Ch. 2 - The Chemistry of Biology

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Matter

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Architecture

80 Terms

1

Matter

all materials that occupy space and have mass

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2

What is matter composed of?

atoms

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3

Atom

simplest form of matter not divisible into simpler substances

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4

Protons

(+) subatomic particles

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5

Neutrons

neutral subatomic particles

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Electrons

(-) subatomic particles

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4 Fundamental Forces

  1. Gravity

  2. Electromagnetism

  3. Strong nuclear force

  4. Weak Force

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8

Electromagnetism

like charges repel, unlike attract

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Strong nuclear force

Holds nucleus together

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10

Weak force

Radioactivity (neutron)

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11

What do all atoms share?

The same fundamental structure

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12

Element

pure substances w/ a characteristic number of protons, neutrons, and electrons and predictable chemical behaviors

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Atomic number

number of protons

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14

Atomic mass

number of protons and neutrons

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15

Isotopes

variant forms of the same element that differ in the number of neutrons

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Atomic weight

average mass numbers of all isotopic forms

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Electron orbitals

volumes of space surrounding the atomic nucleus where electrons are likely to be found

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18

Molecule

a chemical substance that results from the combination of two or more atoms

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19

Compounds

molecules that are combinations of two or more different elements

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Formula/Mass Weight

sum of all of the atomic masses of the atoms a molecule contains

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21

Chemical bonds

when 2 or more atoms share, donate, or accept electrons to form molecules and compounds

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22

What are the three different types of chemical bonds?

  1. Covalent bonds

  2. Ionic bonds

  3. Hydrogen bonds

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23

Covalent bonds

  • electrons are shared among atoms

  • strongest

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Polar covalent bonds

  • unequal sharing (negative and positive pole)

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Nonpolar covalent bonds

equal sharing

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Ionic bonds

  • one or more electrons from one atom are removed and attached to another atom which forms positively charge cations and negatively charged anions

  • least important

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Hydrogen bonds

weak bonds between hydrogen and other atoms

  • electrons are not shared, lost, or gained

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Organic chemicals

compounds containing carbon bonded to hydrogens

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Ionization

aqueous dissociation of an electrolyte into ions

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Functional group

a particular molecular combination that reacts in predictable ways and confers particular properties on a compound

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What can functional groups help define?

The chemical class of certain groups of organic compounds

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C Hopkins Cafe Mg NaCl

  • Carbon

  • Hydrogen

  • Oxygen

  • Phosphate

  • Potassium

  • Iodine

  • Nitrogen

  • Sulfer

  • Calcium

  • Iron

  • Magnesium

  • Sodium

  • Chlorine

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Functional Groups of Organic Compounds

  • accessory molecules that bind to organic compounds

  • confer unique reactive properties on the whole molecule

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Hydroxyl Formula

R-OH

<p>R-OH</p>
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Where can hydroxyl be found?

Alcohols and carbohydrates

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Carboxyl formula

R−COOH

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Where can carboxyl be found?

Fatty acids, proteins, organic acids

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Amino formula

R-CH(NH2)-COOH

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Where can amino be found?

Proteins, nucleic acids

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Ester formula

R-COO-R

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Where can ester be found?

Lipids

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Phosphate formula

knowt flashcard image
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Where can phosphate be found?

DNA, RNA, ATP

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Carbohydrate

A compound containing primarily carbon, hydrogen, and oxygen in a 1:2:1 ratio

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What is the general formula for Carbohydrates?

(CH2O)n

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Dehydration synthesis

loss of water in a polymerization reaction

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What is the function of carbohydrates?

polysaccharides provide cell structure, adhesion and metabolism

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48

How does cellulose affect cell walls?

Cellulose provides the strength and rigidity of the cell wall

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49

Chitin

  • Polysaccharide similar to cellulose in chemical structure

  • Major compound in the cell walls of fungi and the exoskeletons of insects

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Peptidoglycan

  • When polysaccharides are linked to peptide fragments

  • Provides the main source of structural support to the bacterial cell wall

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51

Gram-negative bacteria’s cell wall contains what?

Lipopolysaccharide

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Lipopolysaccharide

LPS of gram-negative bacteria is an endotoxin w/ generalized pathologic effects such as fever

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Glycocalyx

  • attachment to other cells

  • site for receptors

  • carbohydrate-rich molecule

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Glycosidic bonds

link of subunits of disaccharides and polysaccharides

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Peptide

Molecule composed of short chains of amino acids, such as a dipeptide, tripeptide, and a tetrapeptide

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Phosphodiester bond

Forms when two hydroxyl groups in phosphoric acid react w/ a hydroxyl group on other molecules, forming ester bonds

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Disulfide bonds

Occurs between sulfur atoms on the amino acid cysteine

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Lipids (what are they? created by? classification?)

  • long hydrophobic, C-H chains attached to a glycerol molecule

  • created by dehydration synthesis

  • triglycerides, phospholipids, steroids and waxes

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Triglycerides

  • 3 fatty acids bound to glycerol

  • Saturated/unsaturated

  • Energy storage

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Saturated fatty acid

has all carbons in the chain bonded to hydrogen w/ single bonds

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Unsaturated fatty acids

Has at least one carbon-carbon double bond

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62

Give an example of a more saturated fat?

Solid fats (butter)

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Example of unsaturated fats

Oils (liquid fats)

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Name some bad things saturated fats can do to you

  • Raise your cholesterol levels

  • Increase risk of heart disease

  • low density lipoproteins

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Name good things unsaturated fats can do to you

  • Lower cholesterol levels

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Structure of phospholipids

  • Glycerol w/ 2 fatty acids + a phosphate group

  • Bilayers of phospholipids form membranes

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What does the structure of phospholipids provide?

Impenetrable barrier that accounts for the selective permeability and transport of molecules

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68

How are amino acids attached in order to form proteins?

Through peptide bonds

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69

Functions of proteins

support, enzymes, defense, transport, movement

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Primary structure of a protein

  • Series of amino acids bound in a chain

  • Amino acids display small charged functional groups

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Secondary structure of a protein

  • Develops when CO- and NH- groups on adjacent amino acids form hydrogen bonds

    • then folds the chain forming an alpha helix and beta pleated sheet

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Tertiary structure of a protein

  • forms when parts of the secondary structure interact by forming covalent disulfide bonds and other interactions

  • creates a 3-D mass

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Quartenary structure of a protein

  • exists only in proteins that consist of more than 1 polypeptide chain

  • typical of antibodies and some enzymes that act in cell synthesis

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Structure of DNA

  • adenine & thymine, cytosine & guanine

  • Double Helix

  • formed by 2 very long polynucleotide strands linked along their length by hydrogen bonds between the nitrogenous bases

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Structure of RNA

  • polynucleotide that consists of a long chain of nucleotides

  • single strand that contains ribose sugar instead of deoxyribose

  • uracil instead of thymine

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Three types of RNA

mRNA: messenger RNA

tRNA: transfer RNA

rRNA: ribosomal RNA

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Purines

  • two rings

  • 2 types: adenine & guanine

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Pyrimidines

  • one ring

  • 3 types: thymine, cytosine, and uracil

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ATP

  • adenosine triphosphate

    • nucleotide: adenine, ribose, 3 phosphates

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80

Function of ATP

transfer and storage of energy

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