biochemistry. all matter is composed of atoms the structure of the atom electrons: negative...
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Biochemistry
All Matter is composed of
Atoms
The Structure of the AtomElectrons: Negative electrical charge
Protons: Positive electrical charge
Neutrons: No net electrical charge
Molecules
• Two or more atoms held together by
Chemical bonds
Chemical Bonds
• form because of the interactions between the electrons of the atoms
The atom’s ELECTRONEGATIVITY
(ability to attract electrons)
• Determines the type and strength of the Chemical bond
Ions• Ions are atoms that have either a
positive or negative
electrical charge because the
electron number is NOT equal to
the proton number
IONIC BONDS
• Form between atoms when electrons are TRANSFERED
from one atom to another forming ions of opposite
electronic charges• http://www.dac.neu.edu/physics/b.maheswaran/phy1121/data/ch09/
anim/anim0904.htm
Covalent Bonds• Form when atoms share
electrons• Occur when the
electronegativities between the atoms are similiar
• http://www.dac.neu.edu/physics/b.maheswaran/phy1121/data/ch09/anim/anim0904.htm
• Some molecules have Single Covalent Bonds… which means
the atoms share one pair (a single pair) of electrons
• Some molecules have Double Covalent Bonds… which means
the atoms share two pairs of electrons
• Some molecules have Triple Covalent Bonds… which means the atoms share Three pairs of
electrons
Nonpolar Covalent Bonds
• Occur when the electronegativities of both atoms are identical and the
electrons are shared equally
Polar Covalent Bonds
• Occur when the electronegativities of both atoms are Different and the
electrons are shared unequally
Negative Pole
Positive Pole
Hydrogen Bonds
• Hydrogen bonds are weak bonds which form between molecules
Hydrogen Bond
Bond Strengths• Ionic Bonds are weak and are easily
broken in water
• Covalent Bonds are generally strong
• Hydrogen Bonds are very weak
The Properties of Water
• 1. Water is the UniversalUniversal Solvent.
• Ionic compounds and Polar covalent molecules readily
dissolve in water
Hydrophilic Molecules (water-loving)
• Are substances that dissolve in water…. Salts,
sugars, etc….
Hydrophobic Molecules (water-fearing)
• Are substances that do not dissolve in water… oils,
waxes, etc…
Water Has A High Specific HeatCapacity…. The capacity of a
substance to change temperature in response to a gain or loss of heat… water changes temperatures very
slowly• Specific Heat - the amount of heat needed to
raise 1 g of the substance 1 degree C.
• Why? ……… Hydrogen bonding.
Water Has A High Heat Of Vaporization
• Heat of Vaporization: the quantity of heat a liquid must absorb for 1g of it
to convert to a gaseous state.
Liquid Water Is Cohesive
• Water sticks to water.
• Why?
Because the polarity of water results in hydrogen bonding.
Liquid Water is Adhesive
• Water sticks to other molecules.
• Why?
Hydrogen bonding.
Water transport in trees uses Cohesion and Adhesion
Water Has A High Surface Tension• The surface
of water is difficult to stretch or
break.
• Why?
• Hydrogen bonding.
Water Stabilizes Temperature
• Water can absorb and store a huge amount of heat from the sun.
• Result - climate moderation
• Result - organisms are able to survive temperature changes.
Evaporative Cooling
Result:• Water cools organisms from
excessive heat buildup.
• Why?
As water evaporates it takes the heat with it.
Water Expands and becomes less dense when It Freezes….so
it floats
• The distance between water molecules INCREASES from the liquid to the solid form.
• Why?
• Hydrogen bonding
Water Benzene
Floats Sinks
Result
• Ice floats and forms an blanket of insulation during the
winter……….Aquatic life
can live under ice.
Water is used to make Solutions
• A Solution is a Homogeneous mixture of two or more
substances.
• Solvent + Solute Solution
• Sugar water, Saltwater, Pepsi
Solvent
• The dissolving agent
• Present in a greater proportion
Examples:
• Water
• Methane
Solute
• The substance that is dissolved.
• Present in smaller quantity
Examples:• Salt in saltwater
• Sugar in sugar water
Solution Concentration
• Usually based on Molarity
• Molarity - the number of moles of solute per liter of solution.
• A mole is = 6.021x1023
One Mole of each
Sulfur
Sugar
Copper Sulfate
Mercury Oxide
Copper
Sodium Chloride
Dissociation of Water
• Water can sometimes split into two ions.
• In pure water the concentration of each ion is 10-7 M
• Adding certain solutes disrupts the balance between the two
ions.
• The two ions are very reactive and can drastically affect a cell.
Acids• Materials that can release H+
Example: HCl HCl H+ + Cl-
Hydrochloric acid, vinegar, etc…
Effects of Acid Rain
Bases
• Materials that can absorb H+
• Often reduce H+ by producing OH-
Example: NaOH NaOH Na+ + OH-
Drano, Soaps, etc…….
pH Scale
• A logarithmic scale for showing H+ concentration in a solution.
pH = - log [H+]
pH Scale
Acids: pH < 7Acids: pH < 7Neutral: pH 7Neutral: pH 7Bases: pH >7Bases: pH >7
• Acids: pH <7 etc.
• Bases: pH >7 etc.
Each pH unit is a 10x change in H+
Buffers• Materials that have both acid
and base properties.• Resist pH shifts.• Cells and other biological
solutions often contain buffers to prevent damage.
Organic Molecules
• Contain carbon atoms, exceptions are carbon monoxide and carbon dioxide
• Carbon has 4 electrons available to form 4 chemical bonds….therefore large molecules
are easily formed using carbon as the backbone.
• Large carbon based molecules are usually found as long chains or rings.
Macromolecules
• Most macromolecules are “polymers”“polymers” ….molecules that consist of a single unit (monomermonomer) repeated many times.
Functional Groups
• Many organic molecules share similar properties because they have similar clusters of atoms, called the….. Function GroupsFunction Groups
• Each Functional Group gives the Each Functional Group gives the molecules a particular property, molecules a particular property,
such as acidity or polarity.such as acidity or polarity.
Functional Groups
Four Main Types Of Macromolecules
• CarbohydratesCarbohydrates
• LipidsLipids
• ProteinProtein
• Nucleic acidsNucleic acids
Carbohydrates
• Used for fuel, building materials, and receptors.
• Made of C,H,O
• General formula is CH2O
• C:O ratio is 1:1
Types Of Carbohydrates
• Monosaccharides
• Disaccharides
• Polysaccharides
Monosaccharides• Mono - single• Saccharide - sugar• Simple sugars.• Can be in linear or
ring forms.• Glucose, Fructose,
Galactose…. all with the chemical formula C6H12O6….. Same chemical formula, different shapes.
• Most words ending with the letters OSE are carbohydrates.
Glucose, Fructose, Galactose
Disaccharides
• Sugar formed by joining two monosaccharides together thru the process of Dehydration
Synthesis….(removing water)…aka…. Condensation Synthesis.
• all with the chemical formula C12H22O11
• glucose + fructose = sucrose (table sugar) + H2O
• glucose + galactose = lactose ( the sugar in milk) + H2O
• glucose + glucose = maltose + H2O
Condensation Synthesis or
Dehydration Synthesis • The chemical
reaction that joins monomers into polymers.
• Covalent bonds are formed by the removal of a water molecule between the monomers.
Hydrolysis
• Reverse of condensation
synthesis.• Using water (Hydro),
to split (Lysis)• Breaks polymers
into monomers by adding water
Examples of Disaccharides produced through Dehydration Synthesis
• Maltose = glucose + glucose
• Lactose = glucose + galactose
• Sucrose = glucose + fructose
Polysaccharidesall with the chemical formula (CH2O)n
• Many joined simple sugars.• Used for storage or structure.
• Examples: Starch - a polymer of -glucose molecules, principle
energy storage molecules in plants Glycogen - a polymer of -glucose molecules, principle
energy storage molecules in animals, stored in the liver and muscles cells
Cellulose - a polymer of -glucose molecules, principle structural molecules in plant cell walls…. Major component of wood
Chitin - a polymer of -glucose molecules, each modified with a nitrogen group, principle structural molecule in the cell walls of fungi and the exoskeletons of the arthropods.
Lipids (Fats)
• Diverse hydrophobic molecules which are insoluble in water (and other polar molecules) and
soluble in non-polar molecules like ether and chloroform
• Made of C,H,O• No general formula.
• C:O ratio is very high in C
Types of Lipids (Fats)
• Triglycerides
• Phospholipids
• Steroids
Triglycerides
• Three fatty acids joined to one glycerol.
• Joined by an “ester” linkage between the -COOH of the fatty acid and the -OH
of the alcohol.
• Differ in which fatty acids are used.
• Used for energy storage, cushions for organs, insulation.
Acid Fat
Fats and Oils
• Fats - solid at room temperature.
• Oils - liquid at room temperature.
• Saturated - solid at room temperature.
• Unsaturated - liquid at room temperature.
Saturated Fats
• Saturated - no double bonds.
Unsaturated Fats• Unsaturated - one or more C=C
bonds. Can accept more Hydrogens.
• Double bonds cause “kinks” in the molecule’s shape.
Question ?
• Which has more energy, a kg of fat or a kg of starch? …. (Hint) in Fats there are more C-H bonds which provide more energy per mass.
• Answer… carbohydrates (starch) have 4 calories per gram, lipids have 9 calories per gram
Phospholipids
• Similar to fats, but have only two fatty acids.
• The third -OH of the glycerol is joined to a phosphate group replacing a fatty acid
• Major component of the Plasma
Membrane of all cells
Result
• Phospholipids are amphipathic which means they have a nonpolar, hydrophobic tail, but a polar, hydrophilic head.
• Self-assembles into bilayers, an important part of cell membranes.
Steroids
• Characterized by a backbone of four fused carbon rings.
• Differ in the functional groups attached to the rings.
• Examples:
–cholesterol
–sex hormones
Proteins
• Made of C,H,O,N, and sometimes S.
• No general formula
• Polymers of amino acids
Uses Of Proteins
• Structural Proteins: used to make skin, hair, muscles, etc…
• Enzymes: Control Metabolism• Antibodies: Provide protection
against foreign substances• Transport Proteins: Transport
molecules across membranes• Storage: such as ovalbumin in
eggs
Proteins
Proteins are Polypeptide chains of Amino Acids
linked by peptide bonds.
Amino AcidsAmino Acids• All have a Carbon
with four attachments:
-COOH (acid)
-NH2 (amine) -R group• 20 different kinds
of amino acids because there are 20 different kinds of R groups
Amino GroupCarboxyl Group AKA: Acid Group
Amino Acids
Amino Acids
R groups
The properties of the R groups
determine the
properties of the protein.
Polypeptide Chains
• Formed by dehydration synthesis between the carboxyl group of one
amino acid and the amino group of the second Amino Acid.
Levels Of Protein Structure
• Organizing the polypeptide into its 3-D functional shape.– Primary– Secondary– Tertiary– Quaternary
Primary Structure
• Order of amino acids in the
polypeptide chain.
• Many different sequences are possible with
20 AAs.
Secondary Structure• 3-D structure
formed by hydrogen bonding between the R groups.
• Two main secondary structures:
helix
- pleated sheets
Tertiary• 3D shape as bonding
occurs between the R groups.
• Examples:
– Hydrophobic interactions
– Ionic bonding
– Disulfide bridges– Hydrogen Bonding
Quaternary• When two or more polypeptides
unite to form a functional protein.
• Example: hemoglobin
Is Protein Structure Important?
Denaturing Of A Protein
• Events that cause a protein to lose structure (and function).
• Example:
–pH shifts
–high salt concentrations
–heat
Nucleic Acids
• Stores the genetic Information
• Polymers of nucleotides
• Made of C,H,O,N and P
• No general formula
• Examples: DNA and RNA
Nucleotides of DNA and RNANucleotides have three parts:
– Nitrogenous Base
– Pentose sugar (Deoxyribose in DNA and Ribose in RNA)
– Phosphate Group
Nitrogenous Bases• Rings of C and N
• Two types:– Pyrimidines (single ring) Thymine, Cytosine– Purines (double rings) Adenine, Guanine
Pentose Sugar• 5-C sugar
• Ribose - RNA
• Deoxyribose – DNA
DNA: Deoxyribonucleic Acid• Double Helix Structure• The two strands of DNA
are antiparallel, oriented in opposite directions… one strand is arranged in the 3’ – 5’ direction while the other is arranged in the 5’ – 3’ direction (5’ means the phosphate group is attached to the 5th carbon on the Deoxyribose molecule.
• Makes up genes.
RNA: Ribonucleic Acid
• Important molecule in protein synthesis.
• Genetic information for a few viruses only.
Differences between DNA and RNA
• RNA is a single strand
• DNA has Deoxyribose, RNA has ribose
• Thymine is replaced by Uracil
Chemical Reactions in Metabolic ProcessesChemical Reactions in Metabolic Processes
• In order for chemical reactions to occur, the reacting molecules must first collide and then have enough energy (Activation energy) to trigger the formation of new bonds.
• Some reactions require catalysts. Catalysts are molecules which trigger or accelerate chemical reactions without being chemically altered themselves.
Metabolism• Chemical reactions which occur within
living organisms are called Metabolic reactions…..
• Two types of Metabolic Reactions:
*Anabolic Reactions:
Build molecules and store energy
*Catabolic Reactions:
Breakdown Molecules and release energy
Chemical Equilibrium
• The net direction of metabolic reactions, forward or reverse, is determined by the concentration of the reactants and the products.
Enzymes: Globular proteins which catalyze metabolic reactions.
• Enzyme: Catalyzes the Reaction
• Substrate: molecule acted upon
• Products: Resulting molecules• Enzyme + Substrate Enzyme – Substrate Complex Enzyme + Products
• Maltase + Maltose Maltase + Maltose Complex Maltase + glucose + glucose
Active Site
Enzymes
• Most Enzymes end with the letters - ASE
• Enzymes are substrate specific….. Examples:
• Maltase can only breakdown Maltose
• Sucrase can only breakdown Sucrose
• Amylase can only breakdown Amylose
EnzymesThe efficiency of Enzymes
is affected by:
- pH shifts: pepsinogen is only activated when stomach acids
lower the pH
- Heat: denatures enzymes
Cofactors• Are nonprotein molecules that
assist enzymes… since they are nonproteins they are used up in the reactions.
• A holoenzyme is the union of a cofactor and enzyme.
• The enzyme is called an Apoenzyme when it’s part of a holoenzyme
Inorganic Cofactors
Are usually metals, like Iron (Fe+2), Magnesium (Mg+2)
CoEnzymes
Are organic molecules which aid in enzyme reactions…….
Some vitamins are coenzymes. Since they are nonproteins they
are also used up in the reactions.
ATPAdenosine TriPhosphate
Source of Activation energy for Metabolic Reactions
Allosteric Enzymes• Have two types of binding sites….
One for the substrate and one for the allosteric effector.
• Two types of Allosteric Effectors:
• 1. Allosteric Activator – binds to the enzyme and changes its shape to induces a reaction
• 2. Allosteric Inhibitor – binds to the enzyme and induces inactivity
Allosteric Enzymes
Competitive Inhibition
Is when an enzyme mimic occupies
the active site preventing a
reaction.
Noncompetitor InhibitorNoncompetitor Inhibitor
Prevents enzyme reactions by binding to the substrate at locations other than the active or allosteric site.
Cooperativity
• Occurs when an enzyme becomes receptive to additional substrate molecules after one substrate molecule attaches to an active site.
• Example: Hemoglobin…… its binding capacity to additional oxygen molecules increases after the first oxygen fills the active site.
Cooperativity