BSC 450 ch5: protein function

muscle fibers

skeletal muscle consists of parallel bundles of ______ _____, which are very large multinucleated cells fused together - often spans the length of the entire muscle - contains 1000 myofibrils

haptens

small molecules that are covalently attached to proteins in the lab to elicit and immune response

R state

state of hemoglobin known to be relaxed due to less ion interactions

T state

state of hemoglobin known to be tense due to a great number of ion interactions - binding of oxygen disrupts some of these bonds

sequential model

states that ligand binding can induce a change of conformation in a single subunit - makes similar change in adjacent subunit

A band

stretches the length of a thick filament and includes the region where parallel thick and thin filaments overlap

carbonic anhydrase

the CO2 produced by by oxidation in mitochondria is hydrated to form bicarbonate, which is catalyzed by _______ _______

electron donating

the _______ ________ character of the nitrogen groups in heme prevent the iron atom to convert from its ferrous to its ferric state

bohr effect

the affinity of hemoglobin for oxygen decreases as it binds more H+ and CO2 and the pH decreases, once the CO2 is let go of and the pH increases, hemoglobins affinity for oxygen increases

left

the alpha helices created by the heavy chains form a _____ handed coiled coil

proximal histidine

the amino acid side chain in globins that sequesters one of the two open coordination bonds in iron

Fab

the antigen binding fragments cleaved from from immunoglobulin G that are the antigen binding sites

binding site

the area of protein where the ligand binds. it will compliment the molecules: - size - shape - charge - hydrophobic/philic character

ligands

the binding of a ligand is regulated by another _______ which cause conformational changes in the protein that affect binding

glutamate valine

the cause of sickle cell anemia is a mutation in which ________ is replaced with ________ at position 6 which changes the charge in the two beta chains

induced fit

the conformational change a protein goes through to be more complementary to the ligand and vide versa

dissociation constant

(Kd) reflects the energy released from breaking non covalent interactions that stabilize binding.

cytoglobin

a monomeric globin is found in the walls of blood vessels: regulates levels of nitric oxide

heme

a protein bound prosthetic group that iron is incorporated into for multicellular organisms

enzyme configuration composition

There are two types of ways proteins interact with molecules: one way uses an _________ to alter the chemical configuration or composition, the other does not affect the proteins ________ or ________

globular

at myosin's amino terminus, the heavy chains each have a ______ domain where ATP is hydrolyzed. - light chains are also associated with this

marine mammals

myoglobin is abundant in diving ______ ______ because of its oxygen storage property

amino acid iron copper

no ______ ____ residues are suitable for the reversible binding of oxygen so multicellular organisms use transitional metals with a strong affinity to oxygen such as ______ or ______

R T

oxygen has a higher affinity for the ___ states of hemoglobin than the ___ state

concerted model

(also known as MWC) - subunits of a cooperatively binding protein are functionally identical and each subunit can exist in two or more conformations - move between simultaneously

immunoglobulins

(antibodies) bind to bacteria, viruses, or foreign proteins and mark them for destruction - produced by B cells

epitope

(antigenic determinant) the particular molecule within an antigen that an antibody or T cell binds to

elisa

(enzyme linked immunosorbent assay) - used to rapidly screen for and identify an antigen 1. proteins in the sample are absorbed to an inert surface 2. the surface is washed with nonspecific protein 3. the surface is treated with primary antibody 4. surface is treated with secondary antibody that is linked to a enzyme that produces a colored product 5. substrate is added - product formation is proportional to the concentration of the protein of interest in the sample

western blot

(immunoblot assay) proteins that are separated by gel electrophoresis are transferred to nitrocellulose membrane and treated with primary and secondary antibody linked to an enzyme and substrate. - colored precipitate forms showing where protein of interest is - detection of minor component and approx. molecular weight

BPG

a molecule that interacts with hemoglobin and decreases its affinity towards oxygen - binding site separate from oxygen binding site - regulates binding in relation to the pressure of O2 in the lungs - binding site between beta subunits and T state

carbon monoxide nitric oxide

______ _______ and ______ _____ are toxic because they have a greater affinity to iron than oxygen

myosin actin

_________ and _______ are the proteins that generate the contractile force in muscles

myoglobin hemoglobin

__________ and _______ are the most studied and understood proteins. - illustrate almost every aspect of irreversible ligand binding

neuroglobin cytoglobin plants invertebrates

__________, ________, and globins in some _______ and ________ have distal his directly coordinated with heme iron at locations where ligand must end - o2 or other ligands must displace the distal his in the process of binding - hydrogen bond still forms after

protoporphyrin

a complex organic ring structure in heme which binds to a single ferrous iron atom

myosin

a contractile protein with 6 subunits (2 heavy chains and 4 light chains). mostly composed of the heavy chains at the carboxyl terminal arranged as extended alpha helices

sarcomere

a functional and structural unit of the muscle contractile system - entire contractile unit

hemoglobin

a heme protein in erythrocytes that functions in oxygen transport

modulators

a metabolite that, when bound to the allosteric site of an enzyme, alters kinetic characteristics

substrate

a molecule acted on by an enzyme

ligand

a molecule that is bound reversibly to a protein

allosteric protein

a protein usually with multiple subunits and multiple ligand binding sites in which different sites affect ligand binding at other sites

myoglobin

a single polypeptide of 153 amino acid residues with one molecule of heme. - 8 alpha helical segments - 78% of amino acid residues found in alpha helix

M line

a thin line that bisects the A band - region of high electron density in the middle of thick filaments

myofibril

a unit of thick and thin filaments of muscle fibers

globins

a widespread family of proteins found in eukaryotes of all classes. function in: - oxygen transport/storage - sensing oxygen, nitric oxide, and carbon monoxide

ATP hydrolysis

actin molecules use ___ ______ to assemble into a thin filament - each actin molecule is complexed to ADP

homotropic

an allosteric modulator that is identical to the normal ligand

radioactive label

an analytical technique attaches a _______ _____ to an antibody to reveal the location of the target protein in a gel or living cell

Z disk

anchor that is perpendicular to the thin filaments and holding them in place

Chromatography

antibodies can used in _________ to recognize a specific protein that can be salted out or stay in a column while others are washed out

monoclonal antibodies

antibodies produced by a population of identical B cells which all recognize the same epitope.

polyclonal antibodies

antibodies produced by many different B cells in response to one antigen. they bind to different specific epitopes on that antigen

AIDS

causes by HIV virus which attacks helper T cells which blocks the entire immune system

heterotrophic

describes an allosteric modulator that is different from the normal ligand

variable domain

each light chain has a _______ ______ where most of the variability in amino acid sequence is found to create the antigen binding region

protease trypsin

enzyme that cleaves off myosin's fibrous tail, dividing it into light and heavy meromyosin

sarcoplasmic reticulum

flat membranous vesicles that surround each microfibril

2 ferric sequestering

free heme molecules leave ___ coordination bonds of the iron atom open which can result in irreversible conversion to its ______ state. This is prevented in globins by _______ the heme deep into the protein

hydroxyl radicals sequester

free iron promotes the formation of destructive _______ _______ and therefore is bound in forms that _________ it

monomeric neuroglobin

globin largely expressed in neurons and helps protect the brain against hypoxia and ischemia

tetrameric hemoglobin

globin responsible for oxygen transport in the blood stream

monomeric myoglobin

globin that facilitates oxygen diffusion into muscle tissues

cellular immune system

immune system that destroys host cells infected by viruses also destroys some parasites and foreign tissues

humoral immune system

immune system that is directed at bacterial infections, extracellular viruses, and some foreign proteins - found in the body fluids

D E

immunoglobulin ___ and ___ are similar in structure to immunoglobulin G

E

immunoglobulin ___ plays an important role in the allergic response - binds to mast cells at Fc and when foreign body also binds, mast cells secrete histamine

A

immunoglobulin ____ is typically found secretions such as saliva, tears, and milk. can be monomer, dimer, or trimer.

M

immunoglobulin ____ occurs either in a monomeric, membrane bound form, or a secreted form that is a cross linked pentamer - first antibody to be made by B cells

cellular respiration

in addition to carrying oxygen, red blood cells also carry the products of _______ _______ (H+ and CO2) to the lungs and kidney to be excreted

ferrous

iron in its _______ state: Fe2+

ferric

iron in its _______ state: Fe3+

F actin

long polymer of actin made by many G actin molecules

thin filament

made up of F actin along with the proteins troponin and tropomyosin

immunoglobin G

major class of antibody molecule composed of two heavy polypeptide chains and two light polypeptide chains. - heavy chains interact together and then branch off into the two light chains

G actin

monomeric actin

hemocytoblasts

precursor stem cells that form erythrocytes (red blood cells) - produces daughter cells that form large amounts of hemoglobin and then lose their organelles

helper T cells

produce soluble signaling proteins (cytokines). Interact with macrophages - stimulates the proliferation of Tc and B cells that can bind to a particular antigen

papain

protease that cleaves immunoglobulin G at its hinges to give Fc and Fab

papain

protease that cleaves myosin subfragment 1 (S1 or globular domain) from heavy meromyosin leaving sub fragment 2

actin

protein that makes up the thin filaments of muscle - also important for the cytoskeleton in many eukaryotic cells

flexing

rapid molecular _______ in myoglobin amino acid side chains produces cavities for oxygen to enter and leave

Fc

receptors on a macrophage bind to the ___ portion of IgG and when this receptor binds an antibody-pathogen complex the macrophage engulfs the complex by phagocytosis

I band

region of the bundle that would only contain thin filaments in a cross section - lighter

thick filaments

rodlike structure of myosin aggregating that form the core of the contractile unit. - associate to form a long bipolar structure

immunoglobulin fold

the constant domains in immunoglobulin G have a characteristic structure known as the ___________ _____ - a well conserved structural motif in the al beta class of proteins - three in each heavy chain and one in each light chain

Fc

the heavy chains that are cleaved from immunoglobulin G and readily crystalized

6 4 2

the iron atom has ____ coordination bonds to heme, ___ to nitrogen atoms that are part of the flat ring system, and ___ that are perpendicular to the porphyrin ring

oxygen

the last open coordination bond in iron is the binding site for ______

catalytic active

the ligand-binding site of an enzyme is called a ______ or _____ site

s1 fragment

the motor domain of myosin that makes muscle contraction possible - also called myosin head group - can be crystalized

clonal selection

the process of helper T cells stimulating the proliferation of Tc and B cells that bind to a particular antigen

Z disc

the thin actin filaments are attached at one end of the __ ____ in a regular pattern by these proteins: actinic, design, vimentin, nebulin

true

true/ false: a protein can have multiple binding sites for different ligands

cytotoxic T cells

uses T cell receptors to recognize and bind extracellular ligands triggering changes in the cell

less

when [L] < Kd, ______ than half of the binding sites are occupies

half

when [L] = Kd, _____ the binding sites are occupied

distal histidine

when heme is bound to myoglobin, its affinity for O2 is selectively increased by the presence of _______ _____ (His64) - partial negatives in oxygens reactive with positive histidine side chain

deoxygenated insoluble aggregate

when hemoglobin from sickle cells is ___________, it becomes _________ and forms polymers that _________ into tubular fibers

greater

when the concentration of a ligand is much _______ than that of ligand binding sites, [L] stays constant