Enzymes, Metabolism, and Genetics Unit 4 Enzymes, Metabolism, and Genetics

Metabolism Metabolism is the sum of all the chemical reactions in a cell Anabolism – Chemical reactions that build molecules by using available energy to form bonds Catabolism – Chemical reactions that break down larger molecules to release energy, making it available to do work Chemical reactions occur when atoms or molecules (reactants) exchange or share electrons to become more stable and result in new molecules (products) with new properties (unique compared to original reactants).

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Chemical Reactions Types of reactions: Synthesis (Anabolism) A + B  AB Glucose + Fructose  Sucrose + water Decomposition (Catabolism) AB  A + B Sucrose + water  Glucose + Fructose Exchange AB + CD  AC +BD NaOH + HCl  NaCl + H20 Redox: Oxidation – loses electrons or gains oxygen atom Reduction – gains electrons or loses oxygen atoms

Energy Flow in Chemical Reactions During some reactions energy is released - this is an exergonic reaction (for “release” (ex) of “energy” (erg)) During some reactions energy is absorbed – this is an endergonic reaction (end = abosorb or into) Coupling reactions – When energy is given up by one reaction and absorbed in another reaction.

Chemical Reactions need a little help These reactions require a large amount of “Activation Energy” which makes most reactions virtually impossible on their own. Enzymes are organic catalysts – substances that lower the activation energy and allow the reaction to occur more easily.

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Properties of Enzymes Defined: Organic catalysts - Make reactions happen more quickly Activation Energy: energy required to start a reaction 1. Enzymes lower the activation energy 2. Not consumed but are recycled (used but not used up) 3. Not permanently affected by the reactions they catalyze.

Lock and Key concept Substrates bind to an “active” site on the enzyme - forming an “enzyme-substrate complex” Substrate goes through chemical changes Product released from enzyme is chemically different from substrate

Active sites Certain critical areas of the enzyme that have a shape that matches the substrate of the reaction. Shape dictates function – therefore, if the shape of the active site changes, the function is altered. Enzymes are made of protein – therefore temperature and pH are critical conditions required for enzymatic functioning.

Naming of Enzymes Enzymes are generally (but not always) named after the reaction they will catalyze or the substrate that they act on. For example: Lipase – breaks down lipids ATP synthase – helps synthesize ATP Carboxypeptidase – removes an amine group from the carboxyl end of a peptide (protein) chain.

Biochemical Pathways Biochemical pathways are a series of steps that allow the products of one reaction to be used in a second reaction. The intermediate products are not usually shown in the overall equation. A + B  C C + D  E E + F  G Overall equation: A + B + D + F  G Intermediate products: C and E Reactants: A, B, D, and F End Product: G

Catabolism of Glucose Cellular Respiration – a series of biochemical reactions in which energy is liberated – then used to synthesize ATP. The overall reaction is exergonic – not all energy released is used to make ATP. Formula: C6H12O6 + 6O2  6CO2 + 6H2O + 36-38 ATP

Cellular Respiration The ATP molecules that provide energy to eukaryotic cells are produced during cellular respiration. During cellular respiration, the mitochondria take in O2 and release CO2. Cellular respiration is the reason that animals breathe.

Cellular Respiration (cont.) • Oxidation, the removal of hydrogen atoms from a molecule, is a central reaction in cellular respiration. reduction 6 CO2 + 6 H2O + energy C6H12O6 + 6 O2 oxidation

Cellular Respiration (cont.) The breakdown of glucose during cellular respiration releases energy. The slow oxidation of glucose in the mitochondria allows the energy to be removed slowly and stored as ATP.

Cellular Respiration (cont.)

Phases of Complete Glucose Breakdown Cellular respiration involves a metabolic pathway of enzymes assisted by coenzymes. The two coenzymes involved in cellular respiration, NAD+ and FAD+, receive the hydrogen atoms removed from glucose.

Phases of Complete Glucose Breakdown (cont.) The complete oxidation of glucose involves four phases. – Glycolysis, the splitting of glucose into two 3-carbon molecules The preparatory (transition) reaction, which divides each 3-carbon molecules into a 2-carbon molecule and CO2 The citric acid (Kreb’s) cycle, which produces CO2, NADH, FADH2, and ATP The electron transport chain, which assists in the production of the largest amount of ATP

Phases of Complete Glucose Breakdown (cont.)

Outside the Mitochondria: Glycolysis Glycolysis takes place in the cytoplasm of the cell. During glycolysis, glucose (a 6-carbon molecule) is broken down to two pyruvate (3-carbon) molecules. Glycolysis is divided into two stages. – Energy-Investment Steps – Energy-Harvesting Steps

7.2 Outside the Mitochondria: Glycolysis (cont.)

Energy-Investment Steps Some molecules must be energized before they can be broke down. To facilitate glucose breakdown during glycolysis, 2 ATP molecules energize glucose by donating their phosphate groups.

Energy-Harvesting Steps During the energy-harvesting steps, substrates are oxidized and the hydrogen atoms removed are used to form NADH. This oxidation also produces substrates with high-energy phosphate groups, which can be used to synthesize ATP. The transfer of a phosphate group from a molecule to form ATP is called substrate-level ATP synthesis.

Energy-Harvesting Steps (cont.) Glycolysis produces a total of four ATP. Since two ATP were used to initiate glycolysis, the net ATP production from glycolysis is two ATP. The metabolic fate of pyruvate, the product of glycolysis, depends upon the presence of oxygen.

Energy-Harvesting Steps (cont.)

Inside the Mitochondria The remaining stages of cellular respiration occur in the mitochondria. These steps require the presence of oxygen. The structural features of the mitochondria contribute to cellular respiration.

Inside the Mitochondria (cont.)

Preparatory (transition) Reaction The preparatory (prep) reaction of glycolysis, which occurs twice for each glucose molecule, produces the substrate that enters the subsequent citric acid cycle. Several events occur in the preparatory reaction. – Pyruvate is oxidized and releases a molecule of CO2 and a 2-carbon acetyl group. NAD+ accepts a hydrogen atom, producing NADH. The acetyl group is attached to coenzyme A (CoA) to form acetyl-CoA.

The Citric Acid (Kreb’s) Cycle The citric acid cycle occurs in the matrix of the mitochondria. Several events occur during the citric acid cycle. The acetyl group is oxidized to CO2. Both NAD+ and FAD+ accept hydrogen atoms, forming NADH and FADH respectively. Substrate-level ATP synthesis occurs, forming ATP. The citric acid cycle turns twice for each glucose molecule.

The Citric Acid Cycle (cont.)

The Electron Transport Chain The electron transport chain is located in the cristae of the mitochondria. The members of the electron transport chain accept electrons from the hydrogen atoms accepted by NADH and FADH2. As the electrons are passed down the electron transport chain, energy is released and captured for ATP production.

The Electron Transport Chain (cont.) At the end of the electron transport chain, the electrons are donated to oxygen atoms to form water. The number of ATP molecules formed depends upon the electron donor. The electrons from NADH provide energy for the synthesis of three ATP molecules. The electrons from FADH2 provide energy for the synthesis of two ATP molecules.

The Electron Transport Chain (cont.)

The Cristae of a Mitochondrion The members of the electron transport chain are imbedded in the cristae of the mitochondria in a specific pattern. As the members of the electron transport chain accept electrons from NADH and FADH2, the H+ are pumped into the intermembrane space.

The Cristae of a Mitochondrion (cont.) This pumping creates an H+ reservoir in the intermembrane space. This reservoir can be released through an ATP synthase complex to synthesize ATP.

The Cristae of a Mitochondrion (cont.)

Energy Yield from Glucose Metabolism The complete breakdown of glucose yields 36 ATP molecules. Glycolysis provides 2 net ATP. The NADH produced by the prep reaction and the citric acid cycle yield 30 ATP. The electron transport chain uses FADH2 to produce 4 ATP.

Energy Yield from Glucose Metabolism (cont.)

Nucleic Acid Structure Monomer - Nucleotide Nucleotide parts: Nitrogen base Sugar Phosphate group Nucleoside: Nitrogen base and Sugar Adenosine: Adenine + Ribose

Nucleic Acid Structure and Chromosomes DNA Nucleotide Sugar Deoxyribose Phosphate 1/nucleotide Base Adenine, Guanine, Cytosine, Thymine RNA Nucleotide Sugar Ribose Adenine, Guanine, Cytosine, Uracil

Nitrogen Bases Nitrogen bases: Bases in DNA: A, T, C, and G Bases in RNA: A, U, C, and G Base in ATP: A

Purines 2 ringed structure Adenine and Guanine Pyrimidines 1 ring structure Thymine, Uracil, and Cytosine

Phosphate groups in Nucleic Acids DNA and RNA: 1 phosphate group/nucleotide ATP: 3 phosphate (Adenosine Triphosphate)

Sugars Sugars in nucleic acids: Ribose for Ribonucleic Acid and Adenosine Triphosphate (RNA and ATP) 5 carbon (pentose) sugar Deoxyribose in Deoxyribonucleic acid (DNA) 5 carbon sugar (lacking an oxygen, but otherwise exactly the same as ribose)

Function of Nucleic Acids DNA - contains the "blueprint for life" RNA - transfers that information to the organelles of the cell to make proteins ATP - provides the "energy for life" - it is "spendable" energy - just the right amount for cellular functions

Steps from DNA to Proteins Same two steps produce all proteins: 1) DNA is transcribed to form RNA Occurs in the nucleus RNA moves into cytoplasm 2) RNA is translated to form polypeptide chains, which fold to form proteins

Three Classes of RNAs Messenger RNA Ribosomal RNA Transfer RNA Carries protein-building instruction Ribosomal RNA Major component of ribosomes Transfer RNA Delivers amino acids to ribosomes

A Nucleotide Subunit of RNA uracil (base) phosphate group ribose (sugar)

Base Pairing during Replication and Transcription DNA G C A T RNA G C A U DNA C G T A DNA C G T A base pairing in DNA replication base pairing in transcription

Adding Nucleotides 5’ growing RNA transcript 3’ DNA direction of transcription 5’ 3’

The Genetic Code (cont.)

Transcription During transcription, a strand of mRNA is formed that is complementary to the sequence within the DNA. Transcription begins when RNA polymerase binds to the DNA promoter for a gene. The DNA helix is unwound and the primary mRNA strand is formed.

Transcription (cont.)

Transcription (cont.) The primary mRNA strand is then processed to remove introns. The remaining sequence of genetic information, the exons, are retained in the mature mRNA for protein synthesis.

Transcription (cont.)

Translation: An Overview The translation of a mature mRNA into proteins requires several enzymes, tRNA, and rRNA. The tRNA is a single-stranded RNA molecule with an amino acid bound to one end and an anticodon on the other end.

Translation: An Overview (cont.)

Translation: An Overview (cont.) The anticodon is complementary to the corresponding mRNA codon. As a mature mRNA moves to a ribosome, the sequence of codons in the mRNA dictates the sequence of anticodons. The order of the tRNA molecules determines the order of the amino acids.

Translation: An Overview (cont.)

Translation: An Overview (cont.)

Translation Has Three Phases In initiation, the small ribosomal subunit, large ribosomal subunit, the mRNA, and a tRNA carrying a methionine bond to the mRNA to start transcription. The amino acid sequence of the protein is extended during the elongation phase. • Termination occurs when protein synthesis is completed.

Translation Has Three Phases (cont.)

Translation Has Three Phases (cont.)

Genes and Gene Mutations A gene mutation changes the sequence of bases in the DNA. Mutations in DNA are rare (one in 100 million cell divisions). Mutations can be caused by mutagens. Radiation (radioactivity, X-rays, UV light) Chemicals (pesticides, cigarette chemicals)

Effects of Mutations Mutations that are inherited are called germ-line mutations. • Somatic mutations occur in an organism after birth and can lead to cancer. • Point mutations involve the mutation (change) of a single DNA nucleotide.

Effects of Mutations (cont.) In a frame shift mutation, the triplet sequence of the DNA is altered, throwing the mRNA codons out of phase. Although not a mutation, transposons are genes that jump to a different position within the DNA.

Effects of Mutations (cont.)