Chapter 3-Nonenzymstic Protein Function

Question 1

What are examples of structural proteins in the human body?

Answer 1

Collagen, elastin, keratin, actin, tubulin

Question 2

What are examples of motor proteins in the human body? 

Answer 2

Myosin, cilia, flagella of bacteria and sper, kinesics, Dyneins

Question 3

What are examples of binding proteins?

Answer 3

Hemoglobin, calcium binding proteins, DNA binding proteins

Question 4

What are the three families of CAM’s cell adhesion molecules?

Answer 4

Cadherins (glycoproteins) mediate calcium dependent cell adhesion
Integrins contain alpha and beta membrane spanning chains (bind and communicate with the extracellular matrix
Selectins bind to carbohydrate molecules that project from other cell surfaces

Question 5

Name one type of immunoglobulins?

Answer 5

Antibodies

Question 6

What are the three possible outcomes when a antibody is bound to an antigen?

Answer 6

Neutralization: the antibody neutralizes the antigen making the pathogen or toxin unable to exert its effects on the body

Opsonization: Marking the pathogen for destruction by other white blood cells is called

Agglutination: The antigen and antibody club together into large insoluble protein complexes that can be digested by macrophages

Question 7

What is biosignaling?

Answer 7

The process in which cells receive and act on signals

Question 8

Ion channels

Passive or active?
Up or down concentration gradient?
What molecules utilize ion channels?

Answer 8

Passive
Down concentration gradient
Large charged or polar molecules

Question 9

What are the three types of ion channels?

Answer 9

Ungated
Voltage gated
Ligand gated

Question 10

Ungated ion channel

Answer 10

Having no gates, therefore unregulated.

Question 11

Voltage gated channels

Answer 11

Gate is regulated by the membrane potential charge near the channel

membrane depolarization causes a protein confirmational change that allows them to quickly open and then close of the voltage increases

Question 12

Ligand gated channels

Answer 12

The binding of a specific substance or leg into the channel causes it to open and close

Ex. Neurotransmitters

Question 13

Enzyme linked receptors

Answer 13

Contain three primary protein domains:
membrane spanning domain: that anchors the receptor in the cell membrane,
ligand binding domain: which is stimulated by the appropriate like deuces and confirmational change that activates the
catalytic domain: Often results in the initiation of a second messenger cascade

Question 14

G Protein Coupled Receptor

Answer 14

Large family of integral membrane proteins

involved in signal transduction

they contain seven membrane spanning alpha helices.

Question 15

Electrophoresis separates proteins based on what?

Answer 15

Subjects compounds to electric field moves them according to their charge and size

Negative to positively charged anode
Positive to negatively charged cathode

Smaller particles pass easily and large molecules migrate slower or not at all

Electrically neutral molecules migrate slower

Question 16

Native Page separates compounds on what characteristic

Answer 16

Analyzes proteins in their native state

Compares the molecular size or charge of proteins known to be similar in size from using other analytic methods like SDS page

One useful aspects of native page is that you can recover the compound as long as you don’t use stain and stain denatures proteins

Question 17

SDS Page separates compounds based on what characteristic?

Answer 17

Separates compounds on relative molecular size alone

The detergent SDSD disrupts all non-covalent interactions and binds to proteins and create large chains with negative net charges thereby neutralizing the proteins original charge and denaturing the proteins

Question 18

Isoelsctric Focusing deprecated proteins based on what characteristic

Answer 18

The pI of the amino acid

Mixture of proteins placed in a gel with a pH gradient (acidic gel at the positive anode basic gel at the negative cathode neutral in the middle)

Positively charged proteins migrate towards the negatively charged cathode

negatively charged proteins migrate towards the positively charged anode.

When the protein reaches the portion of the gel where the pH=pI the protein takes on a neutral charge and stops moving.


Question 19

Chromatography separate compounds based on what property?

Answer 19

Polarity

Components that have a high affinity for the stationary phase will hardly move while those having a high affinity for the mobile phase will migrate much more quickly.

Question 20

Column chromatography separates compounds based on

Answer 20

Size and Polarity

Smaller/less polar move faster

Question 21

Ion exchange chromatography differs from other forms of chromatography in the following ways.

Answer 21

beads coated c charged substances so they attract or bind compounds that have opposite charge.

Question 22

Size exclusion chromatography differs from other forms of chromatography in what ways?

Answer 22

The beads in the columns contain tiny pores of varying sizes. Tiny compounds get stuck while larger compounds are elites first.

Question 23

Affinity chromatography differs from other forms of chromatography in what ways?

Answer 23

Beads are coated with a receptor that binds of the protein/antibody causing the protein to be retained in the column.

Protein is eluted by washing the column with free receptor

Question 24

What ways can you determine protein structure?

Answer 24

X-ray crystallography, nuclear magnetic resonance spectroscopy (NMR)

X-ray crystallography more popular and reliable (small dots in diffraction pattern interpreted to determine the proteins structure.

Question 25

What process best analyzes small proteins?

Answer 25

Edman degradation uses cleavage to sequence 50-70 amino acids. Removes n terminal of amino acids in a protein then analyzed by mass spec

Question 26

What process best analyzes larger proteins?

Answer 26

Digestion c chymotrypsin, trypsin and cyanogen bromide

Cleaves at specific amino acid residues creating smaller fragments that can be analyzed c electrophoresis/edman degradation

Question 27

What ways can you determine protein concentration?

Answer 27

Colorimetrilly

By UV spectroscopy or through a color change reaction.

Question 28

What is one way you can determine activity levels for enzymatic samples?

Answer 28

Color change

Question 29

Three specific reactions that utilize colorimetric changes to determine protein concentration

Answer 29

BCA assay: bichorionic acid assay
Lowry reagent assay, Bradford protein assay

Branford is the most common because of its reliability and simplicity

Question 30

General details of the Bradford Protein Assay

Answer 30

Proteins mixed with a blue dye. Dye is protonated and starts off green/brown. Turns blue in the process of binding to amino acids. In the process the dye gives up proteins

Increased protein concentration=darker blue color