cell bio test 3

Which of the following is NOT a function of proteins?

movement, immune defense, membrane transport, hormones/hormone receptors, enzymes, genetic information

genetic information

Describe primary protein structure:

amino acid sequence

Describe secondary protein structure:

alpha helices and beta sheets

Describe tertiary protein structure:

overall three-dimensional shape

Describe quaternary protein structure:

several subunits joined together

Which statement about alpha helices and/or beta sheets is FALSE?

Two or more alpha helices can spiral around each other to form a strong coiled coil structure.

Alpha helices can form membrane-spanning domains in membrane-associated proteins.

Beta sheets can stack together to form rigid amyloid structures.

They’re both always made entirely from nonpolar amino acids.

They both form through multiple hydrogen bonds between different parts of their polypeptide backbones.

They’re always made entirely from nonpolar amino acids

What helps determine, either directly or indirectly, the final 3D conformation of a particular protein?

The sequence of amino acids that make up the protein.

The pH of the organelle (or other environment) in which the protein functions.

The sequence of nucleotides in the gene that codes for the protein.

Hydrogen bonding between different parts of the polypeptide backbone.

Interactions of the amino acids’ side chains.

Why are the side chains of amino acids so important?

They function as a biochemical “tool belt” which determines what the protein can do.

They interact with each other to help the protein fold and remain folded.

What amino acids help to stabilize protein structure by clustering inside of the protein and contributing to its overall shape?

Hydrophobic

What amino acids often participate in the protein’s activities because they’re more likely to be on the outside and interact with other molecules?

Hydrophilic

What are different regions of the same polypeptide which perform distinct functions, and often fold somewhat independently from the rest of the polypeptide?

Protein domains

What are encoded by different genes, transcribed and translated separately, then assembled into a larger functional protein?

Protein subunits

T/F A protein’s preferred conformation is the one with the lowest free energy.

True

What exactly happens when an enzyme becomes denatured?

It unfolds from its normal three-dimensional shape, and therefore no longer fits the reactants on which it used to act

Proteins denatured in the lab will often spontaneously refold into their correct conformation when the denaturing agent is removed. Yet denatured proteins within living things (or in the kitchen) do NOT generally refold correctly. What are some reasons for this?

When large numbers of protein molecules are unfolded, they stick to each other to form tangled aggregates.

The cytoplasm is very crowded with other proteins and molecules. It’s too easy for a denatured polypeptide to stick to these and be prevented from folding correctly.

These laboratory refolding experiments are conducted under simplified ideal conditions which don’t closely match the conditions inside living cells.

What do chaperone proteins do?

They help newly made polypeptides to fold correctly, mostly by shielding then from other cellular components which could potentially interfere with proper folding

At low substrate concentrations:

the rate of the reaction is directly proportional to the substrate concentration

At higher substrate concentrations:

the active sites of all the enzyme molecules are constantly occupied, and the reaction rate approaches the maximum rate possible for that enzyme

What are some of the means by which an enzyme can lower activation energy to catalyze a reaction?

Forming temporary bonds with the substrate to redistribute electron density.

Distorting and straining the conformation of the substrate.

Precisely aligning reactants.

What are small molecules which bind as part of an enzyme-substrate complex to enhance catalytic efficiency or function as activated carriers?

cofactors/coenzymes

What is a mechanism for enzyme regulation in which binding of a molecule at one site changes the conformation of the protein, so that the shape of the catalytic site changes?

Allosteric regulation

What is a mechanism for enzyme regulation in which another molecule, similar in shape to the enzyme’s normal substrate, binds in the active site and prevents the substrate from binding?

Competitive inhibition

What is a mechanism for enzyme regulation in which the product of a metabolic pathway binds to and downregulates an enzyme near the beginning of the pathway to prevent wasteful overproduction?

Feedback initiation

What is a long, flexible, largely unstructured polypeptide or noncoding RNS, which binds to various protein components and helps them assemble into a larger multi-protein complex?

Scaffold

What is a dense collection of molecules different enough from their surroundings that they form a distinct phase-separated structure without an enclosing membrane?

Intracellular condensate

What is a membrane-bounded enclosure, whose internal chemical environment may be quite different from the surrounding cytoplasm?

Vesicle

What can antibodies do?

Help fight infections directly and by activating other parts of the immune system.

Be linked to drugs for delivery to specific tissues or tumors, while minimizing systemic side-effects.

Be used as selective filters to bind and purify specific molecules from a mixture.

Be linked to dyes to detect specific molecules on gels or in micrographs.

A centrifuge separates materials by differences in their:

density

How does ion-exchange chromatography separate substances?

electric charge

How does affinity chromatography separate substances?

strong and specific binding to other molecules

How does gel-filtration chromatography separate substances?

size

What research technique measures the mass and charge of vaporized protein fragments deflected through a magnetic field then searches against predicted protein sequence databases?

Mass spectrometry

What research technique measures radio waves emitted by atomic nuclei aligned with a perturbed magnetic field and matched with patterns of characteristics of known molecular features?

NMR spectroscopy

SDS-PAGE uses _____ to separate proteins by _____

an electric voltage across a porous gel matrix, size

What modeling technique uses thousands of perfectly aligned proteins to make one image?

X-ray crystallography

What modeling technique images thousands of randomly oriented proteins then assembles those images into an overall 3D model?

Cryo-electron microscopy

Which type of noncovalent interaction can involve either the polypeptide backbone or amino acid side chains?

Hydrogen bonds

A folded protein structure with which free-energy (G) value - 10, 5, 15, 1 - would likely have the most stable conformation?

1

If protein folding is determined by the sequence of amino acids in the polypeptide chain, why are chaperone proteins needed to assist folding in the cell?

Certain proteins easily aggregate with other proteins

Hydrogen bonding between N-H and C=O groups of every fourth amino acid within a polypeptide chain results in which type of folding pattern?

alpha helix (D)

What is true about amyloid protein structures?

They consist of stacked beta sheets

A stretch of amino acids in a polypeptide chain that is capable of independently folding into a defined structure is called a:

domain

What level of protein structure involves the interaction of more than one polypeptide chain into a three-dimensional structure?

quaternary

Order the protein organizational units from smallest to largest

domain < subunit < complex

A binding site on the surface of a protein interacts specifically with another protein through:

many weak noncovalent interactions

Disulfide bonds stabilize protein shape outside the cell by:

covalent bonds between cysteines

The figure shows a depiction of an antibody. Which label correctly identifies the region(s) of the antibody that contains variable amino acids for binding of a specific antigen?

A

The Michaelis constant (Km) of an enzyme is a measure of:

the binding strength of enzyme to substrate

How do enzymes lower the activation energy of a reaction?

Encourage the substrates to change shape toward a transition state that favors the reaction.

Align substrates to promote a reaction between them.

Rearrange electrons in the substrates in a way that favors the reaction.

The function of the feedback inhibition of an enzymatic pathway is to:

turn off synthesis of a product when it is in abundance

When a ligand binds to an allosteric enzyme’s regulatory site, it changes the activity of that enzyme by:

inducing a conformational charge

How does phosphorylation of a protein affect its activity?

Could increase or decrease activity

How does binding of GTP to a GTP-binding protein affect its activity?

Always activates the protein

Chemical modifications like phosphorylation and acetylation of proteins occur on ____ of amino acids and can affect interaction of proteins with other cell components or structures.

side chains

Shown is the ATP hydrolysis cycle of a motor protein. Describe the state of the motor protein in “C”.

The hydrolysis of ATP to ADP caused a conformational change in the protein

Biochemical subcompartments that form inside the nucleus are distinct from their immediate surrounding because of the:

high concentrations of interacting proteins and RNA

What method is used for separating proteins based on specific interactions with other molecules?

Affinity chromatography

What method is most suitable for determining the three-dimensional structure of an extremely large integral membrane protein complex?

Cryo-electron microscopy

What is a protein family?

Structurally related group of proteins

Which parts of amino acids are involved in a peptide bond?

amino group of one amino acid and carboxyl group of another

What part of an amino acid gives it its unique properties?

side chain

What is the best type of model for visualizing the surface of a protein?

space-filling

What are the two types of beta sheets?

parallel and antiparallel

What does the primary structure of a protein refer to?

the linear amino acid sequence of the protein

What determines the specificity an antibody has for its antigen?

polypeptide loops in its variable domains

For a given protein, hydrogen bonds can form between:

atoms in the polypeptide backbone

atoms of two peptide bonds

atoms in two side chains

a side chain and water

How does an allosteric inhibitor work?

It binds to a site other than the active site, causing a conformational change in the enzyme that makes the active site less accommodating to the substrate

How does phosphorylation control protein acitivity?

the phosphate group induces a change in the protein’s conformation

What kind of enzyme adds a phosphate group to another protein?

kinase

What kind of enzyme removes a phosphate group from a protein?

phosphatase

What is the purpose of active and regulatory sites of an enzyme?

The binding of CTP at a regulatory site on the protein causes decreased production of carbamoyl aspartate

Electrophoresis separates proteins based on:

the proteins net charge and the protein’s size

What are methods for isolating a protein of interest?

chromatography and electrophoresis

What can be used to determine the amino acid sequences of a complex mixture of different proteins?

Mass spectrometry

What is the toughest and most durable of the different types of cytoskeletal filaments?

intermediate filaments

Intermediate filaments are found in what structure?

nuclear lamina

What term describes the structure of intermediate filament monomers?

ropelike

What type of intermediate filaments are found in all animal cells?

nuclear lamins

GTP hydrolysis and whether GTP or GDP is bound to tubulin is an important mechanism to control the dynamic instability of microtubules. Certain aspects of dynamic instability can be viewed using GFP-EB1. What process is it useful for visualizing and why?

growing microtubules; EB1 binds to the GTP-tubulin cap on microtubules

How would microtubule dynamics change after adding a non-hydrolyzable analog of GTP to the cells expressing GFP tubulin?

microtubules would grow longer

What transports cargo to the cell body via backward transport?

dynein

What transports cargo to the axon terminal via outward transport?

kinesin

What does the cellular motility of sperm depend on?

microtubules and dynein

What cytoskeletal structure is the most common for providing tracks for guiding intracellular transport?

microtubles

What do microtubules resemble?

hollow tubes

Dynamic instability in microtubules stems from the intrinsic capacity of tubulin molecules to hydrolyze what?

GTP

Describe the structure of an actin filament.

a twisted chain of actin molecules

What is the name of the thin, sheetlike structures that a fibroblast regularly extends during cell crawling?

lamellipodia

Myosin-1 iis present in what kinds of cells?

all types of cells

What actin-binding proteins would be most involved in the assembly of the contractile ring?

formins

An actin filament undergoing treadmilling at the leading edge of a lamellipodium can do what?

remain the same size

What does not contain both actin and myosin?

the lamellipodium at the leading edge of a crawling cell

In a muscle fiber, what triggers sarcomeres to contract?

a sudden rise in cytosolic Ca2+

What organelle sequesters Ca2+ inside muscle fibers?

sarcoplasmic reticulum

When a muscle is stimulated to contract, what does Ca2+ bind to, and what effect does that have?

troponin, which moves the tropomyosin that otherwise blocks the interaction of actin and myosin

What cytoskeletal structures are made up of protein subunits that are fibrous?

intermediate filaments

What is an important function of intermediate filaments?

providing tensile strength to the cell and the nucleus

How do the intermediate filament proteins keratin, vimentin, and neurofilaments differ from each other?

they are different at the head and tail domains that are exposed at the surface

In terms of structure, if cytoplasmic intermediate filaments are described as ropes, nuclear lamins could be best described as _____

mesh

Microtubules extend from organizing centers in the cell. What is an example of an organizing center?

basal body of a cilium