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Forms of Energy
There are two basic forms of energy. Kinetic energy is the energy of motion. Potential energy is stored energy. Food eaten has potential energy because it can be converted into kinetic energy. Potential energy in foods is chemical energy. Organisms can convert chemical energy into a form of kinetic energy called mechanical energy for motion.
Flow of energy
and energy is released. Endergonic reactions have a positive G and occur only if there is an input of energy. Energy released from exergonic reactions is used to drive endergonic reactions inside cells. ATP is the energy carrier between exergonic and endergonic reactions.
Coupled Reactions
In coupled reactions, energy released by
an exergonic reaction drives an endergonic reaction.
Coupled reactions
Function of ATP
Cells make use of ATP for: Chemical work ATP supplies energy to
synthesize macromolecules, and therefore the organism Transport work ATP supplies energy needed to pump substances across the plasma membrane Mechanical work ATP supplies energy for cellular movements
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Anabolism
Anabolism provides the substances needed for cellular growth and repair Dehydration synthesis type of anabolic process used to make polysaccharides, triglycerides, and proteins produces water
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Anabolism
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Catabolism
Catabolism breaks down larger molecules into smaller ones Hydrolysis a catabolic process used to decompose carbohydrates, lipids, and proteins water is used reverse of dehydration synthesis
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Catabolism
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Energy of Activation
The energy that must be added to cause
molecules to react with one another is called the energy of activation (Ea). The addition of an enzyme does not change the free energy of the reaction, rather an enzyme lowers the energy of activation.
Enzyme-Substrate Complexes
Every reaction in a cell requires a specific
enzyme. Enzymes are named for their substrates: Substrate Enzyme Lipid Lipase Urea Urease Maltose Maltase Ribonucleic acid Ribonuclease
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Enzyme names commonly reflect the substrate have the suffix ase sucrase, lactase, protease, lipase
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Enzymatic reaction
Temperature and pH
As the temperature rises, enzyme activity
increases because more collisions occur between enzyme and substrate. If the temperature is too high, enzyme activity levels out and then declines rapidly because the enzyme is denatured. Each enzyme has an optimal pH at which the rate of reaction is highest.
Enzyme Inhibition
Enzyme inhibition occurs when an active
enzyme is prevented from combining with its substrate. When the product of a metabolic pathway is in abundance, it binds competitively with the enzymes active site, a simple form of feedback inhibition. Other metabolic pathways are regulated by the end product binding to an allosteric site on the enzyme.
Feedback inhibition
Enzyme Cofactors
Presence of enzyme cofactors may be
necessary for some enzymes to carry out their functions. Inorganic metal ions, such as copper, zinc, or iron function as cofactors for certain enzymes. Organic molecules, termed coenzymes, must be present for other enzymes to function. Some coenzymes are vitamins.
Cellular Respiration
The overall equation for cellular respiration
is opposite that of photosynthesis: C6H12O6 + 6O2 6CO2 + 6H2O + Energy In this reaction, glucose is oxidized and oxygen is reduced to become water. The complete oxidation of a mol of glucose releases 686 kcal of energy that is used to synthesize ATP.
Chapter Summary
Two laws of thermodynamics state that
energy cannot be created or destroyed, and energy transformations result in a loss of energy, usually as heat. As a result of these laws, we know the entropy of the universe is ever increasing, and that it takes energy to maintain the organization of living things.
Each reaction requires a specific enzyme. Substrate concentration, temperature, pH, and
enzyme concentration affect the rates of reactions. Most metabolic pathways are regulated by feedback inhibition. Cellular respiration involves oxidation-reduction reactions and accounts for the flow of energy through all living things.
Cellular Respiration
Occurs in three series of reactions 1. Glycolysis 2. Citric acid cycle 3. Electron transport chain Produces carbon dioxide water ATP (chemical energy) heat Includes anaerobic reactions (without O2) - produce little ATP aerobic reactions (requires O2) - produce most ATP
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reaction (releases energy) which drives ATP synthesis, which is an endergonic reaction (energy is required). The overall equation for cellular respiration shows the coupling of glucose breakdown to ATP buildup. The breakdown of one glucose molecule results in a maximum of 36 to 38 ATP molecules, representing about 40% of the potential energy within the glucose molecule.
ATP Molecules
each ATP molecule has three parts:
an adenine molecule a ribose molecule three phosphate molecules in a chain third phosphate attached by high-energy bond when the bond is broken, energy is transferred when the bond is broken, ATP becomes ADP ADP becomes ATP through phosphorylation phosphorylation requires energy released from cellular respiration
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Cellular respiration
reactions that give off CO2 and produce one ATP per cycle; occurs twice per glucose molecule Electron transport system a series of carriers that accept electrons removed from glucose and pass them from one carrier to the next until the final receptor, O2 is reached; water is produced; energy is released and used to synthesize 32 to 34 ATP If oxygen is not available, fermentation occurs in the cytoplasm instead of proceeding to cellular respiration.
Glycolysis
series of ten reactions breaks down glucose into 2 pyruvic acids occurs in cytosol anaerobic phase of cellular respiration yields two ATP molecules per glucose Summarized by three main events 1. phosphorylation 2. splitting 3. production of NADH and ATP
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Energy-Investment Steps
As glycolysis begins, two ATP are used to
activate glucose, a 6-carbon molecule that splits into two C3 molecules known as PGAL. PGAL carries a phosphate group from ATP. From this point on, each C3 molecule undergoes the same series of reactions.
Glycolysis
Event 1 - Phosphorylation two phosphates added to glucose requires ATP Event 2 Splitting (cleavage) 6-carbon glucose split into two 3-carbon molecules
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Energy-Harvesting Steps
Oxidation of PGAL now occurs by the
removal of electrons that are accompanied by hydrogen ions, both picked up by the coenzyme NAD+: 2 NAD+ + 4H 2 NADH + 2 H+ The oxidation of PGAL and subsequent substrates results in four high-energy phosphate groups used to synthesize ATP in substrate-level phosphorylation.
Glycolysis
Event 3 Production of NADH and ATP hydrogen atoms are released hydrogen atoms bind to NAD+ to produce NADH NADH delivers hydrogen atoms to electron transport chain if oxygen is available ADP is phosphorylated to become ATP two molecules of pyruvic acid are produced
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Glycolysis Summary
Inputs: Glucose 2 NAD+ 2 ATP 4 ADP + 2 P Outputs: 2 pyruvate 2 NADH 2 ADP 2 ATP (net gain)
Anaerobic Reactions
If oxygen is not available electron transport chain cannot accept NADH pyruvic acid is converted to lactic acid glycolysis is inhibited ATP production declines
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Aerobic Reactions
If oxygen is available pyruvic acid is used to produce acetyl CoA citric acid cycle begins electron transport chain functions carbon dioxide and water are formed 36 molecules of ATP produced per glucose molecule
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Transition Reaction
The transition reaction connects glycolysis to the
citric acid cycle, and is thus the transition between these two pathways. Pyruvate is converted to a C2 acetyl group attached to coenzyme A (CoA), and CO2 is released. During this oxidation reaction, NAD+ is converted to NADH + H+; the transition reaction occurs twice per glucose molecule.
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the end of the electron transport system. Next, oxygen combines with hydrogen, and water forms: O2 + 2 e- + 2 H+ H2O When NADH carries electrons to the first carrier, enough energy is released by the time electrons are accepted by O2 to produce three ATP; two ATP are produced when FADH2 delivers electrons to the carriers.
Organization of Cristae
The electron transport system is located in the
cristae of the mitochondria and consists of three protein complexes and two mobile carriers. The mobile carriers transport electrons between the complexes, which also contain electron carriers. The carriers use the energy released by electrons as they move down the carriers to pump H+ from the matrix into the intermembrane space of the mitochondrion.
established with few H+ in the matrix and many in the intermembrane space. The cristae also contain an ATP synthase complex through which hydrogen ions flow down their gradient from the intermembrane space into the matrix. The flow of three H+ through an ATP synthase complex causes a conformational change, which causes the ATP synthase to synthesize ATP from ADP + P.
Organization of cristae
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Carbohydrate Storage
Excess glucose stored as glycogen (primarily by liver and muscle cells) fat converted to amino acids
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Structure of DNA
The structure of DNA was determined by James
Watson and Francis Crick in the early 1950s. DNA is a polynucleotide; nucleotides are composed of a phosphate, a sugar, and a nitrogen-containing base. DNA has the sugar deoxyribose and four different bases: adenine (A), thymine (T), guanine (G), and cytosine (C).
resembles a ladder. The sides of the ladder are the sugarphosphate backbones, and the rungs of the ladder are the complementary paired bases. The two DNA strands are anti-parallel they run in opposite directions.
Replication of DNA
DNA replication occurs during chromosome
duplication; an exact copy of the DNA is produced with the aid of DNA polymerase. Hydrogen bonds between bases break and enzymes unzip the molecule. Each old strand of nucleotides serves as a template for each new strand.
complementary positions are joined by DNA polymerase. The process is semiconservative because each new double helix is composed of an old strand of nucleotides from the parent molecule and one newly-formed strand. Some cancer treatments are aimed at stopping DNA replication in rapidlydividing cancer cells.
Gene Expression
A gene is a segment of DNA that specifies
the amino acid sequence of a protein. Gene expression occurs when gene activity leads to a protein product in the cell. A gene does not directly control protein synthesis; instead, it passes its genetic information on to RNA, which is more directly involved in protein synthesis.
RNA
RNA (ribonucleic acid) is a singlestranded nucleic acid in which A pairs with U (uracil) while G pairs with C. Three types of RNA are involved in gene expression: messenger RNA (mRNA) carries genetic information to the ribosomes, ribosomal RNA (rRNA) is found in the ribosomes, and transfer RNA (tRNA) transfers amino acids to the ribosomes, where the protein product is synthesized.
Structure of RNA
Central Concept
The central concept of genetics involves
the DNA-to-protein sequence involving transcription and translation. DNA has a sequence of bases that is transcribed into a sequence of bases in mRNA. Every three bases is a codon that stands for a particular amino acid.
Transcription
During transcription in the nucleus, a
segment of DNA unwinds and unzips, and the DNA serves as a template for mRNA formation. RNA polymerase joins the RNA nucleotides so that the codons in mRNA are complementary to the triplet code in DNA.
Processing of mRNA
DNA contains exons and introns. Before mRNA leaves the nucleus, it is
processed and the introns are excised so that only the exons are expressed. The splicing of mRNA is done by ribozymes, organic catalysts composed of RNA, not protein. Primary mRNA is processed into mature mRNA.
Function of introns
Translation
Translation is the second step by which
gene expression leads to protein synthesis. During translation, the sequence of codons in mRNA specifies the order of amino acids in a protein. Translation requires several enzymes and two other types of RNA: transfer RNA and ribosomal RNA.
Transfer RNA
During translation, transfer RNA (tRNA)
molecules attach to their own particular amino acid and travel to a ribosome. Through complementary base pairing between anticodons of tRNA and codons of mRNA, the sequence of tRNAs and their amino acids form the sequence of the polypeptide.
Ribosomal RNA
Ribosomal RNA, also called structural
RNA, is made in the nucleolus. Proteins made in the cytoplasm move into the nucleus and join with ribosomal RNA to form the subunits of ribosomes. A large subunit and small subunit of a ribosome leave the nucleus and join in the cytoplasm to form a ribosome just prior to protein synthesis.
binding sites for two tRNA molecules at a time. As the ribosome moves down the mRNA molecule, new tRNAs arrive, and a polypeptide forms and grows longer. Translation terminates once the polypeptide is fully formed; the ribosome separates into two subunits and falls off the mRNA. Several ribosomes may attach and translate the same mRNA, therefore the name polyribosome.
Chain Initiation
During chain initiation, a small ribosomal
subunit, the mRNA, an initiator tRNA, and a large ribosomal unit bind together. First, a small ribosomal subunit attaches to the mRNA near the start codon. The anticodon of tRNA, called the initiator RNA, pairs with this codon. Then the large ribosomal subunit joins.
Initiation
Chain Elongation
During chain elongation, the initiator tRNA
passes its amino acid to a tRNA-amino acid complex that has come to the second binding site. The ribosome moves forward and the tRNA at the second binding site is now at the first site, a sequence called translocation. The previous tRNA leaves the ribosome and picks up another amino acid before returning.
Elongation
Chain Termination
Chain termination occurs when a stopcodon sequence is reached. The polypeptide is enzymatically cleaved from the last tRNA by a release factor, and the ribosome falls away from the mRNA molecule. A newly synthesized polypeptide may function along or become part of a protein.
Termination
Gene Mutations
A gene mutation is a change in the
sequence of bases within a gene.
Frameshift Mutations
Frameshift mutations involve the addition
or removal of a base during the formation of mRNA; these change the genetic message by shifting the reading frame.
Point Mutations
The change of just one nucleotide causing
a codon change can cause the wrong amino acid to be inserted in a polypeptide; this is a point mutation. In a silent mutation, the change in the codon results in the same amino acid.
resulting protein may be too short to function; this is a nonsense mutation. If a point mutation involves the substitution of a different amino acid, the result may be a protein that cannot reach its final shape; this is a missense mutation. An example is Hbs which causes sicklecell disease.
Structure of DNA
two polynucleotide chains hydrogen bonds hold nitrogenous bases together bases pair specifically (A-T and C-G) forms a helix DNA wrapped about histones forms chromosomes
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RNA Molecules
Messenger RNA (mRNA) delivers genetic information
from nucleus to the cytoplasm single polynucleotide chain formed beside a strand of DNA RNA nucleotides are complementary to DNA nucleotides (exception no thymine in RNA; replaced with uracil) making of mRNA is transcription
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RNA Molecules
Transfer RNA (tRNA) carries amino acids to mRNA carries anticodon to mRNA translates a codon of mRNA into an amino acid Ribosomal RNA (rRNA) provides structure and enzyme activity for ribosomes
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Protein Synthesis
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Protein Synthesis
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DNA Replication
hydrogen bonds break between bases double strands unwind and pull apart new nucleotides pair with exposed bases controlled by DNA polymerase
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Mutations
Mutations change in genetic information Result when extra bases are added or deleted bases are changed May or may not change the protein Repair enzymes correct mutations
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Clinical Application
Phenylketonuria PKU
enzyme that breaks down the amino acid phenylalanine is missing build up of phenylalanine causes mental retardation treated by diets very low in phenylalanine
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