biochem unit 1 flashcards

what is the hydrophobic effect + when does it happen

when non-polar things group tg in water to reach a more stable state - they r found in the interior of proteins-

it happens when something is insoluble in water

2 different water molecules connect thru ____

the actual bonds in a single water molecule are _____

hydrogen bonds

covalent bonds

for something to be soluble in water, it has to be able to

form hydrogen bonds with water

1 Å =

1 × 10 ^ -10

if the bond energy is 355 kj/mol is it a ionic or covalent bond?

covalent bond

name the 4 types of non covalent bonding

• hydrophobic interactoins

• hydrogen bonds

• electrostatic interactions

• van der Waals interactions

T/F electrostatic interactions are the strongest non covalent bonding type

TRUE

in electrostatic interactions what happens

theres 2 rules -

its between a cation and anion and happens because of attractions between partial charges

• the closer they are the stronger the bond

• +2 is more attracted to a negative than a +1

rule for relationship between the dielectric constant (D) and electrostatic interactions

the higher the dialectic constant, the weaker the electrostatic interactions

if the dielectric constant is low like 2, is it in a oily or watery environment?

what does mean about the electrostatic interactions?

oily and this makes the electrostatic interaction strong and they will be close TG

to make a hydrogen bond H needs ____ or ____ partner

O or N

do hydrogen bonds have electrostatic interactions

yes

O is a partial neg and H is a partial positive

for hydrogen bonds, what is the bond length _______ Å

what is the bond energy ______ kj/mol

2-3

4-20 kj/mol

since there are hydrogen bonds in proteins and dna, water can compete with those things to make hydrogen bonds so theres an ______

equilibrium

explain what happens in van der Waals interactions

a molecule creates a temporary positive and negative side causing nearby atoms to make the opposite dipole and attract

explain the relationship with van der Waals and boiling points

the more van der Waals interactions = the higher the boiling point

also the longest chain = the strongest van der Waals interactions

van der Waals bond length ________ Å

bond energy ______kj/mol

4 Å

2-4 kj/mol

acid ____ H+

bases ______ H+

donates

accept

a big Ka means that the acid…..

is a stronger acid and breaks apart more

pka relationship with acidity

low pka = strong acid

high pka= weak acid

in the ph equation, (H+) in the equation =

10 ^ -pH

when do buffers work the best?

what do they do?

when pka=pH

they delay a change in pH

what happens if u add a strong acid to a buffer

decreases the pH

whats the effective buffer range

± 1 of pka

at a buffers half equivalence point, whats the relationship between the ph and pka?

what does it mean with the concentrations?

pka= pH

its when the concentration of acid= concentration of base

describe the 3 relationships between ph and pka and protenation

if ph is less then pka = groups protenated

the ph is greater then pka = groups deprotenated

if ph =pka the groups 50% protenated, 50% deprotenated

amino acids have 2 isomers, L ad D but which is the only one in human proteins

L

which amino acids are non polar aliphatic (5)

proline

methionine

valine

isoleucine

leucine

which amino acids are non polar aromatic (3)

• phenylalanine

• tryptophan

• tyrosine

tyrosine structure has an OH so its a little more _____ and reactive

polar

the non polar aromatic ones are a little less hydrophobic because they have …

N and O which can create hydrogen bonds

relationship between r group length and hydrophobic

the longer the r groups chain the more hydrophobic

the non-polar groups have _____ r groups

hydrophobic

the polar and small uncharged groups (7)

serine

theronine

asparagine

glutamine

glycine

alanine

cystine

tell me 2 crazy things about cystine

only amid acid that makes covalent disulfide bonds

the sh group makes it more reactive

in the polar and small uncharged groups, which 2 are neutral amino acids

glycine

alanine

groups in the polar charged + basic groups (3)

lysine (postive polar)

arginine (postive polar)

histidine (charge can change)

groups in polar charged + acidic (2)

aspartate (neg)

glutamate (neg)

amino acids whose r groups can change w pH (7)

histidine

aspartate

glutamate

cystine

tyrosine

lysine

arginine

describe briefly the primary structure of proteins

just a sequence of amino acids held tg by peptide bonds

describe briefly the secondary structure of proteins

sections of the amino acid chain folds into shapes held tg by hydrogen bonds

describe briefly the tertiary structure of proteins

3d shape of 1 polypeptide

describe briefly the quantenary structure of proteins

multiple chains of polypeptides tg

what are peptide bonds?

where do they connect?

covalent bonds that connect amino acids

removes h2o between a carboxylic acid of one group and amino of other group

are peptide bonds hydrophobic or hydrophilic?

do u need energy to make them? break them?

very hydrophilic and can make hydrogen bonds

u need energy to make them so u need energy to make proteins

breaking a peptide bond is spontaneous u just need water

where do we start the peptide bond? in fancy terms

N termous towards c terminus

disulfide bonds on sulfur happen thru

oxidation/ reduction

T/F peptide bonds have resonance stabilization and rigid planar geometry

TRUE

peptide bonds are in the cis or trans

trans

what is this

bond between the N and alpha carbon

in proteins secondary structure what are hydrogen bonds between

start @ N of one amino acid and count 4 N’s

it goes from H of the first amino acid to the o of he carboyl attached on the 4th amino

are all alpha helixes right or left handed?

whats their shape? where do their r groups point?

right

spiral shape- r groups point away from the backbone

b- sheets are what shape?

where r the r groups?

linear

r groups alternate sides of the backbone

what are the interactions in a polypeptide folding of tertiary structure

hydrophobic interactions

disulfide bonds

van der waals

salt bridge

hydrogen bonding

what allows for the teriartty structure to happen?

the hydrophobic effect, the hydrophobic residues only @center of protein

what does myoglobin do?

what does hemoglobin do?

bring oxygen to the muscles

transports oxygen from air to blood

what does myoglobin + hemoglobin have that lets them bond oxygen

heme group with iron @ the surface of protein

which (hemoglobin or myoglobin) is a globular protein meaning its chain folds up into a sphere shape

myoglobin

protein function is directly related to which structure (primary secondary or tertiary)

tertiary

• Myoglobin has ________ heme → can bind ____ O₂

• Hemoglobin has _______heme → can bind ____ O₂

1, 1

4,4

which (hemoglobin or myoglobin) is called tetramer and has 4 polypeptide chains in quantanary structure?

which doesn’t hv a quantanary structure?

hemoglobin

myoglobin

whats the difference btw multiple domain proteins and quantenary structure?

multiple domain proteins have 1 chain

quantenary structure has multiple chains

what did anfinsen look to find in his experiment?

how’d he do it?

if we break amino acid interactions, will it get back to the shape it was automatically?

• he used ribonucleus and added urea to break the noncovalnet interactions and b-me to break the disulfide bonds

what did anfinsen find when he just removed b-me?

the sulfides form but not correctly so 1% active only

how does protein folding start?

whats the process called?

hydrophobic amino acids come tg and start the process called nucleation

what bonds have rigid geometry and why

peptide bonds and its bc they have resonance and partial double bond character preventing free rotation

why are the r groups along the polypeptide trans?

so the side chains dont clash and it limits steric hindering

what type of interaction is critical to proper protein folding

Non-covalent interactions the hydrophobic effect

What type of secondary structure does misfolded APP form, how do these misfolded subunits interact, and how does this affect their solubility in water

Misfolded APP forms beta-sheets that stick together making them insoluble in water.

why do non polar amino acids cluster in the middle of proteins

bc of the hydrophobic effect and it minimizes unfavorable interactions

_____ amino acid is a helix breaker.

why?

proline

its ring structure and that it cant form hydrogen bonds

when a protein has many glycine residues in a turn region why is it good?

glycine is small and flexible and has tight coiling

if you replace leucine with aspartate at the core of a protein how does this effect stability and folding?

it makes the protein unstable because leucine is nonpolar and hydrophobic and it stabilizes the core.

in each an alpha helix structure and beta pleated what are the hydrogen bondings like?

alpha- intrachain

beta- interchain

with madcow/scrapies disease, what are the misffolded proteins called and what do they do

prions ; it has correct folding but the prions influence the good proteins

in deoxymyoglobin where is the heme group? and whats going on with the coordination site?

in oxymyoglobin where is the heme group? and whats going on with the coordination site?

deoxy- the iron is slightly out of plane of the heme group; the 6th coordination site is empty

oxy- the iron is in the plane of the heme group; Oxygen binds to the 6th coordination site

where does histadine bind to iron?

5th coordination site

how does myoglobin/ hemoglobin bind to oxygen (whats the binding curve for each?)

why is hemoglobins that?

myoglobin - hyperbolic

sigmoidal ; important because it lets oxygen be delivered to the lungs and tissues

whats the p50 for myoglobin and hemoglobin and what does it mean

myoglobin is low

the smaller the p50 the stronger the protein binds to oxygen

hemoglobin is high

whats hemoglobins R and T states mean? and which is hyperbolic state and linear state?

T = low affinity for oxygen; helps hemoglobin release oxygen into tissue -linear-

R= high affinity for oxygen; you’ll find it in places with high amounts of oxygen -hyperbolic-

what is cooperative binding

the binding of 1 oxygen increases the binding affinity

whats 2,3 BPG and what does it do

its an allosteric effector and stabilizes the T state

when 23BPG is released, and more oxygen sites become available what does that induce in terms of a state change

T state to R state

whats the role of chymotrypsin

breaks proteins into smaller peptides that can be more broken down into amino acids and absorbed by cells

chymotrypsin is an _______ meaning it breaks the proteins ___

endoprotease

in the center

chymotrypsin cuts the bonds after which amino acids

Phenylalanine

tyrosine

tryptophan

whats the active site of chymotrypsin

what are they called all tg

ser 195, his 57, asp 102

catalytic tryiad

what does the oxyanion hole do

stabilizes the negative charge/ transition state and makes the reaction faster

whats the is pocket?

where chymotrypsin recognizes the substrate

what does saying chymotrypsin is a covalent catalyst mean

chymotrypsin temporarily forms a covalent bond with the substrate

explain how the acyl-enzyme intermediate is formed

ser 195 attacks the substrate and one piece of the broken peptide leaves, while on piece becomes temporarily attached to serine

chymotrypsin mechanism explained

the substrate binds

his 57 activates ser and ser becomes the alkoxide ion

the set 195 is the nucleophile, and it attacks the substrate

transition state forms and oxyanion hole stabilizes the neg charge

peptide bond gets broken

acyl enzyme intermediate is formed

water hydrolysis (breaks the temporary covalent bond)

product leaves and enzymes regenerated

whats an example of aspartyl protease

and its the only 1 that cuts @

HIV protease

multiple pieces

how does waters high dielectric constant weaken electrostatic interactions

because it reduces electrostatic attractions and that weakens ionic interactions

what wld happen to protein folding If water was non polar

they wouldn’t fold correctly and the hydrophobic resides wouldn’t cluster in the middle

why are polyprotic acids like phosphoric acid are useful

they can buffer at multiple PH’s

why’s proline rigid

the ring structure and cause it breaks helices

How many residues per turn are present in an α-helix?

3.6

whats the shape and solubility difference in globular proteins and fibrous proteins

g- compact anf soluble

fibrous- elongated and insoluble

if u substitute a hydrophobic amino acid with a polar one in a protein’s hydrophobic core how would it affect protein stability

it would destabilize the hydrophobic core and the protein may misfold