basic chemistry and biochemistry
DESCRIPTION
BASIC CHEMISTRY AND BIOCHEMISTRY. BASIC CHEMISTRY. MEET THE ELEMENTS. http://www.youtube.com/watch?v=d0zION8xjbM. ATOMIC THEORY OF MATTER (vocabulary). Atoms = building blocks of matter that cannot be divided any further by ordinary chemical means - PowerPoint PPT PresentationTRANSCRIPT
BASIC CHEMISTRYAND
BIOCHEMISTRY
BASIC CHEMISTRY
MEET THE ELEMENTS
http://www.youtube.com/watch?v=d0zION8xjbM
ATOMIC THEORY OF MATTER(vocabulary)
1.Atoms = building blocks of matter that cannot be divided any further by ordinary chemical means
2.Molecule = two or more atoms combined that act as a single particle, the smallest particle that retains the properties
3.Elements = substances made of only one kind of atom
ATOMIC THEORY OF MATTER(vocabulary)
4. Compounds = two or more kinds of atoms in a substance in definite proportions
5. Isotopes = varieties in the normal number of neutrons on the nucleus(The atomic number stays the same, the mass number changes)
6. Radioactivity = a nuclear process in which an atom is undergoing changes by emitting charged particles
STRUCTURE OF THE ATOMparticle charge mass locationproton (+) 1 amu in nucleuselectron (-) 0 in orbitalsneutron ( ) 1 amu in nucleusA “Happy Atom” has
all its orbital places filled.
7. Atomic number = # of protons (also the number of electrons in a neutral atom)
8. Atomic mass or mass number = number of protons plus the number of neutrons in the nucleus.
ATOMIC ORBITALS(energy levels)
nucleus
Level 12 electrons orbit
Level 28 electrons orbit
Level 38 electrons orbit
Remember: A “Happy Atom” has all its orbital places filled.
CHEMICAL BONDINGChemical bond = force of attraction that holds atoms
together
There are two kinds of bonds between atoms1. Covalent Bonds = chemical
bond that is formed by the sharing of electrons
2. Ionic Bonds = chemical bond that is formed by transfer of electrons
COVALENT BOND
Covalent Bond = chemical bond that is formed by the sharing of electrons (covalent bonds form molecules)
HYDROGEN ATOM HYDROGEN ATOM
OXYGEN ATOM
Remember: A “Happy Atom” has all its orbital places filled.
IONIC BONDIonic bond = chemical bond that is formed by transfer
of electrons
Remember: A “Happy Atom” has all its orbital places filled
Sodium (Na) has 1 electron in its outer energy level – is it happy?
Chlorine (Cl) has 7 electron in its outer energy level – is it happy?
IONIC BONDSodium and Chlorine ions are formed –
What is an ion?Ion = atom with an excess charge by the loss or gain of
electronsSodium has lost one electron (one less (–) charge) so it now has a net charge of +1
Chlorine has gained one electron (one more (–) charge) so it now has a net charge of -1
The (+) charge of Na is attracted to the (-) of the Cl and this attraction forms an ionic bond!
Na Cl
Na Cl
CHEMICAL FORMULASEach element (symbol)
and its proportions (subscripts)
are represented information
All elements are listed in the periodic table
6 atoms of Carbon (C)12 atoms of hydrogen (H)6 atoms of oxygen (O)
For example C6H12O6 means:
CHEMICAL FORMULASExamples are:
H2O
CO2
C6H12O6
CH4
STRUCTURAL FORMULASA Structural formula shows the kinds and
number of atoms as well as the chemical bonds
H
HO
H HCC
benzene
water
glucose
acetylene
CHEMICAL EQUATIONS
Reactants = the original substances before a chemical reaction (left of the arrow)
Products = new substances formed after a chemical reaction (right of the arrow)
Law of Conservation of Mass = mass can neither be created or destroyed (chemical reaction formulas must
balance)
+
2 molecules of hydrogen(2H2)
+ 1 molecule of oxygen (O2)
2 molecules of water(2H2O)
Complete pages 6 and 7 in your packet
BIOCHEMISTRYThe Chemical Compounds of Life
BIOLOGICALLY IMPORTANT COMPOUNDS
ORGANIC COMPOUNDS:Species that naturally contain carbon and
hydrogen (living organisms and their products)Most also contain O (oxygen) and N (nitrogen)Only a few elements are found in organic
compoundsMay also have P (phosphorous), S (sulfur), Fe
(iron), Ca (calcium), Na (sodium), Cl (chlorine), Mg (magnesium), K (potassium)
BIOLOGICALLY IMPORTANT COMPOUNDS
INORGANIC COMPOUNDS:
DO NOT CONTAIN CARBON (with hydrogen)May have carbonate compounds (CO2, CaCO,
etc.) but not carbon with hydrogen.Living organisms do contain inorganic
compounds
IMPORTANT INORGANIC COMPOUNDS
1. WATER• The most important inorganic compound in living
organisms• 65% of the body• Many biological processes require water2. SALTS• Help maintain water balance in the cells• Provide ions for many biological processes3) ACIDS and BASES• Help maintain homeostasis
The Structure of Organic Compounds• Organic compounds are large and complex because of the
carbon atom• Four vacancies for electrons allow 4 covalent bonds
Carbon has an atomic # of 6 which means it has 6 protons and 6 electronsIt has 4 vacancies in the outer energy level
2.1.
4.
3.
6 +
CHEMICAL COMPOUNDS OF LIFELiving organisms depend upon a variety of molecules for their
survival. Some are used to build complex parts of an organism; some supply energy; while others provide instructions for the operation of the organism.
There are many organic compounds found in organisms, but they can be classified into 4 main types:
I. CARBOHYDRATESII. LIPIDSIII. NUCLEIC ACIDS IV. PROTEINS
CARBOHYDRATES • Carbohydrates are compounds of C (carbon),
H (hydrogen), and O (oxygen)• They have the same ratio H:O as in water
(H2O) = 2:1 (twice as many H as O)* Monosaccharides = simple sugars = C6H12O6
• ALWAYS END IN “OSE”EX: MALTOSE, FRUCTOSE, GLUCOSE
• RELEASE ENERGY WHEN BREAKING DOWN GLUCOSE INTO CO2 AND H2O
• C6H12O2 CO2 + H2O
• MOST ORGANISMS USE GLUCOSE AS A SOURCE OF ENERGY
CARBOHYDRATES
THIS IS A MONOSACCHARIDE MOLECULE!THIS IS A SIMPLE SUGAR!THIS IS GLUCOSE!THIS IS C6H12O6 !
CARBOHYDRATESDISACCHARIDE = two simple sugars joined
POLYSACCHARIDE = several simple sugars joined
POLYMERS = long chains of repeating molecules(many) (molecules)
CARBOHYDRATESSugars stored in plants are called STARCH
Sugars stored in the liver of animals are called GLYCOGEN
Glycogen will be changed into glucose when the body needs it for energy!
CARBOHYDRATESBUILDING BLOCKS OF CARBOHYDRATES ARE SIMPLE SUGARS OR MONOSACCHARIDES
LIPIDS(fats, oils, and waxes)
• Made of carbon, oxygen, and hydrogen(there less oxygen in lipids than in carbohydrates)
• Reserve energy supply in an organism2 times as much energy as carbohydrates
»Plants store oils in seeds»Mammals store fats under the skin
• Waxes are formed from fatty acids and substances similar to glycerol
• Fats and oils are formed from fatty acids and glycerol
LIPIDS(fats, oils, and waxes)
BUILDING BLOCKS of LIPIDS (fats and oils) ARE 1 GLYCEROL + 3 FATTY ACIDS
The Structure of a Fatty Acid
Lipid molecule
The Fatty Acid has 2 parts:1.Chain of carbon atoms with hydrogen atoms bonded
(hydrocarbon chain)2.Carboxyl group
SATURATED vs UNSATURATED FATTY ACIDS
SATURATED FATTY ACIDS:Fats that have all single carbon-to-carbon bonds•Tend to be solids at room temperature (ie. butter)•Tend to increase the amount of cholesterol in the body•Cause deposits that lead to hardening and narrowing of arteries
SATURATED vs UNSATURATED FATTY ACIDS
UNSATURATED FATSFats that have a double or triple carbon-to-carbon bond•Tend to be oils at room temperature•Tend to decrease blood cholesterol
Polyunsaturated fats = a chain that has more than one double or triple bond
Complete the crossword puzzle on page 11 in your
packet
NUCLEIC ACIDS
• Compounds that contain phosphorus (P) and nitrogen (N)
• Also carbon, hydrogen, and oxygen
Two types of Nucleic Acids:
1.DNA2.RNA
NUCLEIC ACIDS(DNA)
DNA = deoxyribonucleic acid
• Found in the nucleus of the cell
• Directs and controls heredity information and the development and activities of the cell
THE STRUCTURE OF DNA
DNA is made of:Repeated chains of nucleotides
Nucleotides are made of:• 5 carbon sugar
(deoxyribose)• Phosphate group (PO4)
• Nitrogenous base (A,T,C,G)
THE STRUCTURE OF DNADNA• The DNA molecule is made of repeating
chains of nucleotides• The sugar and phosphate groups are the
sides of the ladder• Nitrogenous base pairs are the rungs of
the ladder• The bases are adenine (A), thymine (T),
cytosine (C), and guanine (G)• adenine (A) always pairs with thymine (T)• cytosine (C) always pairs with Guanine
(G)
RNA RNA = ribonucleic acidRNA structure:• A single strand or chain of
bases• The sugar is ribose• The base thymine is replaced
with uracil• RNA is involved with protein
synthesis
PROTEINS• Compounds that contain nitrogen, carbon,
hydrogen, and oxygen• Many contain sulfur and phosphorus• Great range of properties that give live
complexity• 20 different amino acids found in proteins
AMINO ACIDS ARE THE BUILDING BLOCKS OF PROTEINS
STRUCTURE OF AN AMINO ACID
1. One central carbon atom (C)2. One carboxyl group (COOH)3. One amino group (NH3)4. One hydrogen atom (H)5. One side chain (R)
GLYCINE is the simplest amino acid – the side chain is only one H atom
Examples of the
different amino acids
PROTEIN VOCABULARYDipeptide = two amino acids bonded together
The peptide bond = the bond between amino acids
Polypeptide = a long chain of amino acids
ORGANIC COMPOUND ATOMS BUILDING
BLOCKS EXAMPLES USES
CARBOHYDRATES C H OH:O is 2:1ex: C6H12O6
glucose
•Monosaccharides(simple sugars)•Disaccharides(2 sugars)•Polysaccharides(many sugars)
•glucose, fructose, galactose•maltose, sucrose, lactose•starch, cellulose, glycogen, chitin
Quick energy
“ose” ending
carbon ring shape
ORGANIC COMPOUND ATOMS BUILDING
BLOCKS EXAMPLES USES
CARBOHYDRATES C H OH:O is 2:1ex: C6H12O6
glucose
•Monosaccharides(simple sugars)•Disaccharides(2 sugars)•Polysaccharides(many sugars)
•glucose, fructose, galactose•maltose, sucrose, lactose•starch, cellulose, glycogen, chitin
Quick energy
“ose” ending
carbon ring shape
LIPIDSC H O H:O is › 2:1ex: C20H24O3
1 glycerol3 fatty acids(hydrocarbon chain)
fats, oils, waxes
Stored energymakes up cell membrane
ORGANIC COMPOUND ATOMS BUILDING
BLOCKS EXAMPLES USES
CARBOHYDRATES C H OH:O is 2:1ex: C6H12O6
glucose
•Monosaccharides(simple sugars)•Disaccharides(2 sugars)•Polysaccharides(many sugars)
•glucose, fructose, galactose•maltose, sucrose, lactose•starch, cellulose, glycogen, chitin
Quick energy
“ose” ending
carbon ring shape
LIPIDSC H O H:O is › 2:1ex: C20H24O3
1 glycerol3 fatty acids(hydrocarbon chain)
fats, oils, waxes
Stored energymakes up cell membrane
PROTEINS
C H O N
20 amino acidsdipeptide (2)polypeptide (many)
glycine, alanine
insulin, hemoglobin
Build and repair
ie: muscles hormonesenzymes
ORGANIC COMPOUND ATOMS BUILDING
BLOCKS EXAMPLES USES
CARBOHYDRATES C H OH:O is 2:1ex: C6H12O6
glucose
•Monosaccharides(simple sugars)•Disaccharides(2 sugars)•Polysaccharides(many sugars)
•glucose, fructose, galactose•maltose, sucrose, lactose•starch, cellulose, glycogen, chitin
Quick energy
“ose” ending
carbon ring shape
LIPIDSC H O H:O is › 2:1ex: C20H24O3
1 glycerol3 fatty acids(hydrocarbon chain)
fats, oils, waxes
Stored energymakes up cell membrane
PROTEINS
C H O N
20 amino acidsdipeptide (2)polypeptide (many)
glycine, alanine
insulin, hemoglobin
Build and repair
ie: muscles hormonesenzymes
NUCLEIC ACIDS
C H O P NNucleotides (sugar, phosphate nitrogenous base)
DNA = deoxyribonucleic acidRNA = ribonucleic acid
hereditary material
protein synthesis
Complete page 15 in your packet
DEHYDRATION SYNTHESISDEHYDRATION = to remove waterSYNTHESIS = to make more complex
H and OH are removed from the glucose molecules (to make water), this is the dehydration part
Then the two glucose molecules have open bonding sites so they can join together to make more complex, this is the synthesis part.
Dehydration synthesis = to make more complex by removing water
HYDROLYSISTo break down by adding water
Turn to page 17 in your packet
Dehydration Synthesis of a Carbohydrate
In carbohydrates, two monosaccharides form a bond to create a disaccharide
Dehydration Synthesis of a Protein
In proteins, two amino acids form a peptide bond to create a dipeptide molecule
Dehydration Synthesis of a Fatty Acid
In lipids, we remove 3 molecules of water!Then the glycerol molecule bonds with the 3 fatty acids
Vocabulary Review
1. monomer =
2. polymer =
3. dehydration synthesis =
4. hydrolysis =
A small molecule that will combine with other small molecules to form a chain
A large molecule (chain) formed from combined repeated smaller units (monomers)
Combining molecules by the removal of water
Breaking down molecules by the addition of water
Complete pages 18, 19, and 20 in your
packet
ENZYMESThe importance of enzymes:• Enzymes are proteins• Enzymes enter the chemical reaction
temporarily and are not changed• Enzymes are used over and over again• Enzymes are organic catalysts
ENZYMESA catalyst is a substance that brings about
a chemical reaction without being changed itself
The substrate is the substance the enzyme acts upon
HOW ENZYMES WORK• The active site matches up with the substrate• Forms enzyme-substrate complex• Enzyme will either break down or bond
molecules• Enzymes are very specific – one specific
enzyme matches one specific substrate
http://www.kscience.co.uk/animations/anim_2.htm
ENZYME SPECIFICITYHow do enzymes work?
substrate: molecules upon which an enzyme acts. The enzyme is shaped so that it can only lock up with a specific substrate molecule.
Each enzyme is specific for one and ONLY one substrate
(one lock - one key)
active site: part of the enzyme that fits with the substrateNote that the active site has a specific fit for this particular substrate and no other.
(enzyme)substrate -------------> product
REMEMBER:Each enzyme is specific for
one and ONLY one substrate
If the substrate and enzyme are not a match – the reaction will not proceed
TWO ENZYME THEORIES
1. LOCK AND KEY THEORY
2. INDUCED FIT THEORY
Naming the Enzyme• The prefix comes from the substrate (the
material acted upon)• Enzymes end in “ase” (the suffix)For example:
Maltase (malt/ase) = an enzyme that breaks down ________
Lipases (lip/ases) = enzymes that break down ______
Proteases (prote/ases) = enzymes that break down ________
lipids
proteins
maltose
FACTORS AFFECTING ENZYME FUNCTION:
• REMEMBER…• Enzymes are powerful• one enzyme molecule can catalyze thousands
of substrate reactions each second• enzymes speed up the reaction without
raising the temperature of the environment • BUT…
ENZYME REACTION vs TEMPERATURE• Enzymes work the best at certain temperatures,
usually the temperature of the natural environment
Enzymes become denatured at high temperatures (the high temp will change the shape of the active site so the enzyme no longer fits)
ENZYME REACTION vs pH
• Enzymes work the best at a certain pH, usually the pH of the natural environment
ENZYME REACTION vs CONCENTRATIONS
• The rate of an enzyme controlled reaction depends upon the concentrations of enzymes and substrates
COENZYMES
SOME ENZYMES NEED SUBSTANCES CALLED COENZYMES IN ORDER TO FUNCTION
• Coenzymes are organic substances• Coenzymes are not proteins• Most coenzymes are vitamins
A COENZYME ALLOWS AN ENZYME TO PERFORM ITS CATALYTIC FUNCTION
Acids, Bases, and Salts
TERMS
• Acids = any compound that produces hydrogen ions (H+) in solution
HCl = H+ + Cl-
• Base = any compound that produces hydroxide ion (OH-) in solution
NaOH = Na+ + OH-
TERMS
• Neutralization = when quantities of acids and bases are mixed together and no extra H+ or OH- remain
HCl + NaOH NaCl + H2O (acid) + (base) (salt) + (water)
TERMS
• Salts = the ionic compound obtained from the neutralization reaction between and acid and a base
HCl + NaOH --- Na+ + Cl- + H2O Solid NaCl (salt) found if water is
evaporated
The pH scale
H2O --- H+ + OH-
Neutral pure water, no excess of H+ or OH-
(not an acid or a base)
• If the H+ concentration increases, it becomes acidic
• If the OH- concentration increases, it becomes basic
The pH scalepH measures the concentration
of H+ Scale runs 0 - 14
• if the [H+] > [H2O] = acid
• if the [H+] < [H2O] = base
The Scale• high [H+] = acids = low pH
values = 0 - 6• neutral = 7• low [H+] = bases = high pH
values = 8 – 14
IndicatorsIndicator: substance that changes color
when pH goes above or below a certain value
• Litmus: Red = acid / Blue = base• Methyl orange: red to yellow indicates
base• Phenolphthalein: colorless to red
indicates base(compare to indicator paper to read
actual pH)