Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Dr. Ford Review > Comprehensive Review > Flashcards

Comprehensive Review Flashcards

1
Q

What are the 4 Noncovalent Interactions?

A

Hydrogen Bonding- Protein Secondary Structure, Nucleotide Base Pairing

Ionic Bonds (Charge-Charge Interacting)- Salt Bridges

Van Der Waals- Nucleotide Stacking

Dipole-Dipole (Partial Charge)- Selectivity Filter of the K+ Channel

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What does it mean if:
pH < pKa
pH > pKa
pH=pKa

A

pH < pKa Protonated
pH > pKa -> Deprotonated
pH=pKa -> Just as likely to be protonated or deprotonated

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What is Ka?

A

A dissociation constant that predicts how likely an acid is going to donate its proton.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What are weak acids used as?

A

Buffers

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What happens when something is reduced? oxidized?

A

Reduced species gain an electron

Oxidized species have lost electrons

OIL RIG

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What amino acid is important during redox reactions.

A

Cysteine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What are the 3 important electron carriers in cellular metabolism? (Give the oxidized and reduced versions)

A

Oxidized:
NAD+
FAD
FMN

Reduced:
NADH
FADH2
FMNH2

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What kinds of reactions are NADPH used for?

What kinds of reactions are FAD/FMN used for?

A

NADPH- Anabolic reactions and is becoming oxidized

FAD/FMN- Catabolic reactions and is becoming reduced

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What is the definition of equilibrium?

A

Forward and reverse rates are equal. No net formation or destruction.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

How does Le Chatlier fit into cellular metabolism?

A

It drives an unfavorable pathway by using up the products. It is used as an equilibrium way to drive rxns.

Can also drive an unfavorable pathway by coupling it with ATP hydrolysis.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What is the thermodynamics equation?

A

∆G=∆H-T∆S

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What does a negative ∆S mean?
What does a positive ∆S mean?

What does a negative ∆G mean?
What does a positive ∆G mean?

What does a negative ∆H mean?
What does a positive ∆H mean?

A

Negative ∆S- Disorder decreases
Positive ∆S- Disorder increases

Negative ∆G- Free energy is released; Exergonic; Favorable; Spontaneous
Positive ∆G- Free energy is added; Endergonic; Unfavorable; Nor Spontaneous

Negative ∆H- Energy is released from the system
Positive ∆H- Energy is added to the system

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

How does Thermodynamics relate to protein folding?

A

As the protein folds, it loses its disorder but the surrounding area gains in disorder

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

How does Thermodynamics relate to Catalysis?

A

With Enzyme the reaction is faster
Without Enzyme the reaction is slower

∆G stays the same because this does not affect the thermodynamics

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What does positive cooperativity mean?
What does negative cooperativity mean?
What is No Cooperativity mean?

A

Positive Cooperativity- the binding site affinity for the ligand increases with each subunit.

Negative Cooperativity- the binding site affinity for the ligand decreases with each subunit.

No Cooperativity- Binding sites are Independent. Michaelis Menten Enzymes.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What is the definition of Km, Kcat, Vmax, Kcat/Km?

A

Km- Michaelis Menten. Substrate concentration that gives half-maximal velocity of an enzymatic reaction. A measure of the affinity of enzyme and substrate with the higher the KM, the lower the affinity.

Kcat- Turnover Number. The number of times each enzyme site converts substrate to product per unit time.

Vmax- The reaction rate when the enzyme is fully saturated by the substrate.

Kcat/Km- Specificity Constant. Measure of enzyme performance by predicting the fate of ES.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Look up graphs for competitive inhibition, noncompetitive inhibition, and uncompetitive inhibition.

A

Slide 8

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What are the similarities and differences between Substrate Level Control and Feedback Control?

Give 2 Examples of each?

A

Similarities- Alters the ability of a reaction to proceed.

Differences- Substrate Level Control (Acts on a single reaction)
Feedback Control- Acts on a different reaction in the pathway

Examples:
Substrate Level Control:
G6P and Hexokinase
Acetyl Coa Inhibits PDH

Feedback Control:
Nucleotide de novo synthesis
Amino Acid Biosynthesis

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

What are the similarities and differences between Activation and Inhibition?

Give an example of each?

A

Similarities- Alters the ability of a reaction to proceed. Can be substrate level or feedback control.

Differences- Activation- adds new or increases existing functions. Inhibition- Decreases or stops existing function.

Examples:
Activation- Dephosphorylation of pyruvate kinase
Inhibition- Phosphorylation of pyruvate kinase

20
Q

What are the similarities and differences between Reversible Covalent Modifications and Irreversible Covalent Modifications?

Give examples of each?

A

Similarities- Activates the molecule
Differences:
-Reversible Covalent Modification- Can be inhibitory and reversible.
-Irreversible Covalent Modification- Never inhibitory and is irreversible.

Examples:
Reversible Covalent Modification:
-Histone Modifications
-Adenylation/Uridylation and Glutamine Synthetase
-Phosphorylation

Irreversible Modification:

  • Protease Cascade/Digestive Enzymes
  • Blood clotting factors
  • Insulin
21
Q

What are the similarities and differences between Allosteric Effector and Competitive Effector?

Give examples of each?

A

Similarities- Inhibits function
Differences- Allosteric Effector- does not bind to the active site. Competitive Effector- Binds at the active site, is never activating

Examples:
Allosteric Effector:
-ATCase
-Ribonucleotide Reductase
-Phosphofructokinase

Competitive Effector:

  • Methotrexate versus Dihydrofolate
  • Dihydrofolate Reductase
22
Q

What is the description for Isozymes and Enzyme Level Control?

Give examples of each?

A

Isozymes- Functional variants of a single enzyme.
Enzyme Level Control- Altering how much of an enzyme is produced.

Isozyme Examples:

  • Hexokinase and Glucokinase
  • LDH 1-4
  • Sirtuins

Enzyme Level Control Examples:

  • Hexokinase and Glucokinase
  • LDH 1-4
23
Q

Draw out the structures for Adenine, Thymine, Guanine, and Cytosine.

Draw out the structures of nucleotides.

A

Look these up online

24
Q

Know the difference between a nucleotide and nucleoside structure.

A

Difference in phosphate bonds. Loop up structure.

25
Q

Know the structures of pyrimidines versus Purines.

A

Pyrimidines- 1 ring

Purines- 2 rings

26
Q

Know the structure of deoxyribose and ribose.

A

Deoxyribose does NOT have a hydroxyl group at carbon 2 whereas ribose HAS a hydroxyl group at carbon 2 of the sugar.

27
Q

Know the difference between a furanose and a puranose.

A

Look up structures.

28
Q

Know the difference between alpha and beta anomers.

A

Alpha- “fish” are in the sea so the hydroxyl points down.

Beta- hydroxyl is up in the air

29
Q

Know fisher versus Hawthorne projections and which sugar is which.

A

Fisher is the linear form of the sugar

Hawthorne is the ring form of the sugar

30
Q

What is the name of the bonds between nucleotides?

A

Phosphodiester bonds

31
Q

What is the name of the bonds between amino acids?

A

Peptide bonds

32
Q

What is the name of the bonds between monosaccharides?

A

Glycosidic bonds

33
Q

What is the typical direction of growth for a nucleotide?

Which end is the next nucleotide monomer added to?

A

5’ -> 3’

The next monomer is added to the 3’ end

34
Q

For amino acids, know which ones are hydrophobic and hydrophilic, very large and small.

A 
Hydrophobic:
•	Alanine - Ala - A 
•	Isoleucine - Ile - I 
•	Leucine - Leu - L 
•	Methionine - Met - M 
•	Phenylalanine - Phe - F 
•	Valine - Val - V 
•	Proline - Pro - P 
•	Glycine - Gly - G 
Hydrophilic:
•	Glutamine - Gln - Q 
•	Asparagine - Asn - N 
•	Histidine - His - H 
•	Serine - Ser - S 
•	Threonine - Thr - T 
•	Tyrosine - Tyr - Y 
•	Cysteine - Cys - C

Very Large:
Tyrosine- Y
Phenylalanine- F
Tryptophan- W

35
Q

What end is the next amino acid added to, the N terminus or C terminus?

A

C-terminus.

36
Q

What are the essential amino acids?

A

PVT TIM HALL

37
Q

What are the 4 catalytic strategies? Describe each.

A

Covalent catalysis- Share electrons
Acid-base catalysis- Share protons
Approximation- orientation
Electrostatic Catalysis- Noncovalent interactions

38
Q

What are the 6 classes of enzymes? Give examples of each.

A

Oxidoreductase- Redox, move electrons. Ex. Dehydrogenases (oxidizes) Reductases (reduce)

Transferases- Moves a functional group. Ex. Kinases/Phosphatases

Hydrolases- Break a bond by adding water. Ex. Citrate Synthase/ Lactase

Lyases- Break a bond without water. Ex. Aldolase in Glycolysis

Isomerases- Rearrange the order of atoms. Ex. TPI

Ligases- Make a covalent bond. Ex. Aldolase in Gluconeogenesis

39
Q

What are two differences between Active and Passive Transport?

A

Use of energy

Direction of movement in relation to concentration gradient

40
Q

What are the features of the 6 families of transport proteins we considered in the lecture. Give examples of each.

A

Active Transport:
P-Type ATPase- Phosphorylates itself to transport ions. Ex. Na/K pump

ABC Transporter- Transports small molecules without the need to phosphorylate itself. Contains an ATP-binding cassette (ABC). Ex. Multidrug-resistant protein.

2º Transport- Uses gradient established by 1º active transport. Moves ions against its gradient without using energy. Ex. Na-Glucose cotransport.

Passive Transport:
Ion Channel- selectivity filter. Voltage or ligand gated. Ex. K+ channel.

Aquaporin- Selectivity filter, but no gate

Gap Junction- No selectivity filter, no gate

41
Q

What is another type of transport protein that you learned about that does not fall into any of the previous families?

A

F-Type ATP Synthase

F stands for Phosphorylation Factor

42
Q

Review the energy production pathways. (Pictures are on phone)

A

Glycolysis
TCA cycle
Oxidative phosphorylation

43
Q

Review the macromolecule recycling (Catabolic) pathways. (Pictures are on phone)

A 
Glycogenolysis
Amino acid catabolism and urea cycle
Nucleotide catabolism/salvage
Beta-oxidation of fatty acids
Ketone bodies
44
Q

Review the macromolecule synthesis (Anabolic) pathways. (Pictures are on phone)

A 
Gluconeogenesis
Pentose phosphate pathway
Nucleotide de novo synthesis
Amino acid biosynthesis
Fatty acid synthesis
45
Q

Review the 2 storage polymers pathways. (Pictures are on phone)

A

Glycogenesis

TAG synthesis

Dr. Ford Review (1 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions