chemistry and biological molecules bio 9 feb 18, 2010
TRANSCRIPT
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Chemistry and Biological Molecules
Bio 9Feb 18, 2010
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In covalent bonding, pairs of valence electrons are shared, and molecules are formed
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Carbon (always) forms 4 bonds
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Carbon can form double bonds
1-Butene 2-Butene
Skeletons may have double bonds, which can vary in location.
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Carbon also forms ring structures upon itself
Skeletons may be arranged in rings.
Cyclohexane Benzene
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The variety of carbon compounds is limitless
All terrestrial life is based on carbon
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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
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Functional groups can radically change the function of a molecule
Estradiol
TestosteroneMale lion
Female lion
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Figure 3.5
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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
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Most molecules in living things fall into four categories
• Carbohydrates• Lipids• Proteins• Nucleic acids
These all exhibit modular construction
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Modular housing
Made of interchangeable parts
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Freight trains have modular assembly
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Modular assembly allows a wide variety of products from a few pieces
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Most biopolymers are formed by dehydration synthesis
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Hydrolysis is the reverse
reaction (Catabolic)
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Metabolism
• all chemical reactions in body• Anabolism- building up• Catabolism- breaking down
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Major Macromolecules of Life
• Carbohydrates• Lipids• Proteins• Nucleic Acids
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Carbohydrates
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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
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A Glucose monomer can cyclize to form a ring structure
Atoms in bonds are free to rotate around the bonds
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Glucose + Glucose = Maltose (monosaccharide + monosaccharide = disaccharide)
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Glucose + fructose = sucrose
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A polysaccharide chain can be extended to thousands- it is theoretically limitless
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Glycogen and cellulose
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Lipids
Nonpolar molecules of living things: Fats, oils, waxes, steroids, etc.
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Lipids
• Non-polar• High-energy molecules• For energy storage• Forms cell membranes• Hormones• Members of family
include oils, fats, waxes, and cholesterol (steroids)
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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
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Triglycerides are a primary lipid structure
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Dehydration synthesis links fatty acids to glycerol
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Fatty acids can be saturated and unsaturated (“cis” and “trans”)
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Monounsaturated vs. Polyunsaturated
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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
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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
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Phospholipids are the primary constituent of cell membranes
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Proteins
Amino acid polymers which make us what we are
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Proteins have incredible versatility of structure and function
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Proteins are incredibly diverse at the molecular level
Insulin
ATP synthase
Rubisco
NitrogenaseFibrin
A few examples
Protein function depends greatly on shape
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Figure 2.12
Amino Acids
• Proteins consist of subunits called amino acids
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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
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Some amino acids are polar, others nonpolar
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Others have sulfur, others are acidic, still others are
basic
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Many are sold as nutritional supplements
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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
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DNA carries the information to make a specific protein
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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
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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
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Figure 2.15a
Levels of Protein Structure
• The primary structure is a polypeptide chain
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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
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Alpha-helix and Beta-sheet are two important 2o structural motifs
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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
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A lightbulb filament has multiple levels of structure
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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)
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Changes in the 1o structure of a protein can have far-reaching effects
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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
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Enzymes-Catalytic proteins
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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
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How enzymes work Structure aids
function An active site
naturally fits substrate
Enzyme specificity depends on shape
Shape changes to fit substrate- induced fit
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Enzymes increase the rates of reactions by 108 or more
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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
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-galactosidase
11
lactose
galactose
glucose
H2O
- galactosidase(aka lactase in humans)
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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
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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
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In salad dressings, oil quickly separates from vinegar because oils are
1. heavier than water. 2. polar. 3. nonpolar. 4. hydrophilic. 5. amphiphilic.
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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
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Nucleic acids
DNA, RNA, and ATP
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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
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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
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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
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There are 4 kinds of DNA bases
• Adenine and Thymine, Cytosine and Guanine
• A, T, C, and G• RNA has Uracil instead
of Thymine
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RNA’s major task is to carry out the instructions of DNA
• DNA is double-stranded, RNA single
• DNA has thymine, RNA has uracil
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ATP
A nucleotide-based
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ATP, a single RNA nucleotide, is the basic energy currency of all cells
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LE 8-12
Pi
ADP
Energy for cellular work(endergonic, energy-consuming processes)
Energy from catabolism(exergonic, energy-yielding processes)
ATP
+
The Regeneration of ATP
What powers this cycle?