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Chapter 2: Biochemistry
Elements and Atoms
• 92 natural elements arranged on a periodic table– cannot be broken down into simpler substances– represented by 1-2 letter symbols– C,H,O, and N
• 4 most abundant elements in living organisms• makes up 96% of the entire mass of the human
body
Trace Elements• ex: Fe, I, and Mg
• are present in very small amounts
• help maintain healthy cells
• elements are made of atoms
–basic building blocks
–smallest particle of an element
• protons: positive charge • neutrons: neutral or no charge • electrons: negative charge
– small– attracted to the nucleus– travel around the nucleus in energy levels
• nucleus: consists of protons and neutrons– the nucleus is always positively charged because of
the positive protons
• energy levels hold a certain amount of electrons
• 1st energy level only holds 2 electrons (e-)
• 2nd energy level holds 8 electrons
• 3rd energy level holds 18 electrons
• an atom’s identity is based on the number of protons it has (atomic number)
• most atoms have no overall charge because the number of protons equals the number of electrons
– ex: Carbon has 6 protons and will have 6 electrons (+6 + -6 = 0)
• ions: charged atoms
– have lost or gained an electron to give the atom an overall + or – charge
• isotopes: atoms of the same element – have the same number of protons but different
number of neutrons– ex: Carbon (normally has 6 protons and 6 neutrons to
equal a mass of 12: C-12)• C-13: 6 protons + 7 neutrons=13• C-14: 6 protons + 8 neutrons=14
• Radioactive isotopes: used in science and medicine– Can be unstable and break apart, giving off radiation
• Compounds: substance composed of atoms of 2 or more different elements that are chemically combined
– Ex: NaCl, H20, C6H12O6
• Covalent: atoms share electrons (nonmetals with nonmetals)
– H20, C6H12O6 (sugars), fats, and proteins
– Weaker bonds– Force that holds atoms together– Molecule: group of atoms held together by covalent
bonds– Has no overall charge
• Ionic: atoms transfer electrons (nonmetals with metals)
• Gain or lose electrons• Ex: NaCl• Attractive force between 2 ions of opposite charge• Stronger bonds• Many ions are very important in living things
– Na and K: help conduct nerve impulses– Ca: help with muscle contraction
Bonding Venn Diagram
Ionic CovalentBoth
Chemical Reactions• Bonds are formed or broken
• Causes substances to recombine into different substances
• Metabolism: all the reactions that occur within a living organism
– Break down and build molecules
Chemical Equations• Reactants (undergo reactions) --------->
Products (formed by reactions)
• EQUATIONS MUST BE BALANCED!!
• Ex: 2H2 + O2 ---------> 2H2O
# of molecules of each substance
# of atoms of each substance
EQUATIONS MUST BE BALANCED!!
Bell Ringer:
1. The nucleus, the center of the atoms, is made up of ___________ and ____________.
2. The negatively charged particles in atoms are called __________.
3. Different isotopes of the same element have different numbers of __________.
4. In a ___________ bond, electrons are transferred from one atom to another.
5. The process that produces a new set of chemicals is called a ___________________.
Water
• The most important compound in living organisms• Makes up 70-95% of most cells• Water is a polar covalent molecule
– Has an unequal distribution of charge• Has a positive end and a negative end• Opposites attract: forms a weak hydrogen bond
• Hydrogen bonds help hold molecules together– Ex: proteins
Characteristics of Water• Cohesion: high surface
tension• Adhesion: able to creep up
tubes (capillary action)• High heat of vaporization
– Resists changes in temperature
– Ex: sweat cooling• High specific heat (internal
and external temperature stability)
• Expands when it freezes (ice floats)
• Great solvent
Mixtures• Different substances
are not chemically combined
– Individual components keep their own properties
– Ex: sand and sugar
Solution• 1 or more substances are distributed evenly in another
substance (well-mixed)
– Can be a solid, liquid, or gas
– Ex: powdered drink mix (Kool-Aid)
– Important in living things
• Solute: what is getting dissolved
• Solvent: what does the dissolving (what dissolves the solute)
– In greater amounts
• Ex: saltwater
– Concentration of the solution:
• Amount of solute
Amount of solvent
Acids and Bases
• pH: a measure of how acidic or basic a solution is
• pH scale: indicates the concentration of H+ ions in solution
• Ex: stomach juice (pH = 2); blood (ph = 7.2)
• pH below 7 acids (form H ions (H+) in H20)• pH above 7 bases (form hydroxide ions
(OH-) in H20)• pH = 7 is neutral (water)
Buffers• pH of fluids in humans must be kept
between 6.5 and 7.5 (to maintain homeostasis)– Higher or lower than this will affect chemical
reactions within cells
• Buffers: weak acids or bases that can react with strong acids or bases – Prevents sharp, sudden changes in pH
Review:1. Match the term with appropriate description:
Polarity Acidic Basic___________ unequal sharing of electrons
___________ lemon juice, pH 1.5
___________ lower concentrations of H+ ions than pure water
___________ ammonia, pH 11.5
___________ a slight negative charge at one end of a molecule, a slight positive charge at the other end
___________ pH values that are below 7
___________ alkaline solutions
2. A dissolved compound that prevents sharp swings in pH is called a __________.
• organic substances contain carbon (found in all living things)
• carbon is the backbone of living things
– has 4 valence electrons
• can bond with other carbon atoms to form chains, branched chains, or rings
• can form single, double, or triple bonds
• C-C C=C C≡C
• Some compounds have the same molecular formula but different structural formulas (called isomers)
– Ex: fructose and glucose- C6H12O6
Macromolecules (polymers)
• Many carbon molecules bond to form long chains• Ex: proteins and starch• Condensation reaction: water molecule is
removed– Dehydration synthesis– □ + □ = □□
• Hydrolysis: breaking down a polymer– Adding water to break bonds– □□ □□ + water □ + □
Organic Molecules• basic units
are called monomers
• 4 major types
Carbohydrates• Elements: Composed of
C,H, and O
• Monomers: Made up of simple sugars called monosaccharides– 2 monosaccharides combine
to make a disaccharide– many monosaccharides
combine to make a polysaccharide
• Function: Used by cells to provide energy
• Special features: examples of polysaccharides– starch (energy storage
in plants)– glycogen (energy
storage in animals)– cellulose (supports cell
walls in plants)
• Examples: breads, pasta, glucose
Lipids• Elements: Made of C,H, and O• Monomer: 3 fatty acids and a
glycerol molecule• Functions:
– Energy storage– Insulation (blubber in some animals)– Waterproof– Important component of the cell
membrane
• Special features:– Insoluble in water– Structure: May be saturated (C-C) or
unsaturated (C=C)
• Examples: fats, oils, waxes, steroids
Proteins
• Elements: Composed of C,H,O,N, and sometimes S• Monomer: Long chains of amino acids (20) joined by
peptide bonds• Functions:
– Structure: hair, nails, hooves, horns, claws, beaks– Contracting muscle tissue– Transport oxygen in blood– Provide immunity
• Special features:– Basic building material for all living things– Enzymes increase reactions
• Examples: Insulin, hemoglobin, enzymes, meat, fish
Enzymes• Proteins that change the rate
of a chemical reaction• Called a biological catalyst
(lowers the activation energy)– Energy needed to start a
reaction
• Enzyme animation
Nucleic Acids• Elements: Composed of
C,H,O,N, and P• Monomer: nucleotides (3
parts)– Nitrogen base (N-base)– Sugar– Phosphate group
• Functions: – Genetic code
• Special features:– DNA: holds all genetic
information– RNA: copies and carries out
instructions from DNA
• Examples: DNA and RNA
How do you test for the presence of organic compounds?
• Carbohydrates:– Starches- Iodine test
• Turns starches blue/black– Sugars- Benedict solution
• Changes from sky blue to orange
• Lipids:– Brown paper bag test-
leaves grease stain• Proteins:
– Biuret: changes from lavender to black
Bell Ringer:
1. The two basic kinds of nucleic acids are ______ and ______.
2. Biological catalysts, or enzymes, act by lowering the _________ required for a reaction.
3. A _______ is a large compound formed by the joining of small compounds called monomers.
4. Protein monomers are called ________.
5. A ______ stores and transmits genetic information.
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