Chemistry Review

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Chemistry Review
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Chemistry

• Atom the smallest unit of matter that enters
  into chemical reactions
• Atoms interact to form molecules
• Three components of atoms
• Electrons (-)
• Protons ()
• Neutrons (neutral)

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Atoms

• Protons and neutrons are in the nucleus
• Electrons move around the nucleus and participate
  in chemical reactions
• Each chemical element has a unique number of
  protons (atomic number)

Figure 2.1
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Most abundant in living matter
Table 2.1
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How Atoms Form Molecules Chemical Bonds

• Atoms want to achieve a full outer electron
  shell
• An unfilled outermost electron shell has either
  vacant spaces or extra electrons, depending on
  whether it is easier for the atom to gain or lose
  electrons

It is easier for oxygen to gain 2 electrons to
attain a full outer shell
Atoms combine (form molecules) to achieve a full
complement of electrons in their outermost shells
It is easier for magnesium to lose 2 electrons
to attain a full outer shell
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How Atoms Form Molecules Chemical Bonds

• Chemical bonds the attractive forces that hold
  atoms together in a molecule
• Ionic bonds electrons are gained and lost
• Covalent bonds electrons are shared
• Hydrogen bonds weak attraction due to partial
  charges (often between molecules)

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How Atoms Form Molecules Chemical Bonds

• Ions atoms that have gained or lost electrons
  and are charged

anion
cation
Figure 2.2a
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Ionic Bonds

• Ionic bonds attractions between ions of opposite
  charge
• one atom loses electrons and another gains
  electrons

Figure 2.2b
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Covalent Bonds

• Covalent bonds form when two atoms share one or
  more pairs of electrons
• Much stronger than ionic bonds

Figure 2.3a
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Covalent Bonds
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Hydrogen Bonds

• Hydrogen bonds form when a hydrogen atom
  covalently bonded to an O or N atom is attracted
  to another O or N atom
• Due to polarity of molecules
• Weaker than ionic bonds constantly formed and
  broken

Figure 2.4
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Chemical Reactions

• Chemical reactions involve the making or breaking
  of bonds between atoms (bond rearrangement)
• A change in chemical energy occurs during a
  chemical reaction
• Endergonic reactions absorb energy
• i.e. formation of a new bond
• Exergonic reactions release energy
• i.e. breaking of a bond

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Important Biological Molecules

• Organic compounds always contain carbon and
  hydrogen
• Inorganic compounds typically lack carbon
• Example H2O
• H2O makes up an average of 65-75 of every cell

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Inorganic Compounds Water

• Due to waters polar nature, it has important
  properties
• Water is in its liquid state on most of Earths
  surface
• Temperature buffer
• Excellent solvent

Figure 2.4a
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Inorganic compoundsAcids, Bases, and Salts

• Acid a substance that dissociates into one or
  more H(a proton donor)
• HCl ? H Cl?

Figure 2.6a
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Inorganic compoundsAcids, Bases, and Salts

• Base a substance that dissociates into one or
  more OH?
• (proton acceptor)NaOH ? Na OH?

Figure 2.6b
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Inorganic compoundsAcids, Bases, and Salts

• Salt a substance that dissociates into cations
  and anions, neither of which is H or OH?NaCl ?
  Na Cl?

Figure 2.6c
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Inorganic compoundsAcid-Base Balance

• Biochemical reactions are extremely sensitive to
  changes in pH
• The amount of H in a solution is expressed as pH
• Increasing H?more acidic (lower pH)
• Increasing OH??more alkaline (higher pH)
• Most organisms grow best between pH 6.5 and 8.5
• Living cells contain natural pH buffers to resist
  intracellular pH changes

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Inorganic compoundsAcid-Base Balance
Figure 2.7
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Organic CompoundsMacromolecules

• Small organic molecules can combine into large
  macromolecules
• Macromolecules polymers consisting of many small
  repeating molecules (monomers)
• Four major classes of organic macromolecules in
  living cells
• Carbohydrates
• Lipids
• Proteins
• Nucleic acids

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Organic CompoundsMacromolecules

• Monomers join by condensation or dehydration
  synthesis reactions
• Involve the release of a water molecule
• Produce covalent bonds between monomers

Figure 2.8
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Organic CompoundsCarbohydrates

• Carbohydrates (Polysaccharides)
• Sugars and starches
• Important energy sources
• Cellular structural components

Figure 2.8
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Organic CompoundsCarbohydrates

• Subunits monosaccharides
• Monosaccharides are simple sugars with 3 to 7
  carbon atoms
• Polysaccharides consist of tens or hundreds of
  monosaccharides joined through dehydration
  synthesis
• Starch, glycogen, dextran, and cellulose are
  polymers of glucose that are covalently bonded
  differently

Figure 2.8
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Organic CompoundsLipids

• Lipids
• Primary components of cell membranes
• Energy storage
• Consist of C, H, and O
• Fatty acids are nonpolar and insoluble in water

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Organic CompoundsLipids

• Simple lipids (fats or triglycerides)
• Subunits glycerol and fatty acids
• Formed by dehydration synthesis
• Unsaturated fats have one or more double bonds in
  the fatty acids

glycerol
Fatty acids
Figure 2.9c
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Organic CompoundsLipids

• Complex lipids
• Contain C, H, and O P, N, or S
• Cellular membranes are made of phospholipids
• Polar and nonpolar regions (amphipathic)

Phospholipid structure
Figure 2.10a
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Organic CompoundsProteins

• Proteins
• Contain C, H, O, N and S
• Essential in cell structure and function
• Enzymes are proteins that speed chemical
  reactions
• Transporter proteins move chemicals across
  membranes
• Bacterial flagella are made of proteins
• Some bacterial toxins are proteins

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Organic CompoundsProteins

• Subunits amino acids

Table 2.4.1
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Organic CompoundsPeptide Bonds in Proteins

• Peptide bonds between amino acids are formed by
  dehydration synthesis

Figure 2.14
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Organic CompoundsLevels of Protein Structure

• Four levels of organization primary, secondary,
  tertiary and quaternary structure
• Overall structure is directly related to its
  function!
• Correct function absolutely relies on correct
  structure
• Primary structure the amino acid sequence of a
  polypeptide chain (genetically determined)
• Relies on covalent bonds

aa1
aa6
aa5
aa2
aa3
aa4
Figure 2.15a
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Organic CompoundsLevels of Protein Structure

• Secondary structure localized folding or
  twisting into pleated or helical domains
• Due to hydrogen bonding
• Predictable based on amino acid sequence

Figure 2.15b
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Organic CompoundsLevels of Protein Structure

• Tertiary structure overall three-dimensional
  structure of a polypeptide chain
• Unpredictable folding
• Many bond types/interactions are involved

Figure 2.15c
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Organic CompoundsLevels of Protein Structure

• Quaternary structure consists of two or more
  individual polypeptide chains that compose a
  single functional unit
• Not all proteins have quaternary structure

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Organic CompoundsNucleic Acids

• Nucleic acids (DNA and RNA)
• Subunits nucleotides
• Nucleotides consist of a
• Pentose sugar
• Phosphate group
• Nitrogen-containing base

Figure 2.16
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Organic CompoundsATP

• Adenosine triphosphate (ATP)
• Principal energy-carrying molecule of all cells
• Has ribose, adenine, and 3 phosphate groups

Figure 2.18

• Hydrolysis of ATP liberates a high amount of
  useful energy for the cell

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