Ch 4: Energy and Cellular Metabolism Energy as it relates to Biology Energy as it relates to Biology Chemical reactions Chemical reactions Enzymes Enzymes and how they speed rxs Metabolism and metabolic pathways Metabolism and metabolic pathways Catabolism (ATP production) Catabolism (ATP production) Anabolism ( ) Anabolism (Synthesis of biologically important molecules)

Energy in Biological Systems Review on your own!

Chemical Reactions 1. Transfer energy 2. or use energy to do work Substrates / reactants Products Bioenergetics Bioenergetics: Study of energy flow through biol. systems Reaction rate = speed of reaction A + B C + D

Activation Energy Starts Reaction Reversible (most biol. rxs.) vs. irreversible reactions Fig 4-3

Endergonic vs. Exergonic Reactions Coupling endergonic and exergoinic rxs D irect coupling vs. indirect coupling Which kind?

Enzymes are Proteins acting as Biological Catalysts 1. chemical reaction rate by lowering activation energy 2. are not changed themselves not changednot changed 3. do not change nature of rx nor result 4. are specific 4 important characteristics of enzymes Fig 4-8

Enzymes lower activation energy: All chemical reactions in body must be conducted at body temp.!! How do enzymes lower activation energy ?

Enzymes bind to reactant molecules and bring them together in best position for rx.

Small region of the complex 3D structure is active (or binding) site. Enzymes bind to substrate Active Site: Old: Lock-and-key model / New: Induced-fit model Fig 2-16

Enzyme-substrate interaction: The old and the new model

Naming of Enzymes Kinase Kinase Phosphatase Phosphatase Peptidase Peptidase Dehydrogenase Dehydrogenase mostly suffix -ase first part gives info on function examples Not in book

Isozymes = different models of same enzyme (differ in 1 or few aa) Examples: 1. Amylase 2. LDH 2. LDH importance in diagnostics Catalize same reaction under different conditions and in different tissues/organs Review Table 4-3

Enzyme Activity depends on 1. proteolytic activation (for some) proteolytic activation proteolytic activation 2. cofactors & coenzymes (for some) cofactors & coenzymes cofactors & coenzymes 3. temperature temperature 4. pH pH 5. other molecules interacting with enzyme other molecules other molecules

1) Proteolytic Activation Also 1.PepsinogenPepsin 2.TrypsinogenTrypsin

2) Cofactors & Coenzymes structure: ___________ molecules (e.g. ?) function: conformational change of active site structure: Organic molecules (vitamin derivatives, FADH 2....) function: act as receptors & carriers for atoms or functional groups that are removed from substrate

Cofactors bind to active site

3) Breakage of intramolecular bonds lead to ?

TyrosineMelanin Tyrosinase is temperature sensitive does not function at cats core body temperature (101.5° F) Tyrosinase is temperature sensitive does not function at cats core body temperature (101.5° F) tyrosinase Siamese Cats

4)

5) Molecules interacting with enzyme: bind to enzyme away from active site changing shape of active site for better or for worse 5) Molecules interacting with enzyme: Allosteric Modulators bind to enzyme away from active site changing shape of active site for better or for worse Allosteric Activator Allosteric Inhibitor Fig 2-20

5) Molecules interacting with enzyme cont. Competitive inhibitors: reversible binding to active site block active site Also possible: irreversible binding via covalent bonds, e.g.: Penicillin Cyanide Fig 2-19

Reversible Reactions follow the Law of Mass Action Fig 4-9

Three Major Types of Enzymatic Reactions: 1. Oxydation - Reduction reactions Oxydation - Reduction reactions Oxydation - Reduction reactions (transfer of ?) 2. Hydrolysis - Dehydration reactions Dehydration reactionsDehydration reactions (breakdown & synthesis of ?) 3. Addition-Subtraction-Exchange reactions

?

Metabolism Catabolism Anabolism

Metabolism definition: ___________ Metabolic pathways = network of linked reactions Cells regulate metabolic pathways via Control of enzyme concentration Modulator production (allosteric modulators, feedback inhibition, Fig 4-11) Fig 4-11) Different enzymes for reversible rxs, Fig 4- 12) Fig 4- 12) Compartmentation of enzymes ATP / ADP ratio

Metabolic pathways: Network of interconnected chemical reactions Linear pathway Circular pathway Branched pathway Intermediates

= end product inhibition Special case: Fig 4-11

Catabolic Pathways: ATP-Production ATP Amount of ATP produced reflects on usefulness of metabolic pathways: Aerobic pathways Anaerobic pathways Different biomolecules enter pathway at different points

ATP Cycle ATP = Energy Carrier of Cell (not very useful for energy storage) ATP : ADP ratio determines status of ATP synthesis reactions

Glycolysis From 1 glucose to 2 pyruvate molecules From 1 glucose to 2 pyruvate molecules Main catabolic pathway of cytoplasm Main catabolic pathway of cytoplasm Does not require O 2 part of _________ and ____________ catabolism Does not require O 2 part of _________ and ____________ catabolism Starts with phosphorylation (Before doubling your money you first have to invest!) Starts with phosphorylation (Before doubling your money you first have to invest!) Fig 4-13

Anaerobic catabolism: Pyruvate lactate Aerobic catabolism: Pyruvate Citric Acid Cycle Pyruvate has 2 Possible Fates

Citric Acid Cycle Other names ? Takes place in ? Energy Produced: 1 ATP 3 NADH 1 FADH 2 Waste – 2 CO 2 Fig. 4-16

NADH FADH 2 Energy Yield of Krebs Cycle Compare to Fig. 4-16

Final step: Electron Transport System Chemiosmotic theory / oxydative phosphorylation Transfers energy from NADH and FADH 2 to ATP (via e - donation and H + transport) Transfers energy from NADH and FADH 2 to ATP (via e - donation and H + transport) Mechanism: Energy released by movement of e - trough transport system is stored temporarily in H + gradient Mechanism: Energy released by movement of e - trough transport system is stored temporarily in H + gradient NADH produces a maximum of 2.5 ATP FADH 2 produces a maximum of 1.5 ATP NADH produces a maximum of 2.5 ATP FADH 2 produces a maximum of 1.5 ATP 1 ATP formed per 3H + shuttled through ATP Synthase Fig 4-17

Cellular Respiration Maximum potential yield for aerobic glucose metabolism: ATP synthesized from ADP H 2 O is a byproduct

Synthetic Pathways Unit molecules Macromolecules Polysaccharides Lipids DNA Protein nutrients & energy required Anabolic rxs synthesize large biomolecules

Glycogen Synthesis Made from glucose Stored in all cells but especially in Liver (keeps 4h glycogen reserve for between meals) Liver (keeps 4h glycogen reserve for between meals) Skeletal Muscle muscle contraction Skeletal Muscle muscle contraction Gluconeogenesis Glycolysis in reverse From glycerol, aa and lactate All cells can make G-6-P, only liver and Kidney can make glucose

Proteins are the key to cell function necessary for all cell functions Protein synthesis is under nuclear direction DNA specifies Proteins Protein Synthesis DNA mRNA Protein ? ?

How can only 4 bases in DNA encode > 20 different aa in protein? 1 letter word: 1 base = 1 aa how many possibilities ? 2 letter word: 2 bases = 1 aa how many possibilities ? 3 letter word: 3 bases = 1 aa how many possibilities ? 3 letter words = base triplets or codons 3 letter words = base triplets or codons

1 start codon (AUG = Met) 3 stop codons 60 other codons for 19 aa Redundancy of Genetic Code

Transcription DNA is transcribed into complementary mRNA by RNA Polymerase + nucleotides + Mg 2+ ( = ?) + ? Gene = elementary unit of inheritance Compare to Fig and review Fig 4-26

Translation mRNA is translated into string of aa (= polypeptide) mRNA + ribosomes + tRNA meet in cytoplasm Anticodon pairs with mRNA codon aa determined Amino acids are linked via ______________ bond. 2 important components ?? Fig 4-27

Protein Sorting Due to signal/targeting sequence No targeting sequence protein stays in cytoplasm No targeting sequence protein stays in cytoplasm Targeting sequence protein destined for translocation into organelles or for export from cell Targeting sequence protein destined for translocation into organelles or for export from cell Post – Translational protein modifications: Folding, cleavage, additions glyco-, lipo- proteins

For export proteins: Signal sequence leads growing polypeptide chain across ER membrane into ER lumen Modifications in ER Transition vesicles to Golgi apparatus for further modifications Transport vesicles to cell membrane Compare to Fig 4-28

DNA Replication Semi- conservative Semi- conservative DNA polymerase DNA polymerase

Running problem: Tay-Sachs Disease