Transcript Biochemistry - Ursuline High School

Biochemistry
All Matter is composed
of
Atoms
The Structure of the Atom
Electrons: 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.mahe
swaran/phy1121/data/ch09/anim/anim09
04.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/phy1
121/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 Universal 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 Heat
Capacity…. 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
Sugar
Copper Sulfate
Sulfur
Mercury Oxide
Sodium Chloride
Copper
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 OHExample: NaOH
NaOH
Na+ + OHDrano, Soaps, etc…….
pH Scale
• A logarithmic scale for showing
H+ concentration in a solution.
pH = - log [H+]
pH Scale
Acids: pH < 7
Neutral: pH 7
Bases: 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” ….molecules that
consist of a single unit (monomer)
repeated many times.
Functional Groups
• Many organic molecules share
similar properties because they
have similar clusters of atoms,
called the….. Function Groups
• Each Functional Group gives the
molecules a particular property,
such as acidity or polarity.
Functional Groups
Four Main Types Of
Macromolecules
• Carbohydrates
• Lipids
• Protein
• Nucleic 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
Polysaccharides
all with the chemical formula (CH2O)n
• Many joined simple sugars.
• Used for storage or structure.
• Examples:
Starch - a polymer of a-glucose molecules, principle
energy storage molecules in plants
Glycogen - a polymer of a-glucose molecules, principle
energy storage molecules in animals, stored in the liver
and muscles cells
Cellulose - a polymer of b-glucose molecules, principle
structural molecules in plant cell walls…. Major
component of wood
Chitin - a polymer of b-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 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 Group
Carboxyl 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:
- a 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 RNA
Nucleotides 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 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
•
Maltase + Maltose
Enzyme – Substrate Complex
Maltase + Maltose Complex
Active Site
Enzyme + Products
Maltase + glucose + glucose
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
Enzymes
The 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.
ATP
Adenosine 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 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