14. Amino Acid Metabolism 15. Photosynthesis 16. Metabolism Regulation `17. Nucleic Acids

What 4 ways do dietary amino acids contribute to human metabolism?

• Nitrogen supply

• Support synthesis of nonessential amino acids

• Being catabolized for energy

• Releasing nitrogen for disposal (Urea cycle)

What are essential amino acids?

Amino acids that cannot be synthesized by the body and must be obtained from the diet

What are non-essential amino acids?

Amino acids that can be synthesized by the body

How are some amino acids synthesized?

Transamination

• Swap amino group and carbonyl

How do amino acids generate chemical energy?

Amino Acid Catabolism via Protease

• Metabolize protein from our diet

• Transamination leaves carbon skeleton

• Carbon skeletons (pyruvate, acetyl-CoA, CAC cycle intermediates) provide energy

What is a glucogenic amino acid?

Glycolysis or CAC intermediates → gluconeogenesis

What is a ketogenic amino acid?

Acetyl CoA or Acetoacetyl CoA intermediates → ketogenesis

If an amino acid can be converted to pyruvate, oxaloacetate, or any citric acid cycle intermediate what type is it?

Glucogenic

How is nitrogen disposed in humans?

Urea

• Carbamoyl Phosphate Synthesis (2 ATP used)

• Urea Cycle (1 ATP used)

What are the origins of each of the amines in urea?

• 1st NH₃ from Ammonia in phosphate synthetase rxn

  • NH₃ attacks Carboxyphosphate

• 2nd NH₃ from Aspartate in urea cycle

  • Aspartate combines with citrulline to make arginosuccinate

What is the relationship between the urea cycle and other pathways?

CAC produces ATP to offset ATP requirements of urea cycle

What is the net reaction of photosynthesis?

6 CO₂ + 6 H₂O + Light --> C₆H₁₂O₆ + 6 O₂

What do the light dependent rxns do?

• Make ATP + NADPH

• Oxidize H₂O → O₂

What does the Calvin cycle do?

Fixate CO₂ to make G3P

What are the ways absorbed energy can be dissipated in photosynthesis?

• Heat

• Light

• Exciton transfer

• Photooxidation

How are photosystems able to perform unfavorable redox reactions?

Light energy

• Excite e^- into a high-energy state

• Reduce acceptors they normally couldn’t

What are the locations of the relevant redox reactions, # of e^- transferred, and # of protons transported in photosystem II?

• Redox Rxns:

  • Lumen: 2 H₂O → 4 H⁺ + O₂

  • Thylakoid Membrane: 2 PQ → 2 PQH₂

• 4 e^-

• 4 H⁺ absorb in stroma + 4 H⁺ release to lumen

What are the locations of the relevant redox reactions, # of e^- transferred, and # of protons transported in cytochrome b₆f?

• Redox Rxns:

  • Lumen: 4 Plastocyanin (Cu²⁺) → 4 Plastocyanin (Cu⁺)

  • Thylakoid Membrane: 4 PQH₂ → 2 PQH₂ + 2 PQ

• 4 e^-

• 4 H⁺ absorb in stroma + 8 H⁺ release to lumen

What are the locations of the relevant redox reactions, # of e^- transferred, and # of protons transported in photosystem I?

• Redox Rxns:

  • Lumen: 4 Plastocyanin (Cu⁺) → 4 Plastocyanin (Cu²⁺)

  • Stroma: 4 Ferredoxin_ox → 4 Ferredoxin_red

• 4 e^-

• 4 H⁺ absorb in matrix

What is the equation to find overall yield of ATP and electron carriers per water molecule oxidized?

3 x H⁺ translocated/c subunits

• Chloroplast c-ring has 15 subunits

What is the relationship between light dependent reactions and the Calvin Cycle?

Light dependent reactions make ATP and NADPH for Calvin Cycle use

How is carbon as CO₂ fixated during the first steps of the Calvin Cycle?

Rubisco attaches CO₂ to RuBP → Unstable 6 Carbon Intermediate Split → 2 3-PGA

What are the fates of G3P?

• Glycolysis: make energy

• Gluconeogenesis: make glucose

• Regeneration of ribulose-1,5-biphosphate (RuBP) to continue Calvin Cycle

How is ribulose-1,5-biphosphate (RuBP) regenerated for another round of the Calvin Cycle?

A series of rearrangements that come from 5 G3P molecules to make 3 RuBP molecules

• ATP is consumed

• 1 G3P goes to make glucose

Why is hormonal control of metabolism across tissues and organs necessary for efficient use of dietary energy sources in humans?

Prioritize fuel sources +Regulate opposing pathways

What kind of hormones are insulin and glucagon and what do they do?

Peptide (protein) hormones

• Insulin - signal high blood glucose + stimulate glucose uptake/glycogen synthesis

• Glucagon - signal low blood glucose + stimulate glycogen breakdown/gluconeogenesis

What is the signaling mechanism of insulin? Start with detection of glucose → Change in metabolism

1. Beta pancreatic cells detect high blood glucose

2. Change ATP/ADP ratio induce release of insulin to bloodstream

3. Insulin binds to beta-subunit of receptor

4. Induce conformational change

5. Produce autophosphorylation event → Chain reaction of signal transduction to induce change in gene expression

6. Change metabolism

How much insulin signaling is impaired in type 1 diabetes?

No insulin production (complete loss of signaling)

• Destroy beta pancreatic cells

• Increase of blood glucose levels

• Juvenile onset

How much insulin signaling is impaired in type 2 diabetes?

Insulin resistance (impaired signaling)

• Insulin in blood but no detection

• Adult onset

How are replication and transmission of genetic information represented in the “Central Dogma of Molecular Biology”?

Replication: DNA → DNA

Transmission of Genetic Information: replication of DNA passed on during cell division

What are the hydrogen bond donors and acceptors in the purine and pyrimidine bases that are involved in base pairing?

• Hydrogen Bond Donors: NH groups

• Hydrogen Bond Acceptors: N or O w/ lone pairs

How does a ribonucleotide differ from a deoxyribonucleotide?

• Extra -OH group

• Use (U)racil instead of (T)hymine

What are phosphoester bonds?

Bond that links phosphate group to carbon connected to sugar

What are phosphoanhydride bonds?

Bond between two phosphate groups

What is the nomenclature for bases?

• Adenine

• Cytosine

• Guanine

• Thymine

• Uracil

What is the nomenclature for nucleosides?

• Adenosine

• Cytidine

• Guanosine

• Thymidine

• Uridine

What is the nomenclature for nucleotides?

• Adenylate

• Cytidylate

• Guanylate

• Thymidylate

• Uridylate

What are the salient features of the double helical structure of DNA?

• Base pairs closely stacked + perpendicular

• Phosphodiester backbone (Provides negative charge)

• Major + Minor Groove where proteins interact with bases

• Antiparallel + Base Pairing

What is the chemical basis for the specificity of purine-pyrimidine base pairs?

Ring Structure + Complementary Hydrogen Bond Pairing:

• Pur + Pur = Too Big or Pyr + Pyr = Too small

• G - C: 3 H-Bonds

• A - T/U: 2 H-Bonds

What is the chemical basis for stability of the DNA double helix?

Hydrophobic Effect