Download Molecular Structures

Molecular Structures
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
Proteins &
Amino Acids
• Amino Acid
Properties
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)
Protein Structure
• Peptide bond
A.K.A Amide Bond
Fig 5-1 Essential Cell Biology, Alberts et al
Protein
Structure
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
Protein
Structure
Secondary
Structure
intramolecular
folding of
backbone
-helix
-sheet
Fig 2-10
Protein Structure
• Tertiary structures
– Proteins can have any combination of
secondary structures
Fig 2-11
Fig 2-9
Protein Structure
• Modeling protein
structures
• X-ray
crystallography
Space-filling
Ribbon
Protein Structure
Backbone
Wire
Space-filling
Ribbon
Panel 5-2 Essential Cell
Biology, Alberts et al
Protein Structures
• Structural & Functional Domains
Fig 2-15
Nucleic Acids
• Nitrogenous base
Nucleic Acids
• Pentose sugar
Nucleic Acids
• Nucleoside
• Base + Sugar
– Adenosine
– Guanosine
– Thymidine
– Cytosine
– Uridine
Nucleic Acids
• Phosphate
– 1-3 (mono, di, tri-phosphate)
Nucleic Acids
• Nucleotides
– Nitrogenous base
• Purine
– Adenine
– Guanine
• Pyrimidine
– Cytosine
– Thymine
– Uracil
– Pentose sugar
• 2’-deoxyribose
• Ribose
– Phosphate
• 1-3 (mono, di, triphosphate)
Nucleic Acids
• Polymerization of
nucleotides
– Phosphodiester bond
• 3'-OH of added
nucleotide SN2 attack
on  phosphate
– DNA polymerase
– RNA polymerase
Nucleic Acid Structure
• The Double Helix
– Watson-Crick base pairs
• A-T
• G-C
Nucleic Acid Structure
• RNA secondary
structure
– Intermolecular base
pairing
– Stems & loops
16S rRNA
Phe tRNA
Carbohydrates
• Simple sugars
– Monosaccharides
•
•
•
•
•
•
Glucose
Fructose
Galactose
Mannose
Ribose
Arabinose
6-carbon
5-carbon
Carbohydrates
• Important modifications
glcNAc
glcUA
• Glycosidic bonds
Carbohydrates
• Glycoconjugates
(polysaccharides,
complex carbos)
– Starch (plants)
– Glycogen (animals)
• Branched polymers of
glucose
– Cellulose
• Unbranched polymers
Fig2-27
Carbohydrates
• Important attachments to amino acid
residue side chains
Fig 2-28
Carbohydrates
• Proteoglycans
– Proteins with attached glycosaminoglycans
– Cell surface proteins
– ECM
Fig 31-14
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