Chapter 2

Front 1

2 components of the theory of chemical evolution?

Back 1

-Pattern component: in addition to small molecules, complex C-containing substances exist and are required for life

-Process component: early in earth's history, simple chemical compounds combined to form more complex C-containing substances before the evolution of life

Front 2

What 4 types of atoms make up 96% of all matter found in organisms today?

Back 2

1. H

2. C

3. O

4. N

Front 3

Atomic #

Back 3

characteristic # of protons for a given element

Front 4

Mass number

Back 4

sum of protons and neutrons (superscript to left of symbol)

Front 5

Isotopes

Back 5

element with diff numbers of neutrons

Front 6

Atomic weight

Back 6

-average of all the mass numbers of the naturally occurring isotopes based on their abundance

Front 7

radioactive isotope

Back 7

-unstable isotope--nucleus will eventually decay and release energy (radiation)

Front 8

dalton

Back 8

-unit of measurement of mass for protons, neutrons, electrons

-masses of protons & neutrons virtually identical, usually rounded to 1 dalton

Front 9

how many electrons can each orbital hold?

Back 9

2

Front 10

orbital

Back 10

specific region in which electrons move around atomic nucleus

Front 11

valence

Back 11

number of unpaired electrons found in an atom

Front 12

when is the atom most stable?

Back 12

-when its valence shell is filled

Front 13

how can valence shells be filled?

Back 13

-through formation of strong chemical bonds

Front 14

covalent bond

Back 14

-strong attraction where two atoms share one/more pairs of electrons

-form when the attractive forces overcome the repulsive forces

-electrons participating in covalent bond are not always shared equally b/t the atoms involved--some atoms hold the electrons more tightly

Front 15

why is the H atom not very stable?

Back 15

-has an unpaired valence electron

Front 16

electronegativity

Back 16

during covalent bonding, when some atoms hold the electrons in covalent bond much more tightly than other atoms

Front 17

what's responsible for an atom's electronegativity?

Back 17

-# of protons in the nucleus

-the distance b/t the nucleus and the valence shell

Front 18

what is one of the most electronegative of all elements?

Back 18

-Oxygen--has 8 protons and only 2 electron shells--attracts covalently bonded electrons very strongly

--electronegativities of 4 most abundant elements: O > N > C = H

Front 19

why are electrons in a C-H bond shared equally/symmetrically?

Back 19

-because they have approximately equal electronegativity

Front 20

nonpolar covalent bond

Back 20

when electrons are shared equally/symmetrically

Front 21

polar covalent bond

Back 21

electrons in this type of bond spend most of their time close to the nucleus of the more electronegative atom

Front 22

ionic bonds

Back 22

-similar in principle to covalent bonds, but instead of being shared b/t 2 atoms, the electrons in ionic bonds are completely transferred from 1 atom to another

-transfer occurs because it gives the resulting atoms a full outermost shell

Front 23

ion

Back 23

-An ion (/ˈaɪən, -ɒn/) is an atom or a molecule in which the total number of electrons is not equal to the total number of protons, giving the atom or molecule a net positive or negative electrical charge. Ions can be created, by either chemical or physical means, via ionization.

-atom/molecule that carries a full charge, rather than the partial charges that arise from polar covalent bonds

Front 24

cation vs. anion

Back 24

-cation: positively charged ion

-anion: negatively charged ion

Front 25

4 ways to represent molecules?

Back 25

1. molecular formulas

2. structural formulas: indicate which atoms in a molecule are bonded together, geometry in 2 dimensions (used for planar molecules such as water and O2.

3. ball-and-stick: provide info on 3-dimensional shape of molecules, relative sizes of atoms

4. space-filling models: more accurately depict the spatial relationship b/t atoms

Front 26

Why is water such an efficient solvent?

Back 26

1. both the O-H bonds in water molecule are polar-->O atom has partial - charge, H atom has partial + charge

2. the molecule is bent---> the partial negative charge on the O atom sticks out, away form the partial + charges on the H atoms, giving the molecule an overall polarity

Front 27

What happens when 2 water molecules approach each other?

Back 27

-the partial + charge on H attracts the partial - charge on O--->this weak electrical attraction forms a H bond b/t the molecules

Front 28

Hydrophilic interactions

Back 28

-ions, polar molecules stay in solution b/c of their interactions w/ water's partial charges

-H bonding makes it possible for almost any charged/polar molecule to dissolve in water

Front 29

Hydrophobic interactions

Back 29

-compounds that are uncharged and nonpolar don't interact w/ water through H bonding and don't dissolve in water

-as their interactions w/ water = minimal/non-existent, forced to interact w/ each other

-water molecules surrounding nonpolar molecules form H bonds w/ one another and increase the stability of these hydrophobic interactions

Front 30

cohesion

Back 30

-attraction b/t like molecules

-water is cohesive b/c of H bonds that form b/t individual molecules

Front 31

Adhesion

Back 31

attraction b/t unlike molecules

Front 32

why is water denser as a liquid than as a solid?

Back 32

-in ice, each water molecule participates in 4 H bonds. these bonds cause H20 molecules to form regular, repeating structure (crystal)--relatively large amount of space b/t molecules

-in liquid, H bonds are constantly being formed & broken--molecules packed more closely

Front 33

Why does water have high capacity for absorbing energy?

Back 33

-because when a source of energy hits it, H bonds must be broken

-takes large amount of energy to change temp due to water's overall polarity, ability to form H bonds

Front 34

Acid

Back 34

substances that give up protons during chemical reactions and raise the hydronium ion concentration of water

Front 35

bases

Back 35

molecules/ions that acquire protons during chemical reactions and lower hydronium ion concentration of water

Front 36

Acid-Base reaction

Back 36

-a chemical reaction that involves the transfer of protons

-every acid-base reaction requires a proton donor and a proton acceptor (an acid and a base, respectively)

Front 37

Molarity

Back 37

-# of moles of the substance present/L of solution

Front 38

what is pH?

Back 38

pH = -log [H]

Front 39

buffers

Back 39

compounds that minimize changes in pH--most buffers = weak acids, meaning that they are somewhat likely to give up a proton in a solution

Front 40

endothermic

Back 40

"within heating"

-a change in chemical equilibrium during a chemical reaction in which heat is absorbed during the process

Front 41

exothermic

Back 41

-"outside heating"

-a change in chemical equilibrium during a chemical reaction in which heat is released

Front 42

What is energy?

Back 42

the capacity to do work or supply heat

Front 43

what are 2 forms of energy?

Back 43

1. potential energy: stored energy; when stored in chemical bonds, it is called chemical energy

2. kinetic energy: energy in motion--molecules have kinetic energy b/c they are constantly in motion

Front 44

Kinetic energy

Back 44

-energy in motion

-kinetic energy of molecular motion = thermal energy

-the temperature of an object is a measure of how much thermal energy its molecules possesses; when two objects w/ different temps come into contact, thermal energy transferred between them (heat)

Front 45

First & Second Laws of Thermodynamics

Back 45

1. energy is conserved--cannot be created or destroyed, but only transferred and transformed

2. Entropy always increases in an isolated system

Front 46

What 2 factors determine if a chemical reaction will occur spontaneously?

Back 46

-When the product molecules are less ordered than the reactant molecules (entropy) (eg. heat increases disorder in environment)

-if products have lower potential energy than their reactants

Front 47

LUCA

Back 47

-last universal common ancestor (top-down approach of investigating chemical evolution)

Front 48

2 different model systems that attempt to explain process component of theory of chemical evolution:

Back 48

1. prebiotic soup model

2. surface metabolism model

Front 49

Process Component of Theory of Chemical Evolution

Pre-biotic soup model

Back 49

1. certain molecules were synthesized from gases in the atmosphere or arrived via meteorites

2. afterward they condensed w/ rain and accumulated in oceans

3. formed "organic soup" that allowed for construction of large, more complex molecules

Front 50

Process Component of Theory of Chemical Evolution

Surface metabolism model

Back 50

-dissolved gases came into contact w/ minerals lining the walls of deep-sea vents and formed more complex, organic molecules

Front 51

Organic molecules

Back 51

molecules that contain C bonded to other element

Front 52

Why is C so important in biology?

Back 52

-it is the most versatile atom on earth

-b/c of its four valence electrons, it will form 4 covalent bonds-this results in limitless array of molecular shapes

-C atoms provide the structural framework for virtually all the important compounds associated w/ life, w/ the exception of water

Front 53

Functional groups

Back 53

-the critically important H-, N-, O-, and S- containing groups in organic compounds

-these groups dictate the types of reactions that occur

Front 54

when you encounter an O compound that is new to you, what 3 things are important to consider?

Back 54

1. overall shape and size provided by C framework

2. identify types of covalent bonds present based on the electronegativities of the atoms--use this to estimate polarity of the molecule & amount of energy stored in its chemical bonds

3. locate any functional groups and note the properties these groups give the molecule

Front 55

Organic compounds

How functional groups behave

amino and carboxyl functional groups

Back 55

-tend to attract/drop a proton, respectively

-amino groups function as bases; carboxyl groups as acids

-both groups participate in H bonding

Front 56

Organic compounds

How functional groups behave

Carbonyl groups

Back 56

-this functional group is the site of reactions that link molecules (aldehyde and ketone molecules) into larger, more complex organic compounds

Front 57

Organic compounds

How functional groups behave

Hydroxyl groups

Back 57

-act as weak acid

-these groups are polar, molecules containing hydroxyl groups will form H bonds and tend to be soluble in water

Front 58

Organic compounds

How functional groups behave

Phosphate groups

Back 58

-carry two negative charges

-when phosphate groups transferred for one organic compound to another, dramatically affects charge of recipient molecule

-phosphates bonded together store chemical energy that can be used in chemical reactions

Front 59

Organic compounds

How functional groups behave

sulfhydryl groups

Back 59

-consist of a sulfur atom bonded to a H atom

-sulfhydryl groups can link to one another via disulfide (S-S) bonds