bioc final

when do proteins have more positive charge

when do proteins have more positive charge

low ph

when do proteins have more negative charge

high ph. at 7 about no charge

what do ionizable groups (ex COO-) do to a biomolecule

change ph properties

isoelectric point

the pH at which a protein has no net charge

why is hydronium very mobile

due to h bonding network. can move around very quickly

what does weaker acid mean in relation to its conj base

weaker acid = stronger conj base and vice versa

what is a buffer

weak acids or bases that can react with strong acids or bases to prevent sharp, sudden changes in pH

when does ph= pka

when [a-]/[ha] =1

when does ph = pka+1

when [a-]/[ha] =10. (10 times more product/conj base than reactant/acid)

when does ph = pka-1

when [a-]/[ha] =0.1 (10 times more acid than product/conj base)

when u add acid to a buffer what happens to a-

we lose a- quantity. (subtract from a- and give to ha)

what in an important intracellular buffer

phosphate

major extracellular buffer

Bicarbonate

bicarbonate system

· H+ + HCO3- <-> H2CO3- <-> H20 + CO2

how does equilibrium shift if excess acid in bicarbonate system

shifts right to make more co2

how does equilibrium shift if too little bicarbonate or high co2 in bicarbonate system

shifts left to make h+ and bicarbonate

what is a proteome

The full range of proteins produced by the genome. over 1 mill distinct proteins and they get altered all the time

primary protein structure

amino acid sequence

secondary protein structure

localized folding (alpha helicies and beta sheets)

tertiary protein structure

3D folding pattern of a protein due to side chain interactions

quaternary protein structire

arrangement of protein chains

what are the 3 types of amino acids

non polar, polar, charged

which enantiomeric config are most amino acids

L (or S if using R/S)

what does mercaptoethanol do

breaks disulfide bonds to get them back to sulfhydryl form. reducing agent

What is Glutathione?

intracellular reducing agent. breaks disulfide bonds

where would you most likely find a hydrophobic amino acid

in the interior of a protein

when are proteins soluble

when ph is less than or greater than pI. due to proteins repelling each other when carryng net charge, making them more soluble

when are proteins low solubility

when pH=pI

why is wireframe representation best

gives detailed view to examine chem and binding processes

what is an alpha helix

A coiling of the polypeptide chain caused by hydrogen bonding between every 4th amino acids (i and i+4). it has the r groups pointed away from helix axis.

~ how many residues in a protein

50

what does ribbon view of a protein show

emphasizes secondary structre (alpha helixes and beta sheet)

what does spacefill view of protein show

shows shape

what does backbone view of protein show

overview of protein. main chain shown, side chains not shown

how are residues joined

peptide bonds. formed from dehydration reaction. they limit conformational flexibility

what are dihedral angles

phi and psi

what do dihedral angles do

define direction and shape of peptide chain. prevents roatation

How many residues per turn in an alpha helix?

3.6 residues per turn (36 per 10 turns)

what do alpha helixes need for stability

h bonds

which elements form the peptide bond

the carbon of the carbonyl and the nitrogen

why are peptide bonds important

because of resonance they have 40% double bond character and thus prevent free rotation (rigid)

are peptide bonds planar

Yes. They are flat Due to partial double-bond character

where in a peptide would you find flexibility

alpha carbon

planar meaning

all in the same plane

where are the 2 bonds you could find flexibility in a peptide

dihedral angles phi and psi. dont rotate freely tho, have certain angles they like to avoid steric hindrance

IN AN ALPA HELIX R GROUPS POINT WHERE

OUT

ex of how some r groups can destabilize an alpha helix

if you have a bunch of amino acids with same charge on one side electrostatic repulsion

antiparallel beta sheet

neighboring hydrogen-bonded polypeptide chains run in opposite directions (alternates between N and C ex NCN at top and CNC at bottom). has stronger h bonds therefore more stable since h bonds are in a line

parallel beta sheet

all of the N-termini are oriented in the same direction (N all at top, C all at bottom

what are supersecondary structures

motifs and domains

What is a motif in a protein?

small region with a defined sequence that serves a common fn in different proteins

what is a domain

subregions of a polypeptide chain that can fold and function independently

A solution contains a typical protein containing many acidic and basic amino acid residues if the pH of the solution is less than the PI of the protein what happens

The protein will tend to be protonated, causing it to have a net positive charge

What causes protein folding?

Hydrophobic effect and favourable interactions. hydrophobic effect has largest role in stabilization

can Protein refold

Yes, most can refold on their own

What did the anfinsen experiment show?

Native protein structure is encoded by sequence. Proteins can refold under the correct conditions, disulphide bonds act as a 'lock' on folding

What guides protein folding?

Initial secondary structure elements guide or restrict protein folding, and some intermediate, promote misfolding or aggregation

What are confirmational diseases

Alzheimer's and mad cow disease. in alzheimers amyloids misfold into a fibril and aggregate. has beta sheets where it shouldnt

What stabilizes the native state of a protein

Hydrophobic effect (increase in water entropy), enthalpic interactions (h bonds), and Vanderwaal forces

What might denature protein

Heat pH extreme chemicals and mutations

benefits of subunits in a protein

easier to fold, can reuse subunits, can regulate

quaternary structure

protein complexes contain subunits

how are nitrogenous bases joined

phosphodiester bonds

what does 5' end of dna mean

5' end has phosphate group attached to 5' carbon

how is dna written

5' to 3'

describe dna structure

double helix. polar exterior non polar interior

What is a guanine quadruplex?

4 guanines surround a cation

what stabilizes dna double helix

Hydrogen bonding between base pairs, mg2+ binding to po4 backbone, hydrophobic effect

when does dna melt

under high heat. separates into single strands - denatured

what does cooling denatured dna slowly do

renatures and makes strands rejoin. cooling too fast causes misfolding but can just remelt and try again

what increases Tm - melting point of dna

the mores C and Gs you have (cytosine and guanine). due to base stacking

what does miRNA (micro rna) do

regulates gene expression by blocking mrna translation

can single stranded rna have tertiary structure

yes

what are the stop codons

UAA, UAG, UGA

what are the start codons

AUG (methionine)

what strand of original dna does mrna output match

coding strand (sense)

what gets read by rna polymerase

dna template strand (antisense)

what does degenerate mean

multiple codons for the same amino acid

what is a nucleosome

A region of DNA wound around histone proteins. basic structural unit of chromatin

what causes chromatin coiling

basic histones interacting with acidic dna backbone

what do histones do

help maintain the shape of the chromosome and aid in the tight packing of DNA, also help regulate gene expression

what is a single nucleotide polymorphism

A DNA sequence variation occurring when a single nucleotide differs between members of a species - point mutation

what is copy number variation

when the number of copies of a particular gene varies from one individual to the next ex one person has 3 gc repeats and one person has 2

nonsense mutation

premature stop

missense mutation

different amino acid used

silent mutation

no amino acid change

frameshift mutation

addition or deletion of a nucleotide, shifting reading frame

splice site mutation

intron left in final processed rna and gets translated

what is a dna prober

single stranded dna probes (oligonucleotides) that detect specific dna or rna sequence in a sample. dna binds to complementary probe. very sensitive and can use fluorescence for visualization

what is ammonium sulphate precipitation

method to control protein solubility using ammonium sulfate to isolate proteins. protein solubility changes with salt conc. at low salt protein can interact. at high salt the salt will use up all water making protein insoluble. need middle balance

how does chromatography work

separates molecules based on affinities for mobile or stationary phase. buffer being added is mobile phase. stationary phase is stuff in column that proteins interact with

size exclusion chromatography

separates proteins by size. relies on porous beads; larger molecules elute first because they are not trapped in the beads. can be used to estimate molecular weight

ion exchange chromatography

separates proteins by charge. -stationary phase is made of negatively charged beads (attract & bind compounds that have opposite charge)

-salt is added to elute proteins stuck to column. can also change ph to elute proteins

cation exchange chromatography

Positive proteins stick to negative beads, only negative proteins go through

Anion exchange chromatography

Negative proteins stick to positive beads, only positive proteins go through

affinity chromatography

separates proteins by what they bind.uses a bound receptor or ligand and an eluent with free ligand or a receptor for the protein of interest

affinity tags

provide an easy way for protein purification using affinity chromatography. modifies protein so it wants to bind something. ex 6x histidine which binds nickel. eluted by a molecule that looks like histidine so they compete

electrophoresis

separates charged molecules in an electric field and gel. small molecules move faster

What does the reducing agent in SDS page do?

breaks disulfide bonds

What does SDS in SDS page do

Gives protein a negative charge, and unfolds protein