Proteins

what do r groups produce

structural variability

what do you find in electrically charged r groups

a full positive or a full negative charge

ball-and-stick

highlights the bonding patterns (the actual structures of the bonds itself)

collagen

long and stringy protein; it's job is to connect things between one another in a cell

what holds the alpha helices of keratin together

hydrogen bonds

what are disulfide bridges

covalent linkages between two cysteine amino acids

what happens when a protein misfolds

it becomes sticky and forms aggregates

what does ATPase do

converts atp to adp

how do some proteins bind to other proteins

surface-surface, helix-helix, surface string

most common way of protein binding to other proteins

surface-surface

how does one get prion disease

a prpc will spontaneously misfold and turn into a prpsc and that prpsc will bind to other healthy prpc's and turn them into prpsc's and there can be various affects

is lactose intolerance a mutation

no, the mutated gene is lactose permanence; in the olden days, people didn't drink milk until starvation. some people had the lactase mutation where they survived while others didn't

how do cells regulate enzyme activity

via feedback inhibition

what does protein phosphorylation fo

regulate protein activity - sometimes kinases can activate or deactivate, but sometimes phophotases can activate or deactivate

what are the weak bonds

hydrogen bonds, hydrophobic interactions, van der waals interactions

how do hydrophobic molecules react with water

they are repelled by water, they stick together with other nonpolar molecules and float between water (they interact)

what are the strong bonds

ionic bonds and covalent bonds

what are covalent bonds

they are the atomic staple, which means that they are permanent when they are made

what are proteins composed of

a string amino acids

what reaction are amino acids linked by to form polypeptides

condensation reaction

what charge does the amino group have

positive charge

what charge does a carboxyl group have

negative charge

what is the n terminus

amino group end

what is the c terminus

carboxyl group end

what is the charge of the c terminus

negative

what side is the n terminus always on

the left

why do condensation reactions require atp

eliminating a water molecule requires energy; forming a covalent bind takes a lot of energy

is hydrolysis energetically favorable or unfavorable

energetically favorable (doesn't require atp)

where is atp's energy stored

in the terminal phosphate

the breakage of how many phosphates releases energy which the cell can use to drive other processes?

the last two phosphates

is atp a stable or an unstable molecule

unstable

what happens to atp when the cell needs energy

the cell sends out an enzyme to break off the terminal phosphates and when this happens, atp releases energy and relaxes

what do carbon carbon bonds allow

rotation and flexibility of long molecules

are peptide bonds flexible

no, they are stiff so they won't rotate freely

what kinds of amino acids are there

polar, nonpolar, and charged

what do you find in polar molecules

less hydrocarbons, more oxygen, nitrogens and sulfurs

what are the levels of protein structure

primary, secondary, tertiary, quaternary

are r groups involved in secondary structures

no

why does o have a negative charge in the peptide backbone

because it is attached to a carbon, which has a partial positive and that allows oxygen to be a partial negative. because it is now partially negative, it can form a bond with the partially positive hydrogen

how does humidity alter keratin hydrogen bonds

water molecules hydrogen bond with the alpha helical keratin proteins in the hair. this causes the bonds with themselves to break because they will now want to hydrogen bond with the water in the air. This causes them to become disorder and therefore, it results in frizz.

what proteins is keratin made of

packed alpha helices

how does keratin break with heat

heat breaks the hydrogen bonds within the alpha helices, and it forces the bonds to reshape in whichever way the mold is. this is why when you straighten your hair, you're breaking the hydrogen bonds that are there naturally and you are reforming the hydrogen bonds when you mold them the way you want them to be.

is tertiary structure global or localized folding

global folding

how do polar groups interact in tertiary structure

by hydrogen bonding. they will fold outwards because they like water

how do nonpolar molecules interact in tertiary structure

they will interact with hydrophobic interactions which will cause them to fold within a cell because they don't like water

what is the region where nonpolar side chains hydrophobic interact called

hydrophobic core

what does it mean when proteins fold into the lowest conformation energy

they fold into a way where all the bonds are favorable. you would need to add extra atp to break favotable bonds.

what kind of environment does the cell have

aqueous environment

what is a cysteine amino acid

it is an amino acid that has a sulfhydryl group (SH)

what bonds can cysteine groups form

disulfide bonds

what are disulfide bonds

covalent bonds between two cysteine groups, and they are usually always permanent

what does it mean to form a covalent bond

it is permanent, once a covalent bond is formed, it cannot be broken

why do we not like covalent bonding in proteins

because we want proteins to be used just once, we want them to be reusable

what do symptoms of parkinson's disease result from

reduction of dopamine production by the brain

what is parkinson's disease caused by

a misfolding of a protein called alpha synuclien and a low dopamine production

what encodes a protein domain

each dna exon

how do you make up new proteins

if you scramble the exons around, you make up new genes which make new proteins

how do we have millions of different proteins

new proteins are made by chopping off bits of old proteins and sticking them together

what is recombination

the rearrangement of genetic material

what kinds of bonds are polypeptides held together with in quaternary structure

weak and strong bonds

what does hemoglobin do

it is a protein in red blood cells that bind oxygen

what is a ligand

any molecule that binds to the binding site; can be another protein, dna, polysaccharide, lipid

through what bonds do ligands attach to the binding site

noncovalent bonds

why do ligands only attach via noncovalent bonds to the active site

because covalent means permanent and you want to be able to recycle the proteins, they should be able to let go

what is pseudomonas syringae

a bacterium that lives on the surface of plants

what is a ligand that is a gas

oxygen. hemoglobin binds to oxygen, then delivers it to the tissues of the body

explain evolutionary tracing

the more important the placement of an amino acid, the less likely it is to change over the course of evolution, so evolutionary tracing can figure out binding sites

what is the most important part of a protein and why

the amino acids that bind to the ligand

explain how a change in amino acids can be detrimental

if some amino acids are mutated, it doesn't affect the protein (structural parts), but if the amino acids at the binding site are mutated, then the binding site won't work. then it wont interact with its ligand and the protein wont do its job. that individual wont survive and even if they do, they wont reproduce as well.

cjd

spongiform, dead cell space, exposure can be eating contaminated meat, late onset

scrapie

found in animals, the itch sensor in brain goes off so they eep itching and it never goes away so they keep scraping themsleves

kuru

tradition of eating brains, early onset

familial fatal insomnia

inherited (genetic), limited to soe families in italy, it is a dominant gene, they die because they don't get enough sleep

the prion theory

challenged the central dome rna-dna-protein; he said that protein misfolding was the direct cause of the disease

enzymes vs substrate

enzymes are proteins and a substrate is a ligand changed by the protein

why do we need enzymes

they allow reactions to happen within seconds when it would've taken years without them

what does omp decarboxylase do

makes UMP and UMP makes dctp and dttp in 20 milliseconds which if you didn;t use the enzyme it would have taken you 80 million years

what is the enzyme is contained in cobra venom

phospholipase a2

what is a micelle

it is when there is no bilayer anymore so it causes the target cell membranes to disintegrate

how do some drugs work by blocking the enzyme.substrate binding

sidenafil binds to the active site of pde5 which is an enzyme that dimishes blood flow to the penis, by blocking it, sidenafil allows for an erection to occur with increased blood flow to. the penis. when there is enough blood flow, it will leave and allow pde5 to bind again and diminish the blood flow

explain how a coenzyme works

an enzyme and substrate may not match. the coenzyme will modify the enzyme so it is the right shape for the substrate. the coenzyme is not itself converting the substrate to product, but it is just helping the enzyme fit the substrate

true or false: many dietary vitamins are coenzymes

true

what is folic acid

a coenzyme required for neural tube development

what is folic acid a major ingredient of

prenatal vitamins

why is thiamine an important coenzyme

it is a critical coenzyme in the krebs cycle - it generates the krebs cycle so you can generate atp out of the food you eat

what is phosphorylation

addition of a phosphate group

what are hydrophobic interactions

the tendency of nonpolar covalently bonded molecules to come together and interact; the tendency for the nonpolar molecules to stick together

what do peptide bonds link

amino acids into polypeptides

do condensation reactions require energy input

yes

how does the cell pay to form covalent bonds

with energy (atp)

how many levels of protein structures are there

four

porin

proteins meant to let things pass into or out of the cell, they form channels in the cell membranes to allow selected molecules to go in or out of a cell

can disulfide bonds occur within a cell

no, the cell is a reducing environment so they can only occur in oxidizing environments outside the cell

what happens when you get a perm

disulfide bonds are broken when you add a reducing solution, then you mold the hair you want it and oxidize the hair to reform the disulfide bonds in the shape we want to remold the hair.

what is a common example of a quaternary structure

hemoglobin

what does ehlers danlos result in

hyperelasticity, joint hypermobility, skin scarring, skin wrinkling, skin sagging

what does pseudomonas syringae do

it raises the freezing temperature of water, killing the plant and eating the cell nutrients for the bacteria to survive

prion diseases

cjd, scrapie, kuru, familial fatal insomnia

why are amyloid fibrils bad

they bunch into plaques and clog up the cell and cause cell death

how is cjd transmitted

via surgical instruments (iatrogenic)