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Flashcards in proteins Deck (25):
1

structural proteins

collagen
elastin
keratin
actin
tubulin

2

motor proteins

myosin
kinesin
dynein
muscle contraction, vesicle movement within cell, and cell motility

3

cell adhesion molecules

proteins found on the surface of most cells
aid in binding for the cell to extracellular matrix or other cells
all integral membrane proteins
cadherins, integrins, and selectins

4

cadherins

glycoproteins
mediate calcium-dependent cell adhesion
hold similar cell types together, epithelial cells

5

integrins

group of proteins that have 2 membrane-spanning chains, alpha and beta
bind and communicate with extracellular matrix
important in cell signaling and host defense

6

selectins

bind to carbohydrate molecules that project from other cell surfaces
weakest bonds formed by CAMs
expressed on white blood cells and endothelial cells that line blood vessels
role in host defense, inflammation and white blood cell migration

7

antibodies

proteins produced by B-cells
neutralize targets in body, such as toxins and bacteria
recruit other cells to help eliminate the threat
Y-shaped protein w/ antigen binding region at the tip of the Y

8

outcome of antibodies binding antigens

1. neutralize the antigen, making pathogen tuna able to exert its effects on the body
2. marking pathogen for destruction by other WBC immediately, called opsonization
3. clumping together (agglutinating) the antigen and antibody into large insoluble protein complex that is phagocytize and digested by macrophages

9

electrophoresis

method for separating proteins
subjects compounds to an electric field, which moves them according to their net charge and size
negative migrate toward +anode
positive migrate toward -cathode
small move faster

10

polyacrylamide gel

PAGE
standard medium for protein electrophoresis
slightly porous matrix mixture

11

Native PAGE

method for analyzing proteins in their native states
limited by the varying mass-to-charge and mass-to-size ratios bc proteins may experience same level of migration
most useful to compare the molecular size or the charge of proteins of similar size

12

SDS-PAGE

sodium dodecyl sulfate (SDS)
separates proteins on the basis of mass alone
proteins move through gel only affected by frictional coefficient which depends on mass alone

13

sodium dodecyl sulfate (SDS)

detergent that disrupts all nonequivalent interactions
in electrophoresis it binds to proteins and creates large chains with net negative charges, neutralizing the proteins original charge and denaturing it

14

isoelectric focusing

separates proteins on a basis of isoelectric point, where the protein is electrically neutral
proteins placed in gel with a pH gradient, acidic at +anode, basic at -cathode
electric field is generated across the gel
positive proteins migrate toward cathode and negative proteins migrate toward the anode
when protein reaches portion of gel with pH=pI it stops migrating

15

chromatography

uses physical and chemical properties to separate and identify compounds from a complex mixture
isolated proteins are immediately available for identification and quantification
*the more similar the compound is to its surroundings, the more it will stick to and move slowly through them
preferred over electrophoresis when large amounts of protein are being separated

16

column chromatography

column is filled with polar silica or alumina beads as stationary phase
gravity moves the solvent and compounds down the column
size and polarity have role in how quickly a compound moves
less polar compound moves faster
can be used to collect proteins and other macromolecules, such as nucleic acids

17

ion-exchange chromatography

beads in the column are coated with charged substances
they attract or bind compounds that have opposite charges
positively charged column will attract and hold negatively charged proteins

18

size-exclusion chromatography

beads in column contain tiny pores of varying sizes
small compounds enter the beads, slowing them down
large compounds can't fit in pores so they elute faster
*different bc small compounds are retained longer (opposite)

19

affinity chromatography

customize column to bind any protein of interest, creating a column with high affinity for that protein
beads are coated with a receptor that binds the protein and it is then retained in the column
protein can then be eluted by washing column with a free receptor

20

structure analysis

x-ray crystallography
nuclear magnetic resonance (NMR) spectroscopy
determine protein structure

21

x-ray crystallography

most reliable and common method
measures electron density on a high resolution scale
x-ray diffraction pattern is generated in this method which can be interpreted to determine the proteins structure

22

Edman degradation

analyzes small proteins
uses cleavage to sequence proteins of 50-70 amino acids
selectively and sequentially removes the N-terminal amino acid of the protein which is visualized via mass spec

23

activity analysis

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

24

UV spectroscopy

determines concentration
used bc proteins contain aromatic side chains
sensitive to sample contaminants

25

Bradford Protein Assay

mixes a protein in solution with Coomassie Brilliant Blue dye
when protonated it is brown-green color
the dye is deprotonated by the protein and turns blue
samples of known protein conc. are reacted with Bradford reagent and absorbance is measured to create standard curve
unknown conc. is exposed to same conditions and conc. is determined based on standard curve