BIO 110 Exam 1 Clark 2026 University of Rochester

Approximate percents of human composition?

70% Water

15% Proteins

4% Small molecules

6% RNA

2% Phospholipids

1% DNA

2% Polysaccharides

Defining traits of living things + describe

• Cellular organization

  • cell = smallest structure capable of life processes / basic unit of life on Earth

• Energy

  • acquire and use

• Homeostasis

  • maintaining stable internal environment despite external changes

• Information

  • Hereditary information made mostly of DNA sequences

• Metabolism

  • all chemical reactions that sustain life (acquire/transform/use energy & matter)

  • highly regulated to avoid energy waste

  • enzymes often interconnected in metabolic pathways

• Growth & Reproduction

  • Growth heavily regulated (lack/excess can be lethal/cancerous)

  • Reproduction includes copying hereditary info and is required avoid extinction

  • All cells originate from other cells

• Respond to change/stimuli

• Evolution (long-term over population)

Prokaryotes vs Eukaryotes

Prokaryotes = single-celled, lack nucleus (has nucleoid), lack membrane-bound organelles/internal structures

Eukaryotes = single-celled or multi-cellular, have nucleus, have membrane bound organelles/internal structures

What are the 3 domains of life and what led to what after the last universal common ancestor (LUCA)?

Bacteria, Eukaryotes, Archaea

Eukaryotes merged from Bacteria and Archaea

Which organelles used to be independent bacteria?

Mitochondria and Chloroplasts

Structure determines ______ (for most biological molecules)

function

Anabolism vs. Catabolism

Anabolism = build together, requires energy

Catabolism = breaks apart, releases energy*

*(because the formation of more stable bonds releases more energy than it takes to break the original bonds)

The Scientific Method

1. Observation [and description of phenomenon]

2. Questions

3. Hypothesis (states the relationship between 2 variables; best attempt to answer question)

4. Predictions (including the existence of other phenomena or quantifying what the results may be — “If ___, then ____.”)

5. Experimental tests (+repeat)

What conclusions can we make about a null hypothesis?

Reject or fail to reject

Controlled experiment vs. Comparative experiment

Controlled experiment = starts with groups that are as similar as possible and only manipulates one independent variable to see impact on dependent variable [in comparison to an unmanipulated control group]

Comparative experiment = starts with the prediction that there will be a difference between 2 or more naturally existing groups (based on the hypothesis) and compares unmanipulated data

What characteristics make a project more experimental?

Manipulation + hypothesis test

Independent vs. Dependent variable

Independent variable is manipulated, and dependent variable changes in response

Experimental group vs Control group

Experimental group = exposed to the independent variable

Control group = exposed to all the same conditions as the experimental group EXCEPT the independent variable

Null hypothesis

States that there is no relationship between 2 variables, and any observed differences are due to random chance

Negative vs. Positive control

Negative control = group where no phenomenon is expected (guarantees no effect)*

Positive control = group where the phenomenon is expected (guarantees desired effect)

*careful of double negatives!!! eg) phenomenon we’re looking for is “cells not growing / lack of cell growth,” so the negative control would make sure cells DO grow, while positive control would ensure no cell growth

What was chosen as the indicator for life on mars and why? (1970s experiment)

CO₂ (from oxidizing radioactively-marked carbon)

It assumes that life on mars uses a similar system to cellular respiration, which reflects a broader goal of people possibly being sustained there.

Elements in each biomolecule

Carbohydrates = CHO

Lipids = CHO (less O in comparison to carbs)

Proteins = CHONS

Nucleic Acids = CHONP

How can you test which way a reaction will proceed?

Put equal concentrations of reactants and products;

• if the concentration of products increase, it proceeds forward/right

• if the concentration of reactants increase, it proceeds in reverse/left

• if the concentrations remain the same, the reaction is already at equilibrium

Equilibrium

Rate of forward reaction = rate of reverse reaction

Equilibrium constant equation

Total free energy change equation[s] & explanation[s]

ΔG = [Energy]_products - [Energy]_reactants

• negative if reaction is spontaneous and releases energy (exergonic)

• positive if system isn’t spontaneous and needs energy (endergonic)

or

ΔG = ΔH - TΔS = enthalpy - entropy

• only use if you can explain enthalpy (heat content of system — negative if heat is release / exothermic, positive if heat is taken from surroudnings / endothermic) and entropy (disorder of system — positive = products are simpler / more disordered)

Which way does a reaction proceed relative to the energies on each side?

Higher energy —> Lower energy

Relationship between K_eq, ΔG, and direction that the reaction proceeds

direct relationship between K_eq and ΔG

ΔG = -RTlnK_eq

Endergonic vs. Exergonic reaction

Endergonic = reaction requires energy

Exergonic = reaction releases energy

Energy coupling

Energy from a favorable reaction can go straight into an unfavorable reaction that requires energy

Chemical bonds and interactions + descriptions

• Covalent bond = sharing of electron pairs; strongest

• Ionic attraction = attraction of opposite charges (pretty strong for noncovalent)

• Hydrogen bond = interaction between partially positive H and partially negative O, F, or N (pretty strong for noncovalent)

• Hydrophobic interaction = interaction of nonpolar substances clustering together in the presence of polar substances (like water)

• van der Waals interaction = temporary/brief interactions of moving electrons of nonpolar substances; weakest

Electronegativity

atom’s attraction strength towards electrons (tendency of atom to pull electrons to itself)

Compare electronegativities of H and C, O, and N

C=H

O>H

N>H

(determines partial charges for hydrogen bonding between H and O or N and how C-H bonds are covalent/nonpolar)

Up to how many hydrogen bonds can a water molecule make?

4 max

Explain the hydrophobic interaction with grouped objects in relation to entropy, order, and energy efficiency

Two nonpolar substances being separately surrounded by water = lower entropy, highly ordered, less efficient regarding energy

Two nonpolar substances grouped together and surrounded by water = higher entropy, less order, more efficient regarding energy

Condensation vs. Hydrolysis

Condensation removes water to form a bond between monomers

Hydrolysis adds water to break a bond between monomers

Prokaryote structures

• Single or double plasma membrane

• Sometimes cell wall {made of peptidoglycan}

• Nucleoid (region of free-floating DNA)

• Sometimes flagellum (for locomotion)

• Free-floating ribosomes

Eukaryote structures + descriptions

• Plasma membrane = selective fluid barrier controlling transport in & out of cell through phospholipid bilayer; proteins embedded for transport, signaling, & structure; primarily held by hydrophobic interactions

• Mitochondria = ATP production through cellular respiration; has double membrane

• Cytoskeleton = structural support, transport, and cell movement through network of protein filaments; actin & myosin help cell change shape

• Nuclear pores = protein complexes in nuclear envelope that regulate transport between nucleus and cytoplasm (like with RNA/proteins)

• Nucleolus = rRNA synthesis and ribosome assembly; not membrane-bound (inside nucleus)

• Nucleus = genome storage and transcription; surrounded by double membrane (nuclear envelope); site of RNA synthesis

• Endoplasmic reticulum = membranous tubules connected to the nuclear envelope:

  • Rough ER = has ribosomes; protein synthesis & modification [for secretion / membrane insertion / organelles]

  • Smooth ER = lacks ribosomes; lipid synthesis [+detoxifies chemicals and stores calcium]

• Ribosomes = protein synthesis (free-floating makes proteins for cytoplasm/nucleus; rough ER makes for secretion/membranes); made of rRNA and proteins

• Golgi = stacks of membranous sacs; modifies, sorts, and ships proteins and lipids; one side receives vesicles from ER, other ships vesicles to organelles or plasma membrane

• Vesicles = membranes that transport molecules

• Centrioles = organizes microtubules (which make up spindle fibers & maintain cell shape) for cell division and motility (ability to move)

Interactions between ER and Golgi

• Proteins/lipids from ER go to Golgi to be modified {by glycosylation and phosphorylation}

• Golgi returns some [escaped] proteins/membranes to ER for recycling

-transport between them happens through vesicles

What aspects of mitochondria point to their endosymbosis?

Having its own maternal circular chromosome

Having its own ribosomes

Unique structures of plant cell + descriptions

Central vacuole = maintains turgor pressure (lots of water —> structural support) and stores water & ions {+tonoplast = its membrane and helps maintain cell pressure/homeostasis}

Chloroplasts = carry out photosynthesis

Cell wall = made mostly of cellulose; gives structural support/protection and maintains cell shape {+plasmodesmata = channels between cell walls for direct transport/communication}

How do proteins go where they should?

Their last string of amino acids acts as a signal sequence that is recognized by specific receptors

Motor proteins + examples

move along cytoskeletal filaments to transport organelles and vesicles + help cell movement

eg) Kinesin uses ATP to move along microtubules with cargo; Dynein does the same thing in the opposite direction; Myosin is similar but with actin filaments

Fluorescence microscopy

fluorescent dyes bind to specific cell structure to help visualize them

Immunohistochemistry

visualizes proteins under a microscope by using antibodies that bind to antigens (target molecule; often proteins) — antibodies can then be attached to glowing molecules

Hydroxyl group

Carboxyl group

Amino group

Phosphate group

Biomolecules, their monomers, polymer/macromolecule examples, functions

• Carbohydrates — monosaccharides eg) glucose — polysaccharides eg) starch, glycogen, cellulose — short-term energy storage, structural support

• Lipids — fatty acids — triacylglycerol, membrane lipids — long-term energy storage, insulation, membrane structure (compartmentalization)

• Proteins — amino acids — peptides & polypeptides — build muscle/structure, enzymes facilitate reactions

• Nucleic Acids — nucleotides (1 nitrogenous base, 5-carbon sugar, phosphate group) — DNA, RNA — store genetic information, encode proteins

Amphipathic

Compound with both hydrophilic and hydrophobic regions

Glycosidic bond

covalent bond between sugars formed by condensation

Monosaccharide vs. Polysaccharide solubility

Monosaccharides are very H₂O-soluble, while polysaccharides will need enzymes to speed up dissolving (still soluble, just don’t break as easily)

What does replacing hydroxyl groups (OH) in carbohydrates do? What are some replacement options?

Specializes sugar functions

Can be replaced with H (deoxy), amine (NH₂), phosphate (PO₄), N-acetyl amine

Types of polysaccharide structures, how their bonds affect functions, and examples

Linear = used for structural support; hydrogen bonds between hydroxyls within same molecules, making it stronger but more hydrophobic; eg) cellulose, chitin

Branched = digestible; water can perform hydrolysis with multiple hydroxyl ends at once to release glucose (which can be oxidized for energy); eg) glycogen, starch

Triacylglycerol vs. Membrane lipid

Triacylglycerol = main form of long-term energy storage (+insulation); 3 fatty acid tails connected to 1 glycerol

Membrane lipid = amphipathic to create phospholipid bilayer; 2 hydrophobic fatty acid tails connected to 1 glycerol and a hydrophilic/charged head (like a phosphate group)

Why are lipids more efficient at long-term energy storage than carbohydrates?

Lipids have more energy per carbon because of their oxidation state (carbohydrates are easier to oxidize into CO₂ because they have less high-energy C-H bonds) and don’t have to store water like glucose does, taking up less space

Saturated vs. Unsaturated fatty acids

Saturated = straight single bonds and packs together better

Unsaturated = has kinks from double bonds, which makes harder to pack; can survive lower temperatures

cis vs. trans unsaturated fatty acids

cis = natural and often healthier

trans = associated with processed foods and often less healthy

Draw and label general amino acid structure + circle parts that will make water

N-terminus / amino group = left (NH₃⁺ or NH₂)

C-terminus / carboxyl group = right (COO^- or COOH)

any of the Hydrogens on the amino group can make water, just only choose 2 for NH₃⁺ or 1 for NH₂ — also different than interacting with water; every part can interact with water, though the R-group may not be able to depending on what it contains

~either or for drawing—just stay consistent and be careful with charges

Draw 2 general amino acids making a peptide bond

~either or for drawing—just stay consistent and be careful with charges

Which dimensional isomer are almost all amino acids?

L isomer (the left-handed one, as opposed to D isomer)

Nonessential vs. Conditionally Essential v. Essential amino acids

Nonessential = human body makes on its own

Conditionally Essential = human body can make, though not enough under certain conditions (eg: during pregnancy)

Essential = humans must eat to get (can’t make on their own)

Five types of R groups and how they interact with water

How many amino acid types are peptides chained with? Is this the number of amino acid types that proteins can have?

20 types of amino acids are usually chained as peptides, but proteins can then be modified to allow for many more types

Native structure

functional [folded] state of protein

Residues

Amino acids linked to a peptide chain after losing H₂O

What direction are peptides synthesized (start to end)?

N terminus (amino group) to C terminus (carboxyl group)

Polypeptide/protein structures and bonds that stabilize each

1. Primary structure = linear amino acid sequence; order defines how the protein will fold and function; has covalent peptide bonds

2. Secondary structure = hydrogen bonds between alpha helices (intramolecular H-bonds) and beta sheets (inter- or intramolecular H-bonds between beta strands) [NOT between R-groups] +covalent peptide bonds from before

3. Tertiary structure = folding with help of the 4 types of noncovalent interactions/bonds (especially the hydrophobic effect) & disulfide bonds [between R-groups] +all bonds from past structures

4. Quaternary structure = two or more polypeptide chains bonded with same bonds as past structures (especially those 4 noncovalent and disulfide bonds); just multiple bonded tertiary structures

What is the original method that protein structure was discovered through? What was built off this to do so faster?

X-ray crystallography

AI trained on patterns from^^^

Denaturing + some methods & the bonds they break

Denaturing proteins means to unfold their tertiary structure, which can happen by:

• heat (breaks hydrogen bonds and other weak noncovalent interactions)

• extreme pH (mainly breaks ionic bonds [due to H⁺ ions changing charges] and hydrogen bonds [because of partial charge interference])

• detergents (mainly breaks weak noncovalent interactions like hydrophobic interactions [since it has nonpolar regions] and ionic bonds [if it has a charge])

• mechanical agitation (breaks weak noncovalent interactions)

• urea (breaks hydrogen bonds and hydropobic interactions [because it’s a strong H-bond donor/acceptor])

• mercaptoethanol (breaks disulfide bonds)

Why do denatured proteins tend to be less soluble than the native protein?

Because the unfolding exposes their hydrophobic regions

Can proteins be renatured?

Yes, if their primary structure remains intact

Cooperativity of folding (cooperative process)

Polypeptide/protein bonds are NOT independent—all bonds have to be able to form to bring about the fully functional structure; if even some bonds are broken, the protein won’t properly fold / bond between the correct regions

• in folding, polypeptide chain goes from high energy & high entropy (unstable) to low energy & low entropy (stable)

What is the pattern for α-helix bond formation?

Hydrogen bonds are formed* between every 4 residues (eg: #2, #6, #10…) between C=O and N-H (eg: O of #2 interacts with H of #6, O of #6 interacts with H of #10…)

*only between parts of the polypeptide backbone, NOT R-groups

What from the secondary structure may be maintained in the tertiary structure?

α-helices and β-sheets

Peptide vs. Polypeptide vs. Protein

Peptide = short chain of amino acids

Polypeptide = longer chain of amino acids that may function by itself or form a larger protein

Protein = one or more polypeptides that is folded to its functional/native structure

Antifreeze proteins structures & functions

• Flat, hydrophilic side binds to small ice crystals while its irregular, hydrophobic region repels water to prevent further [larger] crystal growth

  • makes it thermodynamically unfavorable to add water molecules to the ice lattice

• Evenly spaced hydroxyl (OH) groups on flat side allows for H-bonds with the crystalline ice lattice

  • has some hydrophobic parts on the flat side just to line up with crystal shape

Mucin glycoprotein structures & functions

• Carbohydrate chains = hydrophilic and bind to water to create thick, viscous layer of protection (where pathogens get stuck to be destroyed)

• Dimerization domains = regions to chain to more mucins, increasing total thickness

• Cysteine residues = found throughout to allow disulfide bonding between more mucins (again, increasing thickness)

• Only has small hydrophobic sections so that if denatured (like during a fever), those parts will open up for the mucins to group together at (again, increasing thickness)

+these extracellular glycoproteins can be membrane-bound or secreted

When can carbohydrate chains be added to proteins (glycosylation)? Where does this happen?

During post-translational modifications in the Rough ER* and Golgi

*instead of free-floating ribosomes since they lack specialized enzymes

How do K⁺ channels filter for the correct charge & size of ion?

• Channels are lined with negative carbonyl oxygens, ensuring that only positive ions (cations) go through

• Ions that are too big won’t fit through the channel

• Ions that are too small will attract the negative walls together, making the channel close by collapsing in

Enzyme functions + where it gets energy for reaction from

• Catalysts for biochemical reactions

  • almost always proteins

  • stabilize transition state, lowering reaction’s activitation energy requirement and speeding up the process

    • the bonds made between the enzyme and substrate in its induced-fit is where the rest of the energy comes from

  • often end in “-ase” (NOT -ose, which is for carbs)

Why are catalysts highly regulated?

Reactions shouldn’t be happening all the time — this would unnecessarily waste energy

Enzyme cofactors

Additional groups attached to enzyme to allow for specific functions

• common eg) metal ions (for electron transfer)

• eg) coenzymes = cofactors that contain carbon (organic)

6 types of chemical reactions catalyzed by enzymes

Oxidoreductases = oxidation or reduction reactions (electron is removed/added)

Transferases = moving chemical groups from one place to another

Hydrolases = breaking chemical bonds with water (facilitate hydrolysis)

Lyases = breaking chemical bonds without water

Isomerases = changing molecular shape (same atoms/formula, different arrangement)

Ligases = connect two molecules (facilitate covalent bond formation)

Lock-and-Key vs. Induced-Fit Model

Lock-and-Key Model = outdated; idea that substrate fits exactly into complementary enzyme

Induced-Fit Model = more accurate; enzymes are flexible and have a confirmational change in their shape to tightly fit around a substrate {has a more complementary binding site} (+makes more sense for why multiple substrates can bind to one enzyme!)

Specificity (with enzymes) & what it’s based on

Ability of enzyme to choose / bind to a specific substrate amongst similar molecules

Based on the structure of the active site

Why are enzymes globular instead of just having an active site?

The rest of the protein’s structure regulates the protein and is essential in forming the active site with the correct shape (during folding process)

How catalysts relates to equilibrium / ΔG and the activation energy

Catalysts do NOT change the equilibrium / ΔG of a reaction — they just lower the activation energy

Rate enhancement (with enzymes)

Factor by which catalyst increases the rate of reaction

Ways to regulate enzymes

Covalent modification = addition/removal of chemical groups to enzyme’s residues to alter its shape/properties (like charge)

Allosteric modulators = non-substrate molecules that bind to secondary location (allosteric/regulatory site) on enzyme to increase/decrease its catalytic activity (activator increases, repressor decreases)

• repressors are an example of noncompetitive inhibitors = molecule that reduces enzyme’s activity by binding to allosteric site [which changes the enzyme’s shape]

Competitive inhibition = non-substrate molecule blocks enzyme’s active site from binding to the substrate