1. Molecular Structures

2. Classes of Biomolecules
Proteins
polymers of amino acids
alias: polypeptides, peptides, enzymes
Nucleic Acids
polymers of nucleotides
alias: DNA, RNA
Lipids
long chain hydrocarbons tails with carboxylic end
alias: fatty acids, triglycerides, phosphoglycerides, phospholipids, steroids
Carbohydrates
3-6 carbon polyhydroxyl compounds
monosaccharides, disaccharides, polysaccharides, starches, glycogen

3. Proteins & Amino Acids
Amino Acid Properties

4. Proteins & Amino Acids
Common modifications to amino acids in proteins in cells
phosphorylation (kinasing) – signaling, activation/inactivation
acetylation - histones
disulfide bridges – protein folding
hydroxylation – collagen polymerization
glycosylation (see carbohydrates)

5. Protein Structure Peptide bond PEPTIDE A.K.A Amide Bond
Fig 5-1 Essential Cell Biology, Alberts et al
A.K.A Amide Bond

6. Protein Structure Backbone Side chains
Primary Structure
Amino Acid Sequence
Backbone
amide nitrogen-  -carbon-carbonyl carbon
Side chains
R-groups of each amino acid on  -carbon
Peptide bond is planar giving rigidity to backbone
Fig 2-6

7. Protein Structure Secondary Structure
intramolecular folding of backbone
-helix
-sheet
Fig 2-10

8. Protein Structure Tertiary structures
Proteins can have any combination of secondary structures
Fig 2-11

9. Protein Structure Modeling protein structures X-ray crystallography
Fig 2-9
Protein Structure
Modeling protein structures
X-ray crystallography
Space-filling
Ribbon

10. Protein Structure Backbone Wire Space-filling Ribbon
Panel 5-2 Essential Cell Biology, Alberts et al

11. Protein Structures
Structural & Functional Domains
Fig 2-15

12. Nucleic Acids
Nitrogenous base

13. Nucleic Acids
Pentose sugar

14. Nucleic Acids Nucleoside Base + Sugar Adenosine Guanosine Thymidine
Cytosine
Uridine

15. Nucleic Acids
Phosphate
1-3 (mono, di, tri-phosphate)

16. Nucleic Acids Nucleotides Nitrogenous base Pentose sugar Phosphate
Purine
Adenine
Guanine
Pyrimidine
Cytosine
Thymine
Uracil
Pentose sugar
2’-deoxyribose
Ribose
Phosphate
1-3 (mono, di, tri-phosphate)

17. Nucleic Acids Polymerization of nucleotides Phosphodiester bond
3'-OH of added nucleotide SN2 attack on  phosphate
DNA polymerase
RNA polymerase

18. Nucleic Acid Structure
The Double Helix
Watson-Crick base pairs
A-T
G-C

19. Nucleic Acid Structure
RNA secondary structure
Intermolecular base pairing
Stems & loops
16S rRNA
Phe tRNA

20. Carbohydrates Simple sugars Monosaccharides Glucose Fructose Galactose
Mannose
Ribose
Arabinose
6-carbon
5-carbon

21. Carbohydrates
Important modifications
Glycosidic bonds
glcNAc
glcUA

22. Carbohydrates Glycoconjugates (polysaccharides, complex carbos)
Starch (plants)
Glycogen (animals)
Branched polymers of glucose
Cellulose
Unbranched polymers
Fig2-27

23. Carbohydrates Important attachments to amino acid residue side chains
Fig 2-28

24. Carbohydrates Proteoglycans Proteins with attached glycosaminoglycans
Cell surface proteins
ECM
Fig 31-14

25. Carbohydrates Glycosaminoglycans (GAGs, mucopolysaccharidse)
Polymer of disaccharide units
Sulfate common modification
Linked to protein by O- or N- linkage to S/T or N residues respectively
Fig 31-13