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Micro chapter 2

define matter

anything that takes up space & has mass

matter details

1. Matter= anything that takes up space & has mass
2. Can be liquid, solid, or gaseous state
3. Building blocks of matter- atoms
a. Subatomic particles of atoms- protons (p+), neutrons (n0), and electrons (e-)
b. Protons and neutrons make up the (2) _nucleus_______, electrons are in orbit around them (see figure 2.1)
c.Held together by the attraction of positive protons to negative electrons

Note1: nucleus is positive
Note 2: electrons are high energy, a lot of movement

what are the maximum number of electrons in the 1st, 2nd & 3rd shells

1st = 2 (one orbital, w/1 pair)
2nd = 8 (4 orbitals, w/4 pairs)
3rd = 18 (9 orbitals, w/9 pairs)

what is oclet rule

8 in outer ring most complete, makes it stable, non-reactive

different types of atoms: elements & their properties

1. Different numbers of protons, neutrons, and (5)_electrons___ in atoms create different elements (specifically change in the number of protons)
2. Each element has a characteristic atomic structure and predictable (determines) chemical behavior (review figures)
3. Each assigned a distinctive name with an abbreviated shorthand symbol (review periodic table)

Isotopes

(iso- = same, -tope = type)
1. isotope = same # of protons but different # of neutrons. atom w/change in neutrons
2. Radioactive carbon isotopes used in dating fossils and ancient materials
3. Radioactive Iodine isotopes used in studying the (7) __thyroid_________ gland
4. Isotopes have a different mass than the normal atom (more or less neutrons)

Note: also used to track what's in a cell

electron orbitals & shells

1. An atom can be envisioned as a central nucleus surrounded by a "cloud" of electrons (energy, constant motion)
2. Electrons rotate about the nucleus in pathways called orbitals- (8) [define orbital] = volume of space where electron is likely to be found.
3. Electrons occupy energy shells, from lower-energy to higher-energy as they move away from the nucleus
4. Electrons fill the orbitals and shells in (9)__pairs________ starting with the shell nearest the nucleus
5. Each element, then, has a unique pattern of orbitals and shells

Note: careful on questions, is it pairs in a shell or the number of electrons in a shell

orbital

volume of space where electron is likely to be found.

bonds & molecules

1. Most elements do not exist naturally in pure form
Molecule- distinct combination of 2 or more elements
(can be two of the same element, such as O2)
2. Compounds- molecules that are combinations of two or more different (11)__elements________ (such as CO2)
3. Chemical Bonds- When two or more atoms share, donate, or accept electrons
4. Types of bonds formed and to which atoms and element bonds are determined by the atom's valence

Molecules

distinct combination of 2 or more elements
(can be two of the same element, such as O2)

compounds

molecules that are combinations of two or more different elements (such as CO2)

list 5 types of bonds, strongest to weakest

1.covalent bond-triple bond
2. covalent bond-double bond
3. covalent bond-single bond
4. ionic bond
5. hydrogen bond

Covalent bonds and polarity

1. molecules with shared electrons
2. Co= together, valent=strength
3. Covalent bonds- (12)= atoms sharing electrons in order to reach octlet
4. Examples: H2O (water) and H2 (hydrogen gas).
5. The majority of molecules (organic) associated with living things are composed of single and double covalent bonds between C, H, O, N, S, and P. (sometimes triple bonds)
6. Note: organisms on Earth are carbon based

Note 1: carbon can have 4 bonds
Note 2: hydrogen wants to be as far away from each other as possible

covalent bond

atoms sharing electrons in order to reach octlet

polar vs. nonpolar molecules

1. Some covalent bonds result in a polar molecule- an (13)____unequal____ distribution of charge (ex. H2O).
2. Polarity is a significant property of many large molecules, influences both reactivity and structure
3. Important properties of water as a result of polar bonds (14): adhesive, cohesive & solvent
4. An electrically neutral molecule is nonpolar

properties of water

adhesive, cohesive & solvent

ionic bonds

1. electron transfer among atoms
2. Electrons transferred completely from one atom to another, without sharing, results in an ionic bond (ex. NaCl)
3. Molecules with ionic bonds, when dissolved in a solvent, can separate in to charged particles called ions in a process called ionization
4. Cations- (15) positively______ charged ions
5. Anions- (16)__negatively_________ charged ions
6. These ionic molecules that dissolve to form ions are called (17) _electrolytes

atomic number

shows how many protons in the atoms' nucleus

mass number

of an atom is the sum of protons and neutrons in the nucleus

hydrogen bonding

1. Weak bond (easily broken) between a H covalently bonded to one molecule and an O or N atom on the same or different molecule (such as between water molecules)
2. Gives water many of its properties
3. Also seen in DNA (holds together 2 strands) and this important macromolecule (18) = proteins

es. water, dna & protein
Note 1: result of covalent bond
Note 2: H makes 2nd structure of proteins

chemical shorthand: formulas, models & equations

1. Molecular formula- gives atomic symbols and the number of elements involved as (19)__subscript (# below) (H2o, C6H12O6). listing how many atoms are in there.
2. Molecular formulas might not be unique (glucose, galactose, and fructose, for example)
3. Structural formulas illustrate the relationships of the atoms and the number and types of (20)_bonds_________

Chemical equations

1. Equations are used to illustrate chemical reactions
a. Reactants- Molecules entering the reaction
b. Products- the substances left by a reaction. biproduct = production of reaction (metabolism)

Types of reactions (3) 1/2

1. (21) _Synthesis_____: reactants bond together to form an entirely new molecule
A + B  AB
S + O2  SO2
2H2 + O2  2H2O (note that equations must be balanced)
2. Decomposition: bonds on a single reactant molecule are permanently (22)__broken____ to release two or more product molecules
AB  A + B
2H2O2  2H2O + O2

Types of reactions(3) 2/2

3. Exchange: The reactants trade places between each other and release products that are combinations of the two
AB + XY AX + BY (reversible reaction)
(double arrows = one direction but can go in the other direction)

catalyst

substances that increase the rate of reaction w/o changing final product. Typically made out of proteins.

Solutions: Homogeneous mixtures of molecules

1. Solution- a mixture of one or more solutes uniformly dispersed in a (24) solvent___________
2. The solute cannot be separated by filtration or settling
3. The rule of solubility- "like dissolves like"
4. Water- the most common solvent in natural systems because of its special characteristics
a. Hydrophilic molecules- attract water to their surface (polar)
b. Hydrophobic molecules- repel water (nonpolar)
c. (25) Amphipathic__ molecules- have both hydrophilic and hydrophobic properties

Concentration of solutions

1. Concentration- the amount of solute dissolved in a certain amount of solvent
* a. In biological solutions, commonly expressed as molar concentration or molarity (M)
* i. One mole dissolved in 1 L
* ii. One mole is the molecular weight of the compound in grams

* = don't need to know
Note: [ ] = concentration

Acidity, Alkalinity & the pH scale

1. Acidic solutions- when a component dissolved in water (acid) releases excess hydrogen (26) ions_ (H+)
2. Basic solutions- when a component releases excess (27) hydroxyl (hydroxide ion)_____ ions (OH-)
3. pH scale- measures the acid and base concentrations of solutions
Ranges from 0 (most acidic__) to 14 (most (29)___basic________); 7 is neutral (distilled water)
pH = -log[H+]

hydroxide ion

OH- (negative, gained an electron)

function group hydroxyl = -OH (just allowed to attach)

neutralization reactions

1. Neutralization reactions- occur in aqueous solutions containing both acids and bases
2. Give rise to water and other neutral by-products
3. HCl + NaOH ---- H2O + NaCl

The chemistry of Carbon & Organic compounds (2)

1. Inorganic chemicals- usually does not contain both C and H (ex. NaCl, CaCO3)
2. Organic chemicals- Carbon (hydrogen bonds) compounds with a basic framework of the element carbon bonded to other atoms
a. Typically a combination of C, H and O (can also combine w/CHNOPS)
b. Most of the chemical reactions and structures of living things involve organic chemicals

Carbon - the fundamental element of life (5)
(see slide #33)

1. Valence makes it an ideal atomic building block
2. Forms stable chains containing thousands of C atoms, with bonding sites available
3. Can form linear, branched, or ringed bonds
4. Can form single, double, or triple bonds
5. Most often associates with H, O, N, S, and P

functional groups of organic compounds

-unique group of compounds
1. Special molecular groups or accessory molecules that bind to organic compounds- functional groups (ex. hydroxyl group)
2. Help define the chemical class of certain groups of organic compounds
3. Give organic compounds unique (30) reactive___ properties
a. Reactions of an organic compound can be predicted by knowing the kind of functional group or groups it carries

functional group

a particular molecular combination that reacts in predictable ways & confers particular properties on a compound (ex. -COOH, -OH, -CHO)

Phosphate

capable of 5 bonds, which is unique. high energy bonds

macromolecules: superstructures of Life

1. Biochemistry- study of the compounds of life
2. Biochemicals- organic compounds produced by (or components of) living things
a. Four main families- carbohydrates, lipids, proteins, and nucleic acids
b. Often very large, called macromolecules
c. All macromolecules except for lipids are formed by (31) polymerization (making polymers)________.
i. Repeating subunits (monomers) are bound/joined in to chains of various lengths (polymers)

carbohydrates

1. Sugars and Polysaccharides
a. Most can be represented by the general formula (CH2O)n, where n = (32) (n=can equal any #. ex. n=6 then C6H12O6, multiply each element by 6)

2. Exist in a variety of configurations
a. Sugar (saccharide)- a simple carbohydrate with a sweet taste
b. (33)_Monosaccharide__ contains 3-7 carbons (glucose)
c. Disaccharide contains two (34) monosaccharides__ (lactose)
Polysaccharide contains five or more monosaccharides (ex. (35) starch, cellulose & glycogen___)

Carbohydrates - monosaccharide

1. Monosaccharide combine via a dehydration or condensation reaction
a. _Water_____ is created as a result of the bond

2. Monosaccharides and disaccharides are specified by combining a prefix that describes a characteristic of the sugar with the suffix -ose
a. Hexoses- six sided
b. Pentoses- five sided
c. Fructose- for fruit source

Carbohydrates - monosaccharide
1. description
2. examples
3. notes

1. 3-7 carbon sugars
2. glucose & fructose ("-ose")
3. sugars involved in metabolic reactions; building clock of disaccharides & polysaccharides

Carbohydrates - disaccharides
1. description
2. examples
3. notes

1. two monosaccharides
2. Maltose (malt sugar), Lactose (milk sugar) & Sucrose (table sugar)
3. a. maltose=composed of 2 glucoses; an important breakdown product of starch
b. lactose=composed of glucose & galactose
c. sucrose=composed of glucose & fructose

Note: linked by glycosidic bond

Functions of polysaccharides (4)

FUNCTIONS: (36) support, energy (stores), protection & nutrient stores

ex. Cell walls in plants and many microscopic algae from cellulose (in humans cellulose is fiber)

other polysaccharides (7) & their importance

Give the importance for each of the following: (37)
1. Agar - used for solid culture media
2. Peptidoglycan -structural support to bacteria cell wall (Protein & sugar based)
3. starch - energy source, amalyse used to break up. glucose subunits
4. chitin - exoskeletans/cell wall of fungi
5. lipopolysaccharide - gramming cell walls. cell wall of gram-negative bacteria
6. glycocalyx ("sugarcoat") attachment to other cells or as a site for receptors
glycogen - storage unit in fungi & animals

what is required to break a bond btw 2 glucose molecules

water

Lipids characteristics & main types

1. Lipids- a variety of substances that are not soluble in polar substances (b/c of long or complex hydrocarbon chains which are nonpolar/hydrophobic)
2. Will dissolve in nonpolar solvents
3. Main groups of lipids
a. Triglycerides-a single molecule of glycerol bound to three (38) _fatty acids____
i. Includes fats and oils

glycerol

a 3-carbon alcohol (carbon compounds containing OH groups) w/3 OH groups that serve as binding sites.

types of fat (3)

1. Saturated fats - fatty acids have single bonded carbon chains
a. Easily stack, solid at room temperature (butter and lard)
b. Typically from (39) _animal____ sources
2. Unsaturated fats - at least one (40) _C=C double bond___ in fatty acid carbon chain
a.Don't stack well, (41) _liquid___ at room temp
b. Typically from plant sources (oils)
3. Trans fats
a. Unsaturated fat chemically changed into
b. Needs hydrogen and a palladium catalyst

phospholipids

1. Phospholipids- Contain two fatty acids attached to the glycerol with a phosphate group on the third glycerol binding site
a. Important membrane molecules
b. What causes the "kink" in the one tail? (42)

Misecellaneous lipids (2)

1. Steroids- complex ringed compounds commonly found in cell membranes and animal hormones (gives rigidity)
a. Best known- cholesterol (steroid w/OH group) reinforces structure of the cell membrane in animal cells
b. Other steroids include estrogen and testosterone which are "signaling" molecules.
2. Waxes- esters formed between a long-chain alcohol and a saturated fatty acid (ex. fur, feathers, human skin & insect exoskeletans)

proteins: shapers of life

1. Predominant organic molecules
2. Building blocks- (43) Amino acids (AA)
a. 20 different naturally occurring forms
b. Basic skeleton- a carbon (the α carbon) linked to an amino group (NH2), a carboxyl group (COOH), a hydrogen atom (H), and a variable R group
c. (44) __Peptide (covalent)__ bond forms between the amino group on one amino acid and the carboxyl group on another. (polypeptide=20 or more AA, often a subunit of a protein)

AA can have different characteristics & thus respond differently

Protein structure (4) & diversity

1. Primary (1°) structure- the type, number, and order of amino acids in the chain
2. Secondary (2°) structure- when various functional groups exposed on the outer surface of the molecule interact by forming hydrogen bonds causing...
a. Coiled configuration- α helix
b. Accordion pattern- β-pleated sheet
3. Tertiary (3°) structure- created by additional bonds between functional groups
4. Quaternary (4°) structure- more than one polypeptide forms a large, multiunit protein (hemoglobin)

Protein shape

1. Each different type of protein develops a unique shape, so it can only react with molecules that fit its particular surface features (AA help shape)
a. Ex. enzymes (catalysts) and antibodies (target bacteria)
b. Native state- the functional three-dimensional form of a protein
c. Denatured- when the protein's native state has been (45) _disturbed/changed/altered________

denatured

when the protein's native state has been (45) _disturbed/changed/altered________

Nucleic acids: cell computer & its programs

1. DNA- specially coded genetic program
2. DNA transfers its program to RNA
3. Both are polymers of repeating units called nucleotides
a. Nucleotides- composed of three smaller units: a nitrogen base, a pentose sugar, and a phosphate.
b. The nitrogen base can be one of two forms- a purine (two rings) or a pyrimidine (one ring)
i. Two types of purines: adenine (A) and guanine (G)
ii. Three types of pyrimidines: thymine (T) ([46] _DNA___ only), cytosine (C), and uracil (U) ([47] in ___RNA_____ only)
4. The nitrogen base is covalently bonded to ribose in RNA and deoxyribose in DNA
5. Phosphate (PO43-) covalently bonds the sugars in series

nucleotides composed of

three smaller units: a nitrogen base, a pentose sugar, and a phosphate.

nitrogen base can be in 2 forms, what is in each form?

a purine (two rings) or a pyrimidine (one ring)

Two types of purines: adenine (A) and guanine (G)
Three types of pyrimidines: thymine (T) (DNA only), cytosine (C), and uracil (U) (in RNA__ only)

2 types of pentose in nucleotides

ribonucleic & deoxyribonucleic

backbone of nucleic acid strand is

phosphate-sugar molecules

Double helix of DNA

1. Formed by two long polynucleotide strands
2. Linked along their length by hydrogen bonds between complimentary pairs of nitrogen bases
a. Adenine pairs with thymine (=2 H bonds/easier to break)
b. Cytosine pairs with guanine (=3 H bonds)
c. Where is Uracil? (48) in RNA

RNA: organizers of protein synthesis

1. Also consists of a long chain of nucleotides
2. It is single stranded and contains ribose instead of deoxyribose and uracil instead of thymine
3 .Several functional types of RNA formed using the DNA template
a. Messenger RNA (mRNA)- a copy of a gene that provides the order and type of amino acids in a protein
b. Transfer RNA (tRNA)- a carrier that delivers the correct amino acids for (50) __protein____ assembly
c. Ribosomal RNA (rRNA)- a major component of (51)___ribosomes_____

ATP: Energy molecule of cells (5)

1. Adenosine triphosphate (ATP)- a nucleotide containing (32) _adenine__, ribose, and three phosphates
2. High-energy compound that gives off energy when the bond is broken between the outermost phosphates
3. Releases and stores energy for cellular chemical reactions
4. When the terminal phosphate bond is broken to release energy, adenosine diphosphate (ADP) is formed
5. ADP can be converted back to ATP when the third phosphate is restored.

glucose + glucose = ?

maltose + water
in a glycosidic bond by dehydration synthesis

glucose + fructose = ?

sucrose + water
in a glycosidic bond by dehydration synthesis

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