MCAT > Biochem Chapter 3 > Flashcards

Biochem Chapter 3 Flashcards

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1
Q

What do structural proteins do

A

Give cell shape and provide support
Cytoskeleton, anchor proteins

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2
Q

Where are structural proteins found

A

All throughout extracellular matrix

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3
Q

5 main structural proteins

A

Collagen
Elastin
Keratin
Actin
Tubulin

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4
Q

Describe collagen, what its like

What it do

A

Trihelical fibres
Most of extracellular matrix of connective tissue is made of this

Provides strength and flexibility

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5
Q

Describe elastin

Where they found

A

Extracellular matrix of connective tissue

Stretch, recoil like spring and restore original tissue shape

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6
Q

Describe keratin

  • where they found
  • what type of filament
A

Intermediate filament proteins found in epithelial cells

Hair and nails

Regulatory proteins that help with mechanical integrity as well as

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7
Q

What is actin

  • what does it make up
A

Protein that makes up microfilaments
And thin filaments in myofibrils

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8
Q

What is tubulin

  • what it make
  • what it do
A

Make microtubules

Structure, chromosome separation

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9
Q

What are motor proteins for

How do they do what they need to do

A

Movement within cell
Conformational changes occur through ATP ‘s help for them to work, act as ATPase

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10
Q

Most common motor proteins

A

Myosin

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11
Q

What is myosin, what it do and what does it interact with

A

Interacts with actin for muscle contractions

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12
Q

What do kinesin do at 2 phases of cell cycle

A

Align choromosomes during metaphase

Depolymerize microtbules during anaphase of mitosis

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13
Q

What are motor proteins (3)

A

Myosin
Kinesin
Dyenins

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14
Q

What do Dyneins do

A

Sliding movement of cilia and flagella which help cell move

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15
Q

What are some binding proteins

A

Hemoglobin, calcium binding proteins, DNa binding proteins etc

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16
Q

What are binding proteins
- what are the 2 possible things they can do
- what do they not do

A

They bind to specific target an they either hold on to it or help regulate its concentration

DO NOT MODIFY THE MOLECULES THOUGH

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17
Q

What are cell adhesion molecules (CAM)

A

They allow cells to bind to other cells or surfaces

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18
Q

What are the 3 types of cell adhesion molecules (CAM)

A

Cadherins
Integrins
Selectins

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19
Q

What are cadherins
What they do
What they dependant on

A

Calcium dependant glycoproteins

Help cells stick to other similar cells

Stay organized and intact

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20
Q

Where are usually cadherins found

A

Linings of organ and skin

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21
Q

What are integrins

  • what do its two ends attach to
  • what it do (2)
A

One end sticks out of cell to attach to proteins in extracellular matrix, outside of cell for structure

Other end attaches to inside of cell

  • anchors cell in place
  • sense signals from surroundings and respond , so they know when they move or stay or grow
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22
Q

What do selectins do

  • are they stronger or weaker than cadherins and integrins
    = what they do (2)
A

Allow cels to adhere to carbohydrates on surfaces of other cells

Weaker and temporary interactions

Help immune cells slow down and move to affected tissue

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23
Q

Another word for antibodies

What shape are they

What type of cell are they

A

Immunoglobulin Ig

Y shaped

White blood cell

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24
Q

What are antibodies or immunoglobulin used. By immune system for

A

Target specific antigen , which can be protein on surfaces of the pathogen or a toxin

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25
What do immunoglobulin do Opsonizationa and agglutination meaning What’s the other solution
Opsonization is marking it for destruction by other cells Agglutination is digested by macrophages Another solution is to just neutralize the antigen so the toxic effects aren’t able to present
26
What are the 2 regions of immunoglobulin Which one doles antigen binding
Constant region Variable region - variable region does antigen binding
27
What does variable region and constant region do in antigens
Variable region would be antigen binding Constant region is recruitment and binding of cells with macrophages
28
Are motor proteins enzymes
Yes
29
What is biosignalling
Process where cells relieve and act on signals
30
Waht are ion channels
Type of biosignalling class Ion channels are proteins that create specific pathways for charged molecules, facilitated diffusion
31
What are the 3 types of ion channels
Ungated channels Voltage gated channels Ligand gated channels
32
What are ungated channels Give an example
They have no gates so are unregulated Potassium
33
What are voltage gated channels Give example
They are regulated by membrane potential change near the channel Sodium potassium channels Depolarization and repolarizaiton
34
What are ligand gated channels Give an example
Open and close based on binding to specific substances or ligands Neurotransmitter, hormone are ligands
35
What are the two things biosignalling takes advantage of
Ion. Channels Second messenger cascades
36
What are teh 2 types of second messenger cascades
Enzyme linked receptors G protein coupled receptors
37
3 parts of a enzyme linked receptor The 3 domains
Membrane spanning domain: anchors receptor in cell membrane Ligand binding domain: signalling molecule binds here Catalytic domain: activated and carried out enzymatic function inside cell
38
What are G protein coupled receptors
Integral membrane proteins that do signal transduction
39
What do G protein coupled receptors use to transmit signal to effector in the cell
Heterotrimeric G protein
40
The 3 main types of G proteins (Brief )
1. Gs : stimulated adenylate Cyclase, which increases levels of cAMP in cell 2. Gi: inhibits adenlyate cyclase, which decreases levels of cAMP in the cell 3. Gq: activates phospholipase C
41
What does Gq do in G proteins Go in depth
activates phospholipase C . which cleaves phospholipid from membrane to make PIP2. PIP2 is cleaved into DAG and IP3. IP3 then opens calcium channels in ER so calcium levels in cell increase
42
All G proteins are made of 3 things
Alpha Beta Gamma
43
Inactive alpha subunit is always bound to what in G proteins
GDP
44
How does alpha subunit separate form beta and gamma subunit What does it do after separate? Give an example
When it is an active G protein, it binds to GDP. It become activated and converts into GTP. Then It separates from beta and gamma subunits It then separates to either activate or inhibit target enzyme. Like of adenylate cyclase for example.
45
Difference between enzyme linked receptors and G protein coupled receptors - which domains - what type of complex - how it disassociates
Enzyme linked Auto activity Enzymatic activity G protein - two protein complex - dissociation upon activation - trimer Same : - extracellular domain Transmembrane domain Ligand binding
46
How does transport kinetics differ from enzyme kinetics What’s the same
They both have Km and Vmax values They can also be cooperative There are no catalysts for transport so they don’t have analogous Keq values for reactions
47
Protein isolation can be done through what
Electrophoresis
48
How does electrophoresis work
Uses gel matrix to see migration of proteins in response to an electric field Migration towards opposite charge
49
How do you calculate migration velocity in electrophoresis
V = Ez/f Velocity= electric field strength x net charge of molecule / frictional coefficient
50
What’s the most common gel in electrophoresis How does it work , like why this material Which things move faster through it
Polyacrylamide gel Kind of acts like a sieve, smaller particles pass through faster because porous Small ones faster with greater charge
51
3 types of electrophoresis
Native PAGE SDS page Isoelectric focusing
52
What does native page electrophoresis do Like why s it good and whys it bad
Good - maintains protein shape Bad - results hard to compare because mass-to-charge ratio differs for each protein
53
What does SDS page electrophoresis do , how does it work Like why s it good and whys it bad
Denatures protein and masks the native charge so the comparison of the sizes is better Functional protein can’t be recaptured from the gel though Purely separated by size
54
Waht does isoelectric focusing electrophoresis do Like why it good or worse
Separates proteins based on their isoelectric points, which is the pH at which the protein has no charge Proteins will keep migrating until their pH equal to their pI. Then it’ll stop moving .
55
Is isoelectric focusing electrophoresis , where o positively and negatively charged proteins go
Post - cathode Nega - anode
56
For a native page, SDS page, isoelectric focusing , what do they each give us in terms of info
Native page - study function SDs- compare sizes ISO - identify pi of proteini
57
How does chromatography work
Identify compounds by separating them If more similar to surroundings, it will move more slowly
58
What are two phases of chromatography
Stationary - polar solid Mobile phase - liquid or gas that carries sample through it
59
Compound with ______ affinity for stationary phase, Its retardation factor would be ________ Take _______ to pass through
Higher Lower Longer
60
Compounds get separated by chromatography what is this called
Partitioning
61
What material in thin layer and paper chromatography
Thin layer - silical gel or alumina that attached to a plate Paper - medium is paper made of cellulose
62
Stationary phase and mobile phase for thin layer and paper chromatography
Polar is stationary Non polar is mobile phase
63
RF value how to calculate - chromatography
Distance spot moved/ distance solvent front moved
64
What is column chromatography What is used What is stationary and mobile phase
Filled with silica or aluminum beads Stiaionary - the beads Mobile - non polar
65
3 types of column chromatography
Ion exchange chromatography Size exclusion chromatography Affinity chromatography
66
How does ion exchange chromatography work
Beads with coated charge bind to opposite charged molecules
67
How does size exclusion chromatography work
Beads have small pores to trap small compounds, larger compounds travel faster
68
How does affinity chromatography work
High affinity for a compound in the stuff inside , coating the beads with a receptor or antibody, so only your protein of interest will stick to column . Then you use special solution to get out thing you needed.
69
What can be used to determine protein stucrture in protein analysis (2)
X ray crystallography and NMR
70
If you want to know which amino acid is present and how much what can you do
Amino acid composition can be figured out by simple hydrolysis
71
Amino acid sequencing requires what
Seqetntial degradation Edman degradation
72
What does EDman degradation do How long do the amino acids have to be
Selectively and sequentially removes N terminal amino acid of the protein 50-70
73
Activity levels o enzymatic samples are determined by what
Process of a known reaction, usually with colour change
74
Protein concentration is determined how - bad way - better way
Colour change By UV or colour change reaction - better way in spectroscopy
75
Protein concentration most common methods , what assays is most common
Bradford assay
76
How deos Bradford assay work
Brilliant blue is a dye . When it binds to certain amino acids groups, loses protons and shifts to blue form. More dye binds with more protein concentration, more deeper blue .
77
How can Bradford assay limited (2) What they do
Detergents Higher concentration of buffer Interfere with its ability to ion with amino acids groups
78
Which 3 assays work on figuring our protein concentration
Bradford protein assay BCA assay Lowry reagent assay
79
When is Bradford dye not as accurate , as in in terms of number of amino acids groups
If there is more than one protein, then dye will bind differently and not as accurate
80
First step of protein analysis is
Protein isolation
81
Edman degradation proceeds from which terminus
N
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