Biology Chapter 2

Atom and molecules

• Smallest functional units of matter
• form all chemical substance
• cannot be further broken down into other substances by ordinary chemical or physical means

Chemical Element

• protons
• neutrons
• electrons

• positive charged
• found in nucleus
• same number as electrons
• # of atomic number

• neutral
• nucleus
• numbers can vary

• negative charged
• found in orbitals
• same number of protons

No electric charge

• organized by atomic number
• rows correspond to number of electon shells
• columns left to right tell the number of electrons inthe outer shell
• elements within a column are similar b.c they have the same outer shells and have similar chemical bonding properties.

• protons and neutrons = in mass
• hydrogen atom has an atomic mass of 1

• measurement for atomic mass
• 1 (d)= 1/12 the mass of carbon atom
• carbon has an atomic mass of 12 daltons

• 1 mole of any element contains the same number of atoms- 6.022x10^23
• avogadro's number

• Multiple forms of an element that differ in the number of neutrons
• atomic masses are averages of the wieghts of different isotopes of an element.

• Hydrogen
• oxygen
• carbon
• nitrogen

• 95% of atoms in living organisms
• H and O in water
• N in proteins
• C in building block of all living matter

less than 1%

less than 0.015

2 or more atoms bonded together

• Chemical symbols of elements found in a molecule
• subscript indicates how many of each atom are present

• Molecule composed of two or more elements
• H20

• covalent
• hydrogen
• ionic

• atoms share pair of electrons
• strongest of all chemical bonds
• Share:
• Single bond H-F
• Double Bond O=O
• triple bond

• Atoms are stable when their outer shell is full
• outer shell fills with 8 electrons
• exception:hydrogen, fills its outer shell with 2 electrons.

• Attract an electron from another atom
• In a bond, electrons are more likely to be closer to the atom with higher electonegativity-polar covalent bond.

• Polar covalanet
• electrons are more electronegative oxygen atom rather than less electronegative hydrogen atoms
• molecules has partial negative charge region and a partial positive charge region

• Weak polar bonds
• Hydrogen atoms from one molecue is attracted to an electronegative atom from another molecule
• (dash or dotted line)
• Strong bonds
• Holds DNA stands together

• atom or molecule that has gained or lost one or more electrons
• net electric charge
• have a charge if they gain or loose electrons

Postive Charge

Net negative charge

• Cations
• Anions

Cations binds to an anion

• solution
• solvent
• solutes
• adhesion/ surface tension
• Ph
• High boiling point
• Density is lower when frozen
• High heat capacity
• Participates in reactions

• solvent- liquid
• solutes- substances dissolved in solvent

water is the solvent

colvalent bonds

• dissolve in water
• ions and molecules that contain polar covalent bonds

• dont easily dissolve in water
• nonpolar molecules like hydrocarbon

• polar or ionized regions at one or more sites
• nonpolar regions at other sites

concentratino of dissolved solute

• lowers freezing point below 0 degrees C
• raises its boiling point above 100C

• Participates in chemical reactions (hydrolysis or dehydration)
• provides force or support
• remove toxic waste components
• evaporative cooling
• cohension and adhesion
• high heat capacity

• Hydrogen ions (H+)
• hydroxide ions (OH-)

• Hydrogen ions
• ("proton donor")
• a strong acid releases more H+ than a weak acid.

• H+ (base is an H+ acceptor)
• some OH-
• others bind H+

pH=- log10 [H+]

below 7

Above 7

• shapes and function of molecules
• rates of many chemicals reactions
• ability of two molecules to bind to eachother
• ability of ions or molecules to dissolve in water

• keep a constant pH
• acid base buffer system can shift to generate or release H+ to adjust for changes in pH

• organic molecules contain Carbon
• abundant in living organisms
• biologically relevant macromolecules are large, complex organic molecules.

• 4 electrons in its outer shell
• needs 4 more electrons to fill the shell
• make up to four bonds (single or double)
• form non-polar and polar bonds

poorly water soluble

more water soluble

• hydroxyl
• carbonyl
• Both contibute to solubility of biomolecules

• 1 hydrogen paired with 1 oxygen atom
• (-OH)
• not highly reactive, but contribute to making molecules soluble in water.
• Alcohol and sugars are "loaded" w/ them.

• 1 oxygen atom double bonded to C atom
• (C=O)
• contribute to making molecules water soluble.
• sugars one group

• ionize and dissociate into H+ and COO-
• confer acidic properties to molecules

• Basic and often become ionized to form a positive charged NH3+ group.
• NH2-H----> NH3+

• S-H sulfyhydryl
• S-S disulfide

(PO4^2-)

• structual isomers
• stereoisomers

Contain the same atom but in diffrent bonding patterns

identical bonding relationships, but the spatial positiong of the atoms differs in the two isomers.

• carbohydrates
• lipids
• proteins
• nucleic acids
• many biomolecules are large polymers made up of repeating monomer subunits

• Carbon, hydrogen and oxygen atoms
• Cn(H2O)n
• or CnH2n)n

• simples sugars and carbs
• 5 or 6 carbons are common
• (C5H10O6) - pentoses-ribose
• (9C5H10O4)- deoxyribose
• (C6H12O6)- hexose glucose

• carbohydrates composed of two monosaccharids
• joined by dehydration or condensation reaction
• hydrolysis breaks them apart.

inability to cleave lactose into monosaccharids

• monosaccharids linked together to form
• Examples
• engergy storage- startch, gylcogen
• structural role- cellulose, chitin, glycosaminoglycans

ATP form

• Hydrogen and carbon atoms composed
• *nonpolar and very insoluble in water*
• structurally diverse
• store energy

• Triglycerides mixture
• bonds glycerol to three fatty acids
• dehydration or condensation reaction joins them together.
• hydrolysis breaks them
• 3 carbon backbone (glycerol) attatches to a long fatty acid chain.

dehydration reaction in which fatty acids are added to glycerol

• saturated
• unsaturated

• all carbons linked by single covalent bonds
• solid at room temp.

• contain one or more double bonds
• 1 double bond- momounsaturated
• 2 or more- polyunsaturated
• liquids at room temp
• polyunsat- more than one double bond.

• unsaturated fat that are partially hydrogenated through an industrial process
• different isomerization around double bond
• more hazardous to the heart than saturated fats.
• Exaple: crisco, margine

• important for engergy storage
• 1g is twice as much energy as 1 gram of glycogen or starch.
• provide structural in providing cushioning and insulation

• glycerol, 2 fatty acids and phosphate groups
• form membranes (building blocks)

• four interconnected rings of carbon atoms
• not water soluble
• cholestrol
• estrogen and testosterone differ slightly
• important hormoes and signaling molecules

• enzymes catalysis
• defense
• transport
• support
• motion
• regulation
• storage

• amino acids
• common structre with variable R-group
• 20 amino acids
• side chain determines structure and function

• R groups confer different prop to amino acids.
• joined by dehydration/condensation reaction.
• - peptide bond
• forms polypeptides
• proteins are madeup of 1 or more polypeptides
• broken apart by hydrolysis

• Primary- linear chain of amino acids
• Secondary- alpha helices, beta sheets,
• Tertiary- 3D arrangement of 2 elements
• Quaternary- how multiple polyeptide chains interact with each other.

• amino acids sequence
• determined by genes
• represented by either three-letter or one-letter code.
• Alanine - Ala A
• Tyrosine- Tyr Y
• Glutamine- Gln Q

• Chemical and physical interactons cause folding
• Alpha helices and Beta sheets.
• Random coiled regions
• - unstructured regions not alpha=helix or beta= pleated sheets

• Hydrogen bonds- weak
• ionci bonds- cation and anions that are attracted to each other
• hydrophobic effect- like the same
• van der waals forces- attractive forces occur between atoms that are optimal distances apart.
• disulfide bridges

folding of secondary elements gives complex three dimensional shape

• 2 or more polypeptides
• - protein subunits
• - multimeric proteins

• cellular processes involve steps in which two or more different proteins interact with each other
• specific binding at surface

• mad cow
• alzheimers
• cystic fibrosis
• parkinson
• huntingtons

infectious

• responsible for the storage, expression and transmission of genetic info.
• DNA
• - stores genetic info
• RNA
• - decodes dna information into instructions for building polypeptide chain
• has other regulatory and strucural functions

• phosphate group
• 5 carbon sugar (ribosome or deoxyribose)
• single or double ring of Carbon and nitrogen atoms- nitrogenous base

• Dna is usllay found in dbl standed molecule.
• RNA exists as a single bond.

• double helix
• complementary base pairing
• hydrogen bonding
• Thymine

• ribose instead of deoxyribose
• contains uracil in place of thymine
• Uracil
• several forms.