Bio chem exam 1

what is the longest range non covalent force

charge-charge

what non covalent force is nondirectional

charge-charge

what non covalent bond depends on charge attraction

hydrogen bonding

when is hydrogen bonding the strongest

when it is in a line

what non covalent bond occurs when outer electron orbitals overlap

van der waals repulsion

what bond is partialy covalent

hydrogen bond

is water an H donor or acceptor

both

how many hydrogen bonds can H2O form

4 per water molecule

how close connact are the particals in van der waals forces

less than 1nm usally 0.3-0.6n

electrostatic interactions between permanently charged spieces or between ion and permant dipole

ionic (columbic) interactions

electrostatic interactions between uncharged but polar molecules

dipole interactions

what is van der waals interactions attractive component called

dispersion

what is van der waals interactions repulsive component called

steric

complex phenomenon associated with the ordering of water molecules around non polar substances

hydrophobic effect

why is water good at disolving salts

strong electrostatic interactions between water and charged molecules

water surrounds charged molecules and they can leave the crystal lattice

the parcially postitive and negtive parts of water interact with oppositly charded salt molecules

increases the entropy of the system

how does dissociation of water work

its happens constantly and is reversable

what way does the dissociation of water lean and why

H2O→H+ + OH-

way to the left bc vast majority of water is not ionized

how does water ionize

on its own spontaneously

how to calculate pH

-log[H+]

what is the conc of OH- and H+ when pH is 7

they are equal to eachother

what does small pKa mean

strong acid gives up proton easily

what does large Ka mean

strong acid

what does large pKa mean

weak acid holds onto proton tightly

wheb does conc of acid and conjugate acid equal one another

when pH=pKa

when is buffering capacity at its greatest

when pH=pKa

when is buffering capcity lost

when pKa is diffrent from pH by more than 1 unit

what are vivo buffer systems mainly based on

phosphate- millimolar range

bicarbonate-important for blood plasma

histidine- efficient buffer at neutral pH

what are proteins

heteropolymers of amino acids

what is the only amin acid that have an acidic carboxyl group and basic amino group

proline

what is connected to alpha carbon

alpha hydrogen carboxyl and amino group and R group

how to name amino acids

start from alpha carbon and go down the r-group

all amin acids except one are chiral which isnt

glycine

what is the only type of amino acid used in cellular machinery

L-amino acids

how many amino acids are S orentation

19 out of 20

polar uncharge amino acids

serine

threonine

cysteine

asparagine

glutamine

positively charge amino acids

Lysine

arginine

histidine

what amino acids are almost always protonated

lysine arginine

what amino acids are negativly charged

aspartate

glutamate

what amino acids tend to have post transitional changes

ones containing O or N in R group

what type of transitional changes occurs and on what amino acids

phosphorylation

Serine

Threonine

tyrosine

at a low pH what happens to amino acid

carboxyl group is protonates and the amino acid is in the cationic form

at a high pH what happens to amino acid

amino group is nuetral and amino acid is in anionic form

nutral amino group formular

NH2

pKa of carboxyl group of amino acid(buffer)

2.34

pKa of amino group of amino acid(buffer)

9.6

what amino acid can act as a buffer in three pKa values instead of two

histidine

what do free amino acids have and y

mutiple ionizational groups bc of R-group

how long is a peptide

up to 50 amino acids

where does number/naming start on peptide

always from the amino terminus

how long is a protein

at least 100 amino acids generaly

can proteins contain non amino acids

yes they can contain metals organometallic and organic molecules

amino acid sequence

primary structure

local three dimensional structures

Secondary Structure

complete three dimensional structure of a polypeptide chain

Tertiary Structure

multiple polypeptides coming together to form a structure

Quaternary Structure

are other easter or peptide bonds more reactive

easters

peptide bond features and what they are due to

rigid and planar

favors trans configuration

have dipole moment

due to two resonance structures

what type of alpha helix exists

right handed

configuration of alpha helices

peptide bonds are aligned on hical axis while R-groups are sticking out perpendicularly and h bonds occur every 4 amino acids

what amino acids form alpha helices usally

small hydrophoib amino acids like Ala, Leu

what is an alpha helix bond breaker amino acid

proline- N-ca bond is imposible

glycine-r-group cant support other confirmations

where do the R groups stick out from on beta pleated sheets

switching off above and below

what way do the hydrogen bonds run on paralell beta pleated sheet

same direction

what way do the hydrogen bonds run on antiparalell beta pleated sheet

opposite direction

what amino acid is 6% of the time is not in trans configuration in the peptide bond

proline

what does the 6% cis configuration peptide bonds usally do

beta turns

when do beta turns occur

when beta sheet changes direction

what is the rotation degree of beta turn

180

common beta pleated sheet turn positions

proline in position 2 or glycine in position 3

what does tertiary structure refer to

overall spatial arrangement of atoms in a protein

what stablizes teriary sturcture

many week interaction between amino R-groups

what bond can stablize terciary bonds

disulfide bonds

what are quatenary stuctures refred to as

protein complexes

what can protein complexes do

bring together multiple enzematic activities and regulatory protiens and/or protein structures

what is an intrinsically disorded protien

primary protein mis folded

example of intrinsically disordered protein

p53

what do ribosomes do

translate proteins

what can denature a protein

tempeture

pH

organic solevents

chaotropic agents

what are chaotropic agents

molecules that disrupt hydrogen bonding in aqueous solutions

chaotopic agent examples

urea

guanidinium

hydrochloride

what does omega stand for

fraction of occupied binding sites

the faster omega is reaches 0.5 ….

the lower the Kd

what is Kd

dissociation constant

Lock and key ligand binding

the binding site is same shape as ligand and fit no problem

induced fit ligand binding

diffrent binding site and ligand shape but when they interacte the binding site shapes to fit ligand

conformation selection

binding site constantly chaning shape and then ligand will apear and every once in a while fit

what do amino acid side chains lack

an affinity for oxygen

transitional metals bind to oxygen well but form…

reactive oxygen radicals

what is heme

organometalic compound

what does heme oxidize

Fe2+ to Fe3+

myoglobin and hemoglobin are…

heme that is protien bound

myoglobin

oxygen storage protein

hemoglobin

oxygen transport protein

how much more times better is CO better at binding to heme then O2

20,000

why is CO better at binding to heme

carbon in CO has a filled lone pair that can be donated to empty d-orbital on Fe2+

with the protein pocket coat how much more times can CO bind to O2

250

what does CO do

block function of myoglobin and hemaglobin and mitochondrial cytochromes involved in oxidative phosphorylation

pO2 in lungs

13kPa will realse O2

pO2 in tissues

4pka will not realse O2

what is hemaglobin unit type

tetramer of two subunits alpha2 and beta2 (each subunit is similar to myoglobin)