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MCAT ALL > Non-Enzymatic Protein Function and Protein Analysis > Flashcards

Non-Enzymatic Protein Function and Protein Analysis Flashcards

1
Q

Structural Proteins

A
  • Function: Stabilize and protect the integrity of the cell; compose the cytoskeleton, anchoring proteins and extracellular matrix
  • Examples:primary structural proteins in the body are collagen, elastin, keratin, actin, and tubulin
  • Properties: Fibrous proteins; Repetitive secondary structure and super-secondary structure
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2
Q

Collagen (structure, location, and function)

A

Structure: trihelical fiber (three alpha helices woven together to form a secondary helix)

Location: makes most of the extracellular matrix of connective tissue

Function: strength & flexibility`

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3
Q

Elastin ( location, and function)

A

Location: makes most of the extracellular matrix of connective tissue.

Function: stretches an recoils like a spring, restores original shape of the tissue

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4
Q

Keratin (structure, location, and function)

A

Intermediate filament proteins found in epithelial cells

Function: mechanical integrity of the cell and regulatory protein

Location: primary protein that makes up hair and nails

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5
Q

Actin (structure, location, and function)

A

Most abundant protein in eukaryotic cells

Structure: it has a positive and negative side so can travel unidirectionally

Location: It makes up thin filaments and microfilaments in myofibrils

Function: polarity allows motor proteins to travel
unidirectionally.

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6
Q

Tubulin

A

Make up microtubules

-provide structure, chromosome seperation and intracellular transport with kinesin and dynein

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7
Q

Motor Proteins

A
  • Definition: Proteins capable of force generation through conformational change
  • Function: Serve in muscle contraction, cellular trafficking and cell motility
  • Examples:Myosin, kinesin and dynein
  • Properties: contain one or more heads for force generation’ have catalytic ability to break down ATP for force generation (ATPase)
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8
Q

Motor porteins also display ____ activity

A

enzymatic activity

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9
Q

When motor proteins display enzymatic activity, they act as ____

A

They act as ATPases, that power the conformational change for motor function

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10
Q

Motor proteins have transient interactions with either ____ (a) or ____ (b)

A

(a) actin

(b) microtubules

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11
Q

Primary Motor Proteins

A
  • Myosin
  • Kinesins
  • Dyneins
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12
Q

Myosin

A
  • Primary motor protein that interacts with actin
  • It is the thick filament in myofibril
  • It also plays a role in cellular transport
  • Each myosin subunit has a single head and neck: movement at the neck powers sarcomere contraction
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13
Q

Kinesins and Dyneins

A
  • Motor proteins associated with microtubules
  • Have two heads, one remains attached to tubulin at all times
  • Polarity: kinesins (move towards positive end of microtubule) and dyneins (move towards negative end of microtubule)
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14
Q

Key roles of Kinesins and Dyneins

A

Key roles:

  • Alignment of chromosomes during metaphase
  • Depolymerization of microtubules during anaphase
  • Sliding movement of cilia and flagella
  • Vesicle transport in the cell (opposite polarities
  • Kinesins bring vesicles of neurotransmitters to the synaptic terminal (positive end of axonal microtubules)
  • Dyneins bring vesicles of waste or recycled neurotransmitter back toward the soma (negative end of microtubule)
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15
Q

Binding proteins ___ (a) or ___ (b) molecules by binding to them

A

(a) transport

(b) sequester

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16
Q

Examples of Binding Proteins

A
  • Hemoglobin
  • Calcium-binding proteins
  • DNA-binding proteins (often transcription factors)
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17
Q

Cell Adhesion Molecules (CAMs)

A

Proteins found in the surface of most cells

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18
Q

CAMs function

A

Bind cells to matrix or other cells

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19
Q

All CAMs are ___ proteins

A

Integral membrane proteins

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20
Q

Three major families of CAMs

A
  • Cadherins
  • Integrins
  • Selectins
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21
Q

Cadherins

A
  • Glycoproteins
  • Mediate calcium-dependent cell adhesion
  • Hold SIMILAR cell types together (e.g. epithelial cells)
  • Different cells have type-specific cadherins
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22
Q

Integrins

A
  • Group of proteins.
  • All have two membrane spanning chains (alpha and beta)
  • Chains are important for binding and communicating to the extracellular matrix.
  • Cellular signaling (promote cell division,apoptosis and other processes)
  • Host defense
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23
Q

Selectins

A
  • Bind to carbohydrate molecules that project from cell surfaces (weakest bonds formed by CAMs)
  • Expressed on white blood cells and endothelial cells (line blood vessels)
  • Host defense
24
Q

Immunoglobulins

A
  • Y-shaped proteins produced by B-cells

Key roles:

  • Neutralize targets (toxins and bacteria)
  • Recruit other cells (such as macrophages) to eliminate the threat.
25
Q

Structure of immunoglobulins

A
  • Y-shaped proteins
  • Two identical heavy chains and two identical light chains
  • Disulfide linkages and noncovalent interactions hold them together)
  • Antibody binding region at the tips of the Y (sequence specific) the binds antigen
  • Constant region, rest of the antibody.
26
Q

Possible outcomes of antibodies binding to antigen

A
  • Neutralization of antigen
  • Marking the pathogen or Opsonization for destruction by white blood cell
  • Clumping together or agglutinating into large insoluble protein complexes that can be phagocytized and digested by macrophages.
27
Q

Protein act in biosignaling by acting as:

A
  • extracellular ligands
  • transporters (for facilitated diffusion)
  • receptor proteins
  • second messengers
28
Q

Three main types of ion channels

A
  • Ungated
  • Voltage-gated
  • Ligand-gated
29
Q

Ion channels permit ____ diffusion of charged particles

A

Facilitated diffusion-A type of passive transport in which a molecule is transported down a concentration gradient through a pore in the membrane created by a transmembrane protein.

30
Q

Ungated Ion Channels

A
  • They are unregulated, always open

- Example: ungated K+ channels. There will be a net efflux of K ions through these channels unless K+ is at equilibrium

31
Q

Voltage-Gated channels

A
  • Regulated by membrane potential change near the channel

Examples:

  • Voltage-gated Na+ channels in neurons. Closed at resting conditions. Depolarization opens them, which close again very quickly as voltage increases.
  • K+/Na+ voltage-gated channels in cells of the sinoatrial node of the heart. Serve as the pacemaker current
  • lower voltage= channels open
32
Q

Ligand-Gated Channels

A
  • Binding of a specific substance or ligand opens/closes the channel.
  • Km and Vmax parameters also apply to transporters such as ion channels.
  • They do not have Km values because there is no catalysis

Example:
Neurotransmitter GABA binds to chloride channel at the postsynaptic membrane and opens it.

33
Q

Enzyme-linked receptors

A
  • Membrane receptors that display catalytic activity in response to ligand binding
  • participates in cell signaling through extra-cellular ligand binding and initiating a 2nd messenger
34
Q

Structure of enzyme-linked receptors

A

Three primary protein domains:

1) membrane-spanning domain (anchors receptor to in the cell membrane
2) ligand-binding domain
3) catalytic domain

35
Q

Initiation of a second messenger cascade

A

ligand-binding domain is stimulated by the appropriate ligand and induces a conformational change that activates the catalytic domain.

36
Q

Examples of enzyme-linked receptors are:

A
  • Receptor tyrosine kinases
  • Serine/threonine specific protein kinases
  • Receptor tyrosine phosphatases
37
Q

G protein-coupled receptors

A
  • Large family of integral membrane proteins
  • Involved in signal transduction
  • Have 7 membrane-spanning alpha helices
  • Differ in specificity of the ligand-binding area located on the extracellular surface of the cell.
  • They utilize heterotrimeric G protein
  • Binding of a ligand increases affinity of the receptor for the G protein.
  • Binding of the G protein represents a switch to the active state and affects the intracellular signaling pathway
38
Q

G protein

A
  • They have an intracellular link to guanine nucleotides (GPD and GTP)
  • It has 3 subunits: alpha, beta, and gamma
39
Q

In the G proteins inactive form:

A

The alpha subunit binds GDP and is in a complex with beta and gamma subunits.

40
Q

Trimeric G protein cycle

A

(1) inactive α subunit of G protein binds GDP and forms complex with β and γ subunits.
(2) inactive α subunit protein binds GTP then it dissociates from β and γ subunits
(3) activated α subunit alters the activity of adenyl cyclase*
(4) Once GTP in activated α subunit is dephosphorylated to GDP, it will rebind to the β and γ subunits, rendering the G protein inactive

  • as will activate the enzyme, a1 will inhibit the adenyl cyclase
41
Q

Gs _____ (a) adenylate cyclase, which _____ (b) cAMP levels in the cell

A

(a) stimulates

(b) increases

42
Q

G1 _____ (a) adenylate cyclase, which _____ (b) cAMP levels in the cell

A

a) inhibits

(b) decreases

43
Q

Gq _____ (a) phospholipase C, which _____ (b) calcium channels in the ER, _____ (c) calcium levels in the cell

A

(a) activates
(b) opens
(c) increasing

44
Q

homogenization

A

crushing, grinding or blending the tissue of interest into an evenly mixed solution

45
Q

centrifugation

A

isolation of proteins from much smaller molecules before other isolation techniques are employed

46
Q

Polyacrylamide gel

A

the standard medium for protein Electrophoresis; pourous matrix that solidifies at room temperature and acts like a sieve allowing smaller particles to move faster through medium

47
Q

PAGE (Polyacrylamide gel electrophoresis)

A

analysis of proteins in native states - limited by varying charge:mass and size:mass ratios but allows native protein recovery
-maintains protein shape (non-denaturing)

48
Q

SDS-PAGE (sodium dodecyl Sulfate)

A

separates proteins on mass alone by denaturing + forming negative charge on all; followed by staining to make protein bands visual

49
Q

Isoelectric focusing

A

separates on the basis of PI point by migrating proteins through gel with pH gradient; protein stops moving when reaches point where pH = pI and the protein is neutral

50
Q

Mnemonic for isoelectric focusing: A+

A

Anode has acid (H+ rich) gel and a (+) charge.

51
Q

Chromatography

A

fractionation of a homogenized mixture through a porous matrix - the more similar the compound is to the matrix, the slower it will move through

52
Q

Column chromatography

A

used for other macromolecules besides just proteins - column of alumina/silica beads as adsorbent and gravity moves compounds and solvent down at vary speeds based on polarity and size

53
Q

ion exchange chromatography

A

beads in column coated w/ charged substances - attract or bind substances w/ different charge. then a salt gradient is used to elute remaining charged particles that stuck

54
Q

size exclusion chromatography

A

beads in column contain pores of different sizes. small compounds go through pores slowly, large do not fit and elute quickly. used after ion exchange.

55
Q

affinity chromatography

A

coat beads w/ specific receptor of protein of interest to bind it. can be difficult to remove particle of interest from receptor then though.

56
Q

What are the most prevalent extra cellular proteins?

A

Keratin, elastin and collagen

57
Q

What receptor types use second messengers

A

Enzyme linked receptor and G protein coupled receptor

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