Chemistry & Biology of Bonds: Ionic, Covalent, Polar Molecules, Hydrogen Bonds - Prof. Bar, Study notes of Microbiology

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Slide 1

Chemistry for Microbiology

Lecture 2

Slide 2

Biol 240 S

Learning Outcomes

• Review
  • chemical reactions– Bonding– Oxidation and

Reduction reactions

• pH
  • Biological Molecules

Slide 3

Biol 240 S

3

• Atoms want a complete outer electron shell• Losing an electron

Æ

positive cation

• Gaining an electron

Æ

negative anion

• Opposites attract– BUT bonds disrupted by water

Ions and Ionic bonds

Figure 2.2a

11 e

-^

10 e

-^

17 e

-^

18 e

-

What are ions?, and describe how do ionic bonds form between atoms in a compound.

Slide 4

Biol 240 S

Other Bonds

• Iconic Bonds• Ironic Bonds

Slide 7

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7

• Polar

compoundsdissociate,formingsolutes– They

dissolve

Water as a Solvent

Figure 2.

Water is a polar molecule. Explain what this means in terms of water’s ability to act as asolvent At the atomic level, describe what happens when salt (Na

+^ Cl

-^ ) ‘dissolves’ in water

Slide 8

Biol 240 S

• Hydrogen bonds with

attractions between slightlypositive and slightly negative‘poles’ of polar molecules

• Between water molecules• Between hydrogens and

Oxygens or Nitrogens– DNA– Proteins secondary structure

Hydrogen Bonds

Figure 2.

How do hydrogen bonds differ from covalent bonds and provide examples of ahydrogen bond between 2 molecules and within the structure of a macromolecule.

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Biol 240 S

9

• An acid is a

compound thatdissociates inwater (dissolves)adding H

+^

To the

solutionHCl compound

H

+^

+ Cl

−

Acids

Figure 2.6a

Without using the terms “acid” or “basic” what is the difference between a

solution of pH 3 and a solution of pH 5?

Slide 10

Biol 240 S

• A base is a

compound thatdissociates inwater forming OH

−

ions

• NaOH

Na

+^

+ OH

−

• bases remove H

from solution

OH

−^

+ H

+^

Æ

H

O 2

Bases

Figure 2.6b

Without using the terms “acid” or “basic” what is the difference between a

solution of pH 3 and a solution of pH 5?

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Biol 240 S

13

Carbon Atoms

Slide 14

Biol 240 S

• Carbon skeleton.• Functional groups
  • responsible for most

of the chemicalproperties

• The more C-H the

higher the potentialenergy

• Oxidizing replaces C-

H with C-O or C=O

Organic Compounds

How does an organic molecules differ from an inorganic molecule? Provide examples of each type of compound.

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Biol 240 S

15

Respiration as aRedox Reaction

• Food energy =

molecules with– Many or C-H bonds– Many electrons– = reduced carbon

atoms

• In cells food

molecules oxidized– Electrons removed– Energy harvested

• Oxygen terminal

electron acceptor– Oxygen is reduced

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Biol 240 S

16

• Smaller organic molecules monomers• Macromolecules are polymers• Monomers join by dehydration synthesis

Macromolecules

Figure 2.

Explain the difference between dehydration synthesis and hydrolysis.

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Biol 240 S

19

• Are non-polar and insoluble in water• Consist of C, H, and O.• Triglycerides•

3 C glycerol and 3 fatty acid chains–

formed by dehydration synthesis.

• Bacteria and eukarya ester linkage– Archaea ether linkage

Lipids

Explain why lipids are insoluble in water.

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Biol 240 S

• Cell

membranes aremade ofphospholipids

• Polar

Phosphategroup

• Nonpolar fatty

acid chains

• Bacteria
  • Ester linkage
    • Archaea
      • Ether linkage

Phospholipids

Figure 2.10a

1)

Describe how the properties of phospholipids make these molecules well

suited for plasma membranes.Archaea differ from bacteria in the composition of cell membrane lipids. Explain howthey differ at the molecular level

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21

• Consist of

four carbonrings, with an–OH groupattached toone ring.

• Are part of

membranes.– Cholesterol– ergosterol

Steroids

Figure 2.

Slide 22

Biol 240 S

• Are essential in cell structure and

function.

• Enzymes are proteins that speed chemical

reactions.

• Transporter proteins move chemicals

across membranes

• Flagella are made of proteins.• Some bacterial toxins are proteins.• Antibodies are proteins

Proteins

Why are proteins important to life?

Slide 25

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25

Protein Structure

Describe and give examples of each level of protein structure.

Slide 26

Biol 240 S

Ceviche

-^

Shrimp meat (protein)initially translucent

-^

Acid of Lime marinade[H

+^ ] breaks H bonds

-^

Protein structureunravels–

White (scatters light)

-^

Chewy

-^

Why cook fish?

Explain what happens to the structure of the proteins of shrimp when placed in anacidic lime marinade (Viva Ceviche!)

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Biol 240 S

27

• Conjugated proteins consist of

amino acids and other organicmolecules:• Glycoproteins

• mucin
  • Lipoproteins• Nucleoproteins

Conjugated Proteins

Provide examples of two different types of conjugated proteins.

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Biol 240 S

• Consist of nucleotides.• Nucleotides consist of a:
  • Pentose• Phosphate group• Nitrogen-containing (purine or pyrimidine)

base

Nucleic Acids

Figure 2.

What are the complementary base pairs in DNA and RNA?

Slide 31

Biol 240 S

• Has ribose + adenine, and 3 phosphate groups

(ATP)

• Is made by dehydration synthesis.• Is broken by hydrolysis to liberate useful

energy for the cell.

Adenosine Tri-

Phosphate

Figure 2.

Explain how the chemical structure of ATP allows it to perform its biological role.