Chapter 3: Non enzymatic Protein Function and Protein Analysis

Question 1

Structural proteins.

Answer 1

Cytoskeleton can be thought of as three-dimensional web or scaffolding system for the cell. It is comprised of proteins that are anchored to the cell membrane by embedded protein complexes. In addition to intracellular support, extracellular matrices composed of proteins also support the tissue of the body.

Question 2

Motif.

Answer 2

A repetitive organization of secondary structural elements together.

Question 3

Collagen.

Answer 3

Has a characteristic trihelical fiber and makes up most of the extracellular matrix of connective tissue. It provides strength and flexibility.

Question 4

Elastin

Answer 4

It’s another important component of the extracellular matrix of connective tissue. Its primary role is to stretch and then recoil like a spring.

Question 5

Actin

Answer 5

Protein that makes up microfilaments in the thin filaments in myofibrils. It is the most abundant protein in eukaryotic cells. Acting proteins have a positive side and a negative side; This polarity allows motor proteins to travel unidirectionally along an actin filament.

Question 5

Keratins

Answer 5

Intermediate filament proteins found in epithelial cells. They are the primary proteins that make up hair and nails.

Question 6

Motor Proteins.

Answer 6

The more time cilia and flagella, bacteria and sperm are prime examples as the contraction of the sarcomere muscle. Motor proteins also display enzymatic activity, acting as ATPases that power the conformational change necessary for motor function. Myosin Is the primary motor protein that interacts with actin, It can be involved in solar transport. Kinesins and dyneins The motor proteins associated with microtubules. Kinesins has a role in aligning for museums during metaphase and deep polymerizing microtubules during anaphase of mitosis. Dyneins Is involved in the sliding movement of cilia and flagella.

Question 7

Tubulin

Answer 7

Protein that makes up the microtubules. Used in mitosis and meiosis. Tubulin has polarity. The negative end of a microtubule is usually located at next to the nucleus, whereas the positive end is usually in the periphery of the cell.

Question 8

Cell adhesion molecules (CAMs)

Answer 8

Are proteins found on the surface of most cells and aid in binding the cell to extracellular matrix or other cells. The three types are cadherins, integrins, and selectins.

Question 9

Cadherins

Answer 9

Group of glycoproteins that mediate calcium dependent cell adhesion. Austin holds similar cell types together, such as a epithelial cells.

Question 10

Selectins

Answer 10

Unique because they bind to carbohydrate molecules that project from other cell surfaces. They are expressed on white blood cells and the endothelial cells that line blood vessels.

Question 10

Integrins.

Answer 10

Group of proteins. They all have two membrane spanning chains called alpha and beta. They have an important role in cellular signaling.

Question 11

Ion channels.

Answer 11

Proteins that create a pathways for charged molecules. They are facilitated diffusion of charged particles. Facilitated diffusion is a type of passive transport and diffusion of molecules down a concentration gradient through foreign a membrane created by this transmembrane protein. They have three types and can be ungated, voltage gated and ligand gated.

Question 11

Ligand gated channels

Answer 11

The binding of a specific substrate or ligand to the channel causes it to open or close.

Question 12

Antibodies.

Answer 12

They are also called immunoglobulins, and they are proteins produced by B cells that function to neutralize target in the body such as toxins and bacteria, and then recruit other cells to help eliminate the threat. They have two identical heavy chains and two identical light chains. These two five languages in non covalent interactions holding heavy and light chains together. Antigen biting region at the tips of the “Y”. Antibodies bind to their targets, which are called antigens, and they can use one of three outcomes:

1)Neutralize the antigen, making the pathogen or toxin unable to exert its effect.

2) Marking the pathogen for destruction by other white blood cells. This is called opsonization.

3) Clumping together called agglutinating the antigen and antibody into large insoluble protein complexes.

Question 13

Voltage gated channels.

Answer 13

The gate is regulated by the membrane potential change near the channel. These channels are closed under resting conditions, but membrane depolarization causes the protein confirmation change that allows them to quickly open and quickly close as the voltage increases.

Question 14

Ungated channels

Answer 14

They have no gates and are therefore unregulated. This means there will be a net influx of potassium ions through these channels, unless potassium is the equilibrium.

Question 15

G protein coupled receptors (GPCR)

Answer 15

They are a large family of integral membrane proteins involved in signal transduction. They are characterized by their seven membrane spanning alpha helices. In order for this to transmit signals to an effector in the cell, they utilize a heterotrimeric G protein. G proteins are named for their intracellular linked to guanine nucleotides (GDP and GTP). The binding of the G protein represents a switch to the active state and effects the intracellular signaling pathway. Gs Stimulates. Gi Inhibits. Gq Activates phospholipase C, Which increases calcium levels in the cell.

Question 15

Enzyme-linked receptors.

Answer 15

Membrane receptors may also display catalytic activity in response to ligand binding. These enzyme-linked receptors have three primary protein domains: a membrane spanning domain which anchors the receptor into the cell membrane; a ligand-binding domain, which is stimulated by the appropriate ligand and induces a conformational change that activates the catalytic domain. This is often the initiation of a second messenger cascade.

Question 15

Biosignaling.

Answer 15

Can take advantage of either existing ingredients, (ion channels) or second messenger cascades, (enzyme linked receptors, and G protein coupled receptors). Biosignaling is a process in which cells received and act on signals.

Question 16

Centrifugation

Answer 16

Can isolate proteins from which smaller molecules before other isolation techniques must be employed.

Question 17

Homogenization.

Answer 17

Crushing, riding, or blending the tissue of interest into a evenly mixed solution.

Question 18

Electrophoresis.

Answer 18

Subjecting compounds to an electric field which moves them according to their net charge and size. Negatively charged compounds will migrate towards the positively charged anode. And positively charged compounds will migrate towards the negatively charged cathode. Migration velocity (v) of a molecule is directly proportional to the electric field strength (E) and the net charge (z) on the molecule and is inversely proportional to the frictional coefficient (f).

V =Ez / f

Question 19

Polyacrylamide gel.

Answer 19

Standard medium for protein electrophoresis. Proteins travel through this matrix in relation to their size and charge. Allowing smaller particles to pass through easily while retaining large particles. A molecule will move faster through the medium if it is small, highly charged, or placed in a large electric field. It will migrate slower when they are bigger and more convoluted, electrically neutral are placed in small electric field.

Question 19

Polyacrylamide gel electrophoresis (PAGE)

Answer 19

It is limited by varying mass to charge and mass to size ratios of cellular proteins because multiple different proteins may experience the same level of migration. The functional native protein can be recovered from the gel after electrophoresis. It is most useful to compare the molecular size of the charge of proteins known to be similar in size.

Question 20

SDS-PAGE

Answer 20

Sodium dodecyl sulfate (SDS) It’s useful to separate proteins on the basis of relative molecular mass alone. Add detergent that disrupts all non covalent interactions, thereby neutralizing the proteins original charge and denaturing the protein. As the protein moves to the gel, the only variable affecting the velocity is the electric field force and the frictional coefficient, which depends on mass.

Question 21

Isoelectric focusing.

Answer 21

It exploits the acidic and basic properties of amino acids by separating on the basis of isoelectric point. The mixture of protein is placed in a gel with a pH gradient. An electric field is then generated across the gel. Proteins that are positively charged will begin migrating towards the cathode and proteins that are negatively charged will begin migrating towards the anode. As a protein reaches the portion of the gel where the pH is equal to the proteins Pi, the protein takes on a neutral charge and will stop moving.

Question 21

Proteins Atomic mass is typically expressed in ____

Answer 21

Daltons (Da), 1Da = 1 g/ mol

Question 22

Chromatography.

Answer 22

is about the affinity of a substance for the mobile and stationary phases except for size exclusion chromatography. The solid medium is called the stationary phase or adsorbent. We run the mobile phase through the stationary phase. This will allow the sample to run through the stationary phase or elute. Components have a higher affinity for the stationary phase will barely migrate at all. Components with a high affinity for the mobile phase will migrate much more quickly. The amount of time a compound spends in the stationary phase is referred to as retention time.

Question 23

Protein Analysis.

Answer 23

Protein structure is primarily determined through X-ray crystallography after the poaching is isolated, although NMR can also be used. Amino acid composition can be determined by simple hydrolysis, but amino acid sequencing requires a sequential degradation such as the Edman degradation. Activity levels were enzymatic. Samples are determined by following the process of a known reaction, often accompanied by a color change. Protein concentration is also determined colorimetrically, either by UV spectroscopy or through a color change reaction like the Bradford protein assay.