set 4

Question 1

4.1 – State the main difference between prokaryotes and eukaryotes.

Answer 1

Prokaryotes lack a membrane‑bound nucleus; eukaryotes possess a membrane‑bound nucleus.

Question 2

4.1 – List the 3 domains in the current classification.

Answer 2

Bacteria, Archaea, Eukarya.

Question 3

4.1 – What methods are used today to infer evolutionary relationships?

Answer 3

Molecular sequence comparisons (e.g., rRNA genes, whole‑genome DNA), phylogenomics, and comparative genomics.

Question 4

4.1 – What is the Candidate Phyla Radiation (CPR)?

Answer 4

A large set of bacterial lineages discovered by environmental DNA sequencing; many are unculturable and very small (~400 nm).

Question 5

4.1 – Define extremophiles and give 3 archaeal examples.

Answer 5

Organisms thriving in extreme conditions. Examples: methanogens (H₂ + CO₂ → CH₄), halophiles (high salt), thermacidophiles (hot + acidic).

Question 6

4.1 – Why are Archaea considered more similar to Eukaryotes than to Bacteria?

Answer 6

Core information‑processing machinery (DNA replication, transcription, RNA processing, translation initiation) resembles eukaryotic systems.

Question 7

4.1 – Typical sizes of bacteria/archaea vs plant/animal cells?

Answer 7

Bacteria/Archaea: 1–5 μm; Plant/Animal: 10–100 μm.

Question 8

4.2 – List the three limits on cell size.

Answer 8

1) Surface area:volume (SA:V) constraints, 2) Diffusion rates of molecules, 3) Need to maintain adequate local concentrations of reactants/enzymes.

Question 9

4.2 – Explain why SA:V declines as a cell grows.

Answer 9

Volume scales with length³; surface area with length² → larger cells have proportionally less surface area for exchange.

Question 10

4.2 – Give a biological example of maximizing SA:V.

Answer 10

Intestinal microvilli—fingerlike projections that greatly increase surface area for absorption.

Question 11

4.2 – Define diffusion.

Answer 11

Passive movement of molecules from high → low concentration due to random thermal motion.

Question 12

4.2 – How do cells overcome slow diffusion of large molecules?

Answer 12

Use carrier proteins, active transport, and cytoplasmic streaming to move materials.

Question 13

4.2 – Why are many small cells better than one large cell?

Answer 13

Collectively they have greater total SA, shorter diffusion distances, and can specialize.

Question 14

4.2 – What happens to collision frequency of enzymes/substrates as cell size increases at constant concentrations?

Answer 14

It drops; fewer productive collisions per time → reactions slow unless compartmentalized or concentrations increase.

Question 15

4.3 – How does compartmentalization speed metabolism?

Answer 15

By localizing enzymes + substrates (e.g., Krebs cycle enzymes in mitochondria), raising effective concentrations and collision rates.

Question 16

4.3 – Define organelle.

Answer 16

A membrane‑bound compartment in eukaryotic cells with specialized functions.

Question 17

4.4 – Define nuclear envelope and nucleolus.

Answer 17

Nuclear envelope: double membrane surrounding nucleus. Nucleolus: site of rRNA synthesis and ribosomal subunit assembly.

Question 18

4.4 – Where is DNA found in Bacteria/Archaea vs Eukaryotes, and what is its shape?

Answer 18

Bacteria/Archaea: nucleoid, circular DNA (histone‑like proteins in Archaea). Eukaryotes: nucleus, linear DNA bound to histones.

Question 19

4.4 – What R‑groups make histones bind DNA?

Answer 19

Basic/positively charged residues (Lys, Arg) bind the negatively charged DNA backbone.

Question 20

4.4 – List three cytoskeletal systems and a general role.

Answer 20

Microtubules, microfilaments, intermediate filaments → structure, motility, intracellular transport.

Question 21

4.4 – Define exocytosis and endocytosis.

Answer 21

Exocytosis: vesicles fuse with plasma membrane to export contents. Endocytosis: plasma membrane invaginates to import extracellular material.

Question 22

4.4 – How do cells take up cholesterol via endocytosis?

Answer 22

Receptor‑mediated endocytosis: LDL receptors bind LDL‑cholesterol, clathrin‑coated pits internalize → endosome → lysosome to release cholesterol.

Question 23

4.4 – Define binary fission.

Answer 23

Asexual division of prokaryotes: DNA replicates and the cell splits, yielding genetically identical cells.

Question 24

4.4 – Two reasons meiosis generates genetic diversity.

Answer 24

Independent assortment of chromosomes and homologous recombination (crossing over).

Question 25

4.4 – Explain **operons** vs eukaryotic gene expression.

Answer 25

**Bacteria** often transcribe **polycistronic mRNA** (operons) encoding **several proteins**; **eukaryotes** typically produce **monocistronic mRNAs**.

Question 26

4.5 – Main function of **mitochondria** (don’t say powerhouse!)

Answer 26

**Aerobic respiration**: oxidize fuels and capture energy in **ATP** via **TCA cycle** and **oxidative phosphorylation**.

Question 27

4.5 – Define **cristae** and **matrix**.

Answer 27

**Cristae**: folds of the **inner mitochondrial membrane** housing ETC complexes. **Matrix**: internal **aqueous** compartment with **TCA enzymes**.

Question 28

4.5 – How do **number/location** of mitochondria vary with cell type?

Answer 28

Cells with **high ATP demand** have **many mitochondria** positioned near **energy‑using sites** (e.g., **sperm tail**, **muscle fibrils**).

Question 29

4.5 – Key facts about **mtDNA**.

Answer 29

**Circular**, ~**16.5 kb**, encodes **37 genes** (incl. **tRNAs**); many mitochondrial disorders involve **tRNA gene** mutations; **maternal inheritance**.

Question 30

4.5 – Why are **mitochondrial diseases** maternally inherited?

Answer 30

**Zygote cytoplasm** (and mitochondria) comes predominantly from the **oocyte**; sperm mitochondria are **not typically transmitted**.

Question 31

4.5 – Why would mutant **mitochondrial tRNAs** impair function?

Answer 31

Faulty **tRNAs** **block mitochondrial translation**, reducing **ETC/TCA proteins** → **ATP deficiency**.

Question 32

4.5 – Briefly explain the symptoms in **MELAS**: muscle weakness, lactic acidosis, stroke‑like episodes.

Answer 32

**ATP deficit** in muscle → **weakness**; impaired oxidative phosphorylation → ↑**glycolysis** → **lactate** (**acidosis**); **neuronal energy failure** → **stroke‑like** episodes.

Question 33

4.5 – Main functions and compartments of the **chloroplast**.

Answer 33

**Photosynthesis**; **thylakoid** membranes (light reactions), **grana** stacks; **stroma** (CO₂ fixation).

Question 34

4.5 – Name the cycle that reduces **CO₂ to sugar** in chloroplasts.

Answer 34

**Calvin cycle** (occurs in the **stroma**).

Question 35

4.5 – Why do chloroplasts carry **ribosomes and circular DNA**?

Answer 35

They encode/translate **some of their own proteins**, supporting an **endosymbiotic origin**.

Question 36

4.5 – How are **nitrates** formed in soil from **N₂** and why do chloroplasts reduce nitrate?

Answer 36

**Nitrogen‑fixing bacteria** convert **N₂ → NH₃/NH₄⁺**, and **nitrifying bacteria** oxidize to **NO₂⁻/NO₃⁻** (also via lightning/industrial). Chloroplasts reduce **NO₃⁻ → NH₃/NH₄⁺** for **amino acid** synthesis.

Question 37

4.5 – Why are **NH₃/NH₄⁺** essential for protein synthesis?

Answer 37

They provide the **amino group** incorporated into **amino acids**.

Question 38

4.6 – Summarize the **endosymbiont theory**.

Answer 38

**Mitochondria** and **chloroplasts** originated when ancestral **prokaryotes** were **engulfed** by a proto‑eukaryote and became **symbionts**.

Question 39

4.6 – Give **two arguments FOR** endosymbiosis.

Answer 39

**Circular genomes**, **bacterial‑sized ribosomes**, **binary‑fission‑like division**, **double membranes** resembling engulfment.

Question 40

4.6 – Give **one argument AGAINST** or caveat.

Answer 40

Modern organelles depend on **nuclear‑encoded proteins** and cannot **live independently**; genomes are **highly reduced**.

Question 41

4.6 – Define **aerobic heterotrophic** vs **photosynthetic autotrophic** prokaryote.

Answer 41

**Aerobic heterotroph**: uses **O₂** and **organic carbon**; source of **mitochondrion**. **Photosynthetic autotroph**: uses **light** to fix **CO₂**; source of **chloroplast**.

Question 42

4.7 – List the **endomembrane system** components.

Answer 42

**Nuclear envelope, ER (rough + smooth), Golgi apparatus, lysosomes, vesicles**, and the **plasma membrane** (functionally connected).

Question 43

4.7 – General function of **rough ER** vs **smooth ER**.

Answer 43

**Rough ER**: **synthesizes** membrane/secretory proteins. **Smooth ER**: **lipid/steroid synthesis**, **detoxification** (enzymes on cytosolic face).

Question 44

4.7 – General function of the **Golgi apparatus**.

Answer 44

**Modifies, sorts, and packages** proteins/lipids (e.g., adds **polysaccharides** to proteins) for delivery to **lysosomes, plasma membrane, secretion**.

Question 45

4.7 – What are **secretory vesicles**?

Answer 45

Vesicles that **bud from Golgi**, move to the **plasma membrane**, and **fuse** to release cargo (**exocytosis**).

Question 46

4.7 – Define **lysosome** and **hydrolases**.

Answer 46

**Lysosome**: acidic organelle containing **hydrolases** that degrade **all biomacromolecules**; inner membrane is **carbohydrate‑coated** for protection.

Question 47

4.7 – Why can hydrolases digest **any macromolecule**?

Answer 47

Because the set includes **proteases**, **nucleases**, **lipases**, **glycosidases**, **phosphatases**, etc., targeting **peptide, glycosidic, phosphodiester, ester** bonds.

Question 48

4.7 – Explain **I‑cell disease** and **mannose‑6‑phosphate (M6P)**.

Answer 48

A defect in the **GlcNAc‑phosphotransferase** that generates **M6P** tags → enzymes **aren’t targeted** to lysosomes and are **secreted** instead; cells show **inclusion bodies**.

Question 49

4.7 – Why are lysosomal enzymes **secreted** when they **lack M6P**?

Answer 49

Without **M6P**, they **don’t bind the M6P receptor** in Golgi and **follow the default secretory pathway** to the cell surface.

Question 50

4.8 – General function of **peroxisomes**.

Answer 50

**Oxidize** fatty acids and other substrates; generate **H₂O₂** and degrade it via **catalase/peroxidases**.

Question 51

4.8 – How do peroxisomes remove **H₂O₂**?

Answer 51

**Catalase** converts **2 H₂O₂ → 2 H₂O + O₂** (or uses H₂O₂ to **oxidize** other substrates).

Question 52

4.8 – Explain **X‑linked adrenoleukodystrophy (ALD)** biochemically.

Answer 52

**Defective peroxisomal β‑oxidation** of **very‑long‑chain fatty acids (VLCFAs, e.g., C26:0)** → accumulation damages **myelin**.

Question 53

4.8 – Why does **C26:0** accumulation damage **myelin**?

Answer 53

VLCFAs **disrupt membrane lipids** and **myelin stability**, triggering **inflammation** and **degeneration** of myelin sheaths.

Question 54

4.8 – How does **Lorenzo’s Oil** help ALD?

Answer 54

A **4:1 mix of C18:1:C22:1** **competitively inhibits FA elongation**, lowering **C26:0** synthesis → reduces VLCFA accumulation.

Question 55

4.8 – General functions of **vacuoles** in animals/yeast.

Answer 55

**Storage** and **transport**; **phagocytosis** forms a **phagosome** that fuses with lysosomes for digestion.

Question 56

4.8 – Role of the **central vacuole** in plants.

Answer 56

Maintains **turgor pressure** to keep tissues rigid; loss of pressure → **wilting**.

Question 57

4.8 – Define **phagocytosis** and **phagosome**.

Answer 57

**Phagocytosis**: uptake of large particles by membrane **engulfment**; **phagosome**: the internal **vesicle** formed.

Question 58

4.9 – What are **ribosomes** and are they membrane‑bound?

Answer 58

**Ribonucleoprotein complexes** (rRNA + proteins) that **synthesize proteins**; **not** membrane‑bound.

Question 59

4.9 – Explain **Svedberg (S)** units and why subunits don’t add up arithmetically.

Answer 59

**S** measures **sedimentation rate** (size/shape dependent). Combined particles **sediment differently**, so **S values aren’t additive**.

Question 60

4.9 – Contrast **eukaryotic** and **prokaryotic** ribosome **S values**.

Answer 60

**Eukaryote**: **80S** (60S + 40S). **Bacteria/Archaea**: **70S** (50S + 30S).

Question 61

SG – Compute **SA, V, SA:V** for cubes conceptually and explain significance.

Answer 61

**SA = 6ℓ²**, **V = ℓ³**, **SA:V = 6/ℓ** → as **ℓ increases**, **SA:V** decreases, limiting **exchange** and **metabolic rate** per volume.

Question 62

SG – Name **membrane‑bound** organelles covered in this set.

Answer 62

**Nucleus**, **ER**, **Golgi**, **lysosomes**, **peroxisomes**, **vacuoles**, **mitochondria**, **chloroplasts** (plants/algae).