Living and nonliving matter is composed of atoms.

Similar documents
The Chemistry and Energy of Life

`1AP Biology Study Guide Chapter 2 v Atomic structure is the basis of life s chemistry Ø Living and non- living things are composed of atoms Ø

Full file at

2/25/2013. Electronic Configurations

The Chemistry of Microbiology

Ch 3: Chemistry of Life. Chemistry Water Macromolecules Enzymes

Ch. 2 BASIC CHEMISTRY. Copyright 2010 Pearson Education, Inc.

2) Matter composed of a single type of atom is known as a(n) 2) A) element. B) mineral. C) electron. D) compound. E) molecule.

2.1 Atoms, Ions, and Molecules. 2.1 Atoms, Ions, and Molecules. 2.1 Atoms, Ions, and Molecules. 2.1 Atoms, Ions, and Molecules

2.1 Atoms, Ions, and Molecules

Biology 30 The Chemistry of Living Things

Chapter 02 Chemistry of Life

Microbiology with Diseases by Taxonomy, 5e (Bauman) Chapter 2 The Chemistry of Microbiology. 2.1 Multiple Choice Questions

Matter and Substances Section 3-1

Chapter 02 Chemistry of Life

BIOCHEMISTRY GUIDED NOTES - AP BIOLOGY-

UNIT 1: BIOCHEMISTRY

CHEMICAL BONDS. Attraction that holds molecules together Involves valence electrons. Ionic Bonds Covalent Bonds. Involves sharing of.

Chapter 2. Chemical Principles

Chapter 002 The Chemistry of Biology

The Molecules of Life Chapter 2

Basic Chemistry. Chapter 2 BIOL1000 Dr. Mohamad H. Termos

2: CHEMICAL COMPOSITION OF THE BODY

Chemistry in Biology. Section 1. Atoms, Elements, and Compounds

Study Guide: Basic Chemistry, Water, Life Compounds and Enzymes

Atoms. Atoms 9/9/2015

Figure ) Letter E represents a nucleic acid building block known as a. Answer: nucleotide Diff: 3 Page Ref: 54

Chapter 2: Chemical Basis of Life

Chapter 2 The Chemistry of Biology. Dr. Ramos BIO 370

Chemical Principles and Biomolecules (Chapter 2) Lecture Materials for Amy Warenda Czura, Ph.D. Suffolk County Community College Eastern Campus

Copy into Note Packet and Return to Teacher

1/23/2012. Atoms. Atoms Atoms - Electron Shells. Chapter 2 Outline. Planetary Models of Elements Chemical Bonds

The Chemistry of Life

Chapter 6 Chemistry in Biology

A Brief Overview of Biochemistry. And I mean BRIEF!

EVPP 110 Lecture Exam #1 Study Questions Fall 2003 Dr. Largen

MULTIPLE CHOICE. Circle the one alternative that best completes the statement or answers the question.

Atomic weight = Number of protons + neutrons

Living and nonliving things are all made of elements. It is the way that atoms combine that give every element a different characteristic.

Elements and Isotopes

the spatial arrangement of atoms in a molecule and the chemical bonds that hold the atoms together Chemical structure Covalent bond Ionic bond

W2. Chemical structures of protein and DNA

2.1. KEY CONCEPT All living things are based on atoms and their interactions. 34 Reinforcement Unit 1 Resource Book

Chapter 2. Introduction: Chapter Chemical Basis of Life. Structure of Matter:

Foundations in Microbiology Seventh Edition

2.1 Basic Chemistry 1

2: CHEMICAL COMPOSITION OF THE BODY

BIOCHEMISTRY NOTES - UNIT 2-

Chapter 2: The Chemical Level of. Organization. Copyright 2009, John Wiley & Sons, Inc.

Chapter 2: Fundamentals of Chemistry. Question Type: Multiple Choice. 1) Which of the following pairs is mismatched?

2015 AP Biology Unit 2 PRETEST- Introduction to the Cell and Biochemistry

BIOL 1030 Introduction to Biology: Organismal Biology. Spring 2011 Section A. Steve Thompson:

Bio10 Cell and Molecular Lecture Notes SRJC

Hole s Human Anatomy and Physiology Eleventh Edition. Chapter 2

UNIT 2 CHEMISTRY. Atomic Structure: Ionic Bond: Covalent Bond: Hydrogen Bond:

Nature of matter. Chemical bond is a force that joins atoms

Chapter 6 Chemistry in Biology. 6.1 Atoms, Elements & Compounds 6.2 Chemical Reactions 6.3 Water and Solutions 6.4 The Building Blocks of Life

UNIT 2 CHEMISTRY. Atomic Structure: Ionic Bond: Covalent Bond: Hydrogen Bond:

Chapter 6- An Introduction to Metabolism*

Name Biology Chapter 2 Note-taking worksheet

Chapter 2. The Structure of Atoms. The Structure of Atoms. The Structure of Atoms


Essentials of Human Anatomy and Physiology, 11e (Marieb) Chapter 2 Basic Chemistry. 2.1 Multiple Choice Part I Questions

Essentials of Human Anatomy and Physiology, 12e (Marieb) Chapter 2 Basic Chemistry. 2.1 Multiple Choice Part I Questions

Chemistry of Life. Chapter Two

Chemical Principles. PowerPoint Lecture Presentations prepared by Bradley W. Christian, McLennan Community College C H A P T E R

Chapter 2. Chemical Basis of Life

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

Teacher Instructions

Chemistry of Life. Chapters 2 & 3. Credit: Larry Stepanowicz. Learning Objectives

Chapter 02 Testbank. 1. Anything that occupies space and has mass is called. A. an electron. B. living. C. matter. D. energy. E. space.

Human Biology. The Chemistry of Living Things. Concepts and Current Issues. All Matter Consists of Elements Made of Atoms

Chapter 2 The Chemistry of Life

NORTH CENTRAL HIGH SCHOOL NOTE & STUDY GUIDE. Honors Biology I

Ch. 2 Chemistry Comes to Life

CHAPTER 8. An Introduction to Metabolism

Chapter 2 Chemical Aspects of Life

Chapter 2 Chemistry of Life

Review_Unit 2 Biochemistry

Describe how proteins and nucleic acids (DNA and RNA) are related to each other.

Guided Notes Unit 1: Biochemistry

Chapter 02 Testbank. 1. Anything that occupies space and has mass is called. A. an electron. B. living. C. matter. D. energy. E. space.

Metabolism and Enzymes

Biology Unit 2 Chemistry of Life (Ch. 6) Guided Notes

Charged amino acids (side-chains)

SHORT ANSWER. Write the word or phrase that best completes each statement or answers the question.

4) Chapter 1 includes heredity (i.e. DNA and genes) as well as evolution. Discuss the connection between heredity and evolution?

1) What are the four major elements found in the chemicals that comprise the human body?

Hole s Human Anatomy and Physiology Tenth Edition. Chapter 2

An atom is the smallest unit of an element. It has: A general understanding of chemistry is necessary for understanding human physiology.

The Chemistry of Life.

CHAPTER 2 The Chemical Level of Organization

Mr. Carpenter s Biology Biochemistry. Name Pd

Chapter 6. Ground Rules Of Metabolism

Chapter 2! Chapter 2 Chemistry. The Chemical Level of Organization! SECTION 2-1! Atoms are the basic particles of matter! Subatomic Particles!

Name: Date: Period: Biology Notes: Biochemistry Directions: Fill this out as we cover the following topics in class

Chapter Two: The Chemistry of Biology. The molecules of life make up the structure of cells Chemistry of biological molecule

Chemistry Review. Structure of an Atom. The six most abundant elements of life. Types of chemical bonds. U n i t 2 - B i o c h e m i s t r y

Bloom's Level: 1. Remember Learning Outcome: Describe the structure of atoms. Section: Topic: Chemistry

Basic Chemistry. Chemistry Review. Bio 250: Anatomy & Physiology

Transcription:

Chemistry Topics Covered Atomic structure and interactions Properties of Water Biological Molecules: carbohydrates, lipids, nucleic acids, and proteins Central Dogma: DNA à RNA à Protein Protein Structure: Primary structure determines all other structures Enzymes: active site, cofactors, inhibitors, allosteric sites, optimal conditions, Chemical Energy and Activation Energy Concept 2.1 Atomic Structure Is the Basis for Life s Chemistry Living and nonliving matter is composed of atoms. 1

Concept 2.1 Atomic Structure Is the Basis for Life s Chemistry Like charges repel; different charges attract. Most atoms are neutral because the number of electrons equals the number of protons. Concept 2.1 Atomic Structure Is the Basis for Life s Chemistry Element pure substance that contains only one kind of atom Living things are mostly composed of six elements: Carbon (C) Hydrogen (H) Nitrogen (N) Oxygen (O) Phosphorus (P) Sulfur (S) 2

Concept 2.1 Atomic Structure Is the Basis for Life s Chemistry The number of protons identifies an element. Number of protons = atomic number For electrical neutrality: protons = electrons Mass number is the number of protons plus neutrons Concept 2.1 Atomic Structure Is the Basis for Life s Chemistry Bohr model for atomic structure: atom is largely empty space; the electrons occur in orbits, or electron shells. 3

Concept 2.1 Atomic Structure Is the Basis for Life s Chemistry Bohr models are simplified, but useful in understanding how atoms behave. Behavior of electrons determines whether a chemical bond will form between atoms and what shape the bond will have. Figure 2.1 Electron Shells 4

Concept 2.1 Atomic Structure Is the Basis for Life s Chemistry Octet rule: for elements 6 20, an atom will lose, gain, or share electrons in order to achieve a stable configuration of 8 electrons in its outermost shell. When atoms share electrons, they form stable associations called molecules. Concept 2.2 Atoms Interact and Form Molecules A chemical bond is an attractive force that links atoms together in molecules. There are several kinds of chemical bonds. 5

Table 2.1 Concept 2.2 Atoms Interact and Form Molecules Covalent bonds form when two atoms share pairs of electrons. The atoms attain stability by having full outer shells. Each atom contributes one member of the electron pair. 6

Figure 2.2 Electrons Are Shared in Covalent Bonds Concept 2.2 Atoms Interact and Form Molecules Carbon atoms have 6 electrons; 4 in the outer shell. They can form covalent bonds with four other atoms. 7

Figure 2.3 Covalent Bonding Table 2.2 8

Concept 2.2 Atoms Interact and Form Molecules Properties of molecules are influenced by characteristics of the covalent bonds: Orientation length, angle, and direction of bonds between any two elements are always the same. Example: Methane always forms a tetrahedron. Concept 2.2 Atoms Interact and Form Molecules Strength and stability covalent bonds are very strong; it takes a lot of energy to break them. Multiple bonds Single sharing 1 pair of electrons C H Double sharing 2 pairs of electrons C C Triple sharing 3 pairs of electrons N N 9

Concept 2.2 Atoms Interact and Form Molecules Two atoms of different elements do not always share electrons equally. The nucleus of one element may have greater electronegativity the attractive force that an atomic nucleus exerts on electrons. Depends on the number of protons and the distance between the nucleus and electrons. Table 2.3 10

Concept 2.2 Atoms Interact and Form Molecules If atoms have similar electronegativities, they share electrons equally (nonpolar covalent bond). If atoms have different electronegativities, electrons tend to be near the most attractive atom, forming a polar covalent bond. Concept 2.2 Atoms Interact and Form Molecules The partial charges that result from polar covalent bonds produce polar molecules or polar regions of large molecules. Polar bonds influence interactions with other molecules. Polarity of water molecules determines many of water s unique properties. 11

Concept 2.2 Atoms Interact and Form Molecules Hydrogen bonds: Attraction between the δ end of one molecule and the δ + hydrogen end of another molecule. They form between water molecules and within larger molecules. Although much weaker than covalent bonds, they are important in the structure of DNA and proteins. Figure 2.4 Hydrogen Bonds Can Form between or within Molecules 12

Concept 2.2 Atoms Interact and Form Molecules Hydrogen bonding contributes to properties of water that are significant for life: Water is a solvent in living systems a liquid in which other molecules dissolve. Water molecules form multiple hydrogen bonds with each other this contributes to high heat capacity. In-Text Art, Chapter 2, p. 23 13

Concept 2.2 Atoms Interact and Form Molecules A lot of heat energy is required to raise the temperature of water the heat energy breaks the hydrogen bonds. In organisms, presence of water shields them from fluctuations in environmental temperature. Concept 2.2 Atoms Interact and Form Molecules Water has a high heat of vaporization: a lot of heat energy is required to change water from the liquid to gaseous state (to break the hydrogen bonds). Thus, evaporation has a cooling effect on the environment. Sweating cools the body as sweat evaporates from the skin, it absorbs some of the adjacent body heat. 14

Concept 2.2 Atoms Interact and Form Molecules Hydrogen bonds give water cohesive strength, or cohesion water molecules resist coming apart when placed under tension. Hydrogen bonding between liquid water molecules and solid surfaces allows for adhesion between the water and the solid surface. In-Text Art, Chapter 2, p. 24 15

Concept 2.2 Atoms Interact and Form Molecules Cohesion and adhesion allow narrow columns of water to move from roots to the leaves of plants. Surface tension: water molecules at the surface are hydrogen-bonded to other molecules below them, making the surface difficult to puncture. This allows spiders to walk on the surface of a pond. Concept 2.2 Atoms Interact and Form Molecules Any polar molecule can interact with any other polar molecule through hydrogen bonds. Hydrophilic ( water-loving ): in aqueous solutions, polar molecules become separated and surrounded by water molecules. Nonpolar molecules are called hydrophobic ( water-hating ); the interactions between them are hydrophobic interactions. 16

Figure 2.5 Hydrophilic and Hydrophobic Concept 2.2 Atoms Interact and Form Molecules When one atom is much more electronegative than the other, a complete transfer of electrons may occur. This makes both atoms more stable because their outer shells are full. The result is two ions electrically charged particles that form when atoms gain or lose one or more electrons. 17

Figure 2.6 Ionic Attraction between Sodium and Chlorine Concept 2.2 Atoms Interact and Form Molecules Cations positively charged ions Anions negatively charged ions Ionic attractions result from the electrical attraction between ions with opposite charges. The resulting molecules are called salts or ionic compounds. 18

Concept 2.2 Atoms Interact and Form Molecules Ionic attractions are weak, so salts dissolve easily in water. place text art pg 25 here Concept 2.2 Atoms Interact and Form Molecules Proteins formed from different combinations of 20 amino acids Carbohydrates formed by linking sugar monomers (monosaccharides) to form polysaccharides Nucleic acids formed from four kinds of nucleotide monomers Lipids noncovalent forces maintain the interactions between the lipid monomers 19

Concept 2.3 Carbohydrates Consist of Sugar Molecules Carbohydrates Source of stored energy Transport stored energy within organisms Structural molecules give many organisms their shapes Recognition or signaling molecules can trigger specific biological responses Concept 2.3 Carbohydrates Consist of Sugar Molecules Monosaccharides are simple sugars. Pentoses are 5-carbon sugars. Ribose and deoxyribose are the backbones of RNA and DNA. Hexoses (C 6 H 12 O 6 ) include glucose, fructose, mannose, and galactose. 20

Figure 2.9 Monosaccharides Figure 2.10 Polysaccharides (Part 1) 21

Concept 2.3 Carbohydrates Consist of Sugar Molecules Concept 2.3 Carbohydrates Consist of Sugar Molecules Cellulose the main component of plant cell walls. It is the most abundant carboncontaining (organic) biological compound on Earth. Very stable; good structural material 22

Concept 2.3 Carbohydrates Consist of Sugar Molecules Concept 2.4 Lipids Are Hydrophobic Molecules Lipids Hydrocarbons (composed of C and H atoms) that are insoluble in water because of many nonpolar covalent bonds. When close together, weak but additive van der Waals interactions hold them together. 23

Concept 2.4 Lipids Are Hydrophobic Molecules Lipids: Store energy in C C and C H bonds Play structural roles in cell membranes Fat in animal bodies serves as thermal insulation Concept 2.4 Lipids Are Hydrophobic Molecules Triglycerides (simple lipids) Fats solid at room temperature Oils liquid at room temperature Have very little polarity and are extremely hydrophobic. 24

Concept 2.4 Lipids Are Hydrophobic Molecules Fatty acids are amphipathic; they have a hydrophilic end and a hydrophobic tail. Phospholipid two fatty acids and a phosphate group bound to glycerol; The phosphate group has a negative charge, making that part of the molecule hydrophilic. Figure 2.13 Phospholipids (Part 1) 25

Concept 2.4 Lipids Are Hydrophobic Molecules In an aqueous environment, phospholipids form a bilayer. The nonpolar, hydrophobic tails pack together and the phosphate-containing heads face outward, where they interact with water. Biological membranes have this kind of phospholipid bilayer structure. Figure 2.13 Phospholipids (Part 2) 26

Concept 3.1 Nucleic Acids Are Informational Macromolecules Nucleic acids are polymers that store, transmit, and express hereditary (genetic) information. DNA = deoxyribonucleic acid RNA = ribonucleic acid The monomers are nucleotides. Concept 3.1 Nucleic Acids Are Informational Macromolecules Nucleotide: pentose sugar + N-containing base + phosphate group Nucleosides: pentose sugar + N-containing base 27

Concept 3.1 Nucleic Acids Are Informational Macromolecules Bases: Pyrimidines single rings Purines double rings Sugars: DNA contains deoxyribose RNA contains ribose Figure 3.1 Nucleotides Have Three Components 28

Concept 3.1 Nucleic Acids Are Informational Macromolecules Nucleotides bond in condensation reactions to form phosphodiester bonds. The linkage is between the #5 carbon of one ribose and the #3 carbon of the next ribose. Nucleic acids grow in the 5 to 3 direction. Figure 3.2 Linking Nucleotides Together 29

Concept 3.1 Nucleic Acids Are Informational Macromolecules Oligonucleotides have up to 20 monomers. Example: small RNA molecules important for DNA replication and gene expression. DNA and RNA are polynucleotides, the longest polymers in the living world. Concept 3.1 Nucleic Acids Are Informational Macromolecules Complementary base pairing: 30

Concept 3.1 Nucleic Acids Are Informational Macromolecules Base pairs are linked by hydrogen bonds, favored by the arrangement of polar bonds in the bases. There are so many hydrogen bonds in DNA and RNA that they form a fairly strong attraction, but not as strong as covalent bonds. Thus, base pairs can be separated with only a small amount of energy. Concept 3.1 Nucleic Acids Are Informational Macromolecules In RNA, the base pairs are A U and C G. RNA is usually single-stranded, but may be folded into 3-D structures by hydrogen bonding. Folding occurs by complementary base pairing, so structure is determined by the order of bases. 31

Figure 3.3 RNA Concept 3.1 Nucleic Acids Are Informational Macromolecules DNA is usually double stranded. Two polynucleotide strands form a ladder that twists into a double helix. Sugar-phosphate groups form the sides of the ladder, the hydrogen-bonded bases form the rungs. 32

Figure 3.4 DNA Concept 3.1 Nucleic Acids Are Informational Macromolecules Select the correct sequence of events in gene expression: a. DNA; translation; RNA; transcription; polypeptide b. RNA; transcription; DNA; translation; polypeptide c. DNA; transcription; polypeptide; translation; RNA d. DNA; transcription; RNA; translation; polypeptide e. polypeptide; transcription; DNA; translation; RNA 33

Concept 3.1 Nucleic Acids Are Informational Macromolecules DNA s information is encoded in the sequence of bases. DNA has two functions: Replication Information is copied to RNA and used to specify amino acid sequences in proteins. Figure 3.5 DNA Replication and Transcription 34

Concept 3.2 Proteins Are Polymers with Important Structural and Metabolic Roles Major functions of proteins: Enzymes catalytic molecules Defensive proteins (e.g., antibodies) Hormonal and regulatory proteins control physiological processes Receptor proteins receive and respond to molecular signals Storage proteins store amino acids Concept 3.2 Proteins Are Polymers with Important Structural and Metabolic Roles Structural proteins physical stability and movement Transport proteins carry substances (e.g., hemoglobin) Genetic regulatory proteins regulate when, how, and to what extent a gene is expressed 35

Concept 3.2 Proteins Are Polymers with Important Structural and Metabolic Roles Protein monomers are amino acids. Amino and carboxyl functional groups allow them to act as both acid and base. Concept 3.2 Proteins Are Polymers with Important Structural and Metabolic Roles Cysteine side chains can form covalent bonds called disulfide bridges. 36

Concept 3.2 Proteins Are Polymers with Important Structural and Metabolic Roles Primary structure of a protein is the sequence of amino acids. Figure 3.7 The Four Levels of Protein Structure (Part 1) 37

Concept 3.2 Proteins Are Polymers with Important Structural and Metabolic Roles Secondary structure regular, repeated spatial patterns in different regions, resulting from hydrogen bonding α (alpha) helix right-handed coil β (beta) pleated sheet two or more sequences are extended and aligned Figure 3.7 The Four Levels of Protein Structure (Part 2) 38

Concept 3.2 Proteins Are Polymers with Important Structural and Metabolic Roles Tertiary structure polypeptide chain is bent and folded; results in the definitive 3-D shape Figure 3.7 The Four Levels of Protein Structure (Part 3) 39

Concept 3.2 Proteins Are Polymers with Important Structural and Metabolic Roles Interactions between R groups determine tertiary structure: Disulfide bridges hold folded polypeptides together Hydrogen bonds stabilize folds Hydrophobic side chains can aggregate in the protein interior van der Waals interactions between hydrophobic side chains Concept 3.2 Proteins Are Polymers with Important Structural and Metabolic Roles Secondary and tertiary protein structure derive from primary structure. Denaturing heat or chemicals disrupt weaker interactions in a protein, destroying secondary and tertiary structure. The protein can return to normal when cooled or the chemicals are removed all the information needed to specify the unique shape is contained in the primary structure. 40

Concept 3.2 Proteins Are Polymers with Important Structural and Metabolic Roles Quaternary structure two or more polypeptide chains (subunits) bind together by hydrophobic and ionic interactions and hydrogen bonds. Figure 3.7 The Four Levels of Protein Structure (Part 3) 41

Concept 3.2 Proteins Are Polymers with Important Structural and Metabolic Roles Factors that can disrupt the interactions that determine protein structure (denaturing): Temperature Change in concentration of H + High concentrations of polar substances Nonpolar substances Concept 3.2 Proteins Are Polymers with Important Structural and Metabolic Roles Proteins interact with other molecules. R groups on the surface may form weak interactions (e.g., hydrogen bonds) with groups on the surface of another molecule. This can change the tertiary structure and thus the shape of the protein. Protein structure can also be modified by covalent bonding of a chemical group to the side chain of one or more of its amino acids. 42

Figure 3.11 Protein Structure Can Change Concept 3.3 Some Proteins Act as Enzymes to Speed up Biochemical Reactions Enzymes are highly specific each one catalyzes only one chemical reaction. Reactants are substrates: they bind to specific sites on the enzyme the active sites. Specificity results from the exact 3-D shape and chemical properties of the active site. 43

Figure 3.14 Enzyme Action Concept 3.3 Some Proteins Act as Enzymes to Speed up Biochemical Reactions The enzyme substrate complex (ES) is held together by hydrogen bonding, electrical attraction, or temporary covalent bonding. E + S ES E + P Is the enzyme changed at the end of the reaction? 44

Concept 3.3 Some Proteins Act as Enzymes to Speed up Biochemical Reactions Enzymes use one or more mechanisms to catalyze a reaction: Inducing strain bonds in the substrate are stretched, putting it in an unstable transition state. Concept 3.3 Some Proteins Act as Enzymes to Speed up Biochemical Reactions Substrate orientation substrates are brought together so that bonds can form. Adding chemical groups R groups may be directly involved in the reaction. 45

Concept 3.3 Some Proteins Act as Enzymes to Speed up Biochemical Reactions Enzyme 3-D structures are so specific that they bind only one or a few related substrates. Many enzymes change shape when the substrate binds. The binding is like a baseball in a catcher s mitt. The enzyme changes shape to make the binding tight induced fit. Figure 3.15 Some Enzymes Change Shape When Substrate Binds to Them 46

Concept 3.3 Some Proteins Act as Enzymes to Speed up Biochemical Reactions Some enzymes require ions or other molecules (cofactors) in order to function: Metal ions Coenzymes add or remove chemical groups from the substrate. They can participate in reactions with many different enzymes. Prosthetic groups (nonamino acid groups) permanently bound to their enzymes. Concept 3.3 Some Proteins Act as Enzymes to Speed up Biochemical Reactions Rates of catalyzed reactions: There is usually less enzyme than substrate present, so reaction rate levels off when all enzyme molecules are bound to substrate molecules. The enzyme is said to be saturated. 47

Figure 3.16 Catalyzed Reactions Reach a Maximum Rate Concept 3.4 Regulation of Metabolism Occurs by Regulation of Enzymes Systems biology is a new field that describes the components of metabolic pathways mathematically. Computer algorithms are used to make predictions about what would happen if a component were altered. 48

Concept 3.4 Regulation of Metabolism Occurs by Regulation of Enzymes Cells can regulate metabolism by controlling the amount of an enzyme. Cells often have the ability to turn synthesis of enzymes off or on. Activity of enzymes can also be regulated, which is often faster. Concept 3.4 Regulation of Metabolism Occurs by Regulation of Enzymes Chemical inhibitors can bind to enzymes and slow reaction rates. Natural inhibitors regulate metabolism. Artificial inhibitors are used to treat diseases, kill pests, and study enzyme function. 49

Concept 3.4 Regulation of Metabolism Occurs by Regulation of Enzymes Irreversible inhibition: Inhibitor covalently binds to a side chain in the active site. The enzyme is permanently inactivated. Some insecticides act in this way. Figure 3.18 Irreversible Inhibition 50

Concept 3.4 Regulation of Metabolism Occurs by Regulation of Enzymes Reversible inhibition: A competitive inhibitor binds at the active site but no reaction occurs. It competes with the natural substrate. Concept 3.4 Regulation of Metabolism Occurs by Regulation of Enzymes Reversible inhibition: A noncompetitive inhibitor binds at a site distinct from the active site, causing change in enzyme shape and function. It prevents substrate binding or slows the reaction rate. 51

Figure 3.19 Reversible Inhibition Concept 3.4 Regulation of Metabolism Occurs by Regulation of Enzymes Allosteric regulation non-substrate molecule binds a site other than the active site (the allosteric site) The enzyme changes shape, which alters the chemical attraction (affinity) of the active site for the substrate. Allosteric regulation can activate or inactivate enzymes. 52

Concept 3.4 Regulation of Metabolism Occurs by Regulation of Enzymes Allosteric sites can be modified by: Noncovalent binding (reversible) Covalent binding of a molecule or chemical group, such as phosphorylation (reversible) Figure 3.20 Allosteric Regulation of Enzyme Activity 53

Concept 3.4 Regulation of Metabolism Occurs by Regulation of Enzymes Allosteric regulation Working in groups of three, designate one person in each group to be the enzyme, one to be the substrate, and one to be the allosteric regulator. Act out the steps of allosteric regulation with the following exercise: First, the enzyme is active (clasp hands with substrate). The allosteric regulator, a noncompetitive inhibitor, puts hands on the enzyme s shoulders to prevent substrate binding (enzyme, now inactive, puts hands behind back). Second, with the enzyme still inactive, the allosteric regulator activates the enzyme (hands on shoulders), allowing substrate binding (enzyme clasps hands with substrate). Concept 3.4 Regulation of Metabolism Occurs by Regulation of Enzymes Phosphorylation by protein kinases is an important regulatory mechanism. Phosphorylation can change a hydrophobic region to hydrophilic. The enzyme twists and exposes the active site. Protein phosphatases reverse the process by removing phosphate groups. 54

Concept 3.4 Regulation of Metabolism Occurs by Regulation of Enzymes Enzyme-catalyzed reactions operate in metabolic pathways. The product of one reaction is a substrate for the next reaction. Each step is catalyzed by a specific enzyme. Cell have hundreds of enzymes that participate in interconnecting metabolic pathways, forming a metabolic system. Figure 3.17 A Biochemical System 55

Concept 3.4 Regulation of Metabolism Occurs by Regulation of Enzymes Metabolic pathways: The first reaction is the commitment step the other reactions then happen in sequence. Feedback inhibition (end-product inhibition) the final product acts as an inhibitor of the first enzyme, which shuts down the pathway. Figure 3.21 Feedback Inhibition of Metabolic Pathways 56

Concept 3.4 Regulation of Metabolism Occurs by Regulation of Enzymes ph affects protein structure and enzyme activity: Acidic side chains generate H + and become anions. Basic side chains attract H + and become cations. Concept 3.4 Regulation of Metabolism Occurs by Regulation of Enzymes Protein tertiary structure (and thus function) is very sensitive to the concentration of H + (ph) in the environment. All enzymes have an optimal ph for activity. 57

Concept 3.4 Regulation of Metabolism Occurs by Regulation of Enzymes Temperature affects protein structure and enzyme activity: Warming increases rates of chemical reactions, but if temperature is too high, noncovalent bonds can break, inactivating enzymes. All enzymes have an optimal temperature for activity. Figure 3.22 Enzyme Activity Is Affected by the Environment 58

Concept 3.4 Regulation of Metabolism Occurs by Regulation of Enzymes Isozymes catalyze the same reaction but have different composition and physical properties. Isozymes may have different optimal temperatures or ph, allowing an organism to adapt to changes in its environment. Concept 3.3 Some Proteins Act as Enzymes to Speed up Biochemical Reactions Living systems depend on reactions that occur spontaneously, but at very slow rates. Catalysts are substances that speed up the reactions without being permanently altered. No catalyst makes a reaction occur that cannot otherwise occur. Most biological catalysts are proteins (enzymes); a few are RNA molecules (ribozymes). 59

Concept 2.5 Biochemical Changes Involve Energy Chemical reactions occur when atoms have enough energy to combine or change bonding partners. sucrose + H 2 O glucose + fructose (C 12 H 22 O 11 ) (C 6 H 12 O 6 ) (C 6 H 12 O 6 ) reactants products Concept 2.5 Biochemical Changes Involve Energy Chemical reactions involve changes in energy. Energy can be defined as the capacity to do work, or the capacity for change. In biochemical reactions, energy changes are usually associated with changes in the chemical composition and properties of molecules. 60

Concept 2.5 Biochemical Changes Involve Energy All forms of energy can be considered as either: Potential the energy of state or position, or stored energy Kinetic the energy of movement; the type of energy that does work; that makes things change Energy can be converted from one form to another. Concept 2.5 Biochemical Changes Involve Energy Metabolism sum total of all chemical reactions occurring in a biological system at a given time Metabolic reactions involve energy changes. Energy is either stored in, or released from, chemical bonds.. 61

Concept 2.5 Biochemical Changes Involve Energy Two basic types of metabolism: Anabolic reactions link simple molecules to form complex ones. They require energy inputs (endergonic or endothermic; energy is captured in the chemical bonds that form. Figure 2.14 Energy Changes in Reactions 62

Concept 2.5 Biochemical Changes Involve Energy Catabolic reactions: energy is released (exergonic or exothermic) Complex molecules are broken down into simpler ones. Energy stored in the chemical bonds is released. Concept 2.5 Biochemical Changes Involve Energy Catabolic and anabolic reactions are often linked. The energy released in catabolic reactions is often used to drive anabolic reactions to do biological work. 63

Concept 2.5 Biochemical Changes Involve Energy The laws of thermodynamics apply to all matter and energy transformations in the universe. First law: Energy is neither created nor destroyed. Second law: Useful energy tends to decrease. Entropy is a measure of the disorder in a system. As a result of energy transformations, disorder tends to increase. Concept 2.5 Biochemical Changes Involve Energy Metabolism creates more disorder (more energy is lost to entropy) than the amount of order that is stored. Example: The anabolic reactions needed to construct 1 kg of animal body require the catabolism of about 10 kg of food. Life requires a constant input of energy to maintain order. 64

Concept 3.3 Some Proteins Act as Enzymes to Speed up Biochemical Reactions An exergonic reaction releases free energy (G), the amount of energy in a system that is available to do work. Without a catalyst, the reaction will be very slow because there is an energy barrier between reactants and products. An input of energy initiates the reaction (activation energy or E a ), which puts reactants into a transition state. Figure 3.12 Activation Energy Initiates Reactions 65

Concept 3.3 Some Proteins Act as Enzymes to Speed up Biochemical Reactions Enzymes lower the activation energy by enabling reactants to come together and react more easily. Example: A molecule of sucrose in solution may hydrolyze in about 15 days; with sucrase present, the same reaction occurs in 1 second! Figure 3.13 Enzymes Lower the Energy Barrier 66