Comprehensive Review Flashcards
What are the 4 Noncovalent Interactions?
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
What does it mean if:
pH < pKa
pH > pKa
pH=pKa
pH < pKa Protonated
pH > pKa -> Deprotonated
pH=pKa -> Just as likely to be protonated or deprotonated
What is Ka?
A dissociation constant that predicts how likely an acid is going to donate its proton.
What are weak acids used as?
Buffers
What happens when something is reduced? oxidized?
Reduced species gain an electron
Oxidized species have lost electrons
OIL RIG
What amino acid is important during redox reactions.
Cysteine
What are the 3 important electron carriers in cellular metabolism? (Give the oxidized and reduced versions)
Oxidized:
NAD+
FAD
FMN
Reduced:
NADH
FADH2
FMNH2
What kinds of reactions are NADPH used for?
What kinds of reactions are FAD/FMN used for?
NADPH- Anabolic reactions and is becoming oxidized
FAD/FMN- Catabolic reactions and is becoming reduced
What is the definition of equilibrium?
Forward and reverse rates are equal. No net formation or destruction.
How does Le Chatlier fit into cellular metabolism?
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.
What is the thermodynamics equation?
∆G=∆H-T∆S
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?
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 does Thermodynamics relate to protein folding?
As the protein folds, it loses its disorder but the surrounding area gains in disorder
How does Thermodynamics relate to Catalysis?
With Enzyme the reaction is faster
Without Enzyme the reaction is slower
∆G stays the same because this does not affect the thermodynamics
What does positive cooperativity mean?
What does negative cooperativity mean?
What is No Cooperativity mean?
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.
What is the definition of Km, Kcat, Vmax, Kcat/Km?
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.
Look up graphs for competitive inhibition, noncompetitive inhibition, and uncompetitive inhibition.
Slide 8
What are the similarities and differences between Substrate Level Control and Feedback Control?
Give 2 Examples of each?
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
What are the similarities and differences between Activation and Inhibition?
Give an example of each?
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
What are the similarities and differences between Reversible Covalent Modifications and Irreversible Covalent Modifications?
Give examples of each?
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
What are the similarities and differences between Allosteric Effector and Competitive Effector?
Give examples of each?
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
What is the description for Isozymes and Enzyme Level Control?
Give examples of each?
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
Draw out the structures for Adenine, Thymine, Guanine, and Cytosine.
Draw out the structures of nucleotides.
Look these up online
Know the difference between a nucleotide and nucleoside structure.
Difference in phosphate bonds. Loop up structure.
Know the structures of pyrimidines versus Purines.
Pyrimidines- 1 ring
Purines- 2 rings
Know the structure of deoxyribose and ribose.
Deoxyribose does NOT have a hydroxyl group at carbon 2 whereas ribose HAS a hydroxyl group at carbon 2 of the sugar.
Know the difference between a furanose and a puranose.
Look up structures.
Know the difference between alpha and beta anomers.
Alpha- “fish” are in the sea so the hydroxyl points down.
Beta- hydroxyl is up in the air
Know fisher versus Hawthorne projections and which sugar is which.
Fisher is the linear form of the sugar
Hawthorne is the ring form of the sugar
What is the name of the bonds between nucleotides?
Phosphodiester bonds
What is the name of the bonds between amino acids?
Peptide bonds
What is the name of the bonds between monosaccharides?
Glycosidic bonds
What is the typical direction of growth for a nucleotide?
Which end is the next nucleotide monomer added to?
5’ -> 3’
The next monomer is added to the 3’ end
For amino acids, know which ones are hydrophobic and hydrophilic, very large and small.
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
What end is the next amino acid added to, the N terminus or C terminus?
C-terminus.
What are the essential amino acids?
PVT TIM HALL
What are the 4 catalytic strategies? Describe each.
Covalent catalysis- Share electrons
Acid-base catalysis- Share protons
Approximation- orientation
Electrostatic Catalysis- Noncovalent interactions
What are the 6 classes of enzymes? Give examples of each.
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
What are two differences between Active and Passive Transport?
Use of energy
Direction of movement in relation to concentration gradient
What are the features of the 6 families of transport proteins we considered in the lecture. Give examples of each.
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
What is another type of transport protein that you learned about that does not fall into any of the previous families?
F-Type ATP Synthase
F stands for Phosphorylation Factor
Review the energy production pathways. (Pictures are on phone)
Glycolysis
TCA cycle
Oxidative phosphorylation
Review the macromolecule recycling (Catabolic) pathways. (Pictures are on phone)
Glycogenolysis Amino acid catabolism and urea cycle Nucleotide catabolism/salvage Beta-oxidation of fatty acids Ketone bodies
Review the macromolecule synthesis (Anabolic) pathways. (Pictures are on phone)
Gluconeogenesis Pentose phosphate pathway Nucleotide de novo synthesis Amino acid biosynthesis Fatty acid synthesis
Review the 2 storage polymers pathways. (Pictures are on phone)
Glycogenesis
TAG synthesis
