Energy and Cellular Metabolism
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1 1 Chapter 4 About This Chapter Energy and Cellular Metabolism 2 Energy in biological systems Chemical reactions Enzymes Metabolism Figure 4.1 Energy transfer in the environment Table 4.1 Properties of Living Organisms 3 4 KEY Transfer of radiant or heat Sun Transfer of in chemical bonds Energy lost to environment Heat Radiant Energy for work CO2 Photosynthesis takes place in plant cells, yielding: O2 + Energy stored in biomolecules Respiration takes place in human cells, yielding: Energy stored in biomolecules H2O N2 H2O CO2
2 Energy: Capacity to Do Work 5 Energy Comes in Two Forms 6 Two principle forms of Kinetic the of movement Potential stored Energy can be used to do work: that is, to move matter against opposing forces, such as gravity, friction, electric repulsive force Chemical work Making and breaking of chemical bonds Transport work Moving ions, molecules, and larger particles Useful for creating concentration gradients Mechanical work Moving organelles, changing cell shape, beating flagella and cilia Contracting muscles Kinetic Energy of motion Work involves movement Potential Stored In concentration gradients and chemical bonds Must be converted to kinetic to perform work Transformation efficiency Figure 4.2 The relationship between kinetic and potential 7 Thermodynamic Energy 8 First law of thermodynamics Work is used to push a ball up a ramp. Kinetic of movement up the ramp is being stored in the potential of the ball s position. The ball sitting at the top of the ramp has potential, the potential to do work. The ball rolling down the ramp is converting the potential to kinetic. However, the conversion is not totally efficient, and some is lost as heat due to friction between the ball, ramp, and air. Total amount of in the universe is constant Energy cannot be created or destroyed Energy can be converted from one form to another The pathway of conversion is irrelevant, the change between identical initial and final states is equal Second law of thermodynamics Processes move from state of order to randomness or disorder (entropy)
3 Thermodynamic Energy 9 Chemical Reactions 10 Second law of thermodynamics Processes move from state of order to randomness or disorder (entropy) No conversion is 100% efficient. Total useful in a closed system decreases as conversions occur. Entropy Measure of Disorder Closed systems tend to their highest state of disorder Entropy of the universe increases with every conversion Bioenergetics is the study of flow through biological systems Chemical reactions Reactants become products Reaction rate Activation Net free change of the reaction Exergonic versus endergonic reactions Coupled reactions Reversible versus irreversible reactions Table 4.2 Chemical Reactions 11 Figure 4.3a Activation and exergonic and endergonic reactions (1 of 3) 12 Activation Reactants Starting free level Products Final free level Activation is the push needed to start a reaction.
4 Figure 4.3b Activation and exergonic and endergonic reactions (2 of 3) Free of molecule Activation A+B Net free change KEY Reactants Activation of reaction Reaction process Products 13 Figure 4.3c Activation and exergonic and endergonic reactions (3 of 3) Free of molecule Activation E+F G+H Net free change KEY Reactants Activation of reaction Reaction process Products 14 C+D Time Exergonic reactions release because the products have less than the reactants. Time Endergonic reactions trap some activation in the products, which then have more free than the reactants. Figure 4.4 Energy transfer and storage in biological reactions 15 Figure 4.5 Some reactions have large activation energies KEY Reactants 16 Exergonic reactions release. A+B C+D ENERGY released Heat High- electrons Nucleotides capture and transfer and electrons NADPH NADH FADH 2 ATP ENERGY utilized E+F G+H Endergonic reactions will not occur without input of. Free of molecule Activation C+D A+B Net free change Activation of reaction Reaction process Products Time
5 Enzymes: Overview Enzymes Are proteins catalysts (not used up in the reaction) speed up the rate of chemical reactions by lowering the activation They don t change equilibrium! With infinite time in a closed system, the same equilibrium would be reached whether with enzymes or without. Reactants are called substrates Isozymes Catalyze same reaction, but under different conditions May be activated, inactivated, or modulated Modulated by other enzymes: Phosphorylation (kinase) /dephosphorylation (phosphatase) Coenzymes (e.g., vitamins) Chemical modulators temperature and ph 17 Figure 4.7 Enzymes lower the activation of reactions Free of molecule Activation without enzyme A+B Time Lower activation in presence of enzyme C+D 18 KEY Reactants Activation of reaction Reaction process Products Table 4.3 Diagnostically Important Enzymes 19 Figure 4.6 Effect of ph on enzyme activity 20 Rate of enzyme activity ph Most enzymes in humans have optimal activity near the body s internal ph of 7.4. GRAPH QUESTION If the ph falls from 8 to 7.4, what happens to the activity of the enzyme?
6 Table 4.4 Classification of Enzymatic Reactions 21 Metabolism 22 All chemical reactions that take place in an organism Catabolism (break down/degrade) versus anabolism (build up/synthesize) Kilocalories are measures of released from or stored in chemical bonds Molecules in pathways are intermediates Figure 4.8 A group of metabolic pathways resembles a road map 23 Cells Regulate Their Metabolic Pathways 24 Section of road map Glucose Fructose Fructose 1-phosphate Glycerol DHAP DHAP = dihydroxyacetone phosphate Glycogen Glucose 6-phosphate Fructose 6- phosphate Fructose 1,6- biphosphate Glucose 3-phosphate Metabolic pathways drawn like a road map Ribose 5- phosphate 1. Controlling enzyme concentrations 1. Synthesis/degradation 2. Producing modulators that change reaction rates 1. Ex. Feedback inhibition: negative feedback where accumulation of product inhibits production of that product 3. Using different enzymes to catalyze reversible reactions 4. Compartmentalizing enzymes within organelles 5. Maintaining optimum ratio of ATP to ADP
7 Figure 4.9 Feedback inhibition 25 Figure 4.10 The reversibility of metabolic reactions is controlled by enzymes 26 CO 2 H 2 O Glucose PO 4 Glucose PO 4 carbonic anhydrase carbonic anhydrase hexokinase glucose 6- phosphatase hexokinase enzyme 1 enzyme 2 enzyme 3 A B C Z Feedback inhibition Carbonic acid Glucose 6-phosphate Glucose 6-phosphate Some reversible reactions use one enzyme for both directions. Reversible reactions requiring two enzymes allow more control over the reaction. Irreversible reactions lack the enzyme for the reverse direction. FIGURE QUESTION What is the difference between a kinase and a phosphatase? (Hint: See Table 4.4.) ATP Transfers Energy Between Reactions 27 Figure 4.11 ESSENTIALS ATP Production 28 High- phosphate bond ATP production Aerobic metabolism (yeilds more ATP) Citric acid cycle Electron transport chain Anaerobic metabolism Glycolysis
8 Figure 4.12 ESSENTIALS Glycolysis 29 Figure 4.13 ESSENTIALS Pyruvate, Acetyl CoA, and the Citric Acid Cycle 30 Figure 4.14 ESSENTIALS The Electron Transport System 31 Figure 4.15 Summary of yields from catabolism of one glucose molecule 32 Anaerobic Metabolism Aerobic Metabolism 1 Glucose NADH FADH 2 ATP CO 2 1 Glucose NADH FADH 2 ATP CO 2 G LY G LY C O LY S I S C O LY S I S 2* Lactate 2 Pyruvate 2 2 Pyruvate 2 Acetyl CoA 2 2 TOTALS 0 NADH 2 ATP Citric acid cycle O 2 High- electrons and H + ELECTRON TRANSPORT SYSTEM TOTALS 6 H 2 O * Cytoplasmic NADH sometimes yields only 1.5 ATP/NADH instead of 2.5 ATP/NADH ATP 6 CO 2
9 Figure 4.16 Pyruvate is the branch point between aerobic and anaerobic metabolism of glucose Anaerobic Lactate Cytosol NAD + NADH Mitochondrial matrix Aerobic Pyruvate Pyruvate Acetyl CoA CoA Acyl unit CITRIC ACID CYCLE CoA = Carbon = Oxygen = Coenzyme A H and OH not shown 33 Central dogma of molecular biology Transfer of sequence information between biopolymers 3 General transfers of sequence information Transcription (same language, different format) sequence to sequence synthesizes from Translation (different language) sequence to Polypeptide sequence Ribosomes synthesize polypeptides from Replication (same language, same format) sequence to sequence synthesizes new from a template 34 Protein synthesis 35 Figure 4.17 The genetic code as it appears in the codons of Second base of codon 36 Proteins are composed of 20 naturally occurring amino acids (chemical synthesis can produce many many more) The amino acid sequence (primary structure) of proteins is determined by the genetic code stored in Sections of that produce a particular polypeptide (or its variant) are known as genes One gene-one polypeptide hypothesis (doesn t account for alternative splicing Genetic code is comprised of 4 different nucleotides To encode 20 amino acids with 4 letters, the minimum length of a code for amino acids is =16; 4 3 =64 One triplet of nucleotides is known as a codon First base of codon Phe Leu Leu Ile Met Start Val Ser Pro Thr Ala Tyr Stop His Gln Asn Lys Asp Glu Cys Stop Trp Arg Ser Arg Gly Third base of codon
10 Figure 4.18 ESSENTIALS Overview of Protein Synthesis 37 Figure 4.18 ESSENTIALS Overview of Protein Synthesis Slide 1 38 GENE ACTIVATION Gene Regulatory proteins Constitutively active Regulated activity Induction Repression Nucleus Cytosol Figure 4.18 ESSENTIALS Overview of Protein Synthesis Slide 2 39 Figure 4.18 ESSENTIALS Overview of Protein Synthesis Slide 3 40 Gene Regulatory proteins Gene Regulatory proteins GENE ACTIVATION GENE ACTIVATION Constitutively active Regulated activity Constitutively active Regulated activity Induction Repression Induction Repression TRANSCRIPTION (See Fig. 4.19) TRANSCRIPTION (See Fig. 4.19) si PROCESSING (See Fig. 4.20) Alternative splicing Interference Processed silenced Nucleus Nucleus Cytosol Cytosol
11 Figure 4.18 ESSENTIALS Overview of Protein Synthesis Slide 4 41 Figure 4.18 ESSENTIALS Overview of Protein Synthesis Slide 5 42 Gene Regulatory proteins Gene Regulatory proteins GENE ACTIVATION GENE ACTIVATION Constitutively active Regulated activity Constitutively active Regulated activity Induction Repression Induction Repression TRANSCRIPTION (See Fig. 4.19) TRANSCRIPTION (See Fig. 4.19) si si PROCESSING (See Fig. 4.20) Alternative splicing Interference PROCESSING (See Fig. 4.20) Alternative splicing Interference Processed silenced Processed silenced Nucleus Nucleus TRANSLATION (See Fig. 4.21) r in ribosomes t Amino acids Cytosol TRANSLATION (See Fig. 4.21) r in ribosomes t Amino acids Cytosol Protein chain Protein chain POST- TRANSLATIONAL MODIFICATION Folding and cross-links Cleavage into smaller peptides Addition of groups: sugars lipids Assembly into polymeric proteins -CH 3 phosphate Synthesis 43 Figure 4.19 Transcription 44 Promoter Transcription factors Template strand binds to. The section of that contains the gene unwinds. bases bind to, creating a single strand of. Site of nucleotide assembly bases transcript Lengthening strand and the detach from, and the goes to the cytosol after processing. strand released Leaves nucleus after processing
12 Figure 4.20 processing Template strand Gene 45 Figure 4.21 Translation 46 Transcription processing Nuclear membrane Promoter Transcribed section a b c d e f g h i Attachment of ribosomal subunits TRANSCRIPTION Translation Amino acid t Growing peptide chain Incoming t bound to an amino acid Unprocessed A B C D E F G H I Outgoing empty t C Introns removed Processing may produce two proteins from one gene by alternative splicing. Introns removed B D E F H A C E G Exons for protein #1 Exons for protein #2 D H I Termination Ribosomal subunits Completed peptide Ribosome Anticodon Each t molecule attaches at one end to a specific amino acid. The anticodon of the t molecule pairs with the appropriate codon on the, allowing amino acids to be linked in the order specified by the code. Figure 4.21 Translation Slide 1 47 Figure 4.21 Translation Slide 2 48 Transcription Nuclear membrane Transcription processing Nuclear membrane
13 Figure 4.21 Translation Slide 3 49 Figure 4.21 Translation Slide 4 50 Transcription processing Nuclear membrane Transcription processing Nuclear membrane Attachment of ribosomal subunits Attachment of ribosomal subunits Translation Amino acid t Incoming t bound to an Growing peptide amino acid chain Lys Asp Outgoing empty t Phe Trp Anticodon Ribosome Each t molecule attaches at one end to a specific amino acid. The anticodon of the t molecule pairs with the appropriate codon on the, allowing amino acids to be linked in the order specified by the code. Figure 4.21 Translation Slide 5 51 Protein Synthesis 52 Transcription processing Nuclear membrane Attachment of ribosomal subunits BioFlix TM : Protein Synthesis Translation Amino acid t Incoming t bound to an Growing peptide amino acid chain Lys Asp Outgoing empty t Phe Trp Anticodon Ribosome Termination Ribosomal subunits Completed peptide Each t molecule attaches at one end to a specific amino acid. The anticodon of the t molecule pairs with the appropriate codon on the, allowing amino acids to be linked in the order specified by the code.
14 Protein Sorting Directs Proteins to Their Destination 53 Proteins Undergo Post-Translational Modification 54 Signal sequence Protein folding Cross-linkage Cleavage Addition of other molecules or groups Assembly into polymeric proteins Summary 55 Summary 56 Energy in biological systems Chemical reactions Chemical reactions Enzymes Metabolism ATP production Reactants Products Reaction rate Free Activation Exergonic versus endergonic reactions Reversible versus irreversible reactions
15 Summary 57 Summary 58 Enzymes and substrates Metabolism Cofactors versus coenzymes Catabolic versus anabolic reactions Classification of reactions Control of metabolic pathways Oxidation-reduction Hydrolysis-dehydration Addition-subtraction-exchange Ligation Aerobic versus anaerobic pathways Summary 59 ATP production Glycolysis Citric acid cycle Electron transport chain Glycogen, protein, and lipid metabolism Aerobic versus anaerobic metabolism Gene transcription and alternative splicing Translation and transfer and ribosomal Post-translational modifications
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