched

valine, isoleucine, threonine

which amino acids contain sulfur

cysteine and methionine

which amino acids contain carboxylic acid in their side chain

aspartate and glutamate

which amino acids contain hydroxyls in their side chains

serine, threonine, tyrosine

which amino acids contain nitrogen in their side chains

histidine, lysine, arginine, tryptophan

which amino acids contain nitrogen and oxygen in their side chains

asparagine and glutamine

what can amino acids also be metabolized to form

- hormones

- neurotransmitters

- nitrogenous bases

- energy producing intermediates

what is a salt bridge

form between +vely and -vely charged amino acids

which amino acids form disulfide bonds

Cysteines covalently interact with each other

What is an oxidation reaction?

loss of electrons

What is a reduction reaction?

gain of electrons

cysteine vs cystine

cysteine = reduced form of the a.a.

(remember: the e is for electrons... which you still have in reduced form)

cystine = oxidized form of the a.a.

(remember: the absence of the e means loss of electrons, which is what you face in oxidation)

Protein disulfide isomerase (PDI)

An enzyme that catalyzes the oxidation rxn to produce cystine

B-mercaptoethanol

reducing agent that breaks disulfide bonds

why do cytosolic proteins usually contain cysteines

due to the reducing nature of the cytosol

which amino acids are positively charged (basic) at physiological pH

lysine, arginine, histidine

which amino acids are negatively charged (acidic) at physiological pH

aspartate, glutamate

which amino acids are polar

serine, threonine, cysteine, asparagine, glutamine

which amino acids are non polar

glycine, leucine, isoleucine, tryptophan, phenylalanine, alanine, valine, proline, and methionine

amino acid hydrophobicity

most to least hydrophobic

non polar to charged

where are hydrophobic amino acids usually found on proteins

for soluble proteins, the interior

but can still be found on the surface to allow for non covalent interactions

covalent modifications

- phosphorylation

- ubiquitination

- glycosylation

- acetyl, methyl, hydroxyl, carboxyl

post-translational modification

- addition/removal of functional groups

- disulfide bonds

- covalent modifications

- cofactor/ligand binding

can affect structure and function

GFP (green fluorescent protein)

- AAs buried at center of protein

- nucleophilic attack of amide nitrogen found in glycine by serine's carbonyl forms a heterocyclic structure that is important for its fluorescence

- changing these key AAs or the AAs nearby can affect properties like colour or brightness

equation for pH

pH=-log[H+]

ie. lower pH means more H+ present to protonate functional groups

pKa

used to measure the strength of an acid

pka = -logKa

tells you the value of pH at which a functional group loses or gains its H+

acid dissociation constant

Ka = [H+][A-]/[HA]

what kind of Ka and pKa do strong acids have

high Ka (high dissociation) and low pKa

weak acid and conjugate base

protonated HA and deprotonated A-

Henderson-Hasselbalch equation

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

used to determine the pH of a solution depending on the amount of ionization of a weak acid

relationship between pka and ph

pka is the ph at which a weak acid or functional group is 50% protonated and 50% deprotonated

what do buffers do

- solutions of weak acids and conjugate bases that can resist changes in pH (neutralizes small changes)

- maintain the pH +/- 1 pH unit around the pKa

how do you choose the right buffer

- has a pKa closes to the pH you require at a given temp

- consider chemical stability ex side rxns that interfere

- cost/availability

physiological pH

7.4

Aspartate vs aspartic acid

aspartate: conjugate base

aspartic acid: protonated form

What is the buffering region?

- lots of molecules that are buffering or binding to the protons (resist the change in ph)

- around 1 ph unit of the pka value

- flat portion of titration graph

isoelectric point

- The pH value at which the amino acid exists as a zwitterion (charge of molecule is zero)

- average pka values on either side of zwitterion

buffering species of blood

bicarbonate accepts or donates protons

how does blood buffer using bicarbonate

if the [H+] increases, bicarbonate (HCO3-) binds and produces carbonic acid (H2CO3)

carbonic acid breaks down to water and CO2

CO2 exhaled to remove excess H+

what is the bohr effect

- ph can affect O2 carrying ability of hemoglobin

- CO2 made in tissues combines with H2O to make HCO3- (bicarbonate) and a H+

- this helps with O2 release

- at lower ph, his146 is protonated and creates a salt bridge to asp94

- this favours the deoxygenated structure of hemoglobin

levels of protein structure

primary, secondary, tertiary, quaternary

primary protein structure

sequence of amino acids

secondary protein structure

periodic regular structures (a-helix, beta strands, sheets, and turns)

tertiary structure

folding of secondary structures into defined protein motifs and domains

quaternary structure

assembly of distinct chains (many pp chains) into multi subunit structures

what is the backbone of a polypeptide chain

consists of the peptide bonds and alpha carbons while the variable parts are the distinct R side chains

nature of peptide bonds

- peptide bonds are polar but uncharged

- partial double bond character due to resonance, preventing rotation of the peptide bond

where is rotation allowed in a polypeptide chain

- the bonds linking the amide and carbonyl to the alpha carbon

- amide to alpha is phi

- carbonyl to alpha is psi

- range from -180 to 180

- not all angles permitted due to steric clashes

- clash minimized when side chains are trans to one another

a-helix

- right handed helix

- side chains point out

- intra strand h bonds between C=O (h bond acceptor) and N-H (h bond donor) 4 AA along the sequence (1 bonded to 5)

how many residues per 360 turn in alpha helix

3.6 residues (100 degrees between adjacent amino acids) and each residue is 1.5A high

3 types of alpha helices

- polar/hydrophilic

- hydrophobic

- amphipathic

how are beta sheets formed

- intermolecular h bonds link 2 or more beta strands

- h bonds occur between carbonyls and amines

types of beta sheets

- parallel, antiparallel, mixed

- strands alternate pointing above and below the sheet

- different sides of the sheet can have different properties

what are beta turns (reverse turns)

- 4 residue segment that allows the peptide chain to turn 180

- found on surface of globular proteins connecting secondary structures

- h bonds form btwn carbonyl O and amine H

- Pro common at position 2 (structure helps start the turn)

- Gly (small) Asn Ser (side chains can be modified at the surface of the protein) also frequently seen in turns