Basic Cell Chemistry

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Basic Cell Chemistry
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Chapter Goals

• After studying this chapter, students should be
  able to
• describe the structure of an atom and define the
  terms atomic mass, atomic number, and ion.
• explain how covalent bonds are formed and
  distinguish between nonpolar and polar covalent
  bonds.
• describe the structure of an ion and explain how
  ionic bonds are formed.
• describe the nature of hydrogen bonds and explain
  their significance.
• describe the structure of a water molecule and
  explain why some compounds are hydrophilic and
  others are hydrophobic.
• define the terms acid and base and explain the
  meaning of the pH scale.
• explain how the pH of the blood is stabilized by
  bicarbonate buffer, and define the terms acidosis
  and alkalosis.
• describe the different types of carbohydrates and
  give examples of each type.

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Chapter Goals (contd)

• After studying this chapter, students should be
  able to
• describe the mechanisms and significance of
  dehydration synthesis and hydrolysis reactions
  and explain their significance.
• state the common characteristics of lipids and
  describe the different categories of lipids.
• describe how peptide bonds are formed and the
  different orders of protein structure.
• list some of the functions of proteins and
  explain why proteins provide specificity in their
  functions.
• tell what enzymes are and how they work.
• understand the concept of optima
• understand basic enzyme kinetics

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Basic Cell Chemistry

• Matter and elements
• Atomic structure
• Ions

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Atomic Structure

• B-1

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Ionic Bond
Atomic 11 Atomic Mass 23
Atomic 17 Atomic Mass 34

• B-2

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Crystalline Lattice

• B-3

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Covalent Bond

• B-4

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• 2.8

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• 2.8

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• 2.9

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Polar Molecule

• B-5

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Hydrogen Bond

• B-6

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• 2.6

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Acids, Bases and Salts

• Acid - proton donor
• pH -logH
• Scale 1 - 14, with 7 being neutral
• Base - proton acceptor
• Salts - crystalline solids produced by
  neutralization reactions.
• Buffers resist change in pH

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Biomolecules

• Functional Groups
• Carbohydrates
• Lipids
• Nucleic Acids
• Proteins

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• 2.10

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• 2.11

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Carbohydrates (CH2O)

• Monosaccharides
• Triose
• Tetrose
• Pentose
• Hexose
• Disaccharides
• Oligosaccharides
• Polysaccharides

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Hexose Monosaccharide (glucose)

• B-7

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• 2.16

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Polysaccharide (glycogen)

• B-8

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Lipids

• Glycerides (Mono, Di, Tri)
• Phospholipids
• Steroids
• Prostaglandins

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Triglyceride

• B-9

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Phospholipid and Sphingolipids

• 2.19

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Steroid

• B-11

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Steroid Examples

• B-12

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• 2.22

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Proteins

• Basic building blocks (amino acids)
• Primary Structure
• Secondary Structure
• Tertiary Structure
• Quaternary Structure

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Amino Acid
B-13
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Peptide Bond
B-14
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Primary Structure
B-15
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Levels of Structure
B-16
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Side Chain Interactions
B-17
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Nucleic Acids

• Building Blocks (Nucleotides)
• DNA
• RNA

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Structure of Nucleotide Triphosphate
B-18
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Enzymes

• Specific organic catalysts
• Cannot drive reactions
• Direction determined by LeChatlier Principle.
• E S lt--gt ES lt--gt E P
• E enzyme S substrate P product

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4.1a
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4.1b
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4.2
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Induced Fit Model
Binding of substrate causes the enzyme to change
shape such that the enzyme fits around the
substrate.
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4.3
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4.4
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4.5
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4.6
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4.8
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4.9
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4.10
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Chapter Summary

• Atoms, Ions, and Chemical Bonds
• Carbohydrates and Lipids
• Proteins

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Atoms, Ions, and Chemical Bonds

• I. Covalent bonds are formed by atoms that share
  electrons. They are the strongest type of
  chemical bond.
• A. Electrons are equally shared in nonpolar
  covalent bonds and unequally shared in polar
  covalent bonds.
• B. Atoms of oxygen, nitrogen, and phosphorus
  strongly attract electrons and become
  electrically negative compared to the other atoms
  sharing electrons with them.

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Atoms, Ions, and Chemical Bonds

• II. Ionic bonds are formed by atoms that transfer
  electrons these weak bonds join atoms together
  in an ionic compound.
• A. If one atom in this compound takes the
  electron from another atom, it gains a net
  negative charge and the other atom becomes
  positively charged.
• B. Ionic bonds easily break when the ionic
  compound is dissolved in water. Dissociation of
  the ionic compound yields charged atoms called
  ions.

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Atoms, Ions, and Chemical Bonds

• III. When hydrogen is bonded to an
  electronegative atom, it gains a slight positive
  charge and is weakly attracted to another
  electronegative atom. This weak attraction is a
  hydrogen bond.

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Atoms, Ions, and Chemical Bonds

• IV. Acids donate hydrogen ions to solution,
  whereas bases lower the hydrogen ion
  concentration on a solution.
• A. The pH scale is a negative function of the
  logarithm of the hydrogen ion concentration.
• B. In a neutral solution the concentration of H
  is equal to the concentration of OH-, and the pH
  is 7.
• C. Acids raise the H concentration and thus
  lower the pH below 7 bases lower the H
  concentration and thus raise the pH above 7.

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Atoms, Ions, and Chemical Bonds

• V. Organic molecules contain atoms of carbon
  joined together by covalent bonds atoms of
  nitrogen, oxygen, phosphorus, or sulfur may be
  present as specific functional groups in the
  organic molecule.

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Carbohydrates and Lipids

• I. Carbohydrates contain carbon, hydrogen, and
  oxygen, usually in a ratio of 121.
• A. Carbohydrates consist of simple sugars
  (monosaccharides), disaccharides, and
  polysaccharides (such as glycogen).
• B. Covalent bonds between monosaccharides are
  formed by dehydration synthesis, or condensation.
  Bonds are broken by hydrolysis reactions.

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Carbohydrates and Lipids

• II. Lipids are organic molecules that are
  insoluble in polar solvents such as water.
• A. Triglycerides (fat and oil) consist of three
  fatty acid molecules joined to a molecule of
  glycerol.
• B. Ketone bodies are smaller derivations of fatty
  acids.
• C. Phospholipids (such as lecithin) are
  phosphate-containing lipids that have a
  hydrophilic polar group. The rest of the molecule
  is hydrophobic.
• D. Steroids (including the hormones of the
  adrenal cortex and gonads) are lipids with a
  characteristic five-ring structure.
• E. Prostaglandins are a family of cyclic fatty
  acids, which serve a variety of regulatory
  functions

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Proteins

• I. Proteins are composed of long chains of amino
  acids bound together by covalent peptide bonds.
• A. Each amino acid contains an amino group, a
  carboxyl group, and a functional group.
  Differences in the functional groups give each of
  the more than twenty different amino acids an
  individual identity.
• B. The polypeptide chain may be twisted into a
  helix (secondary structure) and bent and folded
  to form the tertiary structure of the protein.
• C. Proteins that are composed of two or more
  polypeptide chains are said to have a quaternary
  structure.
• D. Proteins may be combined with carbohydrates,
  lipids, or other molecules.
• E. Because of their great variety of possible
  structures, proteins serve a wider variety of
  specific functions than any other type of
  molecule.

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Enzymes

• I. Enzymes are specific organic catalysts
• A. Most enzymes are proteins.
• B. Enzymes have a unique 3-D structure that
  enables them to bind to a specific substrate.
• C. Enzymes speed up chemical reactions by
  lowering activation energy.
• D. Since enzymes physically join to their
  substrate, they can become saturated.
• E. The structure of enzymes is encoded in DNA, so
  a mutation can affect enzyme structure.