Biochemistry
Core Objectives:
1. Although life starts at the cellular level, functional variety seen in life is a result of molecular variety so biologists study molecules
2. How the versatile chemistry of carbon helps create a variety of structures and thus functions in life
3. How the breakdown of molecules with many bonds between carbon and hydrogen releases energy that can be used to power life
4. Understand how macromolecules are polymers built from smaller monomers
5. Dehydration synthesis vs. Hydrolysis
6. Macromolecules
Where to find it
Elements in it
Monomers
Functions
Monomer Structure
Bonds that Hold Polymers Together
Polymer Structure
How Structure Ties in with Function
7. Know the role of ATP and its relationship to nucleic acids
Water – The Molecule of Life (See Separate Lecture)
Carbon Chemistry (Organic)
Elements of Life (CHON PS)
Inorganic vs. Organic Compounds
Carbon (Swissknife of Life)
Valence Shell Configuration (4 electrons on last shell)
Number of Bonds (4)
Types of Bonds (Single, Double, Triple, Quadruple)
Types of Structures
Single bonds  Branched Chains / Pyramids
Double Bounds  Kinks / X-Shaped
Tripled / Quadruple  Straight Chains
Carbon Skeletons
Length
Branched vs. Unbranched
Double & Triple Bounds (Number & Location)
Rings vs. Chains
Hydrocarbons
Chemical Bonds / Reactions & Potential Energy
Bonded Atoms More Stable (Lower Energy State)
Bond Formation Releases Energy (Required Activation Energy to Start Process)
Simpler Molecules More Stable (Lower Energy State)
Complex  Simple = Energy Released
Hydrocarbons = Complex Molecules
Store Chemical Energy (Potential Energy)
Burning / Digesting Hydrocarbons
Hydrocarbons  Simple Molecules (CO2, CO, H2O)
Energy Released
Non polar molecules / insoluble / hydrophobic
Functional Groups
Structure = Function
Hydroxyl [-OH] (Alcohols)  Sugars (Carbohydrages) / Vitamins
Carboxyl [-COOH] (Organic Acids)  Amino Acids (Proteins) / Fatty Acids (Lipids) / Some Vitamins
Amino [-NH2] (Amines)  Amino Acids (Proteins)
Phosphate [-PO2] (Energy Molecules)  RNA & DNA (Nucleic Acids) / Nucleoside Triphosphates (e.g.: ATP)
Carbonyl (Aldehydes / Ketones)  Sugars (Carbohydrates)
Make molecules polar / soluble / hydrophilic
Monomers & Polymers
Monomers
Polymers (Macromolecules)
Dehydration Synthesis / Condensation Reaction & Polymerization (Monomers  Polymers)
Join monomers by removing a H from one functional group and an OH to another; making water in the process
Less common in the body
[Requires Energy / Anabolic / Endergonic / Endothermic]
Hydrolysis & Depolymerization / Digestion (Polymers  Monomers)
[Releases Energy / Catabolic / Exergonic / Exothermic]
Destroy by adding water to complete functional groups (H to one and OH to another)
More common in the body
To Know About Each Type of Macromolecule
Where to find it
Elements in it
Monomers
Functions
Monomer Structure (including important functional groups)
Bonds that Hold Polymers Together
Polymer Structure
How Structure Ties in with Function
Carbohydrates
Find it: Grains / Sugars / Cell Walls
Elements: C-H-O in a 1:2:1 Ratio / Water-Soluble
Monomers: Monosaccharides
Over 40 types
Main Types (All C6H12O6)
Glucose
Fructose
Galactose
Pentose Sugars found in nucleic acids: C5H10O5
Ribose
Deoxyribose
Functions:
Energy Storage (Fuel for cellular respiration)
Structure (Cell Walls)
Cell Communication / Recognition
Monomer Structure
Main 3 have same formula, but different structure = Isomers
Form chains when dry
Form rings when in water (Hydrophobic / Hydrophilic interactions)
Functional Groups: Hydroxyl & Carbonyl (Makes it water-soluble)
Bonds Between Monomers: Glycosidic bonds
Alpha  Chains [Starches & Glycogen]
Beta  Walls [Cellulose & Chitin: Cannot be digested by most animals, require symbiotic bacteria]
Polymer Structure
Disaccharides (2 sugars)
Maltose (Grain sugar) = Glucose + Glucose
Sucrose (Table sugar) = Glucose + Fructose
Lactose (Milk sugar) = Glucose + Galactose
Polysaccharides (Many sugars)
Starch (Plant energy storage)  Long straight chains of glucose
Amylose  No linking; one long chain
Pectins  Linking; many short chains
Glycogen (Animal energy storage)  Long branched chains of glucose
Metabolized by the liver
Common in liver, large muscles, and the brain
Cellulose (Plant cell walls)  Brick wall of sugar that forms fibers
Chitin (Fungus cells walls)  Brick wall of sugar that form fibers
Sugar polymers also part of:
Peptidoglycan  Sugar-protein mix that makes up the cell wall of some prokaryotes
Glycoproteins  Cell membrane components involved in cell recognition and communication
Structure / Function Link
Polysaccharide chains store sugar for future use; can be broken one link at a time as needed
Branched chains are more soluble and can be digested faster (animal glycogen for fast digestion and blood transfer)
Wall-like fibers make molecule solid and useful for structural support (cell walls of plans  tree bark)
Beta-Bonds in cellulose cannot be digested by most animal enzymes meaning symbolic relationships with bacteria necessary
Glycoproteins have specific shapes allowing them to serve as markers
There are more types of monomers in cabs (more coding potential), but
They are not used for genetic coding
Have less functional variety than proteins
(probably not original molecules of life)
Lipids
Find it:
Oils
Fats (Triglycerides)
Cell Membranes (Phospholipids)
Steroid (Hormones: Testosterone, Progesterone, Estrogen)
Cholesterol (Cell membrane / cell communication)
Waxes (Sticky, thick, and strong = Bees, Ear, Plant)
Terpenes (Pigmentation)
Prostaglandins (Localized cell communication)
Elements:
Usually: C-H-O not a 1:2:1 Ratio / Hydrophobic / Insoluble
Phospholipids will also have P
Monomers
For Tryglecerides: Glycerol + Fatty Acid Chains
For Phospholipids: Phosphate + Fatty Acid Chains
Functions:
Long-Term Energy Storage (Fat / Oils)
Shock-Absorption (Fat / Oils)
Water-sealing (Fat / Oils)
Insulation / Heat Loss Protection (Fats / Oils)
Structure (Wax)
Protection (Wax)
Communication (Hormones / Steroids)
Cell Membrane Structure (Phospholipids / Cholesterol)
Monomer Structure
Glycerol = 3 Carbons, each bonded to a hydroxyl groups
Fatty Acids = Carboxyl group + Long chains of hydrocarbons
Saturated
No double bonds between carbons
More bonds between carbon and hydrogen
More complex = more energy when converted to simple compounds
More likely to sit together = more solid-like
More health problems (besides making you fatter)
More likely to cause blockage in arteries (arteriosclerosis) since its solid
More common in animal fat (lard, butter, etc.)
Unsaturated
Double bonds between carbons = bend (or kink) in chain
Less bonds between carbon and hydrogen = less energy than saturated
Less likely to sit close together because of bend = more liquid-like
Can help health (though too much will still make you fat)
Can help clear blockages
More common in animal oils (olive oil, canola oil, sunflower oil, etc)
Note: Although hydroxyl groups and carboxyl groups in these monomers make them polar, the fat polymers are not because
these groups loose polar structure during dehydration synthesis.
Bonds Between Monomers: Not important at this level
Polymer Structure
Phospholipids = Hydrophilic head made of compounds including a phosphate group + 2 fatty acid chains
Triglycerides = 1 Glycerol Bonded to 3 fatty acid chains (Dehydration synthesis between hydroxyl groups of glycerol and
carboxyl group from fatty acids)
Waxes = Very long fatty acids chains + alcohol
Steroids = 4 fused hydrocarbon rings
Structure / Function Link
More bonds between carbon and hydrogen = more complex
More energy storage when converted to simpler molecules (saturated fat)
More health hazards
Double bonds in fatty acid chains (kinks) decrease attraction between them
Store less energy = unsaturated fat
more liquid-like (more oily  plants) than solid (fat  animals)
clears blockages rather than cause blockages in blood vessels (arteriosclerosis)
Phospholipid structure allows for formation of cell membranes
Double bonds in phospholipid tails make cell membrane more liquid-like (better for cold environments)
Proteins
Find it:
Meat / Fibers / Beans / Fish
Elements: C-H-O-N-S (Only one that has sulfur)
Monomers: Amino Acids
Functions (WHAT YOU ARE MADE OF AND WHAT DOES THINGS IN YOUR BODY)
Structure (e.g. Colagen  Bones; Keratin  Hair / Nails; Muscles)
Movement (e.g. Actin Fibers  Muscles)
Membrane Transport (e.g. Channel Proteins, Gate / Carrier Proteins, Active Transporters)
Nutrient Transport (e.g. Hemoglobin  Carries oxygen in the blood)
Catalysts (e.g. Enzymes)
Amino acid storage (e.g. Albumin  Egg yolk)
Control/Messengers = Recognition / Regulation / Signaling / Communication / Immune Response (e.g. Neurotransmitters /
Membrane Receptors / Glycoproteins / Antibodies / Transcription Factors / Translation Factors / Kinases / Cell-Cycle
Regulators / Endocrine Hormones, Etc)
Monomer Structure
Parts:
Central Carbon
Amino Group (N-Terminus)
Carboxyl Group (C-Terminus)
Hydrogen
R or Side Chain (Different between amino acids)
Types of Side Chains:
Hydrophillic
Charged
Polar
Hydrophobic
#’s
39+ Types including synthetic ones
10-25 commonly found in life
20-21 found in the human body (and most life forms)
Bonds Between Monomers: Peptide
Polymer Structure
Primary: Amino Acids + Peptide Bonds = Peptide chain
N-Terminus  C-Terminus
Secondary: Simple Folding  Domains
Attraction between backbone
Alpha helix
Beta plates
Tertiary: Complex Folding  Subunits
Hydrophillic & Hydrophobic interactions
Hydrogen bonds between side-chains
Disulfide-bridges between side-chains
Quaternary: Subunits combine  Complex Protein
Hydrogen Bonds
Globular (Enzyme / Regulatory) vs. Fibrous (Structure / Movement)
Structure / Function Link
Domains give proteins specific functions
Overall tertiary/quaternary structure give proteins specific shapes to perform specific functions (e.g. Active sites in enzymes)
Active sites are more common in globular proteins that will be performing catalysis or regulatory functions
Fibrous proteins have structural or movement roles
Denaturation by heat / pH changes causes destruction of protein shape and thus its function
Changes in amino acid sequence can affect protein structure (especially primary and tertiary)
Greatest degree of functional variety in life (like a language written with 20 letters)
Nucleic Acids
Find it:
Every cell
Elements: C-H-O-N-P (Only one that has N & P)
Monomers: Nucleotides
Functions (WHAT DETERMINES WHO YOU ARE)
Genetic information
Genetic message between generations (Heritable information)
Instructions to build proteins
Monomer Structure
Parts:
Pentose Sugar (RNA: Ribose / DNA: Deoxyribose)
Phosphate Group
Nitrogenous Base
Types
Pyramidines (One-ring)
Cytosine
Thymine (DNA) / Uracil (RNA)
Purines (Two-rings)
Guanine
Adenine
Bonds Between Monomers: Peptide
Polymer Structure
Backbones
Sugar-Phosphate bonded together (
Coding
Nitrogenous Bases
Codons (Triple Code) = Every 3  1 Amino Acid in the protein based on that gene
Base-Pairing Rules
Pyramidine (1) + Purine (2) = 3 Rings
A-T
C-G
Hydrogen-Bonding Pattern
Reverse Orientation (3-5 vs. 5-3)
Strands
RNA (Single)
DNA (Double; Twisted; Held Together by Hydrogen Bonds as per base-paring rules)
More Structural Topics
DNA Coiling
RNA Structural / Functional Variety
Nucleoside Triphosphates (e.g. ATP)
Relationship to nucleic acids
Extra phosphate & bonds
Energy currency in the cell
Structure / Function Link
Information for life based on language using 4 letters
Still much better than computer binary code and think of how much that can do
Triple code allows for redundancy in the genetic code (20 amino acids and 64 codes)
Different types of nucleic acid perform different jobs in the protein synthesis and inheritance machinery
Heat can denature the DNA molecule by breaking hydrogen bonds and causing strands to unzip
Heat can also cause changes to RNA types that have structures that rely on hydrogen bonds
Change in DNA sequence can lead to changes in heritable information (mutations  Evolution / disease)
Changes in DNA sequence can lead to changes to amino-acid sequence and thus protein structure / function