PPT Notes: Chapter 2 Flashcards
Matter
Anything that has mass and occupies space
States of matter
- Solid - definite shape and volume
- Liquid - definite volume, changeable shape
- Gas - changeable shape and volume
Energy
Capacity to to do work or put matter into motion
Types of energy
- Kinetic - energy in action
- Potential - stored (inactive) energy
Forms of energy
CREM
- Chemical - stored in bonds of chemical substances
- Radiant or electromagnetic - exhibits wavelike properties (i.e. visible light, ultraviolet light and x-rays)
- Electrical - results from movement of charged particles
- Mechanical - directly involved in moving matter
Energy form conversions
- Energy may be converted from one form to another
- Conversion is inefficient because some energy is lost as heat
Elements
- Cannot be broken down by ordinary chemical means
- Each has unique:
- Physical properties
- Are detectable with our senses or are measurable
- Chemical properties
- How atoms interact (bond) with one another
- Physical properties
Atoms
Unique building blocks for each element
Atomic symbol
one or two letter chemical shorthand for each element
Major elements of the human body
OCHN
- Oxygen
- Carbon
- Hydrogen
- Nitrogen
96% of human body has these elements
Lesser elements of the human body
- Calcium - Ca
- Phosphorus - P
- Potassium - K
- Sulfur - S
- Sodium - Na
- Chlorine - Cl
- Magnesium - Mg
- Iodine - I
- Iron - Fe
3.9% of body mass
Trace elements of the human body
Part of enzymes, e.g.:
- Chromium - Cr
- Manganese - Mn
- Zinc - Zn
<0.01% of body mass
Atomic structure is determined by
3 subatomic particles
- neutrons and protons in the nucleus
- electrons surrounding the nucleus
neutrons
- no charge
- mass = 1 atomic mass unit
Protons
- positive charge
- mass = 1 amu
electrons
- orbit nucleus
- equal in number to protons in atom
- negative charge
- 1/2000 the mass of a proton (0 amu)
Orbital model of the atom
- current model used by chemists
- depicts probable regions of greatest electron density (electron cloud)
- useful for predicting chemical behavior of atoms
Planetary model of the atom
- oversimplified, outdated model of the atom
- incorrectly depicts fixed circular electron paths
- useful for illustrations
An element is…
atoms of one type e.g. gold atoms make up gold
atoms of different elements contain…
contain different numbers of subatomic particles
the atomic number is equal to
the number of protons in the nucleus
the mass number is equal to
the mass of the protons and neutrons
- mass numbers of atoms of an element are not all identical
- isotopes are structural variations of elements that differ in number of electrons they contain
- Hydrogen: 1 proton, 0 neutron = 1 amu
- Hydrogen isotope: 1 proton, 1 neutron = 2 amu
- isotopes are structural variations of elements that differ in number of electrons they contain
Atomic weight is equal to
the average of mass numbers of all isotopes
- listed on the periodic table of elements
Radioisotopes
- heavy isotopes
- prone to spontaneous decay (radioactivity) because they are unstable
- similar chemistry (bonding properties) to stable isotopes
- can be detected with scanners (CT scan, PET scan)
- valuable tools for biological research and medicine
- causes damage to living tissue
- against localized cancers as radiation therapy
- radon from uranium decay causes lung cancer
Molecules and compounds
most atoms combine chemically by bonding with other atoms to form molecules and compounds
Molecule
any two or more atoms bonded together
- e.g. H2 or C6H12O6
A Compound is
two or more different kinds of atoms bonded together
- e.g. C6H12O6
- can be chemically bonded
- all are homogeneous
Mixtures
- Most matter exists as mixtures
- two or more components physically intermixed
- no chemical bonding between components
- can be separated physically by straining or filtering
- heterogeneous (varied makeup) or homogeneous (pure makeup)
Types of mixtures
3 types
- solutions
- colloids
- suspensions
Solutions
- homogeneous mixtures
- usually transparent (e.g. atmospheric air or seawater)
- solvent
- present in greatest amount, usually a liquid
- solute
- present in smaller amounts
- solvent
Concentration of solutions are expressed as…
Expressed as:
- percent, or parts per 100
- Milligrams per deciliter (mg/dl)
- Molarity, or moles per liter (M)
moles
- 1 mole = the atomic weight of an element or molecular weight (sum of atomic weights) of a compound in grams
- 1 mole of anysubstance contains 6.02 x 1023 molecules (Avogadro’s number)
Avogadro’s number
6.02 x 1023
Colloids (aka emulsions)
- eg Mayo
- heterogeneous translucent mixtures eg cytosol
- large solute molecules that do not settle out
- undergo sol-gel transformations
Suspensions
- heterogeneous mixtures eg blood
- large visible solutes tend to settle out
Electrons occupy up to…
seven electron shells (energy levels) around nucleus.
Octet rule
Except for the first shell which is full with two electrons, (duet rule) atoms interact in a manner to have eight electrons in their outermost energy level (valence shell)
Chemically inert elements
- stable and unreactive
- outermost energy level fully occupied or contains eight electrons
- Noble Gases
Chemically reactive elements
- outermost energy level not fully occupied by electrons
- tend to gain, lose or share electrons (form bonds) with other atoms to achieve stability
Types of chemical bonds
- Ionic
- Covalent
- Hydrogen
Ionic bonds
- Ions are formed by transfer of valence shell electrons between atoms
- anions - (– charge) have gained one or more electrons
- cations - (+ charge) have lost one or more electrons
- Attraction of opposite charges results in an ionic bond
Formation of ionic bond (What kind of structure does it form)
- Ionic compounds form crystals instead of individual molecules
- NaCl (sodium chloride)
Covalent bonds
- Formed by sharing of two or more valence shell electrons
- Allows each atom to fill its valence shell at least part of the time
- Sharing of electrons may be equal or unequal
- sharing produces electrically balanced nonpolar molecules eg CO2
- unequal sharing by atoms with different electron-attracting abilities produces polar molecules eg H20
- Atoms with six or seven valence shell electrons are electronegative, e.g., oxygen
- Atoms with one or two valence shell electrons are electropositive, e.g., sodium
Hydrogen bonds
- Attractive force between electropositive hydrogen of one molecule and an electronegative atom of another molecule
- Common between dipoles such as water
- Also act as intramolecular bonds, holding a large molecule in a three-dimensional shape
Chemical reactions occur when… are represented as…
- Occur when chemical bonds are formed, rearranged, or broken
- Represented as chemical equations
- Chemical equations contain:
- Molecular formula for each reactant yields product
- Relative amounts of reactants and products, which should balance
eg
- H+H —>H2 (hydrogen gas)
- 4H+C —> CH4 (methane)
3 patterns of chemical reactions
- Synthesis (combination) reactions
- Decomposition reactions
- Exchange reactions
Synthesis reactions
A + B —> AB
- Always involve bond formation
- Anabolic (building)
Decomposition reactions
AB —> A+B
- Reverse synthesis reactions
- Involve breaking of bonds
- Catabolic
Exchange reactions
AB+C —> AC+B
- also called displacement reactions
- bonds are both made and broken
Oxidation-Reduction (Redox) reactions
- Decomposition reactions: Reactions in which fuel is broken down for energy
- Also called exchange reactions because electrons are exchanged or shared differently
- electron donors lose electrons and are oxidized
- electron acceptors receive electrons and become reduced
Chemical reactions are either…
- All chemical reactions are either endergonic or exergonic
- Exergonic reactions— release energy
- catabolic reactions
- Endergonic reactions—products contains more potential energy than did reactants
- anabolic reactions
- All chemical reactions are theoretically reversible
- A + B —> AB
- AB —> A + B
- Chemical equilibrium occurs if neither a forward nor reverse reaction is dominant
- Many biological reactions are essentially irreversible due to:
- Energy requirements
- Removal of products
Rate of chemical reactions are influenced by…
Influenced by:
- increased temperature = increased rate
- decreased particle size = increased rate
- increased concentration of reactant = increased rate
Catalysts
- increase rate without being chemically changed
- biological catalysts are known as enzymes
Classes of compounds
Inorganic
- water, salts, and many acids and bases
- do not contain carbon
*carbon dioxide and monoxide are both inorganic
Organic
- carbohydrates, fats, proteins and nucleic acids
- contain carbon, usually large and are covalently bonded
Water
- 60-80% of the volume of living cells
- most important inorganic compound in living organisms because of its properties
- high heat capacity
- absorbs and releases heat with little temperature change
- prevents sudden changes in temperature
- high heat of vaporization
- evaporation requires large amounts of heat
- useful cooling mechanism
- polar solvent properties
- dissolves and dissociates ionic substances
- forms hydration layers around large charged molecules e.g. proteins (colloid formation)
- Body’s major transport medium
- reactivity
- a necessary part of hydrolysis and dehydration synthesis reactions
*
- a necessary part of hydrolysis and dehydration synthesis reactions
- high heat capacity
Salts
- ionic compounds that dissociate in water
- contain cations other than H+ and anions other than OH-
- Ions (electrolytes) conduct electrical currents in solution
- Ions play specialized roles in body functions (eg sodium, potassium, calcium and iron)
Acids and bases
both are electrolytes
- acids are proton (hydrogen ion) donors (release H+ in solution)
- HCl —> H+ + Cl-
- bases are proton acceptors (take up H+ from solution)
- NaOH —> Na+ + OH-
- OH- accepts an available proton (H+)
- OH- + H+ —> H2O
- NaOH —> Na+ + OH-
- *Hydrogen* Bicarbonate ion (HCO3-) and ammonia (NH3) are important bases in the body
Acid solutions contain….
H+
- H+ increases, acidity increases
Alkaline solutions contain…
bases (eg OH-)
- as H+ decreases (or as OH- increases), alkalinity increases
pH
the negative logarithm of H+ in moles per liter
pH neutral solutions
- pure water is pH neutral (contains equal numbers of H+ and OH-)
- pH of pure water = pH 7: H+ = 10-7 M
- all neutral solutions are pH 7
pH acidic solutions
- increased H+ , decreased pH (inversely proportionate)
- acidic pH: 0-6.99
- pH scale scale is logarithmic: a pH 5 solution has 10 times more H+ than a pH 6 solution
pH alkaline solutions
- decreased H+, increased pH (inversely proportionate)
- alkaline (basic) pH: 7.01 - 14
pH change interferes with…
function and may damage living tissue
- slight change in pH can be fatal
- pH is regulated by kidneys, lungs and buffers
Buffers
- mixture of compounds that resist pH changes
- convert strong (completely dissociated) acids or bases into weak (slightly dissociated) ones
- carbonic acid-bicarbonate system
Organic compounds
- contain carbon (except CO2 and CO which are inorganic)
- unique to living systems
- include carbohydrates, lipids, proteins and nucleic acids
- many are polymers - chains of similar units (monomers or building blocks)
- synthesized by dehydration synthesis, which is the removal of water
- broken down by hydrolysis reactions
-lysis
to break
Hydro-
water
Carbohydrates
- sugars and starches
- contain C, H and O (CH2O)n
- Three classes
- monosaccharides
- disaccharides
- polysaccharides
- functions
- major source of cellular fuel (eg glucose)
- structural molecules (eg ribose sugar in RNA)
-saccharides
sugars
Monosaccharides
- simple sugars containing three to seven C atoms
- (CH2O)n
Disaccharides
- double sugars
- too large to pass through cell membranes
Polysaccharides
- polymers of simple sugars eg starch and glycogen
- not very soluble
Lipids contain what elements? Solubility in water?
- Contain C, H, O (less in carbohydrates) and sometimes P
- Insoluble in water
Main types of lipids
PENTS
- neutral fats or triglycerides
- phospholipids
- steroids
- eicosanoids
Triglycerides
- neutral fats - solid fats and liquid oils
- found in butter, meats, etc
- composed of three fatty acids bonded to a glycerol molecule
- main functions
- energy storage
- insulation
- protection
Saturated fatty acids
- single bonds between C atoms; maximum number of H
- solid animal fats e.g. butter
Unsaturated fatty acids
- one or more double bonds between C atoms
- reduced number of H atoms
- plant oils, e.g. olive oil
Phospholipids are modified…
- Modified triglycerides:
- glycerol + two fatty acids and a phosphorus (P)-containing group
- head and tail regions have different properties
- important in cell membrane structure
Steroids
interlocking four-ring structure
Examples:
- cholesterol
- vitamin D
- steroid hormones
- bile salts
Eicosanoids (name the two groups and what they are involved in)
come in two broad groups:
- leukotrienes
- prostanoids
both of which are involved in signaling between cells
Other lipids in the body
other fat-soluble vitamins
- Vitamins A, E, K
Lipoproteins
- transport fats in the blood
Proteins
polymers of amino acids (20 types)
- joined by peptide bonds
Contain C, H, O, N and sometimes S and P
*NCHOPS
Fibrous Proteins
Fibrous (structural) proteins
- Strandlike, water insoluble, and stable
Examples:
- keratin
- Elastin
- Collagen
- certain contractile fibers
Globular proteins
Globular (functional) proteins
- Compact, spherical, water-soluble and sensitive to environmental changes
- Specific functional regions (active sites)
Examples:
HAME
- antibodies
- hormones
- molecular chaperones
- enzymes
Protein denaturation
- Shape change and disruption of active sites due to environmental changes (e.g., decreased pH or increased temperature)
- Reversible in most cases, if normal conditions are restored
- Irreversible if extreme changes damage the structure beyond repair (e.g., cooking an egg)
Molecular chaperones (chaperonins)
serve as the rescue team
- Ensure quick and accurate folding and association of proteins
- Assist translocation of proteins and ions across membranes
- Promote breakdown of damaged or denatured proteins
- Help trigger the immune response
- Produced in response to stressful stimuli, e.g., O2 deprivation
Enzymes
Biological catalysts
- lowers the activation energy, increases the speed of a reaction (millions of reactions per minute)
- often named for the reaction they catalyze; usually end in ase (e.g. hydrolases, oxidases)
- examples include:
- hydrolases that add water
- Oxidases that add oxygen
- Not all end in -ase (e.g. pepsin, gastrin, etc)
- examples include:
Summary of enzyme action
- Binding of enzyme’s active site to the substrate(s).
- Formation of the enzyme substrate complex.
- Release of the products from the enzyme.
Nucleic acids
DNA and RNA
- Largest molecules in the body
- Contain C, O, H, N, and P
- Building block = nucleotide, composed of N-containing base, a pentose sugar, and a phosphate group
DNA
- Four bases:
- adenine (A), guanine (G), cytosine (C), and thymine (T)
- double stranded helical molecule in the cell nucleus
- Provides instructions for protein synthesis during normal cell functioning.
- Replicates before cell division, ensuring genetic continuity during cellular reproduction.
RNA
- Four bases:
- adenine (A), guanine (G), cytosine (C), and uracil (U)
- single stranded molecule mostly active outside the nucleus
- Three varieties of RNA carry out the DNA orders for protein synthesis [there are others]
- messenger RNA [mRNA]
- transfer RNA [tRNA]
- ribosomal RNA [rRNA]
ATP: Adenosine triphosphate
- Adenine-containing RNA nucleotide with two additional phosphate groups
- Adenine-Phosphate-Phosphate-Phosphate
- Has the highest potential energy
- Adenine-Phosphate-Phosphate-Phosphate
- Adenine-Phosphate-Phosphate
- ADP : adenosine diphosphate
- Adenine-Phosphate
- AMP : adenosine monophosphate
Function of ATP
Phosphorylation:
- Terminal phosphates are enzymatically transferred to and energize other molecules
- Breaking the bonds between phosphates releases the potential enregy.
- Such “primed” molecules perform cellular work (life processes) using the phosphate bond energy
