Energy and Cellular Metabolism

Energy and Cellular Metabolism
Chapter 4 Energy and Cellular Metabolism

Energy in biological systems Chemical reactions Enzymes Metabolism
About this Chapter Energy in biological systems Chemical reactions Enzymes Metabolism ATP production Synthetic pathways

Energy: Biological Systems
Energy transfer in the environment KEY Transfer of radiant or heat energy Sun Transfer of energy in chemical bonds Heat energy Energy lost to environment Radiant energy Energy for work CO2 + + Photosynthesis takes place in plant cells, yielding: Respiration takes place in human cells, yielding: CO2 Energy stored in biomolecules Energy stored in biomolecules + H2O CO2 N2 H2O Figure 4-1

Energy: Capacity to Do Work
Chemical work Making and breaking of chemical bonds Transport work Moving ions, molecules, and larger particles Can create concentration gradients Mechanical work Used for movement

Kinetic and Potential Energy
Figure 4-2

First law of Thermodynamics
Thermodynamic Energy First law of Thermodynamics Total amount of energy in the universe is constant Second law of Thermodynamics Processes move from state of order to disorder

Chemical Reactions: Overview
Activation energy is the energy that must be put into reactants before a reaction can proceed A + B  C + D Figure 4-3

Chemical Reactions: Exergonic and endergonic
Activation energy Activation energy G+H A+B Net free energy change E+F Net free energy change C+D (a) Exergonic reactions (b) Endergonic reactions KEY Reactants Activation of reaction Reaction process Products Figure 4-4

Chemical Reactions: Coupling
Figure 4-5

May be activated, inactivated, or modulated
Enzymes: Overview Isozymes Catalyze same reaction, but under different conditions May be activated, inactivated, or modulated Coenzymes  vitamins Chemical modulators  temperature and pH

Enzymes: Lower activation energy
KEY Reactants Activation energy Activation of reaction Reaction process Products A+B Net free energy change C+D Figure 4-6

Enzymes: Law of Mass Action
Figure 4-9a

Enzymes: Law of Mass Action
Figure 4-9b

Enzymes: Types of Reactions
Table 4-4

A group of metabolic pathways resembles a road map
Metabolism: Overview A group of metabolic pathways resembles a road map Figure 4-10

Metabolism: Cell Regulation
Controlling enzyme concentrations Producing allosteric and covalent modulators Using different enzymes for reversible reactions Isolating enzymes within organelles Maintaining optimum ratio of ATP to ADP

enzyme 1 enzyme 2 enzyme 3 Feedback inhibition Figure 4-11

+ CO2 H2O Glucose + PO4 Glucose + PO4 carbonic anhydrase carbonic anhydrase glucose 6- phosphatase hexokinase hexokinase Carbonic acid Glucose 6-phosphate Glucose 6-phosphate (a) (b) (c) Figure 4-12

ATP Production: Overview
Glucose Overview of aerobic pathways for ATP production G L Y C O S I Glycerol ADP ATP Amino acids Acetyl CoA Citric acid cycle Amino acids Pyruvate Cytosol High-energy electrons Mitochondrion Fatty acids Acetyl CoA ADP Amino acids CITRIC ACID CYCLE ATP CO2 High-energy electrons and H+ ADP ELECTRON TRANSPORT SYSTEM ATP O2 H2O Figure 4-13

ATP Production: Glycolysis
Glucose ATP ADP Glucose + 2 NAD ADP + P  2 Pyruvate + 2 ATP + 2 NADH + 2 H H20 Glucose 6-phosphate Fructose 6-phosphate ATP ADP Fructose 1,6-bisphosphate Dihydroxyacetone phosphate KEY = Carbon Glyceraldehyde 3-phosphate = Oxygen = Phosphate group NAD+ (side groups not shown) NADH 1, 3-Bisphosphoglycerate ADP ATP This section happens twice for each glucose molecule that begins glycolysis 3-Phosphoglycerate 2-Phosphoglycerate H2O Phosphoenol pyruvate ADP ATP Pyruvate Figure 4-14

ATP Production: Pyruvate Metabolism
Pyruvate can be converted into lactate or acetyl CoA NAD+ NADH Anaerobic Aerobic Lactate Pyruvate Pyruvate Pyruvate Acetyl CoA NAD+ Cytosol NADH CO2 CoA Mitochondrial matrix Acetyl CoA CoA KEY Acyl unit = Carbon = Oxygen CITRIC ACID CYCLE CoA = Coenzyme A H and –OH not shown Figure 4-15

ATP Production: Citric Acid Cycle
Acetyl CoA enters the citric acid cycle producing 3 NADH, 1 FADH2, and 1 ATP KEY = Carbon = Oxygen CoA = Coenzyme A Side groups not shown CoA Acetyl CoA CoA Citrate (6C) Oxaloacetate (4C) NADH Isocitrate (6C) NAD+ Malate (4C) Acetyl CoA NAD+ NADH CO2 Citric acid cycle CITRIC ACID CYCLE H2O High-energy electrons a Ketoglutarate (5C) Fumarate (4C) NAD+ CO2 FADH2 NADH ATP FAD ADP CoA Succinate (4C) Succinyl CoA (4C) GTP GDP + Pi CoA CoA Figure 4-16

ATP Production: Electron Transport
CITRIC ACID CYCLE Mitochondrial matrix Inner mitochondrial membrane 2 H2O O2 + Matrix pool of H+ e– 3 1 ATP 4e– ADP + Pi 4 High-energy electrons ATP synthase H+ 2 H+ H+ H+ Intermembrane space H+ H+ H+ ELECTRON TRANSPORT SYSTEM Outer mitochondrial membrane High-energy electrons from glycolysis Cytosol 1 Energy released during metabolism is captured by high-energy electrons carried by NADH and FADH2. 2 Energy from high-energy electrons moving along the electron transport system pumps H+ from the matrix into the intermembrane space. 3 Electrons at the end of the electron transport system are back to their normal energy state. They combine with H+ and oxygen to form water. 4 Potential energy captured in the H+ concentration gradient is converted to kinetic energy when H+ ions pass through the ATP synthase. Some of the kinetic energy is captured as ATP. Figure 4-17

CITRIC ACID CYCLE Mitochondrial matrix Inner mitochondrial membrane e– 1 High-energy electrons Intermembrane space ELECTRON TRANSPORT SYSTEM Outer mitochondrial membrane High-energy electrons from glycolysis Cytosol 1 Energy released during metabolism is captured by high-energy electrons carried by NADH and FADH2. Figure 4-17, step 1

CITRIC ACID CYCLE Mitochondrial matrix Inner mitochondrial membrane e– 1 e– High-energy electrons H+ H+ H+ 2 Intermembrane space H+ H+ H+ ELECTRON TRANSPORT SYSTEM Outer mitochondrial membrane High-energy electrons from glycolysis Cytosol 1 Energy released during metabolism is captured by high-energy electrons carried by NADH and FADH2. 2 Energy from high-energy electrons moving along the electron transport system pumps H+ from the matrix into the intermembrane space. Figure 4-17, steps 1–2

CITRIC ACID CYCLE Mitochondrial matrix Inner mitochondrial membrane 2 H2O O2 + Matrix pool of H+ e– 3 1 4e– High-energy electrons H+ H+ H+ 2 Intermembrane space H+ H+ H+ ELECTRON TRANSPORT SYSTEM Outer mitochondrial membrane High-energy electrons from glycolysis Cytosol 1 Energy released during metabolism is captured by high-energy electrons carried by NADH and FADH2. 2 Energy from high-energy electrons moving along the electron transport system pumps H+ from the matrix into the intermembrane space. 3 Electrons at the end of the electron transport system are back to their normal energy state. They combine with H+ and oxygen to form water. Figure 4-17, steps 1–3

CITRIC ACID CYCLE Mitochondrial matrix Inner mitochondrial membrane 2 H2O O2 + Matrix pool of H+ e– 3 1 ATP 4e– ADP + Pi 4 High-energy electrons ATP synthase H+ H+ 2 H+ H+ Intermembrane space H+ H+ H+ ELECTRON TRANSPORT SYSTEM Outer mitochondrial membrane High-energy electrons from glycolysis Cytosol 1 Energy released during metabolism is captured by high-energy electrons carried by NADH and FADH2. 2 Energy from high-energy electrons moving along the electron transport system pumps H+ from the matrix into the intermembrane space. 3 Electrons at the end of the electron transport system are back to their normal energy state. They combine with H+ and oxygen to form water. 4 Potential energy captured in the H+ concentration gradient is converted to kinetic energy when H+ ions pass through the ATP synthase. Some of the kinetic energy is captured as ATP. NADH and FADH2  ATP by oxidative phosphorylation Figure 4-17, steps 1–4

ATP Production: Energy Yield
AEROBIC METABOLISM C6H12O6 + 6 O2 6 CO2 + 6 H2O ANAEROBIC METABOLISM C6H12O6 2 C3H6O3 (Lactic acid) 1 Glucose NADH FADH2 ATP CO2 1 Glucose NADH FADH2 ATP CO2 G L Y C O S I G L Y C O S I +4 4 2* 2 –2 –2 2 Pyruvate 2 Pyruvate 2 2 –2 2 Acetyl CoA 2 Lactic acid TOTALS NADH 2 ATP Citric acid cycle 6 2 2 4 High-energy electrons and H+ 6 O2 ELECTRON TRANSPORT SYSTEM 26-28 TOTALS 6 H2O 30-32 ATP 6 CO2 * Cytoplasmic NADH sometimes yield only 1.5 ATP/NADH instead of 2.5 ATP/NADH. Figure 4-18

ATP Production: Large Biomolecules
Glycogenolysis Glycogen Storage form of glucose in liver and skeletal muscle Converted to glucose or glucose 6-phosphate

ATP Production: Protein Catabolism and Deamination
(a) Protein catabolism (b) Deamination NAD + H2O NADH + H+ NH3 + Deamination Ammonia Protein or Peptide Amino acid Organic acid H2O Hydrolysis of peptide bond Glycolysis or citric acid cycle Peptide + Amino acid (c) H+ NH3 NH4+ Urea Ammonia Ammonium Figure 4-20

ATP Production: Lipolysis
Triglyceride Glucose 1 Lipases digest triglycerides into glycerol and 3 fatty acids. 1 G L Y C O S I Glycerol 2 2 Glycerol becomes a glycolysis substrate. Fatty acid Cytosol Pyruvate 3 b-oxidation chops 2-carbon acyl units off the fatty acids. 3 b-oxidation CO2 Acetyl CoA CoA Acyl unit 4 4 Acyl units become acetyl CoA and can be used in the citric acid cycle. CoA CITRIC ACID CYCLE Mitochondrial matrix Figure 4-21

Synthesis: Gluconeogenesis
Glucose Liver, kidney Glucose synthesis Glucose 6- phosphate G L U C O N E S I GLYCEROL AMINO ACIDS Pyruvate AMINO ACIDS LACTATE Figure 4-22

Synthesis: Lipids Figure 4-23 Glucose G L Y C O L 1 Y S I S Glycerol
Pyruvate 3 Acetyl CoA Fatty acid synthetase Triglyceride CoA 2 Acyl unit Fatty acids 1 Glycerol can be made from glucose through glycolysis. 2 Two-carbon acyl units from acetyl CoA are linked together by fatty acid synthetase to form fatty acids. 3 One glycerol plus 3 fatty acids make a triglyceride. Figure 4-23

Synthesis: Lipids Figure 4-23, steps 1 34 Glucose G L Y C O L 1 Y S I
Glycerol Pyruvate Acetyl CoA CoA Acyl unit 1 Glycerol can be made from glucose through glycolysis. Figure 4-23, steps 1 34

Synthesis: Lipids Figure 4-23, steps 1–2 35 Glucose G L Y C O L 1 Y S
Glycerol Pyruvate Acetyl CoA Fatty acid synthetase CoA 2 Acyl unit Acyl unit Fatty acids 1 Glycerol can be made from glucose through glycolysis. 2 Two-carbon acyl units from acetyl CoA are linked together by fatty acid synthetase to form fatty acids. Figure 4-23, steps 1–2 35

Synthesis: Lipids Figure 4-23, steps 1–3 36 Glucose G L Y C O L 1 Y S
Glycerol Pyruvate 3 Acetyl CoA Fatty acid synthetase Triglyceride CoA 2 Acyl unit Fatty acids 1 Glycerol can be made from glucose through glycolysis. 2 Two-carbon acyl units from acetyl CoA are linked together by fatty acid synthetase to form fatty acids. 3 One glycerol plus 3 fatty acids make a triglyceride. Figure 4-23, steps 1–3 36

Synthesis: DNA to Protein
Gene Regulatory proteins 1 GENE ACTIVATION Constitutively active Regulated activity Induction Repression 2 TRANSCRIPTION mRNA siRNA 3 mRNA PROCESSING Alternative splicing Interference mRNA “silenced” Processed mRNA Nucleus • rRNA in ribosomes • tRNA • Amino acids Cytoplasm 4 TRANSLATION Protein chain 5 POST-TRANSLATIONAL MODIFICATION Folding and cross-links Cleavage into smaller peptides Addition of groups: • sugars • lipids • -CH3 • phosphate Assembly into polymeric proteins Figure 4-25

Gene Regulatory proteins 1 GENE ACTIVATION Constitutively active Regulated activity Induction Repression Nucleus Cytoplasm Figure 4-25, steps 1

Gene Regulatory proteins 1 GENE ACTIVATION Constitutively active Regulated activity Induction Repression 2 TRANSCRIPTION mRNA Nucleus Cytoplasm Figure 4-25, steps 1–2

Gene Regulatory proteins 1 GENE ACTIVATION Constitutively active Regulated activity Induction Repression 2 TRANSCRIPTION mRNA siRNA 3 mRNA PROCESSING Alternative splicing Interference mRNA “silenced” Processed mRNA Nucleus Cytoplasm Figure 4-25, steps 1–3

Gene Regulatory proteins 1 GENE ACTIVATION Constitutively active Regulated activity Induction Repression 2 TRANSCRIPTION mRNA siRNA 3 mRNA PROCESSING Alternative splicing Interference mRNA “silenced” Processed mRNA Nucleus • rRNA in ribosomes • tRNA • Amino acids Cytoplasm 4 TRANSLATION Protein chain Figure 4-25, steps 1–4

Gene Regulatory proteins 1 GENE ACTIVATION Constitutively active Regulated activity Induction Repression 2 TRANSCRIPTION mRNA siRNA 3 mRNA PROCESSING Alternative splicing Interference mRNA “silenced” Processed mRNA Nucleus • rRNA in ribosomes • tRNA • Amino acids Cytoplasm 4 TRANSLATION Protein chain 5 POST-TRANSLATIONAL MODIFICATION Folding and cross-links Cleavage into smaller peptides Addition of groups: • sugars • lipids • -CH3 • phosphate Assembly into polymeric proteins Figure 4-25, steps 1–5

Protein: Transcription
RNA polymerase 1 RNA polymerase binds to DNA. 2 The section of DNA that contains the gene unwinds. RNA bases 3 RNA bases bind to DNA, creating a single strand of mRNA. Sense strand Site of nucleotide assembly DNA Lengthening mRNA strand mRNA transcript Antisense strand RNA polymerase 4 mRNA and the RNA polymerase detach from DNA, and the mRNA goes to the cytoplasm. RNA polymerase mRNA strand released Leaves nucleus after processing Figure 4-26

Protein: Transcription
Gene Sense strand Antisense strand Promoter Transcribed section DNA TRANSCRIPTION Unprocessed mRNA Introns removed Introns removed Exons for protein #1 Exons for protein #2 Figure 4-27

Protein: Transcription and Translation
DNA 1 Transcription RNA polymerase 2 mRNA processing Nuclear membrane 3 Attachment of ribosomal subunits Amino acid Incoming tRNA bound to an amino acid tRNA Growing peptide chain 4 Translation Outgoing “empty” tRNA Anticodon mRNA Ribosome 5 mRNA Termination Ribosomal subunits Completed peptide Figure 4-28

DNA 1 Transcription RNA polymerase Nuclear membrane Figure 4-28, steps 1

DNA 1 Transcription RNA polymerase 2 mRNA processing Nuclear membrane Figure 4-28, steps 1–2

DNA 1 Transcription RNA polymerase 2 mRNA processing Nuclear membrane 3 Attachment of ribosomal subunits Figure 4-28, steps 1–3

DNA 1 Transcription RNA polymerase 2 mRNA processing Nuclear membrane 3 Attachment of ribosomal subunits Amino acid Incoming tRNA bound to an amino acid tRNA Growing peptide chain 4 Translation Outgoing “empty” tRNA Anticodon mRNA Ribosome Figure 4-28, steps 1–4

DNA 1 Transcription RNA polymerase 2 mRNA processing Nuclear membrane 3 Attachment of ribosomal subunits Amino acid Incoming tRNA bound to an amino acid tRNA Growing peptide chain 4 Translation Outgoing “empty” tRNA Anticodon mRNA Ribosome 5 mRNA Termination Ribosomal subunits Completed peptide Figure 4-28, steps 1–5

Protein: Post-Translational Modification
Protein folding Cross-linkage Cleavage Addition of other molecules or groups Assembly into polymeric proteins

Protein: Post-Translational Modification and the Secretory Pathway
Nucleus Ribosome Peroxisome mRNA Targeted proteins 3 DNA 1 Growing amino-acid chain 2 Mitochondrion Cytosolic protein 1 mRNA is transcribed from the genes in the DNA. 4 2 mRNA leaves the nucleus and attaches to cytosolic ribosomes, initiating translation and protein synthesis. Nuclear pore Endoplasmic reticulum 5 3 Transport vesicle Some proteins are released by free ribosomes into the cytosol or are targeted to specific organelles. 6 4 Ribosomes attached to the rough endoplasmic reticulum direct proteins destined for packaging into the lumen of the RER. Cis-Golgi complex Retrograde Golgi-ER transport 5 Proteins are modified as they pass through the lumen of the ER. 7 Cisterna 6 Transport vesicles move the proteins from the ER to the Golgi complex. 8 7 Gogli cisternae migrate from the cis-face toward the cell membrane. 9 Secretory vesicle 8 Some vesicles bud off the cisterna and move in a retrograde fashion. Lysosome or storage vesicle Trans-Golgi complex 10 9 At the trans-face, some vesicles bud off to form lysosomes. Cytosol 10 Other vesicles become secretory vesicles that release their contents outside the cell. Cell membrane Extracellular space Figure 4-29

Nucleus Ribosome Peroxisome mRNA Targeted proteins DNA 1 Growing amino-acid chain Mitochondrion Cytosolic protein 1 mRNA is transcribed from the genes in the DNA. Nuclear pore Endoplasmic reticulum Transport vesicle Cis-Golgi complex Retrograde Golgi-ER transport Cisterna Secretory vesicle Lysosome or storage vesicle Trans-Golgi complex Cytosol Cell membrane Extracellular space Figure 4-29, steps 1 53

Nucleus Ribosome Peroxisome mRNA Targeted proteins DNA 1 Growing amino-acid chain 2 Mitochondrion Cytosolic protein 1 mRNA is transcribed from the genes in the DNA. 2 mRNA leaves the nucleus and attaches to cytosolic ribosomes, initiating translation and protein synthesis. Nuclear pore Endoplasmic reticulum Transport vesicle Cis-Golgi complex Retrograde Golgi-ER transport Cisterna Secretory vesicle Lysosome or storage vesicle Trans-Golgi complex Cytosol Cell membrane Extracellular space Figure 4-29, steps 1–2 54

Nucleus Ribosome Peroxisome mRNA Targeted proteins 3 DNA 1 Growing amino-acid chain 2 Mitochondrion Cytosolic protein 1 mRNA is transcribed from the genes in the DNA. 2 mRNA leaves the nucleus and attaches to cytosolic ribosomes, initiating translation and protein synthesis. Nuclear pore Endoplasmic reticulum 3 Transport vesicle Some proteins are released by free ribosomes into the cytosol or are targeted to specific organelles. Cis-Golgi complex Retrograde Golgi-ER transport Cisterna Secretory vesicle Lysosome or storage vesicle Trans-Golgi complex Cytosol Cell membrane Extracellular space Figure 4-29, steps 1–3 55

Nucleus Ribosome Peroxisome mRNA Targeted proteins 3 DNA 1 Growing amino-acid chain 2 Mitochondrion Cytosolic protein 1 mRNA is transcribed from the genes in the DNA. 4 2 mRNA leaves the nucleus and attaches to cytosolic ribosomes, initiating translation and protein synthesis. Nuclear pore Endoplasmic reticulum 3 Transport vesicle Some proteins are released by free ribosomes into the cytosol or are targeted to specific organelles. 4 Ribosomes attached to the rough endoplasmic reticulum direct proteins destined for packaging into the lumen of the RER. Cis-Golgi complex Retrograde Golgi-ER transport Cisterna Secretory vesicle Lysosome or storage vesicle Trans-Golgi complex Cytosol Cell membrane Extracellular space Figure 4-29, steps 1–4 56

Nucleus Ribosome Peroxisome mRNA Targeted proteins 3 DNA 1 Growing amino-acid chain 2 Mitochondrion Cytosolic protein 1 mRNA is transcribed from the genes in the DNA. 4 2 mRNA leaves the nucleus and attaches to cytosolic ribosomes, initiating translation and protein synthesis. Nuclear pore Endoplasmic reticulum 5 3 Transport vesicle Some proteins are released by free ribosomes into the cytosol or are targeted to specific organelles. 4 Ribosomes attached to the rough endoplasmic reticulum direct proteins destined for packaging into the lumen of the RER. Cis-Golgi complex Retrograde Golgi-ER transport 5 Proteins are modified as they pass through the lumen of the ER. Cisterna Secretory vesicle Lysosome or storage vesicle Trans-Golgi complex Cytosol Cell membrane Extracellular space Figure 4-29, steps 1–5 57

Nucleus Ribosome Peroxisome mRNA Targeted proteins 3 DNA 1 Growing amino-acid chain 2 Mitochondrion Cytosolic protein 1 mRNA is transcribed from the genes in the DNA. 4 2 mRNA leaves the nucleus and attaches to cytosolic ribosomes, initiating translation and protein synthesis. Nuclear pore Endoplasmic reticulum 5 3 Transport vesicle Some proteins are released by free ribosomes into the cytosol or are targeted to specific organelles. 6 4 Ribosomes attached to the rough endoplasmic reticulum direct proteins destined for packaging into the lumen of the RER. Cis-Golgi complex Retrograde Golgi-ER transport 5 Proteins are modified as they pass through the lumen of the ER. Cisterna 6 Transport vesicles move the proteins from the ER to the Golgi complex. Secretory vesicle Lysosome or storage vesicle Trans-Golgi complex Cytosol Cell membrane Extracellular space Figure 4-29, steps 1–6 58

Nucleus Ribosome Peroxisome mRNA Targeted proteins 3 DNA 1 Growing amino-acid chain 2 Mitochondrion Cytosolic protein 1 mRNA is transcribed from the genes in the DNA. 4 2 mRNA leaves the nucleus and attaches to cytosolic ribosomes, initiating translation and protein synthesis. Nuclear pore Endoplasmic reticulum 5 3 Transport vesicle Some proteins are released by free ribosomes into the cytosol or are targeted to specific organelles. 6 4 Ribosomes attached to the rough endoplasmic reticulum direct proteins destined for packaging into the lumen of the RER. Cis-Golgi complex Retrograde Golgi-ER transport 5 Proteins are modified as they pass through the lumen of the ER. 7 Cisterna 6 Transport vesicles move the proteins from the ER to the Golgi complex. 7 Gogli cisternae migrate from the cis-face toward the cell membrane. Secretory vesicle Lysosome or storage vesicle Trans-Golgi complex Cytosol Cell membrane Extracellular space Figure 4-29, steps 1–7 59

Nucleus Ribosome Peroxisome mRNA Targeted proteins 3 DNA 1 Growing amino-acid chain 2 Mitochondrion Cytosolic protein 1 mRNA is transcribed from the genes in the DNA. 4 2 mRNA leaves the nucleus and attaches to cytosolic ribosomes, initiating translation and protein synthesis. Nuclear pore Endoplasmic reticulum 5 3 Transport vesicle Some proteins are released by free ribosomes into the cytosol or are targeted to specific organelles. 6 4 Ribosomes attached to the rough endoplasmic reticulum direct proteins destined for packaging into the lumen of the RER. Cis-Golgi complex Retrograde Golgi-ER transport 5 Proteins are modified as they pass through the lumen of the ER. 7 Cisterna 6 Transport vesicles move the proteins from the ER to the Golgi complex. 8 7 Gogli cisternae migrate from the cis-face toward the cell membrane. Secretory vesicle 8 Some vesicles bud off the cisterna and move in a retrograde fashion. Lysosome or storage vesicle Trans-Golgi complex Cytosol Cell membrane Extracellular space Figure 4-29, steps 1–8 60

Nucleus Ribosome Peroxisome mRNA Targeted proteins 3 DNA 1 Growing amino-acid chain 2 Mitochondrion Cytosolic protein 1 mRNA is transcribed from the genes in the DNA. 4 2 mRNA leaves the nucleus and attaches to cytosolic ribosomes, initiating translation and protein synthesis. Nuclear pore Endoplasmic reticulum 5 3 Transport vesicle Some proteins are released by free ribosomes into the cytosol or are targeted to specific organelles. 6 4 Ribosomes attached to the rough endoplasmic reticulum direct proteins destined for packaging into the lumen of the RER. Cis-Golgi complex Retrograde Golgi-ER transport 5 Proteins are modified as they pass through the lumen of the ER. 7 Cisterna 6 Transport vesicles move the proteins from the ER to the Golgi complex. 8 7 Gogli cisternae migrate from the cis-face toward the cell membrane. 9 Secretory vesicle 8 Some vesicles bud off the cisterna and move in a retrograde fashion. Lysosome or storage vesicle Trans-Golgi complex 9 At the trans-face, some vesicles bud off to form lysosomes. Cytosol Cell membrane Extracellular space Figure 4-29, steps 1–9 61

Nucleus Ribosome Peroxisome mRNA Targeted proteins 3 DNA 1 Growing amino-acid chain 2 Mitochondrion Cytosolic protein 1 mRNA is transcribed from the genes in the DNA. 4 2 mRNA leaves the nucleus and attaches to cytosolic ribosomes, initiating translation and protein synthesis. Nuclear pore Endoplasmic reticulum 5 3 Transport vesicle Some proteins are released by free ribosomes into the cytosol or are targeted to specific organelles. 6 4 Ribosomes attached to the rough endoplasmic reticulum direct proteins destined for packaging into the lumen of the RER. Cis-Golgi complex Retrograde Golgi-ER transport 5 Proteins are modified as they pass through the lumen of the ER. 7 Cisterna 6 Transport vesicles move the proteins from the ER to the Golgi complex. 8 7 Gogli cisternae migrate from the cis-face toward the cell membrane. 9 Secretory vesicle 8 Some vesicles bud off the cisterna and move in a retrograde fashion. Lysosome or storage vesicle Trans-Golgi complex 10 9 At the trans-face, some vesicles bud off to form lysosomes. Cytosol 10 Other vesicles become secretory vesicles that release their contents outside the cell. Cell membrane Extracellular space Figure 4-29, steps 1–10 62

Energy Kinetic energy Potential energy Summary Chemical Transport
Mechanical Kinetic energy Potential energy

Free energy and activation energy
Summary Chemical reactions Reactants Products Reaction rate Free energy and activation energy Exergonic versus endergonic reactions Reversible versus irreversible reactions

Enzymes Summary Definition Characteristics Law of mass action
Type of reactions

Metabolism Summary Catabolic versus anabolic reactions
Control of metabolic pathways Aerobic versus anaerobic pathways

Glycogen, protein, and lipid metabolism
Summary ATP production Glycolysis Pyruvate metabolism Citric acid cycle Electron transport chain Glycogen, protein, and lipid metabolism

Synthetic pathways Summary Gluconeogenesis Lipid synthesis
Protein synthesis Transcription Translation Post-translational modification

Energy and Cellular Metabolism

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