bios 3200 exam 1 dr. Moats

enzymes protein

catalyze (speed up) reactions

structural proteins

to support

transport proteins

allow passage of hydrophilic substances across the membrane

motor protein

A protein that interacts with cytoskeletal elements and other cell components, producing

When multiple alpha helices come together, they may form a structure often called a _________________.

coiled coil

How is the small protein ubiquitin used in protein modification?

Ubiquitin marks other proteins for destruction.

What is the function of SDS in polyacrylamide gel electrophoresis?

It coats the protein with uniform negative charge.

storage proteins

A source of nutrients or other compounds

In proteins, alpha helices and beta sheets are examples of ___________.

secondary structure

A _________ is a portion of a protein which folds independently into a specific unit and is used to add functionality to proteins.

domain

ligand

A molecule that binds specifically to another molecule, usually a larger one.

dimer

a compound whose molecules are composed of two identical monomers

primary structure

sequence of amino acids

secondary structure

The second level of protein structure; the regular local patterns of coils or folds of a polypeptide chain.

tertiary structure

The third level of protein structure; the overall, three-dimensional shape of a polypeptide due to interactions of the R groups of the amino acids making up the chain.

Beta sheets may be constructed in 2 ways: parallel and antiparallel. The term "antiparallel" indicates

The polypeptide chains making up the sheet are arranged in opposite directions.

If the folding of a polypeptide chain results in the placement of two cysteine side chains near each other, a ____________ may form.

disulfide bond

Binding sites for additional molecules on a particular protein are usually formed directly by the primary structure of the protein itself.

False

Enzymes which add high-energy phospates onto other proteins are known as __________.

kinases

phosphorylase

An enzyme that breaks down glycogen by catalyzing hydrolysis of the a-glycosidic linkages between the glucose residues.

phosphatases

remove phosphate groups

ATPases

hydrolyze ATP

the sanger reaction

The Sanger reaction breaks all the peptide bonds at once, and so is useful in identifying only 1 particular amino acid in the protein.

The Sanger reaction may be problematic, but its still useful. How?

It adds a fluorescent label to only the N-terminal amino acid in a protein.

Beta sheets may be constructed in 2 ways: parallel

The polypeptide chains making up the sheet are arranged in the same direction.

In gel electrophoresis, SDS is added to the protein samples to

add a negative charge

Mercaptoethanol

breaks disulfide bonds

dye

tracks the protein

Which method of studying proteins usually involves a protein called Cre?

conditional knock-out animals

Western blotting

procedure that uses labeled antibodies to detect specific antigens in a mixture of proteins separated according to their molecular weight

affinity chromatography

uses a bound receptor or ligand and an eluent with free ligand or a receptor for the protein of interest

2-hybrid systems

The purpose of cholesterol in mammalian cell membranes is to ______________________.

reduce membrane fluidity

A great example of the cell cortex and the use of the protein spectrin can be found in the ______________________.

red blood cell

The process in which regulated ion channels may spontaneously open & close is called ____________.

flicker

A lipid bilayer with a high percentage of phospholipids with double bonds in their fatty acid tails ("unsaturation") will display a high degree of __________.

fluidity

Membrane fluidity in animal cells is decreased by the presence of an increasing amount of

cholesterol.

On the extracellular surface of the plasma membrane, you'll find a greater amount of _____________________ when compared to the intracelluar surface.

carbohydrate

Which of these protein features is/are commonly found in proteins passing through the plasma membrane?

alpha helices

Which of these would be considered an "integral" membrane protein?

What might be present in secondary structures of a transmembrane protein that would allow for the creation of a small pore or channel?

hydrophilic amino acids

Respiratory gases, such as O2 and CO2, can pass directly through cell membranes because they are polar.

False (n0n polar)

Identify the driving force for the movement of solutes through the plasma membrane by passive transport.

the concentration gradient of the solute

Why might the passive movement of a charged molecule through the cell membrane be limited even if the concentration gradient for the molecule is high?

The membrane electrical gradient restricts the flow of like charges.

Which of the following is/are TRUE about the action of the Na+/K+ ATPase?

ALL of these answers are TRUE.

3 multiple choice options

What feature of the Na+/K+ ATPase allows it to be categorized as a primary active transporter?

It breaks down ATP directly for energy.

It is very common for a transport protein to use the sodium electrochemical gradient to pump other molecules into or out of the cell.

Because of their dependence on the sodium gradient set up by the Na+/K+ ATPase, these proteins are called ___________________.

secondary active transporters

secondary active transporters

couple the potential energy of ion gradients to transport substances

it need susbatances from the primary to the secpundary

primary active transporters

needs an engery source

atp

light

Which of these are the most rare of the ion channels, occurring in the ear and bone?

mechanically-gated ion channels

ligand-gated ion channel

A protein pore in the plasma membrane that opens or closes in response to a chemical signal, allowing or blocking the flow of specific ions.

mechanically-gated ion channels

respond to mechanical vibration or pressure

voltage-gated ion channels

Channels that open or close in response to a change in the membrane potential.

signal protein

carries signals from cell to cell

receptor protien

receive and transmit messages into a cell

gene regulation protein

process of controlling which genes in a cell's DNA are expressed

petide bond

(-) carbolyic acid

(+) amine

hydrophlic side chain

polar

hydrophic

non polar

noncovalent interactions

allows for folding of the bonds

chaperones

Proteins that assist in protein folding during posttranslational processing

alpha helices

form of a secondary structure of peptides

rod like structure

peptide chain coils clockwise around the central axis

is stabilized by the carbonyl oxygen atom and an amide hydrogen atom four residues down -- hydrogen bonding

side chains of the amino acids point away from the helical core

ex. keratin

beta sheets

can be parallel or antiparallel peptide chains forming rows or strands held together by intramolecular H bonds between carbonyl oxygen atoms and amide H atoms in an adjacent chain;

ex. fibroin - primary protein component of silk fibers

domain type

can be all aplha

can be all beta

can be combined

quaternary structre

involves association of multiple polypeptides to form a monomeric protein

binding proteins

bind a specific substrate, either to sequester it in the body or hold its concentration at steady state

tethering domains within a protein

can be threadted together 2 and 3 to make something new

tethering interacting proteins

allows for scaffolifng so the bits can fold nicelly

disulifde bonds

alllows for 3 and 4 to keep protein shape

proteins work through interactions

basicallt folding mkaes it stable so it can have a cylic amp

enzyme work in phases

reasons for cofactors

they allow for the build of proteins

feedback

basicallt one one cup is filled it will stop to allow the others to bcome filled

conformation change

shape changes

allosteric regulation

The binding of a molecule to a protein that affects the function of the protein at a different site.

nucleotide hydrolysis

allows motor proteins to produce large movements in cells