1
Q
What four elements make up ~96% of cell mass?
A
Carbon (C), Hydrogen (H), Oxygen (O), and Nitrogen (N)
2
Q
Why is carbon the basis of life rather than silicon?
A
1) Si bonds are unstable in water, 2) Si doesn’t like making bonds with itself or double bonds, 3) Si-O bonds form stable solids (rocks) that are hard to break
3
Q
How many covalent bonds can carbon form and why?
A
4 covalent bonds, because carbon has 4 unpaired valence electrons
4
Q
What is a nonpolar covalent bond?
A
A bond where electrons are shared equally between atoms (e.g., C-C, C-H bonds). Creates ‘non-stick’ molecules with no partial charges.
5
Q
What is a polar covalent bond?
A
A bond where electrons are shared unequally due to differences in electronegativity. Creates partial charges (o+ and o-) and makes molecules ‘sticky.’
6
Q
Which element is most electronegative: C, H, or O?
A
Oxygen (O = 3.44), followed by nitrogen (N = 3.04), carbon (C = 2.55), then hydrogen (H = 2.20)
7
Q
What is an ionic bond?
A
A bond where electrons are completely transferred from one atom to another, creating charged ions (cation + and anion -)
8
Q
Are ionic bonds strong or weak in water?
A
Weak in water (water molecules surround and separate the ions), but strong in air
9
Q
What is a hydrogen bond?
A
A weak attraction between a + hydrogen (bonded to O or N) and a o- atom (usually O or N) on another molecule
10
Q
What must exist before a hydrogen bond can form?
A
Polar covalent bonds (creating partial charges on H and O/N)
11
Q
What are Van der Waals interactions?
A
Very weak, brief attractions caused by temporary charge imbalances as electrons move around atoms
12
Q
Rank these bonds from strongest to weakest:
A
Covalent > Ionic (in air) > Hydrogen bonds > Van der Waals interactions
13
Q
What are functional groups?
A
Chemical groups that replace hydrogens on carbon skeletons and confer unique properties (polarity, reactivity, shape)
14
Q
Name three common functional groups:
A
Hydroxyl (-OH), carboxyl (-COOH), amino (-NH2), phosphate (-PO4), methyl (-CH3)
15
Q
Why is water a polar molecule?
A
Oxygen is more electronegative than hydrogen, creating o- on oxygen and + on hydrogens
16
Q
What is cohesion?
A
Water molecules ‘sticking’ to each other through hydrogen bonds
17
Q
What is adhesion?
A
Water molecules ‘sticking’ to other surfaces through hydrogen bonds
18
Q
What is specific heat?
A
The amount of energy needed to change the temperature of 1 g of a substance by 1°C
19
Q
What is water’s specific heat and why is it high?
A
4.2 J/g-°C. High because hydrogen bonds allow water molecules to move (gain kinetic energy) without breaking apart, so water stores thermal energy without large temperature changes.
20
Q
What is evaporative cooling?
A
When the fastest-moving (highest kinetic energy) molecules evaporate, the average kinetic energy (temperature) of remaining molecules decreases.
21
Q
Why does ice float?
A
Ice is less dense than liquid water because hydrogen bonds form a regular crystal structure that spreads molecules farther apart.
22
Q
What does ‘versatile solvent’ mean for water?
A
Water can dissolve many substances, especially polar and charged molecules (hydrophilic substances).
23
Q
What is a hydrophobic substance?
A
A substance with mostly nonpolar bonds that cannot form hydrogen bonds with water (e.g., oils, fats, hydrocarbons).
24
Q
What are hydrophobic interactions?
A
When nonpolar molecules aggregate together in water because they are excluded by water molecules that hydrogen-bond to each other.
25
What is pH?
pH = -log[H+]. A measure of hydrogen ion concentration in solution.
26
What is the pH of pure water?
pH 7 (neutral), where [H+] = [OH-] = 10^-7 M.
27
If pH decreases by 1 unit, how much does [H+] change?
[H+] increases 10-fold (and [OH-] decreases 10-fold).
28
What is the relationship between [H*] and [OH-]?
[H*][OH-] = 1 x 10^-14 M (always!)
29
What is an acid?
A substance that donates H° to solution (increases [H*], lowers pH)
30
What is a base?
A substance that accepts H° from solution (decreases [H*], raises pH)
31
What is a buffer?
A compound that reversibly donates or accepts H* depending on conditions, resisting pH changes
32
Give an example of a biological buffer system:
Carbonic acid (H2CO3) - bicarbonate (HCO3-) buffer system in blood (maintains pH 7.35-7.45)
33
Do organic acids (carboxyl groups) donate or accept H° at pH >7?
Donate H° (act as acids)
34
Do organic bases (amino groups) donate or accept H* at pH <7?
Accept H* (act as bases)
35
What is a polymer?
A long molecule consisting of many similar building blocks (monomers) linked end-to-end by covalent bonds
36
What is a monomer?
A smaller, repeating molecule that serves as a building block for polymers
37
Name the three types of biological polymers:
Carbohydrates, proteins, and nucleic acids (NOT lipids!)
38
What is a dehydration reaction?
A reaction that joins two monomers by removing H,O. Used to build polymers. Endergonic (requires energy).
39
What is a hydrolysis reaction?
A reaction that breaks polymers into monomers by adding H,O. Used to break down polymers. Exergonic (releases energy).
40
Do enzymes catalyze dehydration and hydrolysis reactions?
Yes! Both reactions require enzymes to occur efficiently.
41
What is the general formula for carbohydrates?
(CH,O), - they contain carbon, hydrogen, and oxygen.
42
What is a monosaccharide?
A simple sugar (single sugar unit).
## Footnote
Example: glucose (C,H,,°.)
43
What is a disaccharide?
Two monosaccharides linked by a glycosidic bond.
## Footnote
Examples: maltose, sucrose, lactose.
44
What is a glycosidic bond?
The covalent bond linking sugar molecules, named by the carbons involved (e.g., 1,4 or 1,2).
45
What is the difference between a and f glycosidic bonds?
a-bond: hydroxyl on C1 points DOWN; ß-bond: hydroxyl on C1 points UP.
46
What is a polysaccharide?
Many monosaccharides linked together by glycosidic bonds.
47
What are the main energy storage polysaccharides?
Starch (plants) and glycogen (animals) - both have a (1→4) linkages.
48
Why is glycogen more branched than starch?
More branching allows faster mobilization of glucose for quick energy needs in animals.
49
What is cellulose and what is it used for?
A structural polysaccharide with ß(1→4) linkages. Found in plant cell walls, provides rigidity, is dietary fiber.
50
Why can't humans digest cellulose?
We lack the enzyme to break ß(1→4) glycosidic bonds.
51
Can we digest starch and glycogen?
Yes! We have enzymes that break α(1→4) glycosidic bonds.
52
What are glycoproteins and glycolipids?
Carbohydrates covalently linked to proteins or lipids on cell surfaces.
53
What is the 'sugar code'?
The molecular diversity of surface carbohydrates that acts as unique signatures for cell recognition (e.g., blood types).
54
Are lipids polymers?
No! They are not formed by end-to-end linkages like other macromolecules.
55
What is the unifying feature of lipids?
They are hydrophobic (have little or no affinity for water) because they consist mostly of nonpolar C-C and C-H bonds.
56
What are the three main types of lipids?
Fats (triglycerides), phospholipids, and steroids.
57
What does amphipathic mean?
Having both hydrophobic and hydrophilic regions.
58
Are fatty acids amphipathic?
Yes! They have a hydrophilic carboxyl head (-COOH) and a hydrophobic hydrocarbon tail.
59
What is a saturated fatty acid?
A fatty acid with NO C=C double bonds. Carbons are 'saturated' with hydrogens. Straight, tightly packed, solid at room temp.
60
What is an unsaturated fatty acid?
A fatty acid with one or more C=C double bonds. Creates kinks, prevents tight packing, liquid at room temp.
61
Give examples of saturated fats:
Animal fats (butter, lard).
62
Give examples of unsaturated fats:
Plant oils (olive oil) and fish fats.
63
What is a triglyceride (fat)?
Glycerol + 3 fatty acids joined by ester linkages (formed by dehydration).
64
Are triglycerides hydrophobic or hydrophilic?
Completely hydrophobic (no strongly polar bonds).
65
What is the main function of fats?
Energy storage (store more energy per gram than carbohydrates), insulation, cushioning organs.
66
What are essential fatty acids?
Specific unsaturated fatty acids (like omega-3s) that humans cannot synthesize and must obtain through diet.
67
Are trans fats healthy?
No! Trans fats are associated with ~278,000 deaths per year and behave like saturated fats in the body.
68
What is a phospholipid?
Glycerol + 2 fatty acids + phosphate group (with additional polar groups).
69
Are phospholipids amphipathic?
Yes! Hydrophilic head (phosphate group) and hydrophobic tails (fatty acids)
70
What happens when phospholipids are added to water?
They spontaneously self-assemble into bilayers with heads facing water and tails facing each other
71
What is the main function of phospholipids?
Major component of all cellular membranes
72
How does saturation affect membrane fluidity?
More unsaturated fatty acids = more fluid (kinks prevent tight packing and Van der Waals interactions)
73
How does cholesterol affect membrane fluidity?
Acts as a fluidity buffer: reduces fluidity at high temps (restrains movement) and increases fluidity at low temps (disrupts tight packing)
74
What is the structure of steroids?
Four fused carbon rings (3 cyclohexane + 1 cyclopentane)
75
Give examples of steroids:
cholesterol, estrogen, testosterone, cortisol
76
What is cholesterol's role in membranes?
Essential component of animal cell membranes, helps regulate fluidity
77
Can steroid hormones pass through membranes easily?
Yes! They are mostly hydrophobic so they can cross lipid bilayers directly
78
How many different amino acids are used to build proteins?
20
79
What are the four components of an amino acid?
1) a-carbon (central), 2) amino group (NH2), 3) carboxyl group (COO-), 4) R-group (side chain)
80
At physiological pH (~7.4), what is the charge on the amino group?
Positive (NH3+) - it's ionized and acts as a base
81
At physiological pH (~7.4), what is the charge on the carboxyl group?
Negative (COO-) - it's ionized and acts as an acid
82
What determines the properties of an amino acid?
The R-group (side chain)
83
What are the four categories of amino acids based on R-groups?
1) Nonpolar (hydrophobic), 2) Polar uncharged, 3) Acidic (negatively charged), 4) Basic (positively charged)
84
Give examples of nonpolar amino acids:
Glycine, alanine, valine, leucine, isoleucine, methionine, phenylalanine, tryptophan, proline
85
Give examples of polar uncharged amino acids:
Serine, threonine, cysteine, asparagine, glutamine, tyrosine
86
Give examples of acidic amino acids:
Aspartate and glutamate (negatively charged at pH 7.4)
87
Give examples of basic amino acids:
Lysine, arginine, histidine (positively charged at pH 7.4)
88
What is a peptide bond?
A covalent bond linking amino acids, formed by dehydration between the amino group of one AA and carboxyl group of another
89
What catalyzes peptide bond formation?
Ribosomes (specifically, an RNA molecule in the ribosome - a ribozyme!)
90
What is a polypeptide?
A single polymer chain of amino acids linked by peptide bonds
91
What is the N-terminus?
The amino end of a polypeptide (has free NH₂ group)
92
What is the C-terminus?
The carboxyl end of a polypeptide (has free COO⁻ group)
93
In what direction is a polypeptide sequence written?
N-terminus → C-terminus
94
What is primary structure?
The unique linear sequence of amino acids in a polypeptide
95
What bonds create primary structure?
Covalent peptide bonds
96
What determines primary structure?
DNA sequence (genetic information)
97
What is secondary structure?
Local folding patterns: α-helices (coils) and β-pleated sheets (folds)
98
What bonds stabilize secondary structure?
Hydrogen bonds between backbone atoms (C=O and N-H), NOT between R-groups
99
What is tertiary structure?
The overall 3D shape of a single polypeptide
100
What interactions determine tertiary structure?
Interactions between R-groups: H-bonds, ionic bonds, Van der Waals, hydrophobic interactions, and disulfide bridges (S-S)
101
What is a disulfide bridge?
A covalent bond between two cysteine R-groups (S-S bond)
102
Where are disulphide bridges is more common?
In extracellular proteins where conditions are more challenging
103
What is quaternary structure?
When a functional protein consists of multiple peptide chains
104
What hold quaternary structures together?
Non covalent interactions (H-bonds, ionic, Van der Waals, hydrophobic) and sometimes disulfide bridges
105
Give an example of a protein with quaternary structure
Hemoglobin
106
What is protein denaturation?
Unfolding of a protein due to disruption of noncovalent bonds (from extreme pH, temperature, or salt)
107
Is primary structure affected by denaturation?
No! Peptide bonds remain intact. Only noncovalent interactions are disrupted
108
Can denatured proteins refold?
Often yes, if conditions return to normal (renaturation)
109
How do hydrophobic forces influence tertiary structure?
Non-polar R-groups cluster together in the protein’s interior (away from water), while polar R-groups are on the surface
110
What is sickle cell disease caused by?
A single amino acid change in hemoglobin (glutamate -> valine), changing protein structure and function
111
List seven major functions of proteins
Enzymes (catalysis), structural support, transport, storage, signaling, motion, defence (antibodies)
112
Give an example of transport protein
Aquaporin (transports water), hemoglobin (transports O2)
113
Give an example of a storage protein
Ferritin (stores iron), ovalbumin (egg white)
114
Give an example of a structural protein
Collagen (connective tissue), keratin (hair/nails)
115
Give an example of a motion generating protein
Myosin (muscle contraction), kinesin (intracellular transport)
116
What is an enzyme?
A protein (or RNA) that catalyzes a specific chemical reaction
117
What is a catalyst?
Something that speeds up a reaction without being consumed
118
Can one enzyme catalyze a reaction multiple times
Yes! Enzymes are reusable
119
What is a substrate?
The molecule(s) that an enzyme acts on
120
What is a metabolic pathway?
A series of enzyme-catalyzed reactions where the product of one reaction becomes the substrate for the next
121
What is activation energy (EA)
The energy barrier that must be overcome for reaction to occur
122
How do enzymes speed up reaction reactions
They lower the activation energy
123
What is an exergonic reaction
A reaction where products have lower free energy than reactants, releases, energy, spontaneous
124
What is an endergonic reaction
A reaction where products have higher free energy than reactants, requires energy input
125
Do exergonic reactions still need enzymes?
Yes! Even though they’re spontaneous, they need enzymes to lower EA and occur at useful rates
126
How are endergonic reactions driven forward in cells?
By coupling them to ATP hydrolysis (which is strongly exergonic)
127
What is the active site
The region of an enzyme where substrates bind and catalysis occurs
128
List three ways enzymes lower activation energy
Bring substrates together (proximity), orient substrates correctly, strain/distort bonds to make them easier to break, provide catalytic amino acids
129
What is catabolism
Breaking down large molecules into smaller ones (usually exergonic, hydrolysis reactions)
130
What is anabolism?
Building large molecules from smaller ones (usually endergonic, dehydration reactions)
131
What is metabolism?
All catabolic and anabolic reactions in an organism
132
What is the fluid mosaic model
A model describing membranes as a fluid lipid bilayer with a “mosaic” of embedded proteins
133
What holds membrane components together?
Weak hydrophobic interactions and Van der Waals forces (not covalent bonds!)
134
Can lipids move within membranes
Yes! They move laterally (side to side) very easily
135
Do lipids flip-flop across membranes easily
No! Transverse movement (flip-flops) is very rare because the hydrophilic head must cross the hydrophobic core
136
What is membrane fluidity?
The ability of lipids and some proteins to move laterally within membrane
137
Why must membranes be fluid?
To function properly as selective barriers, and allow protein movement
138
What happens to membrane fluidity at low temperatures?
Decreases (membrane can solidify like butter)
139
What happens to membrane fluidity at high temperatures?
Increases (membrane becomes too fluid)
140
How does fatty acid saturation affect fluidity?
More saturated = less fluid (straight tails pack tightly with strong Van der Waals forces); More unsaturated = more fluid (kinked tails can’t pack tightly)
141
How does cholesterol affect membrane fluidity?
Acts as a buffer: restrains movement at high temps (decreases fluidity) and disrupts tight packing at low temps (increases fluidity)
142
How do cold water fish adapt their membranes
Higher proportion of unsaturated phospholipids to maintain fluidity in cold
143
How do heat-loving bacteria adapt their membranes
Higher proportion of saturated phospholipids to prevent excessive fluidity
144
What is selective permeability?
Some substances cross membranes easily while others cannot
145
What molecules can cross membranes without proteins
Small nonpolar molecules (O2, CO2, N2), hydrocarbons, steroid hormones
146
What molecules cannot cross membranes without proteins
Ions (Na+, K+, Cl-), polar molecules (glucose, amino acids), large molecules
147
What is an integral membrane protein?
A protein embedded in the membrane
148
What is a transmembrane protein
An integral protein that spans the entire membrane
149
What type of amino acids are found in membrane-spanning regions?
Nonpolar/hydrophobic amino acids
150
What is a peripheral membrane protein?
A protein attached to the membrane surface (not embedded)
151
List six functions of membrane proteins
Transport, enzymatic activity, signal transduction, cell recognition, intercellular joining, attachment to cytoskeleton
152
What is passive transport
Movement of substances down their concentration gradient (high->low), no energy required
153
What is facilitated diffusion?
Passive transport, assisted by transport proteins (down concentration gradient)
154
What is active transport?
Movement of substances against their concentration gradient (low->high), requires energy (ATP)
155
Give an example of a channel protein
Aquaporin ( creates a pore for water to pass through)
156
At equilibrium, does movement across membranes stop?
No! Molecules still move, but there’s no NET movement in either direction
bio 1001
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