1. Factors Affecting Rates of Respiration • Temperature- For every 10 degree C rise in temperature between 0-35 C the rate of respiration increases 2X – 4X. • Storage temperature for harvested plant parts is often critical because these parts continue to respire after harvest ( a catabolic process) which causes a build up of heat, and the breakdown of the product.

2. Factors Affecting Rates of Respiration • Most plants grow better when night time temperatures are 5 degrees C lower than day time temperatures. • This is because lower night time respiration reduces the use of carbohydrates and allows more carbohydrates to be stored or used for growth.

3. Factors Affecting Rates of Respiration • Oxygen concentration- Generally speaking, lower oxygen level results in the reduction of respiration. • Controlled atmosphere (CA) storage in which oxygen is decreased is useful in storage of fruits and vegetables because of lower respiration rates.

4. Factors Affecting Rates of Respiration • Soil conditions- Compacted and/or wet soil conditions result in low oxygen in the root zone and reduced root respiration. • Consequently, roots don’t function well in supplying mineral nutrients essential for the activity of respiratory enzymes which decreases overall respiration.

5. Factors Affecting Rates of Respiration • Light- Lower light intensities result in lower respiration rates. • Lower photosynthesis rates in low light supply fewer carbohydrates essential for respiration. • Plant growth- As a plant grows it depends on energy to be supplied by respiration. • The more growth that is occurring, the higher the respiration rate must be.

6. Summary of Respiration • Aerobic Respiration • Glycolysis • Transition Rx. • Kreb’s Cycle • Electron Transport Chain • Anaerobic Respiration • Pyruvate  • Lactic Acid • Mixed Acids • Alcohol + CO2 • Recycle NADH • 2 ATP / Glucose

7. Amino Acid Catabolism

8. Amino Acids • Building blocks for polymers called proteins • Contain an amino group, –NH2, and a carboxylic acid, –COOH • Can form zwitterions: have both positively charged and negatively charged groups on same molecule • 20 required for humans

11. Peptide Bond • Connect amino acids from carboxylic acid to amino group • Produce amide linkage: -CONH- • Holds all proteins together • Indicate proteins by 3-letter abbreviation

12. Sequence of Amino Acids • Amino acids need to be in correct order for protein to function correctly • Similar to forming sentences out of words

13. Transaminaseenzymes (aminotransferases) Catalyze the reversible transfer of an amino group between two a-keto acids.

14. Example of aTransaminasereaction: Aspartate donates its amino group, becoming the a-keto acid oxaloacetate. • a-Ketoglutarate accepts the amino group, becoming the amino acid glutamate.

15. In another example, alanine becomes pyruvate as the amino group is transferred to a-ketoglutarate.

16. Essential amino acidsmust be consumed in the diet. Mammalian cells lack enzymes to synthesize their carbon skeletons (a-keto acids). These include: Isoleucine, leucine, & valine Lysine Threonine Tryptophan Phenylalanine (Tyr can be made from Phe.) Methionine (Cys can be made from Met.) Histidine (Essential for infants.)

17. Amino Acid Metabolism • Metabolism of the 20 common amino acids is considered from the origins and fates of their: (1) Nitrogen atoms (2) Carbon skeletons • For mammals: Essential amino acids must be obtained from dietNonessential amino acids - can be synthesized

18. The Nitrogen Cycle and Nitrogen Fixation • Nitrogen is needed for amino acids, nucleotides • Atmospheric N2 is the ultimate source of biological nitrogen • Nitrogen fixation: a few bacteria possess nitrogenase which can reduce N2 to ammonia • Nitrogen is recycled in nature through the nitrogen cycle

19. Fig 17.1 The Nitrogen cycle

20. An enzyme present in Rhizobium bacteria that live in root nodules of leguminous plants • Some free-living soil and aquatic bacteria also possess nitrogenase • Nitrogenase reaction: • N2 + 8 H+ + 8 e- + 16 ATP • 2 NH3 + H2 + 16 ADP + 16 Pi Nitrogenase

21. Assimilation of Ammonia • Ammonia generated from N2 is assimilated into low molecular weight metabolites such as glutamate or glutamine • At pH 7 ammonium ion predominates (NH4+) • At enzyme reactive centers unprotonated NH3 is the nucleophilic reactive species

22. A. Ammonia Is Incorporated into Glutamate • Reductive amination ofa-ketoglutarate by glutamatedehydrogenase occurs in plants, animals and microorganisms

23. Glutamine Is a Nitrogen Carrier in Many Biosynthetic Reactions • A second important route in assimilation of ammonia is viaglutaminesynthetase

24. Glutamate synthase transfers a nitrogen to a-ketoglutarate Prokaryotes & plants

25. Alternate amino acid production in prokaryotes Especially used if [NH3] is low. Km of Gln synthetase lower than Km of Glu dehydrogenase.

26. The First Step in Amino Acid Degradation is the Removal of Nitrogen • Amino acids released from protein turnover can be resynthesized into proteins. • Excess amino acids are degraded into specific compounds that can be used in other metabolic pathways. • This process begins with the removal of the amino group, which can be converted to urea and excreted. • The -ketoids that remain are metabolized so that their carbon skeletons can enter glycolysis, gluconeogenesis, or the TCA cycle.

27. The Biosynthesis of Amino Acids • Amino acids are the building blocks of proteins and the nitrogen source of many other important molecules including nucleotides, neurotransmitters, and prosthetic groups such as porphyrins. • Ammonia is the source of all nitrogen for all of the amino acids. • The carbon backbones come from the glycolytic pathway, the pentose phosphate pathway, and/or the TCA cycle. • Amino acid biosynthesis is feedback regulated to ensure that all amino acids are maintained in sufficient amounts for protein synthesis and other processes.

28. Summary of Protein and Amino Acid Degradation • Proteins are degraded to amino acids. • Protein turnover is tightly regulated. • The first step in amino acid degradation is the removal of nitrogen. • Ammonium ion is converted into urea in most terrestrial vertebrates. • Carbon atoms of degraded amino acids emerge as major metabolic intermediates. • Inborn errors of metabolism can disrupt amino acid degradation.

29. Summary of Amino Acid Biosynthesis • Microorganisms use ATP and a powerful reductant to reduce atmospheric nitrogen to ammonia. • Amino acids are made from intermediates of the TCA cycle and other major pathways. • Amino acid metabolism is regulated by feedback inhibition. • Amino acids are precursors of many molecules.

30. Overview of Nucleotide Biosynthesis • Nucleotides serve as active precursors of nucleic acids. • ATP is the universal currency of energy. • Nucleotide derivatives such as UDP-glucose participate in bioynthetic processes. • Nucleotides are essential components of signal transduction pathways.

31. Two Classes of Pathways for the Synthesis of Nucleotides. • In the salvage pathway, a base is attached • to a ribose, activated in the form of 5- • phosphoribosyl-1-pyrophosphate (PRPP). • In de novo synthesis, the base itself is • synthesized from simpler starting materials, • including amino acids. • ATP hydrolysis is necessary for de novo • synthesis.

32. Summary of Nucleotide Biosynthesis • In de novo synthesis, the pyrimidine ring is assembled from bicarbonate, aspartate, and glutamine. • Purine bases can be synthesized de novo or recycled by salvage pathways. • Deoxyribonucleotides are synthesized by the reduction of ribonucleotides. • Key steps in nucleotide biosynthesis are feeback regulated. • NAD+, FAD, and Coenzyme A are formed from ATP. • Disruptions in nucleotide metabolism can cause pathological conditions.

33. Proteins

34. Structure of Proteins • Four organizational levels • Primary structure: amino acid sequence • Secondary structure: arrangement of chains around an axis • Pleated sheet • Alpha helix: right-handed helix

35. Pleated Sheets

36. Alpha Helix

37. Tertiary Structure • Spatial relationships of amino acids relatively far apart in protein chain • Globular proteins: compact spherical shape

38. Quaternary Structure • Structure when two or more amino acid sequences are brought together • Hemoglobin has four units arranged in a specific pattern

39. Intermolecular Forces in Proteins • Hydrogen bonding • Ionic bonds • Disulfide linkages • Dispersion forces

40. Protein metabolism Transamination: use the essential AA to synthesize the others!

41. Protein metabolism Another route: Intestinal bacteria -> ammonia (toxic) -> liver uses it to make amino acids

42. Protein metabolism Amino acids: C, H, O plus amine group with N

43. Protein metabolism Amino acids are broken down into: a) ammonia -> urea b) pyruvate or molecules that are part of the krebs cycle -> respired for energy, or converted to fats or glucose

44. Proteins are degraded into amino acids. • Protein turnover is tightly regulated. • First step in protein degradation is the removal of the nitrogen • Ammonium ion is converted to urea in most mammals. • Carbon atoms are converted to other major metabolic intermediates. • Inborn errors in metabolism

45. Amino acids used for synthesizing proteins are obtained by degrading other proteins • Proteins destined for degradation are labeled with ubiquitin. • Polyubiquinated proteins are degraded by proteosomes. • Amino acids are also a source of nitrogen for other biomolecules.

46. Excess amino acids cannot be stored. • Surplus amino acids are used for fuel. • Carbon skeleton is converted to • Acetyl–CoA • Acetoacetyl–CoA • Pyruvate • Citric acid cycle intermediate • The amino group nitrogen is converted to urea and excreted. • Glucose, fatty acids and ketone bodies can be formed from amino acids.

47. 1. Protein Degradation • proteins are a vital source of amino acids. • Discarded cellular proteins are another source of amino acids.

48. Biotechnology

49. What Is Biotechnology? • Using scientific methods with organisms to produce new products or new forms of organisms • Any technique that uses living organisms or substances from those organisms to make or modify a product, to improve plants or animals, or to develop microorganisms for specific uses

50. What Is Biotechnology? • GMO- genetically modified organisms. • GEO- genetically enhanced organisms. • With both, the natural genetic material of the organism has been altered. • Roots in bread making, wine brewing, cheese and yogurt fermentation, and classical plant and animal breeding