Chemistry and Biological Macromolecules Flashcards
(214 cards)
1
Q
Describe the three subatomic particles
A
Protons (positively charged, determines atomic number), neutrons (neutral, contributes to mass), and electrons (negatively charged, determines chemical behavior)
2
Q
Distinguish between the atomic number and the mass number of an element
A
Atomic number is the number of neutrons, mass number is the number of protons plus neutrons
3
Q
Provide examples of isotopes and explain their usefulness in research and medical diagnostics
A
Carbon-12, Carbon-13, and Carbon-14; PET scans measure radioisotopes and we can tell the diets of some animals from the radio of Carbon-12 to Carbon-13 in their bodies
4
Q
Draw the electron configuration of chlorine.
A
[2 in the first shell, then 8, then 7]
5
Q
Distinguish between ionic bonds, polar covalent bonds, and non-polar covalent bonds and provide examples of each
A
Ionic bonds are one atom stealing the electrons from another (ex: NaCl), polar covalent bonds are two atoms unequally sharing electrons (H2O), and non-polar covalent bonds are two atoms equally sharing electrons (H2)
6
Q
Large difference in electronegativity results in _____ bonds, small difference results in _____ bonds
A
Ionic, covalent
7
Q
What makes the properties of CO2 different from H2O?
A
H2O is a polar molecule, while CO2 is not
8
Q
The bonds within a water molecule are _____, while the bonds between water molecules are _____
A
Covalent, hydrogen bonds
9
Q
What properties of water contribute to Earth’s sustainability for life?
A
Universal solvent, cohesion, adhesion, expansion upon freezing, high heat capacity, high heat of vaporization, high specific heat
10
Q
Why does it take longer to heat a cup of water than a cup of oil?
A
Oil has a smaller heat capacity than water, meaning more energy is required to heat water than oil to a specific temperature, meaning it would take longer
11
Q
What happens when a crystal of sucrose dissolves in water?
A
Water molecules pull apart the individual molecules until they are so dispersed they cannot be seen
12
Q
What’s the relationship between the density of water and temperature, and how does this relate to life on Earth?
A
When water freezes, it becomes less dense, causing ice to float to the surface of the water. This insulates the rest of the water, preventing the entire body to freeze. This allowed life on Earth to evolve because the ocean remained liquid
13
Q
Provide examples of the role of weak bonds in biological molecules
A
Hydrogen bonds determine a protein’s secondary structure; hydrogen bonds and van der Waals interactions determine a protein’s tertiary structure
14
Q
Describe the exclusion of hydrophobic molecules by water molecules
A
Hydrophobic molecules can’t form hydrogen bonds, and thus disrupt the hydrogen bond network, forcing water molecules to reform a hydrogen bond cage around them
15
Q
Matter
A
Anything that takes up space and has mass
16
Q
Element
A
A substance that cannot be broken down to other substances by chemical reactions
17
Q
Compound
A
Substance consisting of two or more elements combined in a fixed ratio
18
Q
Essential Element
A
Required by organisms to live and reproduce
19
Q
Trace Elements
A
required by an organism in only minute quantities
20
Q
Atom
A
Smallest unit of matter that still retains the properties of an element
21
Q
Neutron
A
Electrically neutral subatomic particle
22
Q
Proton
A
Subatomic particle with one unit of positive charge
23
Q
Electron
A
Subatomic particle with one unit of negative charge
24
Q
Dalton
A
Unit of mass for atoms and subatomic particles (equal to 1 AMU)
25
Atomic Number
The number of protons composing an element
26
Mass Number
Total number of protons and neutron in the nucleus of an atom
27
Atomic Mass
The actual mass of an atom, very close to, but not exactly the mass number
28
Isotopes
Atoms of the same element with different numbers of neutrons
29
Radioactive Isotopes
An isotope where the nucleus decays spontaneously, giving off particles and energy
30
Half-life
The time it takes for 50% of a parent isotope to decay
31
Radiometric Dating
Measuring the ratio of different isotopes in a substance to calculate how many half-lives have passed since formation
32
Energy
The capacity to do work
33
Potential Energy
The energy that matter possesses because of its location or structure
34
Electron Shells
An average distance (from the nucleus) and energy level occupied by electrons
35
Valence Electrons
Electrons in an atom's outermost shell
36
Valence Shell
The outermost electron shell
37
Orbital
The three-dimensional space where an electron is found 90% of the time
38
Chemical Bonds
Attractions holding atoms together through the share or transfer of valence electrons
39
Molecule
Two or more atoms held together by covalent bonds
40
Single Bond
A pair of shared electrons
41
Double Bond
Two pairs of shared electrons
42
Electronegativity
The attraction of a particular atom to the electrons of a covalent bond
43
Nonpolar Covalent Bond
When electrons in a covalent bond are shared equally because the two atoms have similar electronegativities
44
Polar Covalent Bond
When an atom is bonded to a more electronegative atom, and the electrons of the bond aren't shared equally (electrons are more attracted to one element than the other)
45
The H-H bond in H2 is a (single/double/triple) bond
Single
46
The O-O bond in O2 is a (single/double/triple) bond
Double
47
The O-H bonds in H2O are (single/double/triple) bonds
Single
48
The C-H bonds in CH4 are (single/double/triple) bonds
Single
49
In a water molecule, the hydrogens have a partial _____ charge and the oxygen has a partial _____ charge
Positive, negative
50
Ions
Oppositely charged atoms (or molecules) resulting from an ionic bond
51
Cation
Positively charged ion
52
Anion
Negatively charged ion
53
Ionic Bond
The attraction between cations and anions
54
Ionic Compounds
Compounds formed by ionic bonds
55
Salts
Compounds formed by ionic bonds
56
Hydrogen Bond
Noncovalent attraction between a hydrogen and an electronegative atom
57
Van der Waals Interactions
Individually weak attractive forces that occur only when atoms and molecules are close together, results from the uneven distribution of electrons
58
How does morphine affect pain perception and emotional state?
Its chemical structure mimics that of natural endorphins, allowing it to bind to endorphin receptors
59
Chemical Reactions
The making and breaking of chemical bonds leading to changes in the composition of matter
60
Reactants
The starting materials of a chemical reaction
61
Products
The resulting materials of a chemical reaction
62
Chemical Equilibrium
The point at which the forwards and backwards reactions offset one another exactly
63
Bombardier Beetle
Beetle that sprays a boiling hot liquid as a defense mechanism; the liquid only explodes after the beetle forces it to by adding two catalysts
64
Polar Molecule
When the overall charge of a molecule is unevenly distributed due to one or more polar covalent bonds
65
Cohesion
The property of water where multiple hydrogen bonds link molecules and hold them together, contributing to high surface tension
66
Surface Tension
Measure of how difficult it is to stretch or break the surface of a liquid
67
Adhesion
The clinging of one substance to another (in this case, by water molecules)
68
Kinetic Energy
Energy of motion
69
Thermal Energy
Kinetic energy associated with the random movement of atoms or molecules
70
Temperature
Average kinetic energy of the molecules in a body of matter, regardless of volume
71
Heat
Thermal energy in transfer from one body of matter to another
72
Calorie
Amount of heat it takes to raise the temperature of 1 gram of water by 1 deg. Celsius
73
Kilocalorie
1,000 cal; the quantity of heat required to raise the temperature of 1 kg of water by 1 deg. Celsius; the "calories" found on food packaging
74
Joule
Unit of energy; one calorie equals 4.184 J
75
Specific Heat
The amount of heat a liquid must absorbed or lost for 1 gram of that substance to charge its temperature by 1 deg. Celsius
76
Heat of Vaporization
Quantity of heat a liquid must absorb for 1 gram of it to be converted from the liquid state to the gaseous state
77
Evaporative Cooling
As a liquid evaporates, the surface of the liquid that remains behind cools down
78
Solution
Liquid that is a completely homogeneous mixture of two or more substances
79
Solvent
Dissolving agent of a solution
80
Solute
Substance that is dissolved
81
Aqueous Solution
Solution in which the solute is dissolved in water
82
Hydration Shell
The sphere of water molecules around each dissolved ion
83
Hydrophilic
Any substance that has an affinity for water
84
Hydrophobic
Substances that are nonionic and nonpolar and seem to repel water
85
Molecular Mass
Sum of the masses of all the atoms in a molecule
86
Mole
Represents the number 6.02x10^23 (Avogadro's Number)
87
Molarity
The number of moles of solute per liter of solution; common unit of concentration
88
Acid
A substance that increases the hydrogen ion concentration of a solution
89
Base
A substance that reduces the hydrogen ion concentration of a solution
90
Hydrogen Ion
H+, Single proton with a charge of 1+
91
Hydroxide Ion
(OH-)
92
Hydronium Ion
(H3O+) Created after a free proton binds to a water molecule
93
pH
-log [H+]
94
Buffer
Substance that minimizes changes in the concentrations of H+ and OH- in a solution
95
Ocean Acidification
When CO2 dissolves in seawater, it reacts with water to form carbonic acid, which lowers ocean pH
96
Describe the characteristics of carbon atoms that make them uniquely suited to form the framework of biological molecules
Carbon has four valence electrons, meaning it can form covalent bonds with as many as four other atoms; can form long chains of carbon
97
List the six most common elements found in biological molecules
Hydrogen, carbon, nitrogen, oxygen, phosphorus, and sulfur
98
List the four classes of biological molecules and their building blocks
Carbohydrates & monosaccharides, lipids & fatty acids, proteins & amino acids, and nucleic acids & nucleotides
99
List reactant(s) and product(s): condensation reaction, carbohydrates
monosaccharides → disaccharide
100
List reactant(s) and product(s): hydrolysis, carbohydrates
disaccharide/polysaccharide → monosaccharides
101
List reactant(s) and product(s): condensation reaction, lipids
fatty acids + glycerol → ester bond (triglyceride with three fatty acids)
102
List reactant(s) and product(s): hydrolysis, lipids
triglycerides → glycerol + free fatty acids
103
List reactant(s) and product(s): condensation reaction, proteins
amino acids → dipeptide
104
List reactant(s) and product(s): hydrolysis, proteins
peptides → amino acids (under acidic conditions and high temperatures)
105
List reactant(s) and product(s): condensation reaction, nucleic acids
nucleotides → polynucleotides
106
List reactant(s) and product(s): hydrolysis, nucleic acids
polynucleotides → nucleotides
107
Provide two examples of human proteins and their functions
Hemoglobin, transporting oxygen in blood cells / insulin, regulating the body's energy by storing or using sugar
108
Compare and contrast the structures of sucrose and lactose
Sucrose is glucose-fructose, lactose is galactose-glucose
109
Compare and contrast which organisms synthesize sucrose and lactose
Plants, algae, and cyanobacteria synthesize sucrose; mammals synthesize lactose
110
Compare and contrast which organisms hydrolyze sucrose and lactose
Animals, bacteria, and other organisms that can produce sucrase hydrolyze sucrose; some yeast, bacteria, and mammals when they are able to produce lactase hydrolyze lactose
111
Explain the difference between lactose intolerance and lactose persistence
Lactose persistence is the lifelong production of lactase, lactose intolerance is the result of low lactase activity
112
Sketch amylose
[Unbranched glucose]
113
Sketch amylopectin
[Somewhat branched glucose]
114
Sketch glycogen
[Extensively branched glucose]
115
Relate the structure of amylose to its function
Amylose is unbranched, so it can form a helical structure that takes up less space, and is thus more efficient for energy storage
116
Relate the structure of amylopectin to its function
Amylopectin is someone branched, which means that there are more glucose molecules accessible on the end of chains, making it better for providing a rapid supply of energy
117
Relate the structure of glycogen to its function
Glycogen is extensively branched, which allows for fast energy release in muscle tissue
118
How do the beta 1-4 linkages in cellulose result in different structures and functions than polysaccharides with alpha linkages?
The beta 1-4 linkages crease an elongated, rigid structure, which is needed for maintaining the shape and rigidity of plant cell walls, where cellulose is found
119
Distinguish between the structure and function of fats and oils?
Oils molecules have a carbon-carbon double bond in the hydrocarbon chain, distorting the shape and preventing them from packing together, while fats have no double bonds. The function of both is to store energy
120
What are the advantages and disadvantages of fat as an energy storage molecule as compared to glycogen?
Fats can store six times as much energy as glycogen, but the body must expend more energy to break them down
121
Sketch and label a phospholipid
[Hydrophilic head and hydrophobic tail]
122
Sketch and label a phospholipid bilayer
[Heads on the outside and tails on the inside]
123
Relate the structure of a phospholipid to its function
The head of a phospholipid is a hydrophilic phosphate group, while the tails are hydrophobic fatty acids, causing them to automatically arrange themselves into a bilayer
124
Sketch the general structure of an amino acid
[page 75]
125
Describe the pathway of excess amino acids in body cell
Excess amino acids are converted to into fat for storage or into glucose for energy via gluconeogenesis
126
List the three categories of R-groups
Nonpolar, uncharged polar, and charged polar
127
Essential Amino Acids
Cannot be synthesized from scratch by an organism fast enough to supply its demand, and must therefore come from diet
128
Describe peptide bond formation
Amino acids are joined when the amine group of one undergoes a dehydration synthesis with the carboxylic acid of another
129
Distinguish between the alpha-helices and beta-pleated sheets in the secondary structure of proteins
Alpha-helices are just single chain polypeptides while beta-pleated sheets are composed of at least two segments of a polypeptide chain lined up together
130
Describe the relationship between the primary and tertiary structures of a protein
The tertiary structure is determined by the primary structure, because it results from interactions between the side groups
131
List the four interactions that contribute to a protein's tertiary structure
Disulfide linkages, hydrophobic interactions/van der Waals interactions, ionic bonds, and hydrogen bonds
132
Why is the tertiary structure of a protein dynamic, while the primary and secondary are not?
A protein will form a tertiary structure in the lowest-energy position possible, but there are many positions with similar energy levels, so the protein fluctuates between these similar positions; the primary structure cannot change without changing the amino acid sequence, and the secondary structure is stabilized by specific hydrogen bonding patterns that won't change (hence why they form the same structures across different proteins)
133
Describe the function of carbonic anhydrase, and how it is changed by different pH levels
Carbonic anhydrase catalyzes the buffer system converting between carbon dioxide / water and the ions of carbonic acid; low pH levels will cause it to produce more carbon dioxide and water, while high pH levels will cause it to produce more carbonic acid
134
Describe the structure of carbonic anhydrase
Zinc-containing enzyme with six alpha-helices and ten beta-sheets
135
Protein Denaturation
When the pH, salinity, temperature or other aspects of a protein's environment are altered, the weak chemical bonds and interactions within a protein may be destroyed, causing the protein to unravel and lose its native shape, rendering it biologically inactive
136
Compare and contrast galactosemia and lactose intolerance
Galactosemia is an inability to break down galactose, causing potentially fatal harm, while lactose intolerance is a result of decreased lactase production, causing discomfort
137
What are the three components of nucleotides?
Nitrogenous base, a pentose sugar, and a phosphate
138
What are the structural differences between ribonucleotides and deoxyribonucleotides?
Ribonucleotides have a ribose sugar (hydroxyl group at the second carbon), deoxyribonucleotides have a deoxyribose sugar (hydrogen atom at the second carbon)
139
Sketch and label the parts of a helical DNA
[Sugar-phosphate backbone, nitrogenous base pairs, hydrogen bonds]
140
Describe the relationship between DNA, RNA, and protein
DNA contains protein-encoding information, RNA uses that information to enable to the cell to synthesize a protein
141
Sketch a model of ATP
[Triphosphate group, ribose, and adenine]
142
What is ATP's role as the energy currency in cells?
ATP stores energy in bonds linking the phosphate groups, meaning energy is released when a phosphate group is removed via hydrolysis
143
Organic Chemistry
The study of compounds containing carbon
144
What did the Miller-Urey Experiment demonstrate?
Organic molecules may have been synthesized abiotically on the earth Earth
145
How many single covalent bonds can carbon form?
4
146
Valence
The number of covalent bonds an atom can form
147
Hydrocarbons
Organic molecules consisting of only carbon and hydrogen
148
Isomers
Compounds that have the same numbers of atoms of the same elements but different structures and hence different properties
149
Functional Groups
Chemical groups directly involved in chemical reactions
150
Hydroxyl Group
(-OH)
151
Carbonyl Group
(>C=O)
152
Carboxyl Group
(-COOH)
153
Amino Group
(-NH2)
154
Sulfhydryl Group
(-SH)
155
Phosphate Group
(-OPO3^2-)
156
Methyl Group
(-CH3)
157
Macromolecules
Large carbohydrates, protein, and nucleic acids that are polymers
158
Polymer
Long molecule consisting of many similar or identical building blocks linked by covalent bonds
159
Monomers
Repeating units that serve as the building blocks of polymers
160
Enzymes
Specialized macromolecules (usually proteins) that speed up chemical reactions
161
Hydrolysis
Process that reverses a dehydration reaction by disassembling polymers into monomers
162
Dehydration Reaction
Condensation reaction (connects a monomer to another monomer or a polymer) that involves a water molecule being lost
163
Carbohydrates
Sugars and polymers of sugars
164
Monosaccharides
Monomers from which more complex carbohydrates are built; contain a carbonyl group and multiple hydroxide groups
165
Glucose
Most common monosaccharide
166
Disaccharide
Two monosaccharides joined by a glycosidic linkage
167
Polysaccharide
Polymers with a few hundred to a few thousand monosaccharides joined by glycosidic linkages
168
Starch
Polymer of glucose monomers used by plants for storage
169
Glycogen
Polymer of glucose that is used by animals for storage
170
Cellulose
Structural polysaccharide used by plants in the construction of cell walls; glucose polymer
171
Chitin
Structural polysaccharide used by arthropods to build exoskeletons
172
Lipids
Group of compounds that are hydrophobic
173
Fat
Glycerol molecule joined to three fatty acids
174
Fatty Acid
Long carbon skeleton, usually 18 or 18 carbon atoms in length; the carbon at the end of the skeleton is part of a carboxyl group
175
Saturated Fatty Acid
Fatty acid with a hydrocarbon chain that contains no double bonds between carbon atoms, usually solid a room temperature
176
Unsaturated Fatty Acid
Fatty acid with a hydrocarbon chain that has one or more double bonds, usually liquid at room temperature
177
Trans-Fats
Produced during hydrogenation of vegetable oils, solidifying the oil
178
Phospholipid
Two fatty acids attached to a glycerol and a phosphate group, major components of cell membranes
179
Cholesterol
Common component of animal cell membranes and the precursor from which other steroids are synthesized
180
Catalysts
Chemical agents that selectively speed up chemical reactions without being consumed in the reaction
181
Polypeptide
Polymer of amino acids
182
Protein
Biologically functional molecule made up of one or more polypeptides, each folded and coiled into a specific three-dimensional shape
183
Peptide Bond
Covalent bond joining the carboxyl group of one amino acid to the amino group of another amino acid via a dehydration reaction
184
Amino Acid
Organic molecule with both an amino group and a carboxyl group
185
Methionine
Beginning of every amino acid sequence in protein synthesis
186
Receptor Proteins
Allow cell to respond to chemical stimuli
187
Structural Proteins
Support the cell
188
Contractile and Motor Proteins
Allow for movement within cells
189
Transcription Factors
Proteins that control the rate of transcription of genetic information from DNA to mRNA by binding to a specific DNA sequence
190
Protein Structure
Three-dimensional architecture of proteins
191
Primary Protein Structure
A protein's sequence of amino acids
192
Secondary Protein Structure
Coils and folds in a polypeptide chain that are the result of hydrogen bonds between the repeating constituents of the polypeptide backbone
193
Tertiary Protein Structure
The overall shape of a polypeptide resulting from interactions between the side chains of the various amino acids
194
Quaternary Protein Structure
The overall protein structure that results from the aggregation of two or more polypeptide chains
195
Gene
Discrete unit of inheritance consisting of DNA
196
Nucleic Acids
Polymers made of monomers called nucleotides
197
Deoxyribonucleic Acid
Type of nucleic acid that provides directions for its own replication and also directs RNA synthesis
198
Ribonucleic Acid
Type of nucleic acid that controls protein synthesis
199
Nucleotides
Composed of a five-carbon sugar (pentose), a nitrogen containing (nitrogenous) base, and one to three phosphate groups
200
Pyrimidine
Family of nitrogenous bases containing a six-membered ring of carbon and nitrogen atoms (cytosine, thymine, and uracil)
201
Purine
Family of nitrogenous bases containing a six membered ring fused to a five-member ring (adenine and guanine)
202
Double Helix
The form taken by the two polynucleotides (strands) that wind around an imaginary axis to form a DNA molecule
203
Antiparallel
The arrangement of the two sugar-phosphate backbones which run in opposite 5' → 3' directions from each other
204
Bioinformatics
The use of computer software and other computational tools to analyze large data sets
205
Geonomics
The process of looking at problems by analyzing large sets of genes or comparing whole genomes of different species
206
Proteomics
Analysis of large sets of proteins, including their sequences
207
eDNA
Environmental DNA, can be extracted from an ecosystems to determine the organisms living there
208
Enantiomers
Isomers that are mirror images of each other
209
What's the difference between cis and trans isomers?
Cis isomers have the same connectivity of atoms on both sides of the molecule, while trans isomers have the same side groups on opposite sides of the molecule
210
Peptidoglycan
Structural carbohydrate in bacterial cell walls
211
Sterols
Base template for the production of steroids
212
Selfish Element
Parts of a protein that do not naturally occur, but if introduced, are able to remain, despite being a burden to the cell
213
N-Terminus
Amino end of a polypeptide
214
C-Terminus
Carboxyl end of a polypeptide
