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BIOL 107 > Chapter 2: Chemistry of Life > Flashcards

Chapter 2: Chemistry of Life Flashcards

1
Q

define matter

A
  • any substance that takes up space and has mass
  • made of elements
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2
Q

define element

A
  • has specific chemical and physical properties
  • consists of a certain kind of atom
  • cannot be broken down to any smaller substance by chemical reactions
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3
Q

define atom

A

the smallest unit of matter that still retains the properties of an element

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4
Q

define atomic number

A
  • number of protons
  • unique to each element; won’t change
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5
Q

define atomic mass

A
  • approximation of mass of an atom
  • sum of mass of protons and neutrons (# of protons + # of neutrons)
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6
Q

define proton

A

positively charged subatomic particles with a mass of 1 amu

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7
Q

define neutron

A

neutrally charged subatomic particle with a mass of 1 amu

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8
Q

define electron

A

negatively charged subatomic particle with almost no mass (0 amu)

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9
Q

define isotope

A
  • same element but differs in the number of neutrons in the nucleus
  • element with different mass number due to neutrons
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10
Q

define radioactive isotope

A

unstable isotopes that spontaneously give off particles and energy to become more stable

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11
Q

define radioactive decay

A
  • energy loss that occurs when unstable atoms nucleus releases radiation to become more stable
  • neutrons converted to protons and atom changes element
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12
Q

when was the periodic table created and by who

A
  • 1869
  • Dmitri Mendeleev
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13
Q

how many elements are there and how many are naturally occurring

A
  • 118 elements
  • 92 naturally occurring
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14
Q

what are the three subatomic particles in an atom

A
  • protons
  • neutrons
  • electrons
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15
Q

which subatomic particle(s) account for the weight of the atom

A

protons and neutrons

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16
Q

which subatomic particle(s) account for the size of the atom

A

electrons

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17
Q

where are most of the biologically important elements located on the periodic table

A

1st few rows

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18
Q

what 4 elements are most organisms primarily made of (96.3%)

A
  • oxygen (65%)
  • carbon (18.5%)
  • hydrogen (9.5%)
  • nitrogen (3.3%)
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19
Q

what are some non-primary elements that organisms are made of (not trace elements)

A
  • calcium
  • phosphorus
  • potassium
  • sulfur
  • sodium
  • chlorine
  • magnesium
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20
Q

define trace elements

A

elements required by organisms in very small quantities (less than 0.01% of mass)

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21
Q

examples of trace elements

A
  • boron
  • copper
  • fluorine
  • iodine
  • iron
  • manganese
  • zinc
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22
Q

effect of nitrogen deficiency on plants

A

yellow leaves

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23
Q

effect of iodine deficiency on humans

A

thyroid issues

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24
Q

are most isotopes stable or unstable

A

stable

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25
Q

which carbon isotopes are stable and which are radioactive

A
  • stable: C12, C13
  • radioactive: C14
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26
Q

how do researchers estimate the age of fossils

A

compare C14 in the atmosphere to C14 in the fossil remains

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27
Q

what does C14 decay to

A

N14

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28
Q

what is the formula for carbon dating

A

N(t)=N(1/2)^t/t^1/2

quantity of substance remaining equals initial quantity of substance times 1/2 to the time elapsed over half life of substance

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29
Q

define valence electrons

A

electrons in the outermost/valence shell

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30
Q

define valence shell

A

outermost electron shell

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31
Q

define valency

A

the number of electrons an atom gains, loses, or shares during a chemical reaction

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32
Q

define compound

A

substance consisting of two or more different elements

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33
Q

define molecule

A

two or more atoms bonded together (may or may not be the same element)

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34
Q

define electronegativity

A
  • attraction of a particular kind of atom for the electrons in a covalent bond
  • more electronegative = more strongly it pulls electrons towards itself
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35
Q

define chemical bond

A

attractive forces that link atoms together to form molecules

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36
Q

define covalent bond

A
  • sharing a valence electrons
  • strong
  • used to complete valence shells and produce stable molecules
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37
Q

define polar covalent bond

A
  • electrons are shared unequally
  • elements with different electronegativity
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38
Q

define nonpolar covalent bond

A
  • electrons shared equally
  • elements with similar electronegativity
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39
Q

define ionic bond

A
  • electrical attraction between the charges of anions and cations
  • when atoms are so electronegative that they strip electrons away from their bonding partners
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40
Q

define ion

A
  • created by electrons transfer between two atoms
  • any atom with a charge
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41
Q

define cation

A
  • positively charged
  • number electrons less than number of protons
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42
Q

define anion

A
  • negatively charged
  • number of electrons greater than number of protons
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43
Q

define hydrogen bond

A
  • form when hydrogen atom covalently bonded to a more electronegative atom is also attracted to another electronegative atoms/molecule
  • happens in water
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44
Q

what determines the chemical behavior of an atom

A

electron configuration and distribution

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45
Q

which electron orbital has the lowest energy

A

closest orbital to the nucleus

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46
Q

which electron orbital has the highest energy

A

outer shell; valence shell

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47
Q

when is an atom most stable/unreactive

A

when the valence shell is full

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48
Q

which electron shell is involved with chemical reactions

A

valence shell

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49
Q

what is the octet rule

A

atoms are most stable when their outermost shell is filled with electrons

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50
Q

which bonds dissociate in water: ionic or covalent

A

ionic

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51
Q

define chemical reaction

A
  • changes in distribution of electrons between atoms
  • forming molecules or breaking apart
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52
Q

explain reversible chemical reactions

A
  • reactions go in both directions
  • reactants converted to products and products converted to reactants
  • double sided arrow
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53
Q

explain irreversible chemical reactions

A
  • reactions go in one direction
  • continues until at least one of the reactants is used up
  • one sided arrow
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54
Q

which creates emergent properties: compounds or molecules

A

compounds

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55
Q

what are emergent properties in compounds

A
  • characteristics of the compound are different than those of the elements its made of
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56
Q

where are covalent bonds commonly found

A
  • carbon-based organic molecules (DNA and proteins)
  • some inorganic molecules (H2O, CO2, O2)
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57
Q

compare bond length, strength, and reactivity between single, double, and triple covalent bonds

A
  • single: long bond length, weakest strength, lowest reactivity
  • double: medium bond length, intermediate strength, medium reactivity
  • triple: short bond length, strongest strength, highest reactivity
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58
Q

are electrons shared equally; why or why not

A
  • no; sometimes but not always
  • because of electronegativity
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59
Q

what factors affect electronegativity

A
  • nuclear charge: more protons = more electronegative
  • size of atom: more distance of outer electrons from nucleus = less electronegative
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60
Q

which elements are the most electronegative

A
  • fluorine
  • oxygen
  • chlorine
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61
Q

are cations and/or anions stable

A

no; neither are stable

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62
Q

how do ionic bonds form

A

electrical attraction between ions with opposite charges (cations and anions)

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63
Q

does an ionic bond result in a compound with a positive, negative, or no charge

A

results in a compound with zero net charge

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64
Q

why are weak chemical bonds important in living systems

A
  • allow for dynamic and easily reversible interactions
  • reinforce shapes of large molecules
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65
Q

examples of weak chemical bonds in living systems

A
  • stabilize structure of proteins
  • hold together double stranded DNA; easily unzipped to single strands
  • hydrogens bonds responsible for waters unique properties
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66
Q

define hydrophobic

A
  • water fearing
  • no affinity for water
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67
Q

define hydrophilic

A
  • water loving
  • has affinity for water
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68
Q

define cohesion

A
  • attraction between H2O due to H bonds
  • creates surface tension
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69
Q

define adhesion

A
  • attraction of H2O to non-water molecules
  • creates capillary action that allows water to flow against gravity
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70
Q

define solute

A

substance that is dissolved

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71
Q

define solvent

A

liquid which dissolves a solute

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72
Q

define solution

A

mixture of solute and solvent

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73
Q

how much of the earth’s surface is water

A

75%

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74
Q

what is the most critical molecule on earth

A

water

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75
Q

how much of the human body is water

A

60-70%

76
Q

what characteristic is responsible for the unique properties of water

A

polarity

77
Q

why is polarity in water important

A
  • the attraction of positive and negative charges allow cohesion among water molecules
  • allows formation of hydrogen bonds
  • responsible for waters unique properties
78
Q

explain hydrogen bonds in water molecules

A

the hydrogen of one water molecule forms a weak bond with the oxygen of another water molecule

79
Q

how many hydrogen bonds can a water molecule form

A
  • 4
  • oxygen can form 2
  • each hydrogen can form 1
80
Q

how do waters hydrogen bonds behave in a liquid form

A
  • constantly breaking and forming
  • molecules slide past each other
81
Q

how to waters hydrogen bonds behave in a gas form

A
  • bonds completely broken as heated
  • molecules escape into the air
82
Q

how do waters hydrogen bonds behave in a solid form

A
  • molecules form crystalline structure
  • makes it less dense than liquid form
83
Q

which type of molecules are hydrophobic

A
  • non-polar molecules
  • oils and fats
  • have no charge for water to interact with
84
Q

which type of molecules are hydrophilic

A

ionic and polar molecules

85
Q

what are the four emergent properties of water

A
  • cohesion/adhesion
  • moderation of temperature
  • expansion upon freezing
  • versatility as a solvent
86
Q

what happens to water as temperature increases

A
  • water absorbs the energy/heat
  • H bonds break and reform
  • water molecules are released (evaporation)
87
Q

does water have a high or low heat capacity

A

high

88
Q

what happens to water as temperature decreases

A
  • molecular motion decreases
  • less energy to break H bonds
  • H bonds form rigid lattice structure
  • creates ice
89
Q

why is ice being less dense than water important for life

A

ice floats on top of water in freezing temperatures, allowing organisms to live in the water under ice

90
Q

water is known as the _________ solvent

A

universal

91
Q

what makes water a good solvent

A

polarity

92
Q

define sphere of hydration

A

when the positive H or negative O of a water molecule surround an ion forming H bonds to dissolve ionic compounds

93
Q

define dissociation (relating to solvents/solutions)

A
  • ionic bonds disrupted and atoms break off molecules to form ions
  • due to interactions of individual ions with polar regions of water molecules
94
Q

define pH

A

concentration of H+ ions

95
Q

define acid

A
  • substance that provides hydrogen ions
  • lowers pH
96
Q

define base

A
  • substance that provides hydroxide ions
  • H combines with OH to produce H2O
  • increases pH
97
Q

define buffer

A
  • absorbs excess H or OH
  • stabilizes pH
  • often weak acids or conjugate bases
98
Q

what do changes in pH affect

A
  • formation of acids and bases
  • biological chemistry
  • weak bonds of proteins and cell structures
99
Q

what buffer system allows us to eat acidic or basic things

A

bicarbonate buffer system

100
Q

what pH range do most of our cells operate in

A

7.2 to 7.6

101
Q

equation for pH

A

pH=-log[H+]

102
Q

equation for pOH

A

pOH=-log[OH-]

103
Q

does an acidic substance have more H+ or OH-

A

more H+

104
Q

does a basic substance have more H+ of OH-

A

more OH-

105
Q

what is the relationship between H+, pH, OH-, and pOH (when H+ increases what happens to each)

A
  • H+ increase
  • pH decrease
  • OH- decrease
  • pOH increase
106
Q

pH + pOH =

A

14

107
Q

if [OH-] is 10^-11, what is [H+]

A

10^-3

exponents must equal 14: 11+3=14

108
Q

if pH is 4, what is [H+]

A

10^-4

109
Q

if pH increases from 6 to 7, what is the difference in [H+]

A

decrease [H+] 10x

110
Q

if pH increases from 8 to 10, what is the difference in [H+]

A

decrease [H+] 100x

111
Q

if pH decreases from 4 to 1, what is the difference in [H+]

A

increase [H+] 1000x

112
Q

life is said to be ______ based

A

carbon

113
Q

why is carbon so special to life

A
  • tetravalent
  • will form 4 bonds
  • accounts for diversity of molecular forms
114
Q

what are the four classes of biological macromolecules

A
  • carbohydrates
  • proteins
  • nucleic acids
  • lipids
115
Q

which biological macromolecule is not a polymer

A

lipids

116
Q

how are all monomers linked

A

covalent bonds

117
Q

how many total monomers are there

A

about 40-50

118
Q

define anabolic reactions

A

building of polymers

119
Q

define catabolic reactions

A

breaking of polymers

120
Q

what is the ratio of C to H to O in carbohydrates

A

1:2:1

121
Q

what does saccharide mean

A

sugar

122
Q

define monosaccharides

A
  • simple sugars
  • monomer of carbohydrates
123
Q

how many carbons are in monosaccharides

A

3 to 7

124
Q

how are monosaccharides generally named

A

ending with -ose

125
Q

what are the most common monosaccharides

A
  • glucose
  • galactose
  • fructose
126
Q

what two forms can monosaccharides be in

A
  • linear chain
  • ring-shaped (more common)
127
Q

define disaccharide

A

two monosaccharides joined by a covalent bond

128
Q

how are disaccharides formed

A
  • dehydration reaction
  • release of a water molecule
129
Q

what are three common disaccharides and the monosaccharides they are made of

A
  • lactose: glucose and galactose
  • maltose: glucose and glucose
  • sucrose: glucose and fructose
130
Q

define polysaccharide

A
  • long chain of monosaccharides linked by covalent bonds
  • may be branches or unbranched
131
Q

which polysaccharides are used for storage

A
  • starch
  • glycogen
132
Q

which polysaccharides are used for structural support

A
  • cellulose
  • chitin
133
Q

describe starch

A
  • polysaccharide
  • stored form of sugar in plants
  • amylose and amylopectin
134
Q

describe glycogen

A
  • polysaccharide
  • storage of glucose in humans and other vertebrate
  • made of monomers of glucose
  • highly branched
  • stored in liver and muscles
135
Q

describe cellulose

A
  • polysaccharide
  • makes up cell walls of plants
  • made of monomers of glucose
136
Q

describe chitin

A
  • polysaccharide
  • makes exoskeleton of arthropods
  • made of repeating units of a nitrogen containing carbohydrate
137
Q

what are the monomers of proteins

A

amino acids

138
Q

how many amino acids are there

A

20

139
Q

what is the most abundant and diverse macromolecule

A

proteins

140
Q

6 functions of proteins

A
  • structure
  • regulatory
  • transport within/between cells
  • storage
  • enzymes
  • hormones
141
Q

why is the shape of a protein important

A

shape impacts the function of the protein

142
Q

define denaturation and its causes/effects

A
  • unfolding/loss of shape of proteins
  • causes: changes in temperature, pH, or chemical exposure
  • effects: loss of shape and therefore loss of function
143
Q

what do enzymes do

A

catalyze (speed up) biochemical reactions

144
Q

what is the fundamental structure of amino acids

A
  • central carbon: C
  • amino group: H2N
  • carboxyl group: COOH
  • hydrogen: H
  • R group: differs between different amino acids
145
Q

why is the R group of amino acids important

A
  • determines the chemical nature of amino acids
  • where you see polar and nonpolar amino acids
146
Q

what is the difference between polypeptides and proteins

A
  • polypeptides: chain of amino acids
  • proteins: polypeptide folded into functional protein shape
147
Q

how many levels of protein structure are there

A

4

148
Q

define primary protein structure

A
  • sequence of a chain of amino acids
  • polypeptide chain
149
Q

define secondary protein structure

A
  • hydrogen bonding of peptide chain causes amino acids to fold into a repeating pattern
  • beta pleated sheet and alpha helix
150
Q

define tertiary protein structure

A

3D folding pattern of protein due to interactions between R groups

151
Q

define quaternary protein structure

A
  • protein consisting of more than one amino acid chain
  • multiple proteins interacting
152
Q

what are the two types of nucleic acids

A
  • deoxyribonucleic acid (DNA)
  • ribonucleic acid (RNA)
153
Q

define DNA

A
  • genetic material in all living organisms
  • never leaves nucleus
154
Q

define RNA

A
  • intermediary that communicates with the rest of the cell
  • involved in protein synthesis
  • can leave the nucleus
155
Q

what are the monomers of nucleic acids (DNA and RNA)

A
  • nucleotides
  • 5 total: GCATU
  • DNA: GCAT
  • RNA: GCAU
156
Q

explain the central dogma

A
  • flow of genetic information
  • DNA to RNA to proteins
  • DNA contains information on how to make proteins
157
Q

what are the three parts of a nucleotide

A
  • nitrogenous base
  • pentose (5 carbon) sugar
  • phosphate group
158
Q

which part of a nucleotide differs

A

nitrogenous base

159
Q

describe the structure of DNA

A
  • double helical structure
  • antiparallel strands: strands run opposite of each other
  • strong sugar phosphate backbone
  • strands held together by hydrogen bonds
160
Q

what type of bond holds together the sugar phosphate backbone of DNA

A
  • covalent bond
  • phosphodiester bond
161
Q

what are lipids composed of

A

hydrocarbons: hydrogen and carbon

162
Q

are lipids polar or nonpolar

A

nonpolar; hydrocarbons with similar electronegativity

163
Q

what type of chemical bonds are present in lipids

A

nonpolar covalent bonds

164
Q

what are two characteristics of lipids

A
  • nonpolar
  • hydrophobic (due to non-polarity)
165
Q

examples of lipids

A
  • fats/triglycerides
  • oils
  • waxes
  • phospholipids
  • steroids
166
Q

four functions of lipids

A
  • long term energy storage
  • insulation
  • building blocks for hormones
  • component of cellular membranes
167
Q

explain the structure of saturated fatty acids

A
  • triglycerides
  • straight carbon chains
  • no double bons
  • “saturated” with H
  • tightly packed structure
168
Q

what form are saturated fatty acids in at room temperature

A

solid

169
Q

where are most saturated fatty acids found

A
  • animal origin
  • fats, butter, dairy
170
Q

how do saturated fatty acids affect cholesterol

A
  • increase LDL
  • cause plaque buildup in arteries
171
Q

explain the structure of unsaturated fatty acids

A
  • triglycerides
  • kinked carbon chains
  • at least one double bonded carbons
  • kinks prevent molecules from tightly packing
172
Q

what form are unsaturated fatty acids in at room temperature

A

liquid

173
Q

where are most unsaturated fatty acids found

A

plant and fish fats

174
Q

how do unsaturated fatty acids affect cholesterol

A
  • increase HDL
  • decrease LDL by transporting it to liver for removal
175
Q

what are the two configurations of carbon double bonds in unsaturated fatty acids

A
  • cis configuration
  • trans configuration
176
Q

explain the structure of cis configuration unsaturated fatty acids

A
  • hydrogens on the same side of the carbon chain
  • causes carbon backbone to bend or kink
  • can’t pack tightly and remain liquid at room temperature
177
Q

explain the structure of trans configuration unsaturated fatty acids

A
  • hydrogens on the opposite side of the carbon chain
  • forms linear fatty acid (no kink in the chain)
  • can pack tightly and be solid at room temperature
178
Q

how are trans fats made

A

food processing

179
Q

what type of fatty acid is elaidic acid

A
  • unsaturated trans
  • linear structure
  • double bond
  • H on opposite sides
180
Q

what type of fatty acid is oleic acid

A
  • unsaturated cis
  • bent structure
  • double bond
  • H on same side
181
Q

what type of fatty acid is stearic acid

A
  • saturated
  • linear structure
  • no double bonds
182
Q

what are phospholipids made of

A
  • 2 fatty acid chains
  • chains attached to glycerol
  • phosphate group at the head
183
Q

define amphipathic molecule

A

both hydrophilic and hydrophobic parts

184
Q

which part of a phospholipid is hydrophobic and which is hydrophilic

A
  • hydrophobic: tail, made of C and H (non-polar)
  • hydrophilic: head, made of C H and O (polar)
185
Q

where are phospholipids commonly found

A
  • cell/organelle membranes
  • phospholipid bilayer
186
Q

define steroids

A
  • lipids made of 4 fused carbon rings
  • cholesterol and hormones
187
Q

define waxes

A
  • lipids made of hydrocarbon chain with alcohol group and fatty acid
  • beeswax and lanolin

BIOL 107 (18 decks)

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