1The study of biochemistry is necessary to understand Microbiology

Habitat

Diet

2Why Chemistry?

Conflict between microbe and host.

Vibrio cholera toxin inserting into intestinal cells.

3Terms and Definitions to review and Remember:

• Atom, protons, neutrons, electrons, isotopes, elements, molecules, ions, anions, cations, compounds, covalent bonds, ionic bonds, hydrogen bonds, pH, acids, and bases.

• Solution

•Suspension

4Atom: smallest unit of an elementElements differ by number of protons

http://www.perceptions.couk.com/imgs/atom.gif

5Molecule: atoms joined together with covalent bonds

Electrons are shared between atoms.

Covalent bonds are strong.

When atoms in the molecule are of different elements, the substance is called a “compound”.

http://www.truenorthgb.com/images/molecule.jpg

6Covalent bonds & polar molecules

Water

Covalent Bonds: sharing of electrons between the oxygen and hydrogen atoms. Strong.

Oxygen is an electron hog; the electrons spend more time there leaving the hydrogen’s proton nearly naked (and somewhat positive): Water is a polar molecule

mdp2.phys.ucl.ac.uk/ Talks/Ice/Ice.html

7Hydrogen bonds:• Electrical attraction between electronegative oxygen

atom and nearly naked proton. • Bonds made between polar molecules.• Weak bonds.

8H-bonds hold large molecules together

Example: A-T base pair in DNA

http://www.mun.ca/biology/scarr/Fg10_16a.gif

9Hydrophilic and hydrophobic

Surfaces made of molecules without polar groups (e.g. CH3CH2CH2CH2.) repel water.

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pH= -log [H+]

Logarithmic

pH 7 is neutral

Ranges from 0-14

Molecules that release H+ are acids; those that release OH- are bases.

http://www.btinternet.com/~chemistry.diagrams/ph_scale.gif

H2O H+ + OH- [H+] = 10-7

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Functional Groups

12Chemical Reactions

• Synthesis or decomposition reactions– More when we cover metabolism.

• Reactants Products (general)• Substrate(s) Products (enzymatic)

C12H22O11 + H2O 2 C6H12O6

Hydrolysis (left to right) Dehydration (right to left)

+ H2Ohttp://www.unisanet.unisa.edu.au/08365/timages/sucrose.jpg

The Chemicals of life are large and small

• Cells contain molecules of all sizes but are MADE of large molecules called polymers– Polymer: a large molecule made of many similar or

identical subunits.– “poly” means “many” (polyethylene, polysaccharide)– The small molecules that make up a polymer: monomers

• “mono” means “one”• “oligo” means few (as in oligomer, oligonucleotide)

• In our, not all polymers are biological– Plastics are all polymers too

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14Small molecules (monomers) and macromolecules (polymers)

Ethylene and polyethylene

15Four Classes of Biological Molecules

• Carbohydrates– Sugars and their polymers

• Nucleic acids and nucleotides– DNA, RNA, ATP

• Lipids– Various hydrophobic molecules

• Proteins and amino acids

16Carbohydrates: CH2O

Monosaccharides: glucose, fructose, many others

Disaccharides: sucrose, lactose

Oligosaccharides: found on glycoproteins, in cytoplasm (oligo- means “few”)

Polysaccharides: starch, glycogen, cellulose, agar, chitin, xanthan gum

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20A nucleotide: a monomer of DNA

http://www.emc.maricopa.edu/faculty/farabee/BIOBK/nucleotide.gif

21Nucleic acids are the polymers made from nucleotides.

DNA tRNA

http://www.biochem.uwo.ca/meds/medna/IMG/tRNA.GIF

22Structure of DNA

http://academic.brooklyn.cuny.edu/biology/bio4fv/page/molecular%20biology/16-05-doublehelix.jpg

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Phospholipids are essential building blocks for membranes; sterol-type molecules are rarely found in bacteria.

25A lipid polymer: a biodegradable plastic made by bacteria. Ester bond

Polyesters

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Peptide bond

covalent bond that connects two amino acids.

29Levels of protein structure

Primary: amino acids and the order they are in; determined from the DNA.

Secondary: alpha helix and beta pleated sheet; twisting of chain in space.

Tertiary: 3D shape of protein.

Quaternary: more than 1 polypeptide combining to form a functional unit.

http://www.contexo.info/DNA_Basics/images/proteinstructuresweb.gif

Don’t forget the water

• ALL living things require water– Water is major component of cytoplasm– All small molecules are dissolved in water– All large molecules have water attached to them– Cells modify their chemistry to retain water– You die of dehydration before you starve

• Every polymer, every structure in the cell is surrounded by water.

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http://media.nasaexplores.com/lessons/04-070/images/faucet.jpg