Chemistry Ch 2

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Chemistry Ch 2
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• The stuff of the universe
• Anything that has mass and takes up space
• States of matter
• Solid has definite shape and volume
• Liquid has definite volume, changeable shape
• Gas has changeable shape and volume

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Matter And Energy
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• Graphite layer structure of carbon atoms
  reflects physical properties.

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A Chemists View of Water
Macroscopic
H2O (gas, liquid, solid)
Symbolic
Particulate
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STATES OF MATTER

• _______ have rigid shape, fixed volume.
  External shape can reflect the atomic and
  molecular arrangement.
• Reasonably well understood.
• _______ have no fixed shape and may not fill a
  container completely.
• Not well understood.
• _______ expand to fill their container.
• Good theoretical understanding.

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OTHER STATES OF MATTER

• PLASMA an electrically charged gas Example
  the sun or any other star
• BOSE-EINSTEIN CONDENSATE a condensate that
  forms near absolute zero that has superconductive
  properties Example supercooled Rb gas

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Energy

• The capacity to do work (put matter into motion)
• Types of energy
• Kinetic energy in action
• Potential energy of position stored (inactive)
  energy

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Kinetic and Potential Energy
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Forms of Energy

• Chemical stored in the bonds of chemical
  substances
• Electrical results from the movement of charged
  particles
• Mechanical directly involved in moving matter
• Radiant or electromagnetic energy traveling in
  waves (i.e., visible light, ultraviolet light,
  and X rays)

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Forms of Energy
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Endergonic and Exergonic Reactions
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Composition of Matter

• Elements unique substances that cannot be
  broken down by ordinary chemical means
• Atoms more-or-less identical building blocks
  for each element
• Atomic symbol one- or two-letter chemical
  shorthand for each element

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Atoms and Elements
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Properties of Elements

• Each element has unique physical and chemical
  properties
• Physical properties those detected with our
  senses
• Chemical properties pertain to the way atoms
  interact with one another

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Physical Properties

• What are some physical properties?
• color
• melting and boiling point
• odor

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Physical Changes

• can be observed without changing the identity of
  the substance
• Some physical changes would be
• boiling of a liquid
• melting of a solid
• dissolving a solid in a liquid to give a
  homogeneous mixture a SOLUTION.

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A Chemists View
Macroscopic
2 H2(g) O2 (g) --gt 2 H2O(g)
Particulate
Symbolic
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Chemical Properties and Chemical Change

• Burning hydrogen (H2) in oxygen (O2) gives H2O.

• Chemical change or chemical reaction
  transformation of one or more atoms or molecules
  into one or more different molecules.

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Sure Signs of a Chemical Change

• Heat
• Light
• Gas Produced (not from boiling!)
• Precipitate a solid formed by mixing two
  liquids together

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Physical vs. Chemical

• physical
• chemical
• physical
• physical
• chemical

• Examples
• melting point
• flammable
• density
• magnetic
• tarnishes in air

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Physical vs. Chemical

• Examples
• rusting iron
• dissolving in water
• burning a log
• melting ice
• grinding spices

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Major Elements of the Body

• Oxygen (O)
• Carbon (C)
• Hydrogen (H)
• Nitrogen (N)

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Lesser and Trace Elements of the Human Body

• Lesser elements make up 3.9 of the body and
  include
• Calcium (Ca), phosphorus (P), potassium (K),
  sulfur (S), sodium (Na), chlorine (Cl), magnesium
  (Mg), iodine (I), and iron (Fe)
• Trace elements make up less than 0.01 of the
  body
• They are required in minute amounts, and are
  found as part of enzymes

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Atomic Structure

• The nucleus consists of neutrons and protons
• Neutrons have no charge and a mass of one
  atomic mass unit (amu)
• Protons have a positive charge and a mass of 1
  amu
• Electrons are found orbiting the nucleus
• Electrons have a negative charge and 1/2000 the
  mass of a proton (0 amu)

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Models of the Atom

• Planetary Model electrons move around the
  nucleus in fixed, circular orbits
• Orbital Model regions around the nucleus in
  which electrons are most likely to be found

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Identification of Elements

• Atomic number equal to the number of
  protons
• Mass number equal to the mass of the protons
  and neutrons
• Atomic weight average of the mass numbers of
  all isotopes
• Isotope atoms with same number of protons but a
  different number of neutrons
• Radioisotopes atoms that undergo spontaneous
  decay called radioactivity

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Radiotherapy

• Rapidly dividing cells are particularly sensitive
  to damage by radiation. For this reason, some
  cancerous growths can be controlled or eliminated
  by irradiating the area containing the growth.
  External irradiation can be carried out using a
  gamma beam from a radioactive cobalt-60 source,
  though in developed countries the much more
  versatile linear accelerators are now being
  utilized as a high-energy x-ray source (gamma and
  x-rays are much the same).

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• Internal radiotherapy is by administering or
  planting a small radiation source, usually a
  gamma or beta emitter, in the target area.
  Iodine-131 is commonly used to treat thyroid
  cancer, probably the most successful kind of
  cancer treatment. It is also used to treat
  non-malignant thyroid disorders. Iridium-192
  implants are used especially in the head and
  breast. They are produced in wire form and are
  introduced through a catheter to the target area.
  After administering the correct dose, the implant
  wire is removed to shielded storage. This
  brachytherapy (short-range) procedure gives less
  overall radiation to the body, is more localized
  to the target tumor and is cost effective.

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Molecules and Compounds

• Molecule two or more atoms held together by
  chemical bonds
• Compound two or more different kinds of atoms
  chemically bonded together

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Molecules
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The Nature of Matter
Gold
Mercury

• Chemists are interested in the nature of matter
  and how this is related to its atoms and
  molecules.

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Mixtures and Solutions

• Mixtures two or more components physically
  intermixed (not chemically bonded)
• Solutions homogeneous mixtures of components
• Solvent substance present in greatest amount
• Solute substance(s) present in smaller amounts

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Types of Mixtures

• Variable combination of 2 or more pure substances.

Heterogeneous visibly separate phases
Homogeneous Same throughout
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Concentration of Solutions

• Percent, or parts per 100 parts
• Molarity, or moles per liter (M)
• A mole of an element or compound is equal to its
  atomic or molecular weight (sum of atomic
  weights) in grams

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Colloids and Suspensions

• Colloids, or emulsions, are heterogeneous
  mixtures whose solutes do not settle out
• Suspensions are heterogeneous mixtures with
  visible solutes that tend to settle out

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Mixtures Compared with Compounds

• No chemical bonding takes place in mixtures
• Most mixtures can be separated by physical means
• Mixtures can be heterogeneous or homogeneous
• Compounds cannot be separated by physical means
• All compounds are homogeneous

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Chemical Bonds

• Electron shells, or energy levels, surround the
  nucleus of an atom
• Bonds are formed using the electrons in the
  outermost energy level
• Valence shell outermost energy level containing
  chemically active electrons
• Octet rule except for the first shell which is
  full with two electrons, atoms interact in a
  manner to have eight electrons in their valence
  shell

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Chemically Inert Elements Inert elements have
their outermost energy level fully occupied by
electrons
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Chemically Reactive Elements Reactive elements do
not have their outermost energy level fully
occupied by electrons
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Types of Chemical Bonds

• Ionic
• Covalent
• Hydrogen

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Ionic Bonds

• Ions are charged atoms resulting from the gain
  or loss of electrons
• Anions have gained one or more electrons
• Cations have lost one or more electrons

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Formation of an Ionic Bond

• Ionic bonds form between atoms by the transfer of
  one or more electrons
• Ionic compounds form crystals instead of
  individual molecules
• Example NaCl (sodium chloride)

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Formation of an Ionic Bond
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Formation of an Ionic Bond
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Covalent Bonds

• Covalent bonds are formed by the sharing of two
  or more electrons
• Electron sharing produces molecules

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Single Covlent Bonds
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Double Covlalent Bonds
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Triple Covalent Bonds
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Polar and Nonpolar Molecules

• Electrons shared equally between atoms produce
  nonpolar molecules
• Unequal sharing of electrons produces polar
  molecules
• Atoms with six or seven valence shell electrons
  are electronegative
• Atoms with one or two valence shell electrons are
  electropositive

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Comparison of Ionic, Polar Covalent, and Nonpolar
Covalent Bonds
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Hydrogen Bonds

• Too weak to bind atoms together
• Common in dipoles such as water
• Responsible for surface tension in water
• Important as intramolecular bonds, giving the
  molecule a three-dimensional shape

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Hydrogen Bonds
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Chemical Reactions

• Occur when chemical bonds are formed, rearranged,
  or broken
• Are written in symbolic form using chemical
  equations
• Chemical equations contain
• Number and type of reacting substances, and
  products produced
• Relative amounts of reactants and products

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Examples of Chemical Reactions
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Patterns of Chemical Reactions

• Combination reactions Synthesis reactions which
  always involve bond formation
• A B ? AB
• Decomposition reactions Molecules are broken
  down into smaller molecules
• AB ? A B
• Exchange reactions Bonds are both made and
  broken
• AB C ? AC B

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Oxidation-Reduction (Redox) Reactions

• Reactants losing electrons are electron donors
  and are oxidized
• Reactants taking up electrons are electron
  acceptors and become reduced

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Energy Flow in Chemical Reactions

• Exergonic reactions reactions that release
  energy
• Endergonic reactions reactions whose products
  contain more potential energy than did its
  reactants

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Reversibility in Chemical Reactions

• All chemical reactions are theoretically
  reversible
• A B ? AB
• AB ? A B
• If neither a forward nor reverse reaction is
  dominant, chemical equilibrium is reached

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Factors Influencing Rate of Chemical Reactions

• Temperature chemical reactions proceed quicker
  at higher temperatures
• Particle size the smaller the particle the
  faster the chemical reaction
• Concentration higher reacting particle
  concentrations produce faster reactions
• Catalysts increase the rate of a reaction
  without being chemically changed
• Enzymes biological catalysts

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Biochemistry

• Organic compounds
• Contain carbon, are covalently bonded, and are
  often large
• Inorganic compounds
• Do not contain carbon
• Water, salts, and many acids and bases

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Properties of Water

• High heat capacity absorbs and releases large
  amounts of heat before changing temperature
• High heat of vaporization changing from a
  liquid to a gas requires large amounts of heat
• Polar solvent properties dissolves ionic
  substances, forms hydration layers around large
  charged molecules, and serves as the bodys major
  transport medium

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Properties of Water

• Reactivity is an important part of hydrolysis
  and dehydration synthesis reactions
• Cushioning resilient cushion around certain
  body organs

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Surface tension
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Salts

• Inorganic compounds
• Contain cations other than H and anions other
  than OH
• Are electrolytes they conduct electrical
  currents

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Acids and Bases

• Acids release H and are therefore proton donors
• HCl ? H Cl
• Bases release OH and are proton acceptors
• NaOH ? Na OH

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Acid-Base Concentration (pH)

• Acidic solutions have higher H concentration and
  therefore a lower pH
• Alkaline solutions have lower H concentration
  and therefore a higher pH
• Neutral solutions have equal H and OH
  concentrations

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Acids and Bases Video
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Acid-Base Concentration (pH) Acidic pH 06.99
Basic pH 7.0114 Neutral pH 7.00
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pH Scale Video
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Buffers

• Systems that resist abrupt and large swings in
  the pH of body fluids
• Carbonic acid-bicarbonate system
• Carbonic acid dissociates, reversibly releasing
  bicarbonate ions and protons
• The chemical equilibrium between carbonic acid
  and bicarbonate resists pH changes in the blood

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Organic Compounds

• Molecules unique to living systems contain carbon
  and hence are organic compounds
• They include
• Carbohydrates
• Lipids
• Proteins
• Nucleic Acids

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Carbohydrates
Carbohydrates Contain carbon, hydrogen, and
oxygen Their major function is to supply a source
of cellular food Examples Monosaccharides or
simple sugars
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Carbohydrate Video
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CarbohydratesDisaccharides or double sugars
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CarbohydratesPolysaccharides or polymers of
simple sugars
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Lipids

• Contain C, H, and O, but the proportion of oxygen
  in lipids is less than in carbohydrates
• Examples
• Neutral fats or triglycerides
• Phospholipids
• Steroids
• Eicosanoids

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Neutral Fats (Triglycerides)Composed of three
fatty acids bonded to a glycerol molecule
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Lipids Video
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Other LipidsPhospholipids modified
triglycerides with two fatty acid groups and a
phosphorus group
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Other LipidsSteroids flat molecules with four
interlocking hydrocarbon ringsEicosanoids
20-carbon fatty acids found in cell membranes
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Representative Lipids Found in the Body

• Neutral fats found in subcutaneous tissue and
  around organs
• Phospholipids chief component of cell membranes
• Steroids cholesterol, bile salts, vitamin D,
  sex hormones, and adrenal cortical hormones
• Fat-soluble vitamins vitamins A, E, and K
• Eicosanoids prostaglandins, leukotriens, and
  thromboxanes
• Lipoproteins transport fatty acids and
  cholesterol in the bloodstream

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Amino Acids

• Building blocks of protein, containing an amino
  group and a carboxyl group
• Amino acid structure

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Amino Acids
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Protein Video
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ProteinMacromolecules composed of combinations
of 20 types of amino acids bound together with
peptide bonds
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Structural Levels of Proteins

• Primary amino acid sequence
• Secondary alpha helices or beta pleated sheets

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Structural Levels of Proteins

• Tertiary superimposed folding of secondary
  structures
• Quaternary polypeptide chains linked together
  in a specific manner

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Fibrous and Globular Proteins

• Fibrous proteins
• Extended and strandlike proteins
• Examples keratin, elastin, collagen, and certain
  contractile fibers
• Globular proteins
• Compact, spherical proteins with tertiary and
  quaternary structures
• Examples antibodies, hormones, and enzymes

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What Are Enzymes?

• Most enzymes are Proteins (tertiary and
  quaternary structures)
• Act as Catalyst to accelerates a reaction
• Not permanently changed in the process

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Enzymes

• Are specific for what they will catalyze
• Are Reusable
• End in ase
• -Sucrase
• -Lactase
• -Maltase

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How do enzymes Work?

• Enzymes work by weakening bonds which lowers
  activation energy

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Enzymes
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Enzyme-Substrate Complex The substance (reactant)
an enzyme acts on is the substrate

• Joins

Substrate
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• Induced Fit
• A change in the shape of an enzymes active site
• Induced by the substrate

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Protein Denuaturation Reversible unfolding of
proteins due to drops in pH and/or increased
temperature
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Protein DenuaturationIrreversibly denatured
proteins cannot refold and are formed by extreme
pH or temperature changes
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Factors Affecting Enzyme Activity

• Temperature
• pH
• Cofactors Coenzymes
• Inhibitors

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Temperature pH

• High temperatures are the most dangerous
  reactions denature enzymes (Most like normal
  Body temperatures)
• Most enzymes like near neutral pH (6 to 8)
• Denatured (unfolded) by ionic salts

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Cofactors and Coenzymes

• Inorganic substances (zinc, iron) and vitamins
  (respectively) are sometimes need for proper
  enzymatic activity.
• Example
• Iron must be present in the quaternary
  structure of hemoglobin in order for it to pick
  up oxygen.

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Two examples of Enzyme Inhibitors

• a. Competitive inhibitors are chemicals that
  resemble an enzymes normal substrate and compete
  with it for the active site.

Substrate
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Inhibitors

• Noncompetitive inhibitors
• Inhibitors that do not enter the active site,
  but bind to another part of the enzyme causing
  the enzyme to change its shape, which in turn
  alters the active site.

Substrate
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Molecular Chaperones (Chaperonins)

• Help other proteins to achieve their functional
  three-dimensional shape
• Maintain folding integrity
• Assist in translocation of proteins across
  membranes
• Promote the breakdown of damaged or denatured
  proteins

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Characteristics of Enzymes

• Most are globular proteins that act as biological
  catalysts
• Holoenzymes consist of an apoenzyme (protein) and
  a cofactor (usually an ion)
• Enzymes are chemically specific
• Frequently named for the type of reaction they
  catalyze
• Enzyme names usually end in -ase
• Lower activation energy

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Characteristics of Enzymes
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Mechanism of Enzyme Action

• Enzyme binds with substrate
• Product is formed at a lower activation energy
• Product is released

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Mechanism of Enzyme Action
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Nucleic Acids

• Composed of carbon, oxygen, hydrogen, nitrogen,
  and phosphorus
• Their structural unit, the nucleotide, is
  composed of N-containing base, a pentose sugar,
  and a phosphate group
• Five nitrogen bases contribute to nucleotide
  structure adenine (A), guanine (G), cytosine
  (C), thymine (T), and uracil (U)
• Two major classes DNA and RNA

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Nucleic Acid Video
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Deoxyribonucleic Acid (DNA)

• Double-stranded helical molecule found in the
  nucleus of the cell
• Replicates itself before the cell divides,
  ensuring genetic continuity
• Provides instructions for protein synthesis

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Structure of DNA
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Structure of DNA
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Ribonucleic Acid (RNA)

• Single-stranded molecule found in both the
  nucleus and the cytoplasm of a cell
• Uses the nitrogenous base uracil instead of
  thymine
• Three varieties of RNA messenger RNA, transfer
  RNA, and ribosomal RNA

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Adenosine Triphosphate (ATP)

• Source of immediately usable energy for the cell
• Adenine-containing RNA nucleotide with three
  phosphate groups

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Adenosine Triphosphate (ATP)
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How ATP Drives Cellular Work