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BCHM463 > Material for Exam #1 > Flashcards

Material for Exam #1 Flashcards

1
Q

What are the 3 fundamental principals of biochemistry according to Dr. Capp?

A

1) Equilibrium is everything
2) Structure determines function
3) Nothing is wasted

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2
Q

What is the ΔG equation for a system at standard conditions, and at non-standard conditions?

A

Standard Conditions: ΔG^0 = -RTln(Keq)

Non-Standard Conditions: ΔG = ΔG^0 + RTln(Q)

Q = [products]/[reactants] not at equilibrium

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3
Q

What is the ΔG for ATP going to ADP + Pi

A

ΔG = -30.5 KJ/mol

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4
Q

What are the 5 types of bonds?

A 
Covalent Bonds
Ionic Bonds
Hydrogen Bonds
Dipole-Dipole Interactions
London Dispersion Forces
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5
Q

What are the 2 terms for a molecule with both polar and non-polar components?

A

Amphiphillic/Amphipathic

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6
Q

What is a micelle?

A

A shape formed by amphipathic molecules where the non-polar heads aggregate together away from the polar solvent and the polar ends are facing the solvent (like a cell membrane)

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7
Q

What are the two definitions for an acid?

A

Donates an H+ - Bronstead-Lowry definition

Accepts an electron pair - Lewis definition

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8
Q

What are the two definitions for a base?

A

Accepts an H+ - Bronstead-Lowry definition

Donates an electron pair - Lewis definition

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9
Q

What pH conditions lead to a buffering effect, and in what pH range?

A

When the pH = pKa, there is a buffering effect +/- 1 pH value

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10
Q

What is the pH of blood?

A

pH = 7.4

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11
Q

What is the pKa combo for bicarbonate?

A

pKa = 6.35

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12
Q

What is the pKa of the amino group on an amino acid?

A

pKa = 9.5

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13
Q

What is the pKa of the carboxyl on an amino acid?

A

pKa = 2.2

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14
Q

What is the stereoisomer for all amino acids?

A

“L” stereoisomer

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15
Q

What are the small, non-polar amino acids?

A

GAVIL

glycine, alanine, valine, isoleucine, leucine

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16
Q

What are the weird, non-polar amino acids?

A

MP

methionine, proline

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17
Q

What are the large, non-polar amino acids?

A

TTP

tryptophan, tyrosine, phenylalanine

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18
Q

What are the alcohol and thiol amino acids?

A

STC

serine, threonine, cystine

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19
Q

What are the polar and acidic amino acids?

A

AAGG

aspartic acid, asparagine, glutamic acid, glutamine

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20
Q

What are the base and buffer amino acids?

A

HAL

histidine, arginine, lysine

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21
Q

How many amino acids are generally in a protein?

A

Generally, there are between 100 and 1,000 amino acids in a protein

22
Q

What part of an amino acid is flexible?

A

The alpha carbon is flexible

23
Q

What are 3 examples of secondary structure? What forces are responsible for secondary structure?

A

Alpha helices
Beta sheets
Loops

H-bonding between the amine and carboxyl groups in the backbone are responsible for secondary structure

24
Q

What kind of turn is in an alpha helix, how many amino acids per turn, is the C or N on top, and where do the side chains point?

A

An alpha helix has the C on top and is a right handed turn with 3.6 amino acids per turn and side chains pointing down and out from the helix

25
Q

Where are the H-bonds in a beta sheet, what are two types of ways a beta sheet can be organized, and where do the R groups point?

A

The H-bonds in a beta sheet form between the rows, it can be parallel or anti-parallel, and the R groups are normal to the surface of the sheet

26
Q

What are two kinds of loops and what are their internal structures like? Where do loops usually show up on a protein?

A

Turns: internal H-bonds made up of 3-5 amino acids

Random Coil: very long loop, around 20 amino acids, and have no internal structure

Loops tend to show up on the outside of a protein

27
Q

What are two examples of super secondary structure?

A

Coiled-Coil: 2 alpha helices wrapped around each other

Helix-Turn-Helix: two alpha helices joined by a turn

28
Q

How can the tertiary structure of a protein be characterized?

A

Alpha, beta, or alpha beta depending on the presence of alpha helices or beta sheets

29
Q

What 3 types of interactions seal tertiary structure?

A

1) Salt bridges (amino acid side chains with stable charges forming ionic bonds)
2) Disulfide Bonds (proteins to be exported from cell)
3) Metal ions (stable cations like Zn+2 or Ca+2)

30
Q

What are 3 ways of destroying tertiary structure?

A

1) Changing temperature
2) Changing pH
3) Overcoming the hydrophobic effect (done by detergents which are amphipathic, or chaotropic agents which disrupt water and H-bonding)

31
Q

What are the general steps in the protein folding model?

A 
Random coil
Nucleation
Hydrophobic Collapse
Molten Globule
Native Protein
32
Q

When protein folding goes wrong, the clumps are called _____ and when they are outside of a cell they are called _____ which are long _____.

A

The clumps are called amaloyd fibers and when they are outside of the cell, they are called amaloyd plaques which are long beta sheets

33
Q

Where does a small ligand bind to a protein?

A

The protein’s binding pocket

34
Q

What are 4 things a bound ligand can do?

A

1) Cause a conformational change
2) Catalyze a reaction
3) Regulate protein function
4) Do nothing (just hold the ligand)

35
Q

What are the units of Kd, and what do high and low Kd values mean?

A

Kd is measured in “molar” and a low Kd means good binding (high protein affinity for ligand)

36
Q

What is Y (and Fo) and what are 2 equations for it?

A

Y and Fo are fraction occupancy, meaning the fraction of protein bound to ligand.

Y = [P:L] / [P] + [P:L]
Y = [L] / Kd+[L]
37
Q

When is [L] = Kd?

A

[L] = Kd at 50% occupancy

38
Q

What are two ways of visualizing protein structure and roughly, how do they work?

A

X-ray crystallography: electron clouds interact with x-rays and must be in crystal form which might not be regular structure

NMR (nuclear magnetic resonance): the way an atom responds to a magnetic field is effected by the atoms around it and this has hard math so best for small proteins

39
Q

What kind of cooperativity does hemoglobin display?

A

Hemoglobin displays positive cooperativity

40
Q

What are the two states hemoglobin, and which one lets hemoglobin have oxygen bound to it and which one does not? What part of hemoglobin moves to change states?

A

R (relaxed state) - oxygen can bind

T (taught state) -oxygen cannot bind (stabilized by pH dependent salt bridges)

The movement of residues at the alpha-beta interfaces account for these changes

41
Q

What doe the Bohr effect say about hemoglobin’s oxygen affinity? How does this translate to oxygen loading and unloading in the body?

A

Hemoglobin’s affinity for oxygen increases as pH increases. This means it has a higher affinity in basic conditions.

In the capillaries of the body, the pH is acidic so oxygen is unloaded. In the lungs, the pH is more basic so it causes oxygen to bind to hemoglobin.

42
Q

What are the two models of allosterism, and how are they different?

A

Symmetry model: the allosteric protein has R and T states that are always in equilibrium and a ligand can bind to either one. R and T subunits are never there at the same time

Sequential model: a ligand binds to the allosteric protein which causes a conformational change in that subunit as well as the other subunits

43
Q

What are antibodies made up of?

A

4 polypeptide chains: 2 heavy chains and 2 light chains with 2 identical binding sites

44
Q

How does SDS page work?

A

SDS denatures proteins and makes them negative so they can be separated just by molecular weight (not charge or shape)

The polyacrylamide gel is a medium that has little holes that helps sort the proteins

45
Q

What is the best stain to use for gels?

A

Coomassie Blue

46
Q

How does a western blot work and what does it show?

A

A western blot separates proteins in a gel using SDS-PAGE and then proteins are transferred from the gel to nitrocellulose. The nitrocellulose is then incubated with a primary antibody and then a secondary antibody (that is linked to a detection mechanism). It very specifically shows your protein.

47
Q

What are the two ways you can express a protein, and what are some benefits and drawbacks of these methods?

A

Endogenous expression: express in the protein’s native environment (likely get stable protein and my discover related proteins, may see any post translational modifications, not that much protein)

Exogenous expression: use another organism to harvest protein (usually get a lot of protein and perhaps avoid interfering proteins)

48
Q

What are some methods to quantify a protein?

A

Absorbance at 280nm (tyrosine and tryptophan)

Bradford assay with coomasie blue (red and positive with no protein, blue and negative with protein and then absorbance at 600 nm)

Activity assay

SDS-PAGE followed by coomassie blue staining

SDS-PAGE followed by western blot (identifies presence of protein in impure samples)

49
Q

What are the three general protein isolation methods?

A

1) Salting out (ammonium sulfate)
2) Chromatography
3) Density gradient centrifugation

50
Q

What are the 4 types of chromatography?

A

Ion exchange chromatography (cation and anion sticking or not sticking to column)

Hydrophobic interaction chromatography (load with low salt and elute with high salt)

Affinity chromatography (relies on protein-ligan interaction)

Gel filtration chromatography (separates based on size)

BCHM463 (3 decks)

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