Nonenzymatic Protein Function And Protein Analysis - Ch. 3

Question 1

Collagen

Answer 1

Structural protein - characteristic trihelical fiber makes up most of the extracellular matrix of connective tissue. Deficiency causes brittle bone disease

Question 2

Elastin

Answer 2

Structural protein - another component of extracellular matrix of connective tissue; it stretches and recoils like a spring

Question 3

Keratins

Answer 3

Structural protein - intermediate filament proteins found in epithelial cells
Contribute to mechanical integrity of cell and function as regulatory proteins (hair and nails)

Question 4

Actin

Answer 4

Structural protein - protein that makes up microfilaments and thin filaments in myofibrils.
Most abundant protein in eukaryotic cells
Positive side and negative side polarity allows motor proteins to travel unidirectional along an actin filament

Question 5

Tubulin

Answer 5

Structural protein- makes up microtubules important for providing structure, chromosomal separation in mitosis and meiosis and intercellular transport of kinesin and dynein

Question 6

Motor proteins

Answer 6

Some interact with structural proteins
Display enzymatic activity acting as ATPases that power conformational change
Transient interactions with either actin or microtubules

Question 7

Myosin

Answer 7

Motor protein - primary one that interacts with actin

Thick filament in myofibril and involved in cellular transport sometimes

Question 8

Kinesins and dyneins

Answer 8

Motor proteins- associated with microtubules
They have two heads, one of which is attached to tubulin at all times
Kinesins - role in aligning chromosomes during metaphase and depolymerizing microtubules during anaphase of mitosis - move vesicles to positive end of cell
Dyneins - involved in the sliding movement of cilia and flagella- move vesicles to negative end of cell

Question 9

Binding proteins

Answer 9

Stabilizing functions in individual cells and body
Include hemoglobin, calcium-binding proteins, DNA-binding proteins
Has affinity for its molecule of interest

Question 10

Cell Adhesion molecules

Answer 10

CAMs

Found on surface of most cells and aid in binding the cell to the extracellular matrix of other cells

Question 11

Cadherins

Answer 11

Family of CAMs
Group of glycoproteins that mediate calcium-dependent cell adhesion
Often hold similar cell types together
Different cells - different types of cadherins

Question 12

Integrins

Answer 12

Family of CAMs
Group of proteins that have two membrane spanning chains called alpha and beta important for binding to and communicating with extracellular matrix
Promote cell division, apoptosis and other processes

Question 13

Selectins

Answer 13

Family of CAMs
Group of proteins that bind to carb molecules that project from other cell surfaces
Weaker bonds formed by CAMs than cadherins and integrins
Expressed on WBCs and endothelial cells that line blood vessels
Important in host defense

Question 14

Immunoglobulins

Answer 14

Also called antibodies or immunoglobulins (Ig)
Most prominent type of protein found in immune system
Produced by B cells target threats and recruit cells to help
Y-shaped made of two identical heavy chains and two identical light chains held together by disulfide linkages and noncovalent interactions

Question 15

Antigen binding region

Answer 15

Area of Ig (immunoglobulins or antibodies) in which there is a specific polypeptide sequence that will bind only one specific antigenic sequence

Question 16

Possible outcomes of immunoglobulins binding with antigens

Answer 16

• Neutralizing antigen
• Marking pathogen for destruction (called opsonization)
• clumping together (agglutinating) the antigen so it can be phagocytized

Question 17

Biosignaling

Answer 17

Process by which cells receive and act on signals

Question 18

Ion channels

Answer 18

Proteins that create specific pathways for charged molecules

Question 19

Facilitated diffusion

Answer 19

Ion channels

A type of passive transport - diffusion of molecules down a concentration gradient through a pier in the membrane

Question 20

Ungated ion channel

Answer 20

Unregulated; example potassium channels.

Question 21

Voltage-gate ion channels

Answer 21

Regulated by membrane potential change near channel
Membrane depolarization can cause conformation change to make them quickly open and quickly close again (sinoatrial node in heart is example - pacemaker)

Question 22

Ligand-gated ion channels

Answer 22

Binding of specific substance or ligand to channel causes it to open or close

Question 23

Enzyme-linked receptors

Answer 23

Catalytic activity in response to ligand binding

Three primary protein domains: membrane-spanning domain, catalytic domain, and ligand-binding domain

Question 24

Membrane-spanning domain

Answer 24

Enzyme linked receptor that anchors the receptor in the cell membrane

Question 25

Ligand-binding domain

Answer 25

Enzyme linked receptor that is stimulated by the appropriate ligand and induces a conformational change that activates the catalytic domain

Question 26

G-Protein Coupled Receptors

Answer 26

GPCR

Large family of integral membrane proteins involved in signal transduction

Question 27

G-Proteins

Answer 27

Named for intercellular link to guanine nucleotides (GDP and GTP)
Three main types: Gs which stimulates adenylate cyclase increases levels of cAMP in cell
Gi inhibits and decreases levels of cAMP
Gq activates phospholipase C

Question 28

Subunit of G protein

Answer 28

Alpha binds GDP and in in complex with beta and gamma subunits

Question 29

Protein isolation

Answer 29

Means of separating protein of interest for study
Isolated by cell lysis and homogenization - the act of crushing, grinding, or blending the tissue of interest into an evenly mixed solution.
Centrifugation - then isolates proteins from smaller molecules

Question 30

Electrophoresis

Answer 30

Electric field with positively charged anode end which attracts anions and negatively charged cathode end attracts cations
Polyacrylamide gel is the standard medium

Question 31

Migration velocity equation

Answer 31

In electrophoresis, migration velocity (v) of molecule is equal to electric field strength (E) times net charge on molecule (z) both over frictional coefficient (f) which depends on mass and shape

Question 32

Native PAGE

Answer 32

Polyacrylamide gel electrophoresis - analyzation of proteins in their native states
Drawbacks: limited by varying mass-to-charge and mass-to-size ratios of cellular protein

Question 33

SDS-PAGE

Answer 33

Sodium dodecyl sulfate polyacrylamide gel electrophoresis- separates proteins on the basis of mass alone. Starts with PAGE but adds SDS, a detergent that disrupts all noncovalent interactions
Denatures protein
The only variables affecting velocity are E and f

Question 34

Isoelectric focusing

Answer 34

Electrophoresis separating proteins based on their isoelectric point (pI) - pH at which it is electrically neutral
Based on acidic and basic properties - placed in gel with pH gradient acidic on positive anode and basic gel at negative cathode, neutral in middle.
Movement towards what it needs will cause the pH to equal the pI and the protein to stop migrating.

Question 35

Chromatography

Answer 35

The more similar a compound is to its surroundings (by polarity, charge etc) the more it will stick to and move slowly through them
First sample onto solid medium called stationary phase or adsorbent
Then run motile phase through stationary phase allowing it to elute - affinity for this phase results in fast migration

Question 36

Retention time

Answer 36

Amount of time substance spends in stationary phase in chromatography

Question 37

Partitioning

Answer 37

Separation of components in stationary phase

Question 38

Column chromatography

Answer 38

Column filled with silica or alumina beads as adsorbent
Gravity moves solvent and compounds down the column
Polarity and size effect how fast. The less polar the faster it will move.
Salinity can easily be changed to help elute protein of interest

Question 39

Ion-exchange chromatography

Answer 39

Beads in silica and alumina in column are coated with charged substances so they attract and bind substances of opposite charge

Question 40

Size-exclusion chromatography

Answer 40

Beads in column contain tiny pores and keep small compounds and allow bigger ones to elute

Question 41

Affinity chromatography

Answer 41

Customized columns with high affinity for a particular protein by coating beads with receptor that binds that protein or specific antibody for that protein
Protein is retained

Question 42

X Ray crystallography

Answer 42

Isolated and crystallized protein beforehand
Most reliable and common
Diffraction pattern of small dots can be interpreted to determine protein’s structure

Question 43

NMR Spectroscopy

Answer 43

Nuclear magnetic resonance - accounts for 25% of structural determination

Question 44

Edman degradation

Answer 44

Uses cleavage to sequence proteins of up to 50 to 70 amino acids. Selectively and sequentially removes the n-terminus amino acid of the protein

Question 45

UV Spectroscopy

Answer 45

Proteins have aromatic side chains and can be analyzed with this without treatment. But this is sensitive to contamination.

Question 46

Bradford protein assay

Answer 46

Mixes a protein in solution with Coomassie brilliant blue dye
Protonated, dye is brown-green