Transcript Chapter 2 Biochemistry

Lesson Overview
The Nature of Matter
Lesson Overview
2.1 The Nature of Matter
Lesson Overview
The Nature of Matter
Atoms
What three subatomic particles make up atoms?
 Protons – in nucleus, positive charge
 Neutrons – in nucleus, neutral-no charge
 Electrons – outer shell, negative charge
 QUESTION: What overall charge does
the nucleus have?
Lesson Overview
The Nature of Matter
Elements and the Periodic Table
Elements
 pure substance that consists entirely of one type of
atom
 Found on Periodic Table, represented by one- or twoletter symbols
 Atoms of element MUST have same number of
protons (atomic number); can differ in number of
electrons (ions) or neutrons (isotopes)
Lesson Overview
The Nature of Matter
Elements and the Periodic Table
ATOMIC NUMBER - # of protons in
the nucleus of an atom (equal to #
of electrons in neutral atom)
MASS NUMBER – Number of protons
and neutrons combined
* To get # of neutrons, SUBTRACT
atomic number from mass
number
Lesson Overview
The Nature of Matter
Elements and the Periodic Table
EXAMPLE:
 What atom is shown to the right?
 How do you know?
 What is its atomic number?
 What is the mass number?
 What are the number of protons?
 What are the number of electrons?
 What are the number of neutrons?
Lesson Overview
The Nature of Matter
Isotopes
o
ISOTOPES - Atoms of the same element that differ in the number of
neutrons they contain
o
So isotopes of an elements have different MASS NUMBERS
o
Isotopes have the same chemical properties (same # of electrons)
Lesson Overview
The Nature of Matter
Radioactive Isotopes
Some isotopes are radioactive, meaning that their nuclei are unstable
and break down at a constant rate over time.
Radioactive isotopes have a number of important scientific and practical
uses.
o
Radioactive dating to determine the ages of rocks and fossils
o
Used to detect and treat cancer
o
Used as labels or “tracers”
Lesson Overview
The Nature of Matter
Chemical Compounds
• Chemical compound - formed by the chemical combination of two or more
elements in definite proportions
Compounds represented by chemical formula
Example:
Water
Salt
• properties of a compound different from elements
Lesson Overview
The Nature of Matter
Chemical Bonds
Bonds involve the electrons of atoms
Two main types:
o Ionic bonds – transfer of electrons, forming ions (charged atoms) –
one positive (cation) and one negative (anion)
Example: NaCl
o Covalent bonds – sharing of electrons, complete outer shell; form
MOLECULES
Example: water
Lesson Overview
Ionic Bonds
The Nature of Matter
Lesson Overview
The Nature of Matter
Covalent Bonds
Lesson Overview
The Nature of Matter
Lesson Overview
2.2 Properties of Water
Lesson Overview
The Nature of Matter
The Water Molecule
How does the structure of water contribute to its unique properties?
Because water is a polar molecule, it is able to form multiple hydrogen
bonds, which account for many of water’s special properties.
Lesson Overview
The Nature of Matter
Polarity
oxygen end = slight (-) charge
hydrogen end = slight (+) charge
A molecule in which the charges
are unevenly distributed is said
to be “polar”
Lesson Overview
The Nature of Matter
Hydrogen Bonding
OPPOSITES ATTRACT!
hydrogen bond – attraction
between (+) hydrogen and (-)
oxygen
hydrogen bonding important to
water’s special properties
• Cohesion
• Heat capacity
Lesson Overview
The Nature of Matter
Cohesion, Adhesion, and Heat Capacity
Cohesion - attraction between
molecules of the same substance.
(surface tension) Sticky
Adhesion – attraction between
molecules of different substances
(capillary action)
Meniscus
Heat Capacity - amount of heat
energy required to increase its
temperature
Lesson Overview
The Nature of Matter
Solutions
•
•
Solute—the substance that is dissolved
Solvent—the substance in which the solute dissolves; water known
as “universal solvent”
*Water’s polarity gives it the ability to dissolve both ionic compounds
and other polar molecules (salts, sugars, minerals, gases)
•
Suspensions - mixtures of water and undissolved material
**Example for solution and suspension - BLOOD
Lesson Overview
The Nature of Matter
Acids, Bases, and pH
Water molecules sometimes split apart to form hydrogen ions and
hydroxide ions (DISSOCIATION of WATER)
Lesson Overview
The Nature of Matter
The pH Scale
pH scale - indicates the concentration of H+ ions in solution
Ranges from 0 to 14
pH of 7 = neutral (equal # of H+ and OH-)
below 7 = acidic (more H+ than OH-)
above 7 = basic, or alkaline (more OH- than H+)
Lesson Overview
The Nature of Matter
The pH Scale
Each step on the pH scale represents a factor of 10. For example, a liter
of a solution with a pH of 4 has 10 times as many H+ ions as a liter of a
solution with a pH of 5.
Lesson Overview
The Nature of Matter
Lesson Overview
2.3 Carbon Compounds
Lesson Overview
The Nature of Matter
The Chemistry of Carbon
What do we know about CARBON?

Symbol

Atomic number

Number of valence electrons
***Living organisms are made up of molecules that consist of CHONPS
Lesson Overview
The Nature of Matter
Macromolecules
The smaller units, or monomers,
join together to form polymers.
The monomers in a polymer may
be identical or different.
Lesson Overview
The Nature of Matter
Macromolecules
Four major groups of macromolecules found in living
things:
1. carbohydrates
2. lipids
3. nucleic acids
4. proteins
Lesson Overview
The Nature of Matter
Carbohydrates
• made up of CHO
• usually in a ratio of 1 : 2 : 1.
Functions –
main source of energy
structural purposes
Examples:
glucose
(monosaccharide/monomer)
starch
(polysaccharide/polymer)
Lesson Overview
The Nature of Matter
Lipids
•
Made mostly of C & H’s and are generally not
soluble in water
•
Examples are fats, oils, waxes, and steroids
Functions:
Used to store energy (fat)
Parts of biological membranes (phospholipids)
waterproof coverings (waxes)
chemical messengers (steroids/hormones)
Lesson Overview
The Nature of Matter
Lipids
• Most are made up of glycerol and fatty acid chains
• Saturated vs. Unsaturated
Lesson Overview
The Nature of Matter
Nucleic Acids
• made up of CHONP
• Nucleotides consist of three
parts: a 5-carbon sugar, a
phosphate group
(–PO4), and a nitrogenous base.
Functions:
to store and transmit genetic
information
***Two kinds – DNA and RNA
Lesson Overview
The Nature of Matter
Protein
•
•
made up of CHON
monomer is an amino acid (a.a. come together to make
proteins)
Functions:
Varied functions
controlling the rate of reactions
regulating cell processes
forming cellular structures
transporting substances into or out of cells
helping to fight disease
Lesson Overview
The Nature of Matter
Protein
• Amino acids have an amino group (–NH2), a carboxyl group (–
COOH); R-group make each a.a. different
• Covalent bonds called peptide bonds link amino acids together
to form a polypeptide
Lesson Overview
The Nature of Matter
Levels of Organization
Proteins have four levels of structure.
1. Primary structure is the sequence of
its amino acids
2. Secondary structure is the folding or
coiling of the polypeptide chain.
(alpha/beta)
3. Tertiary structure is the 3-D structure
4. Quatenary structure – subunits come
together
Lesson Overview
The Nature of Matter
Lesson Overview
2.4 Chemical Reactions
and Enzymes
Lesson Overview
The Nature of Matter
Chemical Reactions
Ex.
The elements or compounds that enter into a chemical reaction are known
as reactants.
The elements or compounds produced by a chemical reaction are known
as products.
Lesson Overview
The Nature of Matter
Activation Energy
Activation Energy - the energy that is needed to get a reaction started
The difference between the required energy and the energy of the
reactants is the activation energy (see graphs)
Lesson Overview
The Nature of Matter
Enzymes
Function –
Enzymes speed up chemical reactions that take place
in cells
***Temperature, pH, and regulatory molecules can affect
the activity of enzymes
Lesson Overview
The Nature of Matter
Nature’s Catalysts
Enzymes are proteins that act as biological catalysts
(speed up reactions by lowering activation energy)
*Enzymes very specific
Lesson Overview
The Nature of Matter
The Enzyme-Substrate Complex
•
The reactants of
enzyme-catalyzed
reactions are known as
substrates.
Lesson Overview
The Nature of Matter
The Enzyme-Substrate Complex
Substrates bind to a site on the enzyme called the active site
The active site and the substrates compared to “lock and key”