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Biochemistry > Chapter 3: Nonenzymatic Protein Function / Protein Analysis > Flashcards

Chapter 3: Nonenzymatic Protein Function / Protein Analysis Flashcards

1
Q

List the 5 primary structural proteins:

A

collagen, elastin, keratins, actin, and tubulin

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2
Q

Collagen

A

has a characteristic trihelical fiber

makes up most of the extracellular matrix of connective tissue

found throughout the body and provides STRENGTH AND FLEXIBILITY

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3
Q

Elastin

A

one of the primary structures of protein in the body

important component of the extracellular matrix of connective tissue

for STRETCH AND RECOIL to restore original shape of the tissue

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4
Q

Keratin

A

one of the primary structures of protein in the body

intermediate filament proteins found in epithelial cells

contribute to mechanical integrity of the call and also function as regulatory proteins

primary protein that makes up HAIR AND NAILS

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5
Q

Actin

A

makes up ** microfilaments** and **THIN FILAMENTS **in myofibrils

have ** polarity ** to allow motor proteins to travel unidirectionally along an actin filament

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6
Q

what is the most abundant protein in eukaryotic cells?

A

actin

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7
Q

Tubulin

A

makes up microtubules

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8
Q

3 microtubule functions

A

provide structure, chromosome separation in mitosis and meiosis, intracellular transport with kinesin and dynein

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9
Q

Motor proteins

A

responsible for muscle contraction and cellular movement (cilia / flagell)

may display enzymatic activity such as ATPases (power conformational change for motor function)

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10
Q

list 3 common motor proteins

A

myosin
kinesin
dynein

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11
Q

Myosin

A
  • primary motor protein that interacts with actin (thick filament in myofibril)
  • can be involved in cellular transport
  • each subunit has a single head and neck
  • movement at the neck is responsible for the power stroke of sarcomere contraction
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12
Q

Kinesins and dyneins

A

the motor proteins associated with microtubules

they have two heads; at least one remains attached to tubulin at all times

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13
Q

Kinesin moves towards..

A

the positive end of the microtubule / the outer membrane

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14
Q

Dyneins move toward

A

the negative end of the microtubule / toward the nucleus

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15
Q

Binding proteins

A

acts as an agent to bind two or more molecules together

??

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16
Q

Cell Adhesion Molecules (CAMs)

A

Allow cells to bind to other cells or surfaces

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17
Q

3 categories of cell adhesion molecules

A

cadherins
integrin
selectins

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18
Q

Cadherins

A

calcium dependent glycoproteins that hold similar cells together

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19
Q

Integrin

A

ADHERE A CELL TO A PROTEIN

play important role in cell signaling

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20
Q

Selectins

A

ADHERE A CELL TO A CARB

most commonly used in the immune system

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21
Q

Immunoglobulins (antibodies)

A

neutralize targets in the body, such as toxins and bacteria, and then recruit other cells to help eliminate the threat

Y-shaped proteins made up of 2 identical heavy chains and 2 identical light chains

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22
Q

Antigen binding region

A

a region on the tips of the Y with specific polypeptide sequences that will bind ONE and only one specific antigenic sequence

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23
Q

Antigen constant region

A

the part of the antigen that is NOT the binding region

involved in recruitment of other immune system cells (ex. macrophages)

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24
Q

What are the 3 possible outcomes once an antibody binds to its target antigen?

A
  • neutralize the antigen
    • makes the pathogen unable to exert its effect on the body
  • marks the pathogen for destruction by other white blood cells immediately (opsinization)
  • agglutinate (clump together) the antigen and antibody into large insoluble protein complexes that can be phagocytized and digested by macrophages
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25
Q

Biosignalling

A

process in which cells receive and act on signals

26
Q

Ion channels

A

transmembrane proteins that provide a pathway for ions to enter the cell

facilitated diffusion of molecules down a concentration gradient

27
Q

3 main groups of ion channels

A

ungated
voltage gated
ligand-gated

28
Q

Ungated ion channels

A

ion channels that are always open

29
Q

Voltage-gated channels

A

open or close based on membrane potential charge near the channel

30
Q

Ligand-gated Channels

A

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

ex. neurotransmitters bind to post-synaptic channels (ex. GABA opens chloride channels)

31
Q

Enzyme-linked receptors

A

membrane receptors that also display catalytic activity in response to ligand binding

often participate in cell signaling through initiation of second messenger cascades

32
Q

3 primary protein domains of enzyme-linked receptors

A

membrane-spanning domain
ligand-binding domain
catalytic domain

33
Q

Membrane-spanning domain of enzyme-linked receptors

A

anchors the receptor in the cell membrane

34
Q

Ligand-binding domain of enzyme-linked receptors

A

stimulated by the appropriate ligand and induces a conformational change that activates the catalytic domain

35
Q

Catalytic domain of enzyme-linked receptors

A

activates cellular enzymes; initiates second messenger cascade

36
Q

One of the most common enzyme-linked (catalytic) receptors

A

receptor tyrosine kinases (RTKs)

composed of a monomer that dimerizes upon ligand binding

the dimer is the active form that phosphorylates additional cellular enzymes (included the receptor itself)

37
Q

G protein-coupled receptors (GPCRs)

A

large family of integral membrane proteins involved in signal transduction

7 transmembrane alpha-helices

interact with heterotrimeric G proteins to transmit signals to effector cells

ligand binding increases affinity of the receptor for the G protein

binding of G protein switches to active state and affects intercellular signalling pathway

38
Q

3 main types of G proteins:

A

Gs - stimulates adenylate cyclase which i_ncreases levels of cAMP_ in the cell

Gi - inhibits adenylate cyclase which decreases levels of cAMP in the cell

Gq - activates phospholipase C which cleaves a phospholipid from the membrane to form PIP2; PIP2 is cleaved to DAG and IP3; IP3 opens calcium channels in the ER to increase calcium levels in the cell

39
Q

G protein structure

A

3 subunits: alpha, beta, and gamma

inactive form: alpha subunit binds GDP and is in a complex with beta and gamma subunits

active form: …

40
Q

G protein activation:

A
  • inactive form: alpha subunit binds GDP and is in a complex with B and Y subunits
  • when ligand binds to GPCR, receptor becomes activated and engages the G protein
  • GDP on G protein is replaced with GTP
  • alpha subunit dissociate from B and Y subunits
  • activated alpha subunit alters activity of adenylate cyclase (As vs Ai)
  • Once GTP on A subunit is dephosphorylated to GDP, A subunit will bind to B and Y subunits, rendering the G protein inactive again
41
Q

How are proteins isolated from body tissues / cell cultures?

A

Cell lysis followed by homogenization

42
Q

Homogenization

A

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

43
Q

Centrifugation

A
44
Q

Electrophoresis

A

subjects compounds to an electric field, which moves them according to their net charge and size

45
Q

Electrophoresis

A

uses a gel matrix to observe the migration of proteins in response to an electric field

(proteins move according to their net charge and size)

46
Q

Equation relating electrophoresis factors

A

v = Ez/f

  • v = velocity of molecule
  • E = electric field strength
  • z = net charge of molecule
  • f = frictional coefficient
47
Q

What is a standard medium for protein electrophoresis?

A

polyacrylamide gel

48
Q

Native PAGE

A

polyacrylamide gel electrophoresis (PAGE) a method for analyzing proteins in their native states

maintains the proteins shape

results are difficult to compare because the mass-to-charge and mass-to-size ratios differ for each cellular protein

the functional native protein may be recovered from the gel, but only if the gel has not been stained (most stains denature proteins)

most useful for: compare analytic methods like SDS-PAGE or size-exclusion chromatography

49
Q

SDS Page

A

sodium dodecyl sulfate (SDS) PAGE

SDS denatures the proteins and masks the native charge

allows for comparison of size alone

the functional protein cannot be recaptured from the gel

50
Q

Isoelectric Focusing

A

separates proteins by their isoelectric point (pI)

the protein migrates toward and electrode until it reaches a region of the gel where pH = pI of the protein

recall: PI = pH at which the protein is electrically neutral (zwitterion)

acidic gel @ positive anode; basic gel @ negative cathode

51
Q

Chromatography

A

separates protein mixtures on the basis of their affinity for a stationary phase or a mobile phase

the more similar the compound is to its surroundings (polarity, charge, etc.) the more it will stick to its surroundings (slower movement)

preferred over electrophoresis when large amounts of protein are being separated

52
Q

Column Chromatography

A

uses beads of a polar compound, like silica or alumina (stationary phase) with a non polar solvent (mobile phase)

the less polar a compound, the faster it will elute down the column through the stationary phase

53
Q

Ion-exchange chromatography

A

the beads in the column are coated with charged substances, so they attract or bind compounds with opposite charge

uses a charged column and a variably saline eluent

54
Q

Size-exclusion chromatography

A

the beads in the column contain tiny pores of varying sizes, which allows small compounds to enter the beads (slowing them down)

large compounds can’t fit into the pores, so they travel around the beads and through the column faster

55
Q

Affinity chromatography

A

the columns can be customized to have high affinity for a specific protein of interest

ex. coating beads with receptors that bind the proteins (the protein is retained in the column)

56
Q

How is protein structure determined?

A

primarily by X-ray crystallography: after the protein is isolated and crystallized; measures electron density on an very high resolution scale; can also be used for nucleic acids

Nuclear magnetic resonance (NMR) spectroscopy may also be used

57
Q

How is amino acid composition determined?

A

complete protein hydrolysis and subsequent chromatographic analysis

BUT amino acid sequencing requires sequential degradation, such as the Edman degradation (sequentially removes the N-terminal amino acid of the protein)

58
Q

How is protein activity analyzed?

A

protein activity is generally determined by monitoring a known reaction with a given concentration of substrate and comparing it to a standard

reactions with a colour change have a particular applicability because microarrays can rapidly identify the samples from a chromatographic analysis that contains the compound of interest

59
Q

How is protein concentration determined?

A

colorimetrically, either by UV spectroscopy (b/c proteins contain aromatic side chains) or through a colour change reaction (BCA assay, Lowry reagent assay, Bradford protein assay)

60
Q

Bradford protein assay

A

mixes a protein in solution w/ a dye that is protonated and green-brown prior to mixing

the dye turns blue as it gives up protons to the amino acid groups

increased protein concentrations = larger concentration of blue dye in solution

(samples with known concentrations are first used to create and absorbance standard curve)

Biochemistry (16 decks)

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