Bio EXAM 1

What are proteins composed of?

domains

Can a protein have more than one domain?

yes

What is a modular protein subunit with its own unique function?

domain

How can new proteins be made?

shuffling domains

What are pieces of protein with a function of their own?

protein domain

What encodes a protein domain?

DNA exon

What is scrambled to make new genes and therefore new proteins?

exons

What is quaternary structure?

a protein made up of more than one polypeptide

Not all proteins have quaternary structure but if they do…

it needs to be maintained

What can quaternary structure be bonded by?

R group interactions

disulfide

Hydrogen bonds

peptide backbone

ionic

hydrophobic

What is held together with both strong and weak bonds?

polypeptides

What is an example of a protein that has quaternary structure?

hemoglobin

What disease is caused by misfolded proteins?

Ehlers Danlos syndrome

What is Ehlers Danlos syndrome?

an inherited defect in the synthesis of collagen protein results in skin hyperelasticity, joint hypermobility, skin scarring, skin wrinkling, and skin sagging

Where is collagen found?

hair, skin, nailsW

What is the job of collagen?

provide elasticity

How does the production of collagen change as you age?

less collagen production as one gets older

What does a protein bind to?

ligand

What kind of bond forms between a protein and ligand?

noncovalent, because it is only a temporary bond

What are the forms of a ligand?

DNA, polysaccharide, lipid, water, gas

What is the name of the bacterium that lives on the surface of plants?

Pseudomonas syringae

What kind of proteins does P. syringae produce?

Ice Nucleation Proteins (INP)

What does INP do?

raise the freezing temperature of water, causing billions of dollars of frost damage to crops every year

Why would this bacterium want to encourage plants to freeze?

bacteria are decomposers and want to eat plant; plants have a waxy cuticle layer so plant is protected, but when frozen, ice crystals form and H2O break open plant cells

What are the strongest linkage between ligand and protein?

ionic bonds, even though they will dissolve in water they will quickly reform and other ionic bonds are still formed and holding it together

What is a gas that acts as a ligand?

oxygen, carbon dioxide, monoxide

How does hemoglobin work in the body?

hemoglobin in the red blood cells bind atmospheric oxygen and deliver it to the tissues of the body

What determines a proteins interactions?

binding surface

What is the normal ratio of ligands to proteins?

1:1

When a protein folds where do the R groups go?

together in the middle of the folded protein

Can binding between the backbone and ligand occur?

yes, sometimes

What can evolutionary tracing figure out?

binding sites

What is the most crucial part of the protein?

binding sites

The more important placement of an amino acid…

the less likely it is to change over the course of evolution

What are the three types of protein to protein binding?

surface-string

helix-helix

surface-surface

What is the most common protein-protein binding and why?

Surface-surface because the R groups interact with each other

What is prion disease caused by?

misfolded PrP proteins bind to healthy PrP proteins

Do all mammals make the PrP protein?

yes

Is the prion itself a mutated version or wild type?

mutated version, stable state

What are all prion diseases derived from?

the same PrP protein

What is common between all four prion diseases?

they are all neurodegenerative and irreversible

What is CJD?

creutzfeldt-jakob disease

What is the human version of mad cow disease?

CJD

What happens with CJD?

the brain turns into sponge with pockets of dead tissue; slow process

What is scrapie?

exclusively animal prion disease

What happens with scrapie?

causes animals to obsessively scratch/itch themselves

What is Kuru?

fast process; found in a single tribe passes person to person from eating brains at funerals; short incubation period of CJD

What does FFI stand for?

familial fatal insomnia

What is FFI?

born with problem in PrPc and fold as a PrPsc

What does FFI do to the body?

damaged part of the brain controls sleep; die from lack of sleep

What are the 4 kinds of prion disease?

CJD, scrapie, Kuru, Familial fatal insomnia (FFI)

How does each prion disease have a unique set of symptoms?

each disease’s prions are folded differently

Who is the person who discovered prion diseases?

Stanley “Mr. Prion” Prusiner

What did Stanley Prusiner discover?

prion diseases involve proteins encoding proteins and pass along their own disease, which is an exception to central dogma

What is the central dogma?

DNA is the main encoder which goes to RNA then proteins

What do misfolded proteins aggregate into?

amyloid fibrils

What is the cause of all 4 prion diseases?

prion amyloid plaques

What are amyloid fibrils?

long strips of misfolded beta sheet rich proteins

What do fibrils bunch up into?

plaques

What do plaques do to the cell?

clog it

Are amyloid fibrils stable?

very stable

iatrogenic

obtaining disease from medicine/hospital

How was CJD transmitted iatrogenically?

surgical instruments

enzymes convert substrates into…

products

enzyme

proteins that change their ligands

substrate

ligands that are changed by the protein

What is the job of enzymes?

speed up reactions that would have happened anyway

How many enzymes are in the human body?

>75,000 enzymes

What is the human enzyme that breaks down lactose?

lactase

What kinds of bonds are disulfide bonds?

covalent

What is the human enzyme that breaks down lactose?

lactase

When does the enzyme lactase tend to be turned off?

2-3 years old

What is lactose intolerance?

When people do not produce enough lactase to digest all lactose

Is lactose intolerance a disease type?

No, it is the wild type, lactose tolerance is mutated type

How many different mutations cause lactose tolerance?

6

What kind of molecule is lactose?

disaccharide

What is lactose broken into?

galactose and glucose

What product from the breakdown of lactose can be used by the cell?

glucose

How did lactose tolerance become a thing?

10,000 years ago people domesticated cattle and in desperation drank cow’s milk. 1/100 people were able to digest and survive this. It is suspected this happened 6 times to account for the 6 different mutations for lactose tolerance

If you are lactose tolerant, do you think all cells of your body produce lactase?

No, only the cells involved in digestion in the small intestine produce lactase because it would be a waste of energy for every cell to produce it

What does cobra venom digest?

cell membranes

What enzyme does cobra venom contain that is dangerous to humans?

Phospholipase A2

What does Phospholipase A2 do?

clips a fatty acid chain off phospholipids, leaving one fatty acid side chain

What is it called when one fatty acid side chain remains on a phospholipid?

conical molecule

What do conical molecules form?

micelles

What do the target cells do when they are formed into micelles?

the target cell membrane disintegrates

What composes membranes?

phospholipids

What happens to anything on humans that cobra venom touches?

it disintegrates or crumbles away

some drugs work by…

blocking enzyme/substrate binding

What was the original name for erectile dysfunction?

impotence

What is the name for Viagra?

Sildenafil

What is the active site that sildenafil (viagra) binds to?

Phosphodiesterase 5 (PDE5)

What does the binding between viagra and PDE5 do?

widens the arteries to the penis to allow blood flow so the penis can become hard

What is sildenafil?

an inhibitor that binds to the active site PDE5

What is PDE5?

modulates so the penis does not become too hard that damage occurs

The rate of a reaction depends on…

substrate concentration

Some proteins require …. at active site

coenzymes

Are coenzymes enzymes?

no, they are organic molecules that are nonproteins

What are coenzymes?

passive molecules that help interactions; modifies active side of a protein so that the substrate can stick

What is the definition of coenzyme?

small organic molecule that enhances protein activity