chemistry and biological molecules bio 9. lecture outline organic chemistry polymers and modular...
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Lecture Outline
• Organic chemistry• Polymers and modular structure• Biological macromolecules
– Carbohydrates– Lipids– Proteins– Nucleic Acids
Carbon can form double bonds
1-Butene 2-Butene
Skeletons may have double bonds, which can vary in location.
Carbon also forms ring structures upon itself
Skeletons may be arranged in rings.
Cyclohexane Benzene
FUNCTIONAL GROUPS
A carbon skeleton can be modified by the addition of functional groups- familiar groups of atoms which affect the properties of the molecule
hydroxide group – OHamino group – NH2carboxyl group – COOHphosphate group – PO4methyl group – CH3
Functional groups can radically change the function of a molecule
Estradiol
TestosteroneMale lion
Female lion
Which of the following represents an amino group?
1 2 3 4 5
20% 20% 20%20%20%1. -OH2. -PO4
3. -CH3
4. - NH2
5. -COOH
Most molecules in living things fall into four categories
• Carbohydrates• Lipids• Proteins• Nucleic acids
These all exhibit modular construction
Carbohydrates• “Carbon” + “Hydro”• Formula (CH2O)n
• Different from hydrocarbons
• Soluble in water• Includes: table sugar,
honey, starch, glycogen, cellulose, high fructose corn syrup
• Glucose is the primary monomer
A Glucose monomer can cyclize to form a ring structure
Atoms in bonds are free to rotate around the bonds
Lipids
• Non-polar• High-energy molecules• For energy storage• Forms cell membranes• Hormones• Members of family
include oils, fats, waxes, and cholesterol (steroids)
Lipids are non-polar
• Therefore, they are hydrophobic
• C and H are similarly electronegative
• Do not mix easily with water
• C-H bond is high in energy
• Lipids make good energy storage molecules
Cis- and Trans- fatty acids are isomers
• Melting point is very different because of shape
• Health effects are very different
• Isomers- Same formula, different shape
Triglycerides can be modified to form phospholipids
• Phospholipids are amphipathic- having a polar and nonpolar region
• Hyrophilic head, hydrophobic tails
• Primary constituent of cell membranes
Lecture Outline
• Proteins• Nucleic acids• Ch 23- Nutrient cycling• Ch 24- Human impact on the environment• Finish bacteria lab
Proteins are incredibly diverse at the molecular level
Insulin
ATP synthase
Rubisco
NitrogenaseFibrin
A few examples
Protein function depends greatly on shape
Proteins are made of amino acids
• All amino acids have a backbone and a side group (“R” group)
• Backbone: amino group, carboxyl group, central carbon
• Side group: there are 20 different kinds, each with different chemical properties
Amino acids are added one by one to form a polypeptide chain of a protein
• Dehydration synthesis forms a peptide bond• DNA contains the instructions for the proper
sequence for a specific protein
Proteins have four levels of structure
• Primary- amino acid sequence of polypeptide
• Secondary- coiling of amino acid backbone
• Tertiary- Polypeptide folding from amino acid side groups
• Quaternary- more than one polypeptide
• Protein structure depends on all these levels of interaction
A protein’s Primary (1o) structure is its amino acid sequence
• Determined by the sequence of amino acids
• Amino acids linked by peptide bonds
• Chain is called polypeptide• Sequence proceeds from “N-
terminus” to “C-terminus”• Amino acid sequence
determined by DNA code
Secondary (2o) structure
• Hydrogen bonding between amino acid backbones• Amino group H’s H-bond with O’s from carboxyl end • 2 basic 2o 2o structures: α- helix and β-pleated sheet
Tertiary structure• The folding interactions
from amino acid side chains of a polypeptide
• The folding of 2o domains upon each other
• Interactions can be ionic, H-bonds, hydrophobic, or covalent
• Proper 3o structure depends on pH, temperature
Quaternary structure• The interactions of multiple polypeptides to form a
functional protein• Polypeptides can be the same (collagen is a homotrimer)
or different (hemoglobin is a heterotetramer)
The tertiary structure of proteins is sensitive to denaturation
• Heat or chemicals (incl. acids and bases) can temporarily or permanently change a protein’s 3o structure
Enzymes are a special kind of protein
Enzymes are protein catalysts
• Catalysts- things which speed up chemical reactions
• Catalysts are not consumed in a reaction
• -ase: The enzyme suffix
Catalase
How enzymes work Structure aids
function An active site
naturally fits substrate
Enzyme specificity depends on shape
Shape changes to fit substrate- induced fit
Enzymes are not consumed by the reactions they catalyze
Enzyme availablewith empty activesite
Active site
Glucose
Fructose
Products arereleased
Enzyme(sucrase)
Substrate(sucrose)
H2O
Substrate isconverted toproducts
Substrate bindsto enzyme withinduced fit
Metal ions and vitamins often serve as enzymatic cofactors, serving an essential role in
an enzyme’s function
FeMo and FeS clusters in Nitrogenase
B vitamins often serve as enzyme cofactors
Enzymes are catalysts made of protein. Which of these factors can slow their proper functioning?
1. Temperature2. pH3. Salts4. All of the above5. None of these
Effects of Temperature and pH
• Each enzyme has an optimal temperature in which it can function
• Each enzyme has an optimal pH in which it can function
• Tertiary structure can be radically altered by changes in pH
A protein containing more than one polypeptide chain exhibits the __________ level of protein
structure.
1. A) primary 2. B) secondary 3. C) tertiary 4. D) quaternary 5. E) infinite
Nucleic acids• (Primarily)
Informational molecules in cells
• Include DNA, RNA, and ATP/ADP
• DNA is the code to make a protein
• Living things are made up of protein
Nulceotides are the monomers of nucleic acid polymers
• Consist of a sugar, a phosphate, and a nitrogen-containing base
• Sugar can be deoxygenated
• Bases contain the genetic information
Hydrogen bonds hold the two sides of the DNA ladder together
• DNA bases have –OH and –NH2 groups
• Sides of ladder are covalently bonded
• Rungs held together with H-bonds
There are 4 kinds of DNA bases
• Adenine and Thymine, Cytosine and Guanine
• A, T, C, and G• RNA has Uracil instead
of Thymine
RNA’s major task is to carry out the instructions of DNA
• DNA is double-stranded, RNA single
• DNA has thymine, RNA has uracil