Proteins, Nucleotides, Metabolism and the Cell 8/31

1. Proteins, Nucleotides, Metabolism and the Cell 8/31 • What is the hierarchy of protein folding? • What happens when proteins denature? • What are nucleotides and what do they do? • ATP is the universal energy currency of cells! • How are catabolic and anabolic reactions the “Ying and Yang” of metabolism? • What is “Cell Theory”? • What limits cell size and determines cell shape?

2. For the test/quiz: Draw two peptide bonds that would be required to link three amino acids into a tripeptide.

3. Proteins also have shapes and levels of folding that are important considerations with respect to function and denaturation. Levels of Protein Structure: • PrimarySecondaryTertiaryQuaternary • Primary: This is amino acid order and location of dissulfide bonds in chain sequence • Secondary: H-bond interactions between adjacent backbone of amino acids. 2o structure can create sheets, globular structures and tubes • Tertiary: H-bond and ionic interactions between R-groups on the amino acids. 1o dissulfide bonds may “stabilize” tertiary structure (Consider a hair perm) • Quaternary: Sometimes two or more protein chains stabilize each other when they fit together….consider Hemoglobin. • Prosthetic Groups: iron and the “heme” • Co-factors: vitamins, Calcium, etc

4. Each color is a different protein chain

5. “denaturation” causes loss of enzyme function!1) The more unfolded a protein becomes the less of its original function REMAINs!2) Once a protein is unfolded it may or may not be able to return to its original shape and function. Pepsin and Trypsin are digestive enzymes that cut the peptide bonds of proteins. Why does pepsin work in the stomach? Why does trypsin work in the intestine? What happens if an enzyme is turned “ON” in the wrong place? (i.e. trypsin in the lung)

6. Why can’t a diabetic take insulin as a pill?Insulin actually consists of two small segments of protein held together by disulfide bonds (-S-S-) in a very special shape.

7. Enzymes only become/stay active within a specific pH or temperature! Enzymes also have a specific environment where they are optimally active. Each enzyme has unique optima that may be unique to each different enzyme. Has an understanding of protein structure improved your understanding of how function and structure are linked?

8. Why does a small change in pH have a large effect on enzyme function?pH = -log(H+) pH=-log(0.0000001)= 7pH= 7.5 = 0.00000032 moles H+/liter

9. Parts of a nucleotide: Ribose- Without -OH = DNA With-OH = RNA High energy phosphate chain- Nitrogenous BASE: Adenine (ATP) Thymine (TTP) Guanine(GTP) Cytosine(CTP) Uracil (UTP) “Cyclic”AMP Single vs. Chain Nucleotides are important for energy metabolism, production of proteins and storing genetic information.

10. NUCLEIC ACIDS ARE THE STUFF OF LIFE!DNA: deoxyribonucleic acid RNA: Ribonucleic acidRNA and DNA are both made from nucleotides • DNA stores our genetic information and is used to make RNA 4 Bases: Adenosine, Thymine, Cytosine and Guanine (Not Uracil) ATGC • Ribose has a hydrogen instead of a hydroxyl group • Hydrogen changes solubility and causes two complimentary strands to form a double helix • RNA is used to make proteins AUGC 4 Bases: Adenine, Cytosine, Guanine, Uracil (Not Thymine) • Ribose has the hydroxyl group and cannot form stable double helix • Pattern of nucleotides is used to make a protein with a unique primary sequence • DNA or RNA: Which has ribose? Which has Uracil?

11. DNA makes: RNA Ribose has no –OH “deoxyribose” Double stranded Helix RNA makes: Protein Has –OH on ribose No double helix What does DNA or RNA look like?

12. ATP is broken down to sequentially release energy! Enzymes tightly control this process. • ATP ADP + Pi + Energy • ADP AMP + Pi + Energy • AMP  Adenine + Pi + Energy These two important reactions that create “information” in the cell: • ATP cAMP + PPi + Energy + Information • Effect in lung: • GTP cGMP + PPi + Energy + Information • Effect in reproductive organs:

13. ATP is the energy currency of the body. Most of our ATP is produced in the mitochondria, but some cells (red blood cells) lack mitochondria and can only generate ATP anaerobically.

14. Energy is released when ATP is broken down to ADP and PO4. The energy can be used to overcome the activation energy for many (but not all) enzyme catalyzed chemical reactions. The name of an “enzyme” usually has “–ase” at the end “Kinases” attach phosphate from a nucleotide to a target (add energy). Phosphorylation= Pi attachment to a substrate “Phosphatases” remove the phosphate from a target (release energy). Dephosphorylation= Pi removal from a substrate. Consider energy in a muscular contraction or the movement of a flagella that permits a sperm to “swim”: Energy can also be carried/delivered in the form of a high-energy electron that is temporarily “stored/stabilized” by important co-factor molecules such as FADH2 or NADH NADH is used to shuttle energy rich electrons to the mitochondria where most of our ATP is produced!

15. Catabolism (breakdown) of lipids, carbohydrates and proteins yields energy via aerobic or anaerobic routes. • Glucose is cleanest burning fuel in the body>>CO2 • Fat can also be used to produce ATP • Aerobic Requirements • Anaerobic Fallback: • Conversion of substrates to glucose before entering metabolic routes:

16. Anabolic Reactions in the body use energy to make more complicated molecules (energy storage). • Carbohydrate monomers are stored as polysaccharides for later use • Energy is used to make fatty acids which are stored for use later (Triglycerides) or used to make plasma membranes of cells • Energy is used to create peptide bonds between amino acids….this makes proteins Your metabolism (Metabolic Rate) is the sum of all the catabolic (energy releasing) and anabolic (energy storing) reactions occurring in your body at any given time.

17. What is metabolism? • Sum of all catabolic and anabolic reactions in a cell. • Sum of all catabolic and anabolic reactions in a body. • The Ying and Yang of the chemical reactions that make up our metabolism seek to maintain homeostasis in a cell and the whole body! Are you using Catabolic or Anabolic Reactions? • If you are “gaining” weight? • If you are “losing” weight? • If you sitting quietly? • If you are exercising?

18. The cell is the functional unit of all life. Organisms can consist of a single cell or groups of cells with varying degrees of specialization. Cell Theory: • Organisms are composed of cells • Cell is simplest single unit of life • Cell structure/function relate to activity • All cells come from pre-existing cells • Cells share common similarities Folks that Examine Cells for a Living: • “Cytologist”: • “Hematologist” • “Oncologist”

19. Why do cells have a specific size, shape and function? • Shape is often dependent on the needs of the cells specialized activity: • Size Range: 0.01-0.1 mm diameter (Huge= 1mm oocyte) • What limits cell size? • Plasma membrane holds things in a cell!! • Membrane proteins control movement in/out of a cell!! • Organelles allow for specialization within a cell! • Second messengers are chemicals that allow for information movement in a cell. • Hormones/neurotransmitters carry information between cells!