Proteins

Question 1

Biologically significant proteins

Collagen

Answer 1

A structural protein that provides elastic strength.
Remember that it is a critical component of the extracellular matrix.

Can be found in connective tissues like dermis and cartilage.

Question 2

Biologically significant proteins

Actin

Answer 2

A structural protein that forms microfilaments. Plays a key role in muscle cells.

Question 3

Biologically significant proteins

Tubulin

Answer 3

A structural protein that helps form microtubules. Play a key role in mitosis as they form spindle fibers.

Question 4

Biologically significant proteins

Kinesin and Dynein

Answer 4

These are motor proteins that slide along microtubules.

Kinesin goes away (anterograde) from the nucleus while dynein goes toward (retrograde) the nucleus (think dynein toward)

Question 5

Biologically significant proteins

Myosin

Answer 5

A motor protein that plays a key role in muscle contraction.

Question 6

Three main mechanisms of biological signaling:

Answer 6

1) Altering channel permeability of ion channels
2) Using the second messenger system (ie GPCR)
3) Changes in gene expression

Question 7

Signaling

Endocrine versus paracrine

Answer 7

Endocrine messengers are delivered by bloodstream while paracrine signals act locally between cells.

Question 8

Signaling

Second messenger systems

Answer 8

Two-step process
1) First messenger: initial interaction between a receptor and ligand.

2) Second messenger: downstream effect that is triggered by the initial receptor-ligand-binding.
Common example: GPCR

Question 9

Signaling

Ligand-gated ion channels

Answer 9

Channels that let ions through and change their permeability in response to a signaling molecule such as a neurotransmitter.

Question 10

Classes of proteins

Structural proteins

Answer 10

Fibrous proteins that provide structure and strength to cytoskeleton, extracellular matrix, etc.
Examples: collagen, actin, tubulin

Question 11

Classes of proteins

Motor proteins

Answer 11

Proteins that generate force and motion, generally through the conformation change of a head.
Examples: myosin, kinesin, dynein

Question 12

Classes of proteins

Cell adhesion molecules

Answer 12

Proteins that bind things together.
Examples: cadherins, integrins, selectins.

Question 13

Protein electrophoresis

Answer 13

Proteins are run through an electric field in a gel matrix to separate them based on size or charge.
Note: proteins can also be separated by other properties using chromatography techniques.

Question 14

Protein electrophoresis

Native PAGE

Answer 14

Electrophoresis technique that maintains shape of protein but is limited due to the effect of charge.

Question 15

Protein electrophoresis

SDS-PAGE

Answer 15

Electrophoresis technique that denatures proteins using SDS.

More accurately separates proteins by size because this removes the confounding factor of charge.

Note that after SDS-PAGE, the proteins are no longer usable.

Question 16

Protein electrophoresis

Isoelectric focusing

Answer 16

Proteins are placed between an acidic (+ charge) anode and a basic (- charge) cathode.

They then migrate and separate based on their isoelectric point.

Utilizes the amphoteric nature of amino acids.

Question 17

Protein laboratory techniques

Isolating or purifying a protein

Answer 17

Use chromatography or electrophoresis.

Question 18

Protein laboratory techniques

Determining sequence

Answer 18

Use Edman degradation

Question 19

Protein laboratory techniques

Determining structure

Answer 19

Use crystallography

Question 20

Protein laboratory techniques

Determining concentrations

Answer 20

Use colorimetric techniques such as Bradford protein assay.
Western blot can also be used with comparison to a reference protein.

Question 21

Protein laboratory techniques

Determining absorbance

Answer 21

Use Beer’s law to calculate absorbance
Absorbance = ε C L
ε = extinction coefficient, C = concentration, L = path length

Question 22

G-protein coupled receptor signaling

Answer 22

GPCRs are located on the cell membrane.
Special receptors are associated with G-proteins, which relay extracellular signals inside the cell through a second messenger system.

Question 23

Five steps of G-protein coupled receptor signaling

Answer 23

Step 1
The G-protein coupled receptor binds to its corresponding ligand and induces a conformational change. The ligand is the first messenger.

Step 2
The alpha subunit gets activated as GDP is swapped with GTP (active form).

Step 3
The active subunit comes off and initiates the second reaction, the conversion of ATP to cAMP by adenylyl cyclase .

Step 4
The “second messenger”, commonly cAMP, triggers downstream effect inside the cell.

Step 5
GTP gets hydrolyzed back to GDP and subunit then rejoins the receptor to get ready to go again.

Question 24

Cell adhesion molecules

Cadherin

Answer 24

A cell adhesion molecule that adheres cells together and are dependent on calcium.
Mnemonic: Cadherin = “Ca” + “Adhering”

Question 25

Cell adhesion molecules

Integrins

Answer 25

Cell adhesion molecules that bind to the extracellular matrix.

Question 26

Cell adhesion molecules

Selectins

Answer 26

Cell adhesion molecules that play a role in immune function.

Question 27

Binding affinity

Equilibrium dissociation constant (Kd)

Answer 27

Can be used as a measure of binding affinity, where lower values of Kd indicate greater binding affinity.

Question 28

Binding affinity

Cooperative binding

Answer 28

Ligand binding induces a conformational change in one subunit of a protein, that increases or decreases binding affinity in other subunits.

Classic example: the binding of one oxygen molecule to hemoglobin increases its affinity for other oxygen molecules.

Question 29

Binding affinity

Positive cooperativity

Answer 29

Results in a sigmoidal-shaped binding curve.