Biochemistry Final Exam

What amino acids are Nonpolar?

GIVPALM

• Glycine, Isoleucine, Valine, Proline, Alanine, Leucine, Methionine

What amino acids are Aromatic?

FYM

• Phenylalanine, Tyrosine, Tryptophan

What amino acids are Polar, Uncharged?

STCNQ

• Serine, Threonine, Cysteine, Asparagine, Glutamine

What amino acids are Negative?

ED

• Glutamic Acid, Aspartic Acid

What amino acids are Hydrophobic?

FLAVI

• Phenylalanine, Leucine, Alanine, Valine, Isoleucine

What amino acids are Hydrophilic?

REKHN

• Arginine, Glutamic Acid, Lysine, Histidine, Asparagine

What amino acids are Positive?

KRH

• Lysine, Arginine, Histidine

What nucleic acids are purines?

Adenine and Guanine

“as pure as gold” - 2 rings

What nucleic acids are pyrimidines?

Cytosine, Uracil, Thymine

“cut” - 1 ring

Difference between DNA and RNA

DNA (B Form) - deoxyribose

RNA (A Form) - ribose

Peptide Bonds

C=ONH; strongest bond; cleaved by peptidase

Secondary Structure

Alpha-helix, right handed. Beta-sheets are parallel and antiparallel (antiparallel is stronger since the hydrogen bonding is head on)

Tertiary Stucture

Disulfide bonds stabilize cystine and forms a bond

N terminus

Considered positive therefore negative amino acids are located here

C terminus

Considered negative therefore positive amino acids are located here

Glycine and Proline

Glycine is the only amino acid that is not chiral (has two Hydrogens)

Proline is the only amino acids that is an imino acid (not amino)

Molten Globule

Hydrophobic effect stabilizes the initial intermediate. Hydrophobic collapse determines stability

KD

Dissociation constant, inverse to KA (association constant)

Lower the KD the tighter the binding

Myoglobin

Binds to oxygen in low KD (stays bound) storage molecule

Hemoglobin

High and low KD (in lung low = picks up oxygen); R and T state. Binds to 4 O2 molecules max

Tense

HIS HC3 is protonated (pulls ion out of plate and O2 cannot bind). The ion binds to O2 and HIS HC3 (thermodynamically more stable)

Relaxed

HIS HC3 is deprotonated (less stable thermodynamically). 2,3-bPG stabilizes T state (donut hole of hemoglobin)

What is a nontoxic way to transport ammonia to the liver?

GLN (glutamine)

Urea Cycle: Step 1

Ornithine + carbomyl phosphate → citrulline + Pi

• Catalyzed by ornithine transcarbamolyase

• Citrulline exported to cytosol

Urea Cycle: Step 2

Citrulline + aspartate → arginosuccinate

• Catalyzed by arginosuccinate synthetase. 2 more phosphate bonds cleaved (to adenylate to activate the citrulline). 1 more amino group enters

• Activation of citrulline. AMP excellent leaving group as aspartate is added. Incorporates second amino acid

Urea Cycle: Step 3 and 4

• Arginase catalyzes hydrolysis of arginine

Arginine + H2O → ornithine + urea

• Arginosuccinase catalyzes:

Arginosuccinate → fumarate + arginine

Glycerophospholipids

Will be asked how many times B-oxidation takes place

For example: 8C = 3 steps → 4 AcCoA

Know the general names of the pathway (ex: thiolase, dehydrogenase, etc)

What is the starting material for B-oxidation?

Malonyl CoA (not Acetyl CoA)

What do hydratases work on?

Trans Delta 2 bonds

Metabolic catabolism and anabolism

What units are utilized in fatty acid synthesis?

Acetyl and Malonyl Coa

What is the active group of the acyl carrier protein?

Thiol group (SH)

Fatty Acid Synthesis

Step 1: Condensation

1. KS catalyzes condensation of 2C and 3C units

2. Acetate added to malonate

3. Release of CO₂ drives reaction forward (2C + 3C - 1C = 4C)

Fatty Acid Synthesis

Step 2: Reduction

1. Catalyzed by KR (ꞵ-ketoacyl-ACP reductase)

2. Electron donor is NADPH

Fatty Acid Synthesis

Step 3: Dehydration

1. Catalyzed by DH (ꞵ-hydroxy acyl-ACP dehydratase)

Fatty Acid Synthesis

Step 4: Second Reduction

1. Catalyzes by ER (enoyl-ACP reductase)

2. NADPH is the electron donor

3. Product is an acyl group that is 2C long than the substrate primer linked to ACP

Know the aspects of a Reaction Coordinate Diagram

What does ΔG‡ mean?

How fast a reaction will occur

What does ΔG’o mean?

How likely a reaction will occur

Do enzyme impact ΔG’o?

No

Lower the Km

The higher the affinity for enzyme to substrate

Graph and Equation for Enzyme Kinematics

What state is enzyme kinematics always looked under?

Steady State (Rate of formation = Rate of breakdown)

Solve for Vmax given data

Competitive Inhibition

Binds to enzyme

Calculate for Vmax and Km

Uncompetitive Inhibition

Binds to enzyme substrate complex

Identify values in graph (Km and Vmax are altered)

Mixed Inhibition

Km and Vmax are altered

HIV Protease

Water directly attacks the peptide bond and releases the peptide

Enolase

Utilizes Mg2+ ions to stabilize the transition state

What is Keq?

[Products] / [Reactants]

Know the equation

ΔG = -RTln (K’eq)

How are unfavorable reactions able to proceed?

Via product removal, coupling, or tagging with a good leaving group

What is the movement of electrons?

From lower affinity to higher affinity

Know what an oxidizing and reducing agent is?

OIL RIG

Know what an aldose and ketose is

What is the difference between a D and L isomer?

D (OH is on the right) and L (OH is on the left)

What form of amino acids do we use?

L amino acids

What form of sugars do we use?

D sugars

What is the difference between 𝛂 and 𝛃 anomers?

𝛂 (below the plane) 𝛃 (above the plane)

What are the two phases of glycolysis?

Prep Phase - making intermediates to drive reaction

Payoff Phase - regenerate NADH)

6C sugar to 2 3C sugars

What are the 3 bypass steps?

1, 3 (point of no return), 10

Glucokinase

(Hexokinase IV) has a very low affinity for glucose (found in liver) which is where we store our glucose

What are the energy yielding steps of Glycolysis?

6, 7, and 10

What are the PDH cofactors?

E1 (TPP), E2 (lipoamide), E3 (FAD)

What is the result of the PDH complex?

Removal of CO2 (decarboxylation) and formation of Acetyl-CoA

What is the result of the Citric Acid Cycle?

1 turn = 1 GTP, 3 NADH, 1 FADH2, and 2 CO2

(amphibolic cycle - intermediates can come and leave at various points)

What does high levels of Acetyl CoA do?

It will turn off the PDH complex but activate pyruvate carboxylase (reciprocally regulated)

Malate-Aspartate Shuttle

NADH → NADH2

Glycerol-3-Phosphate Shuttle

NADH → FADH2

Brings electrons to electron transport chain

Electron Transport Chain

Movement of e- from complex I to ubiquinol is a favorable reaction. Ubiquinol donates e- to complex III (half cycle due to cytochrome) e- get dropped off to Complex IV

Electron Transport Chain Complex II

Electron donor is succinate, converted to fumarate

FADH pushes 6 protons (1.5 ATP)

Electron Transport Chain Complex IV

Loose (ADP bound), Tight (ATP bound), Open (nothing)

Glycogenesis

Making of glycogen molecules (highly fed state)

Glucose-6-phosphate → glucose-1-phosphate (via phosphoglucomutase)

What is the starting product for Glycogenesis?

UDP glucose (allows for the synthesis of glycogen)

What does glycogen synthase catalyze the formation of?

𝛂 1→4 linkages (branching enzymes make 1→6 linkages)

How do we get amino acids?

From dietary amino acids, or non-dietary protein breakdown

What occurs in the Liver?

Glutamate acting as a nitrogen sink (transamination reaction) donate amino group to alpha-keto acid to mane an amino acid (glutamate in the liver is the carrier of the amino group)

Transdeamination

Removing of amino group in the cytosol (done by enzyme glutamate dehydrogenase)

What occurs in the extrahepatic tissue?

carry 2 molecules of ammonia

L-glutamate → L-glutamine

What occurs in the muscle?

It can take an alternative pathway (glucose-alanine cycle). Amino acids are broken down and put onto glutamate. Donate NH4 and get converted to alanine

Urea Cycle

Think about what is the input (glutamate or glutamine), how much ATP is being input (1 ATP in step 1) (put in 3 ATP) (get 2.5 molecules ATP out)

Glycerophospholipids

Glycerol + 2 fatty acids + alcohol + PO4

Sphingolipids

Sphingosine + fatty acid + PO4 + Choline

Sterols

Rings (function as hormones in our body)

What are the signaling molecules in our body?

PIP2 (Phosphoenol phosphate)

They are usually going to be something with a phosphate attached to it

Membrane Fluidity

Saturated fatty acid (melting point is high)

Unsaturated fatty acid (low melting point)

Trans fatty acid (extremely low)

What are occurring at the same time?

B-oxidation and gluconeogenesis

Fate of Glycerol

1 net molecule of ATP

Carnitine

Transport of fatty acids from cytosol to mitochondria

Acyl carnitine is what is being transferred across the membrane

4 steps of B-oxidation

Oxidation, hydration, oxidation, cleavage

1st step the e- acceptor is FAH, 2nd step the e- acceptor is NAD

Breakdown of a 16C molecule

Acyl-CoA → Acetyl-CoA and C14 molecule

We then run 7 cycle of B-oxidation

16C molecule yield 106 molecules of ATP

Monounsaturated Fatty Acid

Cis-delta-3 → Trans-delta-2 (via an isomerase)

Polyunsaturated Fatty Acid

1st enzyme is reductase and 2nd is an isomerase allowing B-oxidation to proceed

How can CoA pools be regenerated?

The formation of ketone bodies