Transcript Biochemistry

Biochemistry
The Chemistry of Life
Basic Chemistry
• Atom
– Simplest unit of matter
– Made up of three different “subatomic”
particles
Subatomic Particles
• Protons
– Have a positive charge (+)
– Have mass
– Located in nucleus
• Neutrons
– Are neutral, have no charge (0)
– Have mass
– Located in nucleus
• Electrons
– Have a negative charge (-)
– Almost no mass
– Located in “energy levels” outside of nucleus
• Atomic Number:
– Tells you the number of protons an atom has,
and also the # of electrons
Atoms are neutral
# Protons (+) = # Electrons (-)
• Atomic Mass:
– Add together the number of protons and
neutrons in nucleus of atom
– Electrons hardly contribute any mass
• Isotopes:
– Atoms of one type of element with different
atomic masses
– Same # of protons
– Different # neutrons
– Changes the mass only, the properties are
the same
• Radioactive Isotopes:
– The nucleus of some isotopes is unstable
– The atom with emit radiation
– Radiation can be measured with tools
• ex. Geiger counter
– These isotopes can be used as useful tools in science
– Ex:
• Carbon-14 dating
• Radiation treatment for cancer
• Elements
– Substance made of only one type of atom
– Each element has a unique atomic #
– Elements most commonly found in living
things
•
•
•
•
Carbon (C)
Hydrogen (H)
Oxygen (O)
Nitrogen (N)
• Compounds
– Two or more elements chemically combined
– Atoms held together by bonds.
– Once bonds form, compounds will have new,
and different properties
– Organic Compounds
• Contains carbon and hydrogen (and often O, N)
• Ex: Glucose (C6H12O6), carbohydrate, lipids,
proteins
– Inorganic Compounds
• Doesn’t contain carbon and hydrogen together
• Ex: H2O, CO2, NH3, NaCl
• Why do atoms form compounds?
– Bonds that form between atoms give atoms a
stable outer electron level.
– Called a “stable octet” of valence electrons
(8)
Types of Chemical Bonds
• Ionic Bonds:
– One or more electrons are transferred from
one atom to another.
– Neutral atoms become positive & negative ions
– Forms salts
• (Ex: NaCl)
Ionic bond = attraction between (+) and (-) ions
• Covalent Bonds:
– Electrons are shared between atoms
– Each bond represents a shared pair of electrons
– Can form single, double or even triple bonds
Covalent bonds form molecules
– Subscripts in the formula tell # of each atom
• Ex: H2O, NH3, CO2, CH4
Ionic Bonds:
Transfer electrons
Covalent Bonds:
Share Electrons
Properties of Water
• Water is necessary for life
• Contains covalent bonds
Water Molecules: H2O
(look like Mickey Mouse)
• Water is a “Polar” molecule
(like a magnet)
• The bonds are “polar”
– Oxygen attracts the electrons
more than Hydrogen
• Hydrogen Bonding:
bonding between the (+) H of
one molecule and the (-) end
of another molecule.
– Makes water good at
sticking to itself and other
substances
– Makes water good dissolver
• Cohesion: water sticks to itself
– Ex:
• Water forms “beads” on smooth surface
• Surface Tension allows insect to “skate”
• Adhesion: water
sticks to other
substances
– Ex: Capillary action:
water molecules rise
up small tubes
• Heat Capacity:
– Water has a relatively high heat capacity
– Ex:
• Lakes and oceans can absorb a lot of heat from
sun without a drastic temperature change
• Water as a Solvent:
– Dissolves most ionic and covalent substances
– “Universal Solvent” = many things can
dissolve in it.
– Solute: substance being dissolved
– Solvent: substance in which solute dissolves
– Solution: evenly disbursed mixture
– Suspensions: material in the water but just
suspended not dissolved (ex: blood cells in
blood)
pH of Solutions
• pH Scale: way to measure concentration
of H+ ions in solution
– Ranges from 0 to 14
– Pure water is neutral pH = 7
• Litmus Paper:
– Used to test pH of a solution
• Red = acidic
• Blue = basic
• Acids: Form H+ ions
– pH is <7
– Ex: HCl (stomach acid), lemon juice
• Bases: Produces OH- (hydroxide ions)
– Also called “alkaline”
– pH >7
– Ex: Lye (NaOH) used as drain cleaner
• Buffers:
– Maintain pH at a certain level
– Usually between 6.5 – 7.5 (close to neutral)
– Helps to maintain homeostasis in organism
Major Types of Chemical
Reactions
• Dehydration Synthesis: (Condensation)
– Chemically combine two smaller molecules
– Water is removed
– “Dehydrate” = remove water
– “Synthesis” = to make
• Hydrolysis:
– Break apart large molecule into smaller
pieces
– Water is added
– “Hydro” = water
“Lysis” = to break
• Polymerization:
– Create a large molecule (polymer)
– Join up smaller “monomer” units
– Often a dehydration synthesis reaction
Ex:
Join amino acids (monomer) to make protein (polymer)
Join glucose (monosaccharide) to make starch
(polysaccharide)
Organic Compounds
Carbohydrates
• Sugars and starches
• FUNCTION:
– Used as an energy source
– Energy released during cellular respiration
• Made of carbon, hydrogen and oxygen
Ex:
C6H12O6, C12H22O11
• Ratio of H of O is always 2:1
• Basic Structure:
– “Ring” made of 5 carbons and 1 oxygen
– Rings can join up by dehydration synthesis
3 Types of Carbohydrates
• Monosaccharide's: 1 sugar ring
• Disaccharides: 2 sugar rings
• Polysaccharides: many sugar rings
• Monosaccharide's: (Simple sugars)
– All have formula C6H12O6
– Single ring structure
– End in “-ose”
– Ex: glucose, fructose, galactose
• Disaccharides: double sugars
– All have formula C12H22O11
– End in “-ose”
– Ex: sucrose, lactose, maltose
• Polysaccharides: 3 or more sugar units
• Ex:
– Starch (energy storage in plants)
– Glycogen (how animals store sugar in liver)
– Cellulose (plant cell walls)
– Chitin (insect exoskeletons)
• Simple sugars form into complex sugars by
dehydration synthesis (condensation).
• Combining molecules by removing water
Monosac. + Monosac.  Disac. + Water
C6H12O6 + C6H12O6

C12H22O11 + H2O
and H2O
• Complex sugars are broken down into
simple sugars by hydrolysis.
• Breaking down molecules by adding water
• Also called chemical digestion
Disac.+ Water  Monosac. + Monosac.
C12H22O11 + H2O  C6H12O6 + C6H12O6
Dehydration Synthesis
and Hydrolysis are
OPPOSITE Reactions
**Chemical reactions are often
enzyme mediated.
Lipids
• Fats, oils and waxes
• FUNCTION:
– Long term energy storage
– Insulation
– Protective coating around cells
– Cell membranes
• Made of carbon, hydrogen, and oxygen
• Ratio of H to O is not 2:1
– Ex: C15H26O6 (fewer oxygens)
• Animals store energy mostly as fats
• Plants store energy mostly as oils
Lipids
• Made up of:
– 1 glycerol molecule
– 3 long fatty acid chains
– Looks like a giant letter “E”
– Also called a “triglyceride”
GLYCEROL
Note:
3 “OH” groups
FATTY ACID CHAIN
Note:
CARBOXYL GROUP:
“COOH” group at end of
molecule
Basic Lipid Structure
• Lipids are:
– formed by dehydration synthesis
– broken down by hydrolysis
Saturated vs. Unsaturated Fats
– Saturated:
• all single bonds between carbon atoms
– Unsaturated:
• One or more double bonds between carbon atoms
• Makes fatty acid more bent
Proteins
• Protein Structure:
– Made of carbon, hydrogen, oxygen and
NITROGEN
– Large complex polymer molecules that can
have a large range of sizes, shapes and
properties
Proteins
• FUNCTIONS:
– Enzymes: speed up chemical reactions
– Hormones: chemical messengers
– Antibodies: defend against disease
– Hemoglobin: binds oxygen to red blood cells
– Cell growth and repair
– Cell Membrane Channels
• Amino Acid: basic building block of proteins
Parts of an Amino Acid
• Carboxylic Acid Group
• Amino Group
• “R”-Group (varies depending on amino acid)
Examples of Different
Amino Acids
• There are 20 different amino acids
• All have different “R” groups
Peptide Bond: bond between amino acids
Dipeptide: two amino acids joined.
Polypeptide: many amino acids joined
– Proteins are polypeptides
Forming a Peptide Bond
and H2O
+ H2O
• Amino acids join up to form proteins at ribosome
• The function of the protein comes from it’s
specific sequence of amino acids and the shape
the protein forms
• The “code” for the specific sequence of amino
acids comes from DNA
Nucleic Acids
• Large complex macromolecule
• Stores information in “code”
• Composed of carbon,
hydrogen, oxygen, nitrogen and
phosphorus
Structure of Nucleic Acids:
• Made of chains of nucleotides
Nucleotide: (made of 3 components)
– Phosphate Group
– Sugar
– Nitrogenous Base
Two Types of Nucleic Acids
• DNA: (Deoxyribonucleic Acid)
– Contain genetic information
– Found in nucleus
– Divides when cell divides
• RNA: (Ribonucleic Acid)
– Copies code from DNA
– Takes code to ribosomes for protein synthesis
– Found in nucleus and cytoplasm
Differences Between
DNA & RNA
– DNA:
• Double strand of nucleotides
• Sugar is deoxyribose
• Nitrogenous Bases
– Adenine, Thymine, Cytosine, Guanine
– RNA:
• Single strand of nucleotides
• Sugar is ribose
• Nitrogenous bases
– Adenine, Uracil, Cytosine, Guanine
•