BIO 110 Exam 2 Clark 2026 University of Rochester

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Fluid mosaic model

• Phospholipid bilayer is fluid (flexible)

• Also has proteins embedded or attached to membrane for transport, signaling, structure

• Attached carbohydrates can be recognized by complementary protein receptors on other cells

Endomembrane system

network of membrane-bound orgenelles interacting through bidirectional vesicle trafficking

• ER sends new proteins/lipids to Golgi [which modifies products; eg) glycosylation = attaching carb to protein/lipid]

• Golgi sends recycled ER proteins/membranes back to Golgi

• Golgi sends vesicles into plasma membrane, lysosome, or to be secreted

Triacylglycerol structure and function

• 1 glycerol connected to 3 fatty acid tails; hydrophobic

• long-term energy storage, thermal insulation, mechanical cushioning for organs

  • excess caloric intake of carbs/fats can be converted to this [for storage in adipocytes]

Membrane remodeling

membrane structure can change for organization and supporting endomembrane system

• eg) phagocytosis

Phagosome & Phagocytosis

• Phagosome = a vesicle with material ingested by phagocytosis

• Phagocytosis = process where cell membrane engulfs large particles/microbes into phagosome

Primary lysosome vs. Secondary lysosome

• Primary: contains digestive enzymes but hasn’t ingested material yet

• Secondary: when primary lysosome fuses with phagosome or endosome to digest material

How can membrane lipids be structurally diverse? What is the point of this diversity?

any polar molecule can bind to the glycerol [or be in place of it] to make it amphipathic — any molecule can bind after that requirement

• eg) phosphate group

• eg in place of glycerol = shingosine

the diversity allows for specialization of membrane-bound organelles and various cell types

• eg) membrane oligosaccharide antigens determine blood type

What molecule (besides cholesterol) can restrict membrane lipid movement? What are examples that keep specific lipids in the correct position?

embedded proteins

• Flippase, Floppase, Scramblase

What molecules break down lipids?

enzymes

Cholesterol & function in plasma membrane

amphipathic sterol lipid with small polar -OH head (sticks slighty out of membrane)

• Reduces flexibility in warm temperatures

• Increases flexibility in cold temperatures (against phospholipids’ paracrystalline state)

Membrane protein types/functions

• Transport proteins = selectively allow molecules to pass through membrane

• Receptors = cell-to-cell communication

• Enzymes = catalyze reactions at membrane surface

• Cell recognition proteins = immune / cell identity recognition; often glycoproteins

• Cell adhesion proteins = attach cells to each other or extracellular matrix

• Structural/anchoring proteins = maintain membrane shape/stability + link membrane to cytoskeleton

• generate/stabilize membrane curvature (for vesicle traffic)

Ways membrane proteins associate with membrane

• Integral/transmembrane proteins = embedded in bilayer and span the membrane 1+ times; amphipathic; hard to remove without detergents

• Peripheral membrane proteins = loosely attached to membrane surface or integral proteins; interact with ionic bonds or H-bonds (polar); easier to remove

• Lipid-anchored proteins = covalently attached to lipids

Passive transport vs. Active transport

• Passive = diffusion of molecule from high to low concentration (concentration gradient) through bilayer

  • simple diffusion = small, nonpolar (lipophilic) molecule goes straight through lipid bilayer

  • facilitated diffusion = channel/carrier proteins help large or polar molecules cross

• Active = requires energy to go against concentration gradient

Glucose transporter (GLUT)

• Carrier protein that performs passive transport

• glucose in blood plasma binds to protein site —> conformational change that lets it into the cell —> when glucose is released into cytoplasm, it returns to original shape

Sodium-potassium (Na⁺K⁺ ATPase) pump

• Membrane bound enzyme that performs active transport

• 3 Na⁺ moved out for every 2 K⁺ moved in = maintains negative resting potential inside cell

Valinomycin

• peptide ionophore (carries specific ion across lipid membrane) that encloses K+ in a hydrophobic coat

  • disrupts membrane potential (voltage difference inside/outside cell)

  • naturally made by Streptomyces bacteria to limit growth of surrounding microbes

RNA world-hypothesis theory

RNA used to be main material of heredity, acting as both DNA and proteins

• supporting evidence = RNA ability to fold and act as enzyme; ribosome composition of proteins + rRNA

Drug & target examples

small molecule designed to bind to specific target (usually protein) to change its structure [and therefore function]

• target eg) enzymes, receptors, ion channels, membrane transporters, macromolecules, etc.

• many drugs mimic endogenous (naturally inside organism) molecules [esp with substrates to enzymes or signaling molecules to receptors]

  • competitive inhibitors are common drug designs

Agonist vs. Antagonist

• Agonist = initiates physiological response

• Antagonist = decreases function of target [protein]

  • majority since it’s easier to break than “fix/activate” the enzyme

Why can some drugs be taken orally while others need to be injected?

depends on if stomach acid will break them down

Antibiotic function & types

drug that kill bacterial infections

• selectively toxic (kill the microbe, not the patient)

• works by binding to enzymes to inhibit their use in cell wall / nucleic acid / protein synthesis/maintenance

  • protein interference can be through ribosome inhibition

• Bacteriostatic = inhibits growth enough for the immune system to kill

• Bactericidal = kills directly

Opioids

drugs that are/mimic morphine [from the natural opium poppy plant]

• eg) heroin

• morphine is a mimic of endogenous opioid peptides like endorphins

  • released during physical exercise —> relieve pain/stress

• targets opioid receptors like µ, δ, κ that activate inhibitory G proteins that decreases [pain-signaling] neurotransmitter release

• produces analgesic (pain relieving) effect + ventilatory depression (NOT mental; it’s dangerously slow/little breathing that can stop heartbeat), constipation, immune suppression

Naloxone/Narcane

opioid mimic that’s an opioid antagonist

• has higher affinity for opioid receptors than opioids, displacing them without activating the same pathways

  • can lead to symptoms of opioid withdrawal

• block opioid effects for 30-90 minutes before readministration needed

  • administered by syringe or nasal spray

Types of diabetes, causes, and what can treat the main two

• Type 1 = inability of pancreas to make/release insulin (a hormone)

  • cause = genetic + environmental trigger

  • treatment = injecting fast- or long-acting insulin (depending on needs)

• Type 2 = inability of receptors to properly respond to insulin

  • cause = lifestyle (weight, diet, activity)

  • treatment = Glucagon-Like Petide-1 (GLP-1 = a hormone) mimics like semaglutide (Ozempic), which lowers blood sugar levels and appetite (by suppressing glucagon release & delaying gastric emptying)

    • semaglutide has 3 amino acid changes to make its effects last longer and allow for accurate binding at GLP-1 receptors

• Gestational = temporary form that can occur during pregnancy

Selective serotonin reuptake inhibitors (SSRIs)

blocks the serotonin reuptake transport, increasing serotonin concentrations in the brain (since it won’t be broken down as much)

• work against low levels of serotonin in depression

• serotonin receptors control mood/emotions when serotonin stimulates (which is made from tryptophan)

• drug eg) Prozac

Zonisamide

drug that binds to sodium channels and voltage-sensitive calcium channels to suppress neural hypersynchronization (excessive firing of electrical impulses at once)

• treats seizures

Cannabinoids

chemicals that act on endocannabinoid system in body to influence neuron communication related to appetite, anxiety, learning/memory, pain

• eg) THC, CBD

What did Gregor Mendel suggest?

that there’s a material of heredity in organisms

Gene

functional unit of heredity (often a contiguous {continuously touching} segment of DNA) that is transcribed into RNA [which may or may not be translated into a protein]

• all include a regulatory region (regulates gene expression) and coding region (contains information to produce RNA)

  • all regulatory regions include a promoter & transcription factor binding sites

  • RNA polymerase must bind to promoter to transcribe gene

Allele

form (among many) of gene at a location on a chromosome

Autosome

non-sex chromosome

• humans have 22 pairs

Sex chromosomes

X or Y chromosomes

Thomas Hunt Morgan’s hypothesis and conclusions

alleles for red/white eyes in fruit flies were carried on the X chromosome (aka X-linked)

• built off Nettie Stevens’ demonstration that sex was determined by X and Y chromosome inheritance

concluded that the white-eyed phenotype was X-linked, showing that genes were carried on chromosomes

• but both proteins and DNA make up chromosomes, and people believe at first that proteins’ 20 amino acids match genetic complexity better than DNA’s 4 nucleotides

Mouse experiment that showed whether DNA or proteins were the material of heredity

strains of strep bacteria:

• rough/R = non-virulent (non-deadly)

  • can be transformed into S type by interacting with heat-killed S strain’s hereditary information

• smooth/S = virulent (deadly)

  • can be heat-killed to be non-deadly

• since destroying the S strain’s DNA was the only one to stop death, it likely contained the hereditary information for virulence

  • note, DNA also survives higher heats than most macromolecules

Hershey-Chase Experiment 1952

• bacteriophage = virus that infects bacteria by injecting material of heredity that makes bacteria create more virus

• treatment 1 radio labeled phage protein with ³⁵S (sulfur makes up proteins)

• treatment 2 radio labeled phage DNA with ³²P (phosphorus makes up DNA)

• after bacteriophages injected E. coli and phage ghosts were removed, radioactivity was only seen in the DNA-marked E. coli —> DNA must be the material of heredity

Chargaff’s Rules

1. base composition/proportion in DNA varies from species to species

2. different tissues in same individual have same DNA base composition

3. base composition of DNA doesn’t change with organism age, nutrition, or environment

4. in all DNA, adenosine residues = thymidine residues & guanosine residues = cytidine residues (A=T, G=C) —> knowing 1 strand’s sequence means you know the complement

Purine vs. Pyrimidine

• Purine = 2 rings

  • A, G

• Pyrimidine = 1 ring

  • T, U, C

X-ray crystallography

technique to find 3D protein structure

• by purifying molecule —> turning it into a crystal (changing its properties to bind to itself with a regular pattern) —> shooting X-rays through it —> reverse engineering the electron diffraction paths

5’AGCT3’ sketch of DNA strand & DNA structure

DNA is an antiparallel double-stranded helix

• phosphate group in sugar-phosphate backbone makes negative

• major groove is where most proteins bind

• free-floating nucleotides have 3 phosphates, but 2 detach when nucleotide attaches to DNA strand

How was the double helix hypothesis of DNA structure tested? What were its results?

Dickerson Dodecamer analyzes structure of chemically synthesized DNA [with known sequence] using X-ray crystallography

• showed that DNA had varying bend angles (not all straight) and many slight variations in 3D structure depending on base pair sequence compared Watson & Crick’s ideal model

  • explained how specific proteins could find and bind to specific sequences based on structure — every DNA sequence is a different ligand (binding target)

Central Dogma

genetic information flows from DNA —> RNA —> protein

• never originates from protein

  • DNA or RNA [in some cases] can also replicate itself

  • RNA can also be reverse transcribed into DNA

• original dogma was provocative so people would try [and fail] to disprove

  • one wrong part = possible arrow from DNA straight to protein

Polymerase

enzyme that synthesizes a complement dependent on template (DNA or RNA) with very high accuracy

• “{template}-dependent {product} polymerase”

• works 5’ → 3’, starting from primer

• requires triphosphate forms of nitrogenous bases (ATP, TTP, GTP, CTP)

  • breaking off of two phosphate groups provides energy needed for phosphodiester bond, attaching to daughter strand

• many have exonuclease region that proofreads and removes incorrect bases during synthesis

What did Arthur Kornberg discover?

DNA requires a template for synthesis

• also isolated DNA polymerase I in E. coli (he thought it was a replicating polymerase but it just proofreads)

Polymerase chain reaction (PCR)

process that amplifies small sequence of DNA into millions/billions of copies

• requires DNA template (aka parent strand), nucleotides, primers, and polymerases

• can be used for genetic testing

1. Denaturation = heats to 95ºC to fully separate DNA strands

2. Annealing = primer can bind with hydrogen bonds at ~55ºC and free-floating nitrogenous bases of daughter strand start making hydrogen bonds with complements

3. Extension = at 72ºC, heat-resistant DNA polymerase is added to synthesize 5’ → 3’ strand with phosphodiester bonds and hydrogen bonds forming between nucleotides

• process repeats many cycles

DNA synthesis + proteins and parts involved

From replication fork (Y shape region where the DNA strands split):

• Gyrase = type of topoisomerase that alleviates torsional stress (relaxes supercoiling)

• Helicase = breaks H-bonds so DNA strands split into two

• Single-strand binding (SSB) proteins = temporarily bind to single strands of DNA to prevent H-bonds from reforming

• DNA primase = specialized DNA-dependent RNA polymerase that starts by adding RNA primer (since DNA polymerase can’t begin synthesis)

• [DNA-dependent] DNA polymerase III = synthesizes DNA nucleotides starting from RNA primer

  • can continuously synthesize leading strand by following helicase

  • makes Okazaki fragments at multiple primers of lagging strand

• DNA polymerase I = replaces RNA primers with DNA

  • Ligase = bonds replaced^ fragments with previous Okazaki fragment

• Sliding clamp = protein that attaches to DNA polymerases to prevent them from coming off the template while adding nucleotides

• Polymerases on each side (leading/lagging) are bound by a dimerization domain to prevent the leading strand from getting too far ahead too fast

• Telomerase = RNA-dependent DNA polymerase that uses an internal RNA template to add complementary DNA to the parent strand (called a telomere and is unnecessary for desired product) so that the lagging daughter strand can fully replicate the essential part of the DNA template

Prokaryotic vs. Eukaryotic DNA replication

• Prokaryotes have circular chromosomes —> 1 origin of replication (where unwinding & synthesis is) that terminates once the helicases at each side of replication fork meet

• Eukaryotes have linear chromosomes —> multiple origins of replication that end synthesis at a termination sequence

  • lagging strand can’t fully be replicated because RNA primer takes up space at the end and DNA can’t be added after

    • DNA polymerase I can’t replace that primer unless DNA follows it

  • telomerase adds telomere to remedy (part which doesn’t need to be fully replicated)

Transcription parts involved and steps

1. Initiation = DNA-dependent RNA polymerase binds to promoter [likely with help of transcription factors] and unwinds DNA strand
   —no need for helicase or primer because transcription bubble made is temporary and small)
   —RNA polymerase finds where to bind from recognized signal such as TATA box (conserved DNA sequence)

2. Elongation = RNA polymerase moves along DNA’s 3’ → 5’ while synthesizing RNA 5’ → 3’

3. Termination = RNA polymerase reaches termination sequence, signaling for its release

*note, 5’ cap and poly(A) tail aren’t in prokaryotes

Which side of DNA is the template strand for transcribing a gene?

either depending on gene

Transcription factors vs. General transcription factors

• Transcription factors = proteins that regulate gene expression

  • negative transcription factors = downregulate expression (commonly by binding to promoter to block RNA polymerase)

  • positive transcription factors = upregulate expression (commonly by binding to promoter to help RNA polymerase find and bind to it)

    • ligand often binds to repressor or activator to change its structure and stop downregulation or upregulation

• General transcription factors = used to initiate transcription for almost all genes

Most and least abundant type of RNA

• most = rRNA

• least = mRNA

What percent of human genome is transcribed into RNA? What percent is translated into proteins? Why?

• ~25% into RNA

• ~1% into proteins

• vast majority is non-coding or regulatory region

What main type of RNA does each RNA polymerase correspond to?

• RNA polymerase I = rRNA

• RNA polymerase II = mRNA

• RNA polymerase III = tRNA

this prob isn’t important

Prokaryotic vs. Eukaryotic transcription

• Prokaryotes’ mRNA can go straight from transcription to translation since there’s no nucleus in between

• Eukaryotes need to modify by adding a 5’ cap and poly(A) tail [to 3’] to protect mRNA from degradation on the way (leaving nucleus) to translation and help it find/interact with the ribosome

  • Intron splicing is also much more common = removing noncoding regions

Intron splicing vs. Alternative splicing

• Intron splicing = introns are all removed by proteins, leaving exons to connect

• Alternative splicing = some introns aren’t removed or some exons are removed

  • contributes greatly to protein diversity since the same gene could code for many different proteins

    • explains why DNA can seem less complex than proteins at first but really isn’t

How was the genetic code experimentally found?

• E. coli was grinded to just include ribosomes, tRNAs, and [radio-labeled] amino acids [and existing was mRNA removed]

• synthesized mRNA sequence was added with known nitrogenous bases

  • eg) UUUUUU…

  • eg) U and As in any order UUAAUUUAUAUAAAAUUUUAU…

• reverse engineer codons (sequence of 3 bases) with the amino acids in the peptide they coded for to match to each possible combination

  • then start radio-labeling only certain amino acids to isolate single codon from possibilities

*this worked despite the lack of a start codon due to structural changes that came with excess Mg⁺ in the test tubes

Translation steps and parts involved

1. enzymes attach each amino acid to corresponding tRNA

2. Initiation = ribosome’s small subunit binds to mRNA and initiation factors (helper proteins) —> fMet tRNA anticodon binds to start codon [at P site] —> large subunit binds and locks in place + initiation factors leave

3. Elongation = anticodon of next tRNA matches/binds at A site —> amino acids in P and A sites bond —> tRNA at A site moves to P site; tRNA at P site moves to E site to exit

4. Termination = stop codon doesn’t code for an amino acid, so an RFI (release factor) binds at its place to signal for peptide release and ribosome disassembly

• A = decoding site; P = peptidyl site; E = exit site

• hydrolysis of GTP provides energy for process

• mRNA is translated 5’ → 3’ (ribosome would go right in the picture = towards 3’)

Glycosylation & Phosphorylation are examples of…

post-translational modifications to a peptide

• Glycosylation = adding sugar to peptide

• Phosphorylation = adding phosphate group to peptide

What makes each of your cells unique?

the regulation of their expressed genes

(NOT the genes they have — most all cells in one organism have the same DNA)

Benefit of regulating genes early (at transcription) compared to late (post-translation)

• early avoids wasting energy or letting minimal expression slip through later in the process

• late helps if you still need a gene’s products quick and may just be temporarily disabling them

  • eg) blood clotting proteins

Prokaryotic vs. Eukaryotic gene expression

• Prokaryote genes tend to be “turned on” by default

  • negative regulation is more common

• Eukaryote genes tend to be “turned off” by default

  • positive regulation is more common

*BOTH still use BOTH positive and negative regulation though

Key requirements for regulating gene expression

• being able to sense changing environmental condition

  • being able to activate/repress genes in response to changes

Operon

string of genes on chromosome with a single promoter that regulates their transcription

• often since each coded protein works together and can be regulated together

• most common in prokaryotes

Arabinose operon [is an example of what?]

example with AraC protein that can be both a repressor (when arabinose doesn’t bind) and an activator (when arabinose binds)

Tryptophan operon [is an example of what?]

example of negative feedback, where the final product made by its enzymes (tryptophan), signals for the gene’s downregulation

Nucleosomes & role in gene expression

Eukaryotic nuclear/linear DNA strands [which are negative] wrapped tightly around histone proteins [which are positive] (like string around a spool)

• make up chromatin = mixture of DNA and proteins that makes up chromosomes

  • Heterochromatin = tightly bound histones —> genes are less likely to be transcribed (transcriptionally silent)

  • Euchromatin = less condensed —> genes are more likely to be transcribed

Some methods of regulating gene expression

• transcription factors

• nucleosomes condensing DNA

• intron splicing or alternative splicing (depending on proteins that splice)

• microRNAs helping selectively destroy mRNA that comes from a certain gene

• environmental conditions