Biology 150 Exam 1

Study Guide
Chapter 2.1: Atoms, Ions, and Molecules
The Building Blocks of Chemical Evolution
 C, H, N, and O makes up 96% of all matter
 Two fundamental questions in biology:
o What is the physical structure of these atoms found in living cells?
o What is the structure of simple molecules that serve as building blocks?
 Structure affects function
 Dalton – special unit used for subatomic particles (equal to about 1 neutron/proton)
 Electronegativity: O > N > C ~= H
o C-H nonpolar covalent bond
o O-H polar covalent bond
o Na-Cl ionic bond
 Representations of molecules:
o Molecular formulas (CH4)
o Structural formulas (O=C=O)
o Ball-and-stick models (3D shape, size of atoms)
o Space-filling nodes (most accurate)
 Most simple chemicals are made in AQUEOUS environments

Chapter 2.5: The Importance of Organic Molecules

 Carbon is super important because of its versatility
o 4 valence electrons  can form covalent bonds with itself easily
o Chain or ring formation increases diversity
 Functional groups to know:
 Amino and carboxyl:
o Tend to attract or drop a proton in
solution
o Amino = bases, carboxyl = acids
o Both in amino acids which are very
important
 Also participate in hydrogen
bonding
 Carbonyl:
o Site of reactions that link aldehyde
and ketone molecules in larger,
complicated compounds
 Hydroxyl:
o Act as weak acids usually source for
protonation
o Polar, so soluble in water
 Phosphate:
o Carry two negative charges
o Change in charge when transferred
can alter structure/function of
recipient molecule (signaling!)
o ATP relationship
 Sulfhydryl:
o Can link to another through
disulfide (S-S) bonds  protein
folding
 Dipole (or dipole moment)
o Molecule in which concentration of
(+) is separated by concentration of
(-)
 Moeity
o A part of a whole, building block
o E.g. a subunit of a polymer
 Functional group modify the properties of carbon skeletons, especially in aqueous
solutions (which is the primary conditions of life!)
Chapter 2.2: Properties of Water and the Early
Oceans
 Water is an excellent solvent, or agent for dissolving substances and getting them into
solution
o Why is it so efficient?
 Both of the O-H bonds are polar
 Bent geometry
 ^both of these factors result in a polar molecule
 Hydrophilic – ions and polar molecules
 Hydrophobic – nonpolar, lipids
 Properties of H2O:
o Small size
o Highly polar covalent bonds
o Bent shape
o Leads to…
 Cohesion: attraction between like molecules (water and water)
 Adhesion: attraction between unlike molecules (water and solid)
 Surface tension: cohesion means when water molecules are at the surface,
there are no water molecules above them for H-bonding  exhibit
stronger attractive forces between nearest neighboring molecules
 Water resists any force that increases its surface area
 Denser as a liquid than as a solid (unique to water)
 In ice, form crystal lattice
 In water, no crystal lattice, more packed together
 This is why ice floats in water!
 High capacity for absorbing energy
 High specific heat due to H-bonding
 High heat of vaporization due to H-bonding (evaporative cooling)
 Water in Acid-Base Reactions
o H2O  H+ + OH-
o pH buffers – needed for homeostasis (CH2O3  CHO3- + H+)
o Carbon is always tetrahedral
o Oxygen and nitrogen always at angle  contributes to region’s bonds
 Nonpolar interactions w/ water
o Fats and oils form droplets in H2O
o Cell membrane has a nonpolar zone
 Solid barrier
 Nonpolar bonds = more chemical energy
o Fats and oils have the most stored energy
 Water’s polar nature
o Ice’s density, evaporative cooling, adhesion
  Solubility and pH  important properties to understand
o More polar bond = more soluble
o More polar bonds = less likely to cross cell membrane unaided
 Interactions between polar bonds give molecules 3D shapes
o Main point of unit 2
 Functional groups are important for how they interact
o How proteins fold
o Hold DNA together
o Enzymes + substrates
o How changing one functional group can have devastating consequences
 Functional groups affect the way molecules behave
o There are two carbonyl groups on this molecule contributing to polarity of the
molecule  soluble in H2O
o The oxygens in these groups have a partially negative charge
 We don’t build things to last with ionic bonds because they break very easily in H2O,
which is solvent everything is in

Chapter 2.3: Chemical Reactions, Energy, and

Chemical Evolution
 Simple molecule present in the atmosphere and oceans of early Earth participated in
chemical reaction that eventually produced large, more complex organic molecules
(a.k.a. proteins, nucleic acids, sugars, and lipid)
 Two environments for these reactions:
o Atmosphere
 Dominated by volcano puke
 H2O(g), CO2, N2
 Small amount of H2 and CO
o Dep-sea hydrothermal vents
 Really hot rocks contact deep cracks on seafloor
 CO2 and H2 gas
 Rich in mineral containing reactive metals
 Ni, Fe
 When CO2, N2, H2, CO mingle  very little happens (no hookups)
 Energy: capacity to do work or supply heat
 Stored energy = potential energy
o e- on outer electron shell = greater potential energy than e- on inner shell
 Kinetic energy of molecular motion = thermal energy, measure of how much an object
has = temperature
 First law of thermodynamics: energy is conserved, neither created nor destroyed
 Spontaneity is determined by:
 o Reactions tend to be spontaneous when the product molecules are less ordered
than the reactant molecules (tends to entropy/chaos) – second law of
thermodynamics
o Reactions tend to be spontaneous if the products have lower potential energy
than the reactants
 Summary: physical and chemical processes proceed in the direction that results in
increased entropy and lower potential energy

Chapter 2.4: Investigating Chemical Evolutions:

Approaches and Model Systems
 “Top down” and “bottom up” approaches
o Top down = researchers examine modern cells to identify chemistry that’s shared
throughout tree of life; ancient reactions are possibly involved in evolution that
led to LUCA (last universal common ancestor)
o Bottom up = primarily focus on small molecules and environmental conditions
present in early Earth; attempt to identify reactions that could build molecules
found in life using only what was available at the time
 Two different model systems:
o Prebiotic soup model = certain molecules were synthesized from gases in the
atmosphere or arrived via meteorites; afterwards, condensed with rain,
accumulated in oceans, resulting in an “organic soup”
o Surface metabolism model = dissolved gases came into contact with minerals
lining the walls of deep-sea vents and formed more complex, organic molecules
 Stanley Miller’s 1953 experiment – CH3, NH3, H2, tiny amount of liquid water, and
electric shocks
o Miller’s results came under fire when others pointed out that early atmosphere
dominated by CO, CO2, and H2, not methane and ammonia in experiment
o Followup experiments: formaldehyde synthesis
 CO2(g) + 2H2(g)  CH2O(g) + H2O(g)
 Nonspontaneous – requires a lot of energy
o New model: CO2, H2O, N2, CO, H2 and reactions that occur with sunlight
 Sunlight made up of photons, or packets of light energy
 Photons break up molecules into free radicals = extremely reactive!
 Complete reaction:
 CO2(g) + 2H2(g) + sunlight  CH2O(g) + H2O(g)
 HCN could also have been produced early on
 Surface metabolism model explains dilution effect of formaldehyde and HCN in early
oceans – localized concentration in vents
o Not only would vent-wall minerals be reactants together, but they’d also be
critical to rate at which reaction products are formed (catalysts!)
o 2CO2(aq) + 4H2(aq)  CH3COOH(aq) + 2H20(l)
  Acetic acid can be formed under conditions that stimulate a hydrothermal
vent environment
 Key intermediate in pathway for acetyl CoA, which is kinda the main
freaking thing you need for metabolism!

Recitation Notes: Changing pH to Changes in

Charge
 A + B  AB
 H2O  H+ + OH- 1. Reversible chemical reactions reach an equilibrium (no net change
in concentrations)
 In pH = 7:
o R-NH3+
o COO-
 In acidic conditions (pH < 7):
o R-NH3+
o COO- becomes protonated  COOH
 In basic conditions (pH > 7):
o R-NH3+ becomes deprotonated  R-NH2
o COO-

Chapter 3.1: Amino Acids and their

Polymerization
 Non-ionized amino acid

 Ionized amino acid

 Notable components of an amino acid: amino group, hydrogen atom, carboxyl group, R
group (side hoe chain)
 Why do we care about these charges?
o Help amino acids stay in solution, so they can interacts with each other and with
other solutes
o Affect amino acid’s chemical reactivity
 The Nature of Side Hoes Chains
o R-group variability accounts for the properties unique to each amino acid
 Within these groups are functional groups, which, under the right
settings (*wink*), can participate in chemical reactions
 The polarity of these chains affect solubility
 Nonpolar – hydrophobic – tend to coalesce in aqueous conditions
 Polar – hydrophilic – dissolve in water easily
 Type of amino acid – the signs to look for:
o Side chain = (-)  acidic (will receive a H+)
o Side chain = (+)  basic (will donate a H+)
o Side chain = no charge  depends!
 Has an oxygen  uncharged polar
 Nah?  nonpolar amino acid
 How do they hook up doe?
o Monomers link up to form polymers  polymerization
o Macromolecule  basically an orgy
o Polymerization is NOT spontaneous (increasing order in molecule!)
o Condensation/dehydration = polymerization
 Endergonic
 Water is produced  condensation
o Hydrolysis = de-polymerization
 Exergonic
 Water is removed, lysing of water
 The peptide bond
o C-N covalent bond that results from condensation to link amino acids together
 Three key points to note about the peptide-bonded backbone:
o R-group orientation
 Side chains extend out from the backbone, making it possible for them to
interact with each other and with water
o Directionality
 Amino group on one end, carboxyl group on the other
 N-terminus/amino-terminus
 C-terminus/carboxy-terminus
 Always write amino acid sequences from the N-terminus to C-
terminus
 o Why? The N-terminus is the start of chain when proteins
are made in biological cells!
o Flexibility
 Peptide bond can’t rotate because of its double bonded-ness, but single
bonds surrounding it can!
 Some more sexy terminology!
o Oligopeptide = <50 amino acids in chain (“few”)
o Polypeptide = >50 amino acids in chain (“many”)

Chapter 3.2: What Do Proteins Look Like?

 Proteins are involved in errthang because they’re diverse
 Example – TATA box-binding protein – testament to the most important thing to
remember
 Four level of organization:
o 1° – Primary Structure
 Unique sequence of amino acids in a protein
o 2° – Secondary Structure
 Hydrogen bonding between components of the peptide-bonded backbone
 Only when a polypeptide bends in a way that puts C=O and N-H
groups close together
 α- helix – polypeptide’s backbone is coiled

 β-pleated sheet – segments of a peptide chain bend 180° and then

fold in the same plane
o 3° - Tertiary Structure
 Interactions between R-groups or between R-groups and the backbone
 Five types of interactions matter:
 H-bonding
o Between polar R-groups and opposite partial charges in
either backbone or other R-groups
 Hydrophobic interactions
o In solution, hydrophobic nonpolar side chains coalesce into
globular masses
o Same as Van der Waals
 Van der Waals interactions
o Between hydrophobic nonpolar side chains, weak
attractions result in a tiny asymmetry in charge that
changes with time
o Can increase stability of structure
 Covalent bonding
o Disulfide bonds = bridges
 Ionic bonds
 o 4° - Quaternary Structure
 Combination of polypeptide interactions
o Each structure based on the ones before it

Chapter 3.3: Folding and Function

 Denaturation
 Molecular chaperones – heat shock proteins, protect body’s proteins from denaturing at
high temperatures
 Protein shape is flexible
o Often regulated – calmodulin
o Prions – misfolding can be infectious

Chapter 3.4: Proteins are the Most Versatile

Macromolecules in Cells
 So what do proteins do? Well, a lot!
1. Catalysis
2. Defense
3. Movement
4. Signaling
5. Structure
6. Transport
 Why are enzymes good catalysts?
 Substrates are brought together
 Was the first living entity a protein catalyst?
 Nah, bro

Chapter 8.1: What Happens to Energy in

Chemical Reactions?
 Free energy, bitch
 Chemical reactions involve energy transformations! *
o First law of thermodynamics – conservation of energy
o Enthalpy (H) = total energy in a molecule
 Includes potential energy of the molecule (a.k.a. heat content) plus the
effect of the molecule on its surrounding in terms of pressure and volume
o Change in enthalpy (ΔH) determines if…

 ΔH is (-)  reaction is exothermic

 ΔH is (+)  reaction is endothermic

 o Entropy (ΔS) = amount of disorder
 Second law of thermodynamics: total entropy always increases in a closed
system
 Gibb’s free-energy change (ΔG)

o ΔG = ΔH – TΔS

 ΔG is (-)  reaction is exergonic

 ΔG is (+)  reaction is endergonic

 ΔG is 0  reaction is at equilibrium
 Temperature and concentration rate affect reaction rates

Chapter 8.2: Nonspontaneous Reactions May Be

Driven Using Chemical Energy
 Energetic coupling: allows endergonic reactions to proceed using the energy released
from exergonic reactions
 Redox reactions transfer energy via electrons
o OIL RIG
o Glucose + O2  CO2 + H2O + energy
o Electrons travel from e- donor to e- acceptor
 FADH2 = e- carrier, FAD = e- acceptor
 NAD+ = e- carrier, NADH = e- acceptor
o Not always a transfer of hydrogens!
 ATP – adenosine trisphosphate
 Kilocalorie (kcal) = raises 1 kg of water 1° C
 Hydrolysis of ATP releases free energy
 Used for transferring cleaved PO4 to substrate  phosphorylation

Chapter 8.3: How Enzymes Work

 Enzymes help reactions clear two hurdles
 Reactants need to
1. Collide in a precise orientation
2. Have enough kinetic energy to overcome repulsion between electrons that come
into contact as a bond forms
 The key is enzymes’ active sites
 Enzymes are flexible and dynamic
1. Induced fit
 Activation energy needed to achieve transition state (instability)
 Reactions happen when reactants have enough kinetic energy to reach the transition
state
1. Kinetic energy, in turn, is a function of molecules’ temperature
2. Reaction rates depend on both the kinetic energy of the reactants and the
activation energy of the particular reaction
 Catalysis is a three step process:
1. Initiation
 Enzymes orient reactants precisely as they bind at specific locations
within the active site
2. Transition state facilitation
 Inside a catalyst’s active site, reactant molecules are more likely to reach
their transition state
 The interactions between substrate and R-groups of enzyme’s active site
lower activation energy; thus, the catalyzed reaction proceeds much more
rapidly than the un-catalyzed reaction
3. Termination
 Reaction products have less affinity for the active site than the transition
state does
 Binding ends and products are released
 What limits the rate of catalysis?
1. When substrate concentrations are low, the speed of an enzyme-catalyzed
reaction increases in a steep, linear fashion
2. At intermediate substrate concentrations, the increase in speed begins to slow
3. At high substrate concentration, the reaction rate plateaus at a maximum speed
 The “saturation kinetics” of enzyme-catalyzed reactions was taken as evidence that the
enzyme substrate complex developed by Fischer actually exists
1. After some point, active sites cannot accept substrates any faster, so no matter
how large the concentration gets the rate of the reaction does not increase
 Do enzymes work alone?
 No, bro! They don’t!
 Cofactors:
 Inorganic ions (Zn2+, Mg2+, Fe2+) reversibly interact with enzymes
 Coenzymes:
 Organic molecules that reversibly interact with enzymes, such as the
electron carriers NADH or FADH2
 Prosthetic groups:
 Non-amino acid atoms or molecules that are permanently attached to
proteins, such as the molecule retinal
 These are more important than you think!
Chapter 8.4: What Factors Affect Enzyme
Function?
 Enzymes are optimized for particular environments
o Natural selection, bitch!
o Rate of an enzyme-catalyzed reaction depends not only on substrate
concentration and the enzyme’s intrinsic affinity for the substrate, but also on
temperature and pH
 Most enzymes are regulated
o Other molecules (sometimes even other enzymes) regulate the cell’s enzymatic
activity (often through structural changes)
o Noncovalent modifications
 Reversible
 Competitive inhibition – binds to active site
 Allosteric regulation – binds to other site on protein
o Covalent modifications
 Reversible or irreversible
 Phosphorylation