Chapter 4: Cellular Metabolism
Metabolic Reactions
metabolism: all chemical reactions occurring in cells & necessary to maintain life
anabolism: reactions that build up molecules (larger molecules are built from smaller molecules); generally requires energy
dehydration synthesis is used to join 2 molecules
dehydration synthesis: a bond is formed between 2 molecules with removal of water - OH is removed from 1 molecule and H is removed from the other; the OH and H join to form water (H2O)
2 monosaccharides are joined to form a disaccharide,
chains of monosaccharides joined together are polysaccharides
Fatty acids are joined to glycerol by dehydration synthesis
Amino acids are joined to form a
dipeptide by dehydration synthesis (a peptide bond is formed)
chains
of amino acids joined by peptide bonds are polypeptides, or proteins
catabolism: reactions that break down molecules (larger molecules are broken down into smaller molecules); often releases energy
hydrolysis is used to break apart 2 molecules - the bond between them is broken by addition of water
hydrolysis is the opposite of dehydration synthesis
water is split and OH is added to 1 molecule and H is added to the other
Control of Metabolic Reactions
Enzymes: increase the rate of a chemical reaction by lowering its activation energy
Enzymes are almost always composed of proteins
Enzymes are organic catalysts (catalysts speed up chemical reactions)
An enzyme reacts with a specific substrate to form a specific product; the part of an enzyme molecule where the substrate binds is called the active site
Enzymes bind to specific substrates because the substrate fits into the active site based on its shape (lock & key mechanism)
When the product is released the enzyme is unaltered, that is, not changed or used up - it can then bind more substrate and catalyze the same chemical reaction again and again
Control of Enzyme Activity
Enzyme activity (the rate of product formation) increases with increased concentration of enzyme or substrate
Enzymes (like other proteins) can be denatured by heat, chemicals, altered pH - things that change the shape of the protein change the shape of the active site and the substrate no longer binds
Many enzymes require a nonprotein cofactor to be active; an organic cofactor is called a coenzyme
Metabolic Pathways
Metabolic pathways are a series of chemical reactions, each catalyzed by a different enzyme, that are linked because the product of the first chemical reaction serves as the substrate for the enzyme that catalyzes the next chemical reaction in the pathway.
The final chemical reaction in a metabolic pathway makes the final product of the pathway.
Energy for Metabolic Reactions
Energy: the capacity to do work (change or move matter)
Energy forms: heat, light, sound, electrical energy, mechanical energy, chemical energy
Most metabolic reactions use chemical energy (ATP)
Chemical energy is released when chemical bonds are broken
Heat (burning molecules) breaks chemical bonds to release energy
Oxidation: addition of oxygen (or removal of hydrogen/electrons)
Glucose oxidation in cellular respiration releases energy for cellular reactions
Enzymes reduce the large amounts of energy required for oxidation during cellular respiration
Cellular Respiration: the complete breakdown of glucose to carbon dioxide and water
Includes glycolysis, the citric acid cycle & the electron transport chain
Electrons captured move through the electron transport chain to provide energy to produce ATP (adenosine triphosphate)
Glucose metabolism is a series of oxidation-reduction reactions. Glucose is oxidized (electrons are removed) and oxygen is reduced (ultimately gains the electrons removed from glucose)
During the process, at a couple of steps in the metabolic pathways, an enzyme will directly transfer a phosphate from one of the metabolic intermediates to ADP to form ATP - this is called substrate-level phosphorylation
ATP (Adenosine Triphosphate)
ATP is a nucleotide that provides energy for most of the chemical reactions occurring within cells
Energy (about 7.4 kcal/mole ATP) is released when the terminal (last, or third) phosphate is removed by hydrolysis
Energy released from this reaction is used to power anabolic reactions (synthesis reactions that require energy) in cells
Glycolysis: the oxidation of glucose (a 6 carbon molecule) to 2 pyruvate (3 carbon molecules)
Occurs in the cytoplasm
Net gain of 2 ATP molecules produced directly by substrate-level phosphorylation (4 produced, 2 used to get the glycolysis pathway started) plus high energy electrons
No oxygen is required – anaerobic phase of cellular respiration
Citric acid (Krebs) cycle & electron transport chain: completes the oxidation of glucose by oxidizing the pyruvate molecules to 6 carbon dioxide (CO2) molecules and water
Occurs in mitochondria
Pyruvate is oxidized to acetate ( a 2 carbon molecule) and a CO2 molecule and high energy electrons are released
Acetate is joined to coenzyme A to form acetyl CoA
Acetyl CoA enters the citric acid cycle, where oxidation is completed, releasing 2 molecules of CO2 , and high energy electrons
1 molecule of ATP is generated directly by substrate-level phosphorylation when each acetate molecule is oxidized in the citric acid cycle, for a gain of 2 more ATP molecules per glucose molecule
The high energy electrons from the oxidation of glucose pass down the electron transport chain and energize a process that adds phosphate to ADP to form ATP
This is oxidative phosphorylation: the high energy electrons from oxidation provide the energy to form ATP
Oxidative phosphorylation generates 34 molecules of ATP from the complete oxidation of one glucose molecule but it "costs" 2 ATP to shuttle the high energy electrons from glycolysis into the mitochondria - so you net 32 ATP molecules by oxidative phosphorylation
Oxygen is final electron acceptor – the electrons pass from the electron transport chain to oxygen and hydrogen to form water - aerobic phase of cellular respiration
The complete oxidation of glucose by aerobic celllar respiration produces 4 ATP by substrate-level phosphorylation and 32 ATP by oxidative phosphorylation for a total of 36 ATP per molecule of glucose.
Of course you may wonder about the catabolism of other types of organic macromolecules (food).
Proteins are broken down to amino acids, the amino group is removed (deamination), and the remainder of the molecule enters glycolysis or the citric acid cycle at some point, depending on which amino acid it is and what the structure of its side chain is.
Triglycerides are broken down to glycerol and fatty acids. Glycerol enters glycolysis and the fatty acids are broken down to acetate molecules which enter the citric acid cycle.
Genetic information
Gene: sequence of DNA used to form a polypeptide (contains the code for a ploypeptide)
Genome: all the DNA within the nucleus of a cell
DNA Synthesis:
DNA replication is carried out by the enzyme DNA Polymerase, as well as some additional protein factors
DNA helicase unwinds the double helix in preparation for replication
DNA Polymerase has a proofreading activity to correct replication errors (adding the wrong base). The corrected error rate (after proofreading) is 1 in 1 billion bases
DNA replication is semiconservative: each newly replicated DNA molecule consists of 1 old strand from the original double- stranded DNA molecule, and 1 newly synthesized strand
Gene Expression
Transcription: DNA is transcribed to RNA in the nucleus
3 types of RNA can be made:
mRNA (messenger RNA): directs the synthesis of a protein
rRNA (ribosomal RNA): rRNA along with proteins comprise the structure of the 2 subunits of the ribosome
tRNA (transfer RNA): binds to an amino acid & delivers it to the ribosome during protein synthesis; has anticodon that binds to mRNA codon
Transcription is carried out by a 5’ to 3’ RNA Polymerase, as well as additional protein factors
Translation: mature mRNA is translated to protein in the cytoplasm
Translation occurs at the ribosomes
Many ribosomes may synthesize protein from the same mRNA molecule at the same time (polyribosomes)
tRNA molecules carry amino acids to the ribosome during translation (a tRNA for each amino acid)
Ribosome subunits associate immediately prior to translation, and dissociate following translation
Codon: sequence of 3 nucleotides in mRNA that specify 1 amino acid in a polypeptide
3:1 ratio for # nucleotides in mRNA : # amino acids in polypeptide
Ribosomes bind mRNA and begin translation, usually, at the first AUG (start) codon
One of 3 stop codons (UAA, UAG, UGA) signals the ribosome to stop translation of the mRNA… following translation, a release factor cleaves the complete polypeptide from the last tRNA and the ribosome, and the polypeptide leaves the ribosome
