Cell Biology: Modules 2-1 to 3-4 Study Guide

Comprehensive practice flashcards covering non-covalent chemistry, biological macromolecules, membrane structure and transport, protein folding, nucleic acids, transcription, translation, cell structure, and bacterial growth curves.

What causes a covalent bond to be polar, and why are $C-H$ bonds nonpolar?

Polarity occurs when bonded atoms have different electronegativities (such as $O$ or $N$ bonded to $C$ or $H$), resulting in uneven electron sharing and a permanent dipole. $C-H$ bonds are nonpolar because carbon and hydrogen have similar electronegativities and share electrons nearly equally.

Why is carbon dioxide ($CO_2$) nonpolar overall despite containing polar bonds?

Carbon dioxide has a linear geometry, which causes its polar bond dipoles to point in opposite directions and cancel out by symmetry.

What charge states do carboxyl ($-COOH$) and amino ($-NH_2$) groups adopt at cellular $\text{pH} \approx 7.4$?

The carboxyl group loses an $H^+$ to become negatively charged ($-COO^-$), and the amino group gains an $H^+$ to become positively charged ($-NH_3^+$).

Rank the four major non-covalent interactions and covalent bonds from strongest to weakest.

Covalent bonds $\gg$ ionic interactions (in low-water settings) $>$ hydrogen bonds $>$ van der Waals contacts.

Why is the strength of an ionic bond (salt bridge) reduced to about $1\text{--}5\,\text{kcal/mol}$ in water compared to its strength in a vacuum?

Water molecules shield the full positive and negative charges, weakening the electrostatic attraction between the ions.

What is the primary thermodynamic driving force of the hydrophobic effect?

An increase in the entropy of water. Nonpolar groups force surrounding water molecules into ordered cages; clumping nonpolar groups together releases these water molecules into disorder, which is energetically favorable.

What are the four major classes of macromolecules and their linking covalent bonds?

1. Proteins: peptide bonds. 2. Nucleic acids: phosphodiester bonds. 3. Carbohydrates: glycosidic bonds. 4. Lipids: ester bonds (glycerol-fatty acid).

Why are lipids not considered true polymers?

Lipids are not assembled from identical repeating units linked into covalent chains; rather, they are assembled from smaller distinct components and self-assemble through non-covalent forces (the hydrophobic effect).

What chemical reaction joins biological monomers together, and what small molecule is produced?

A condensation (dehydration) reaction, in which one monomer loses an $-OH$ and the other loses an $H$, releasing a molecule of water ($H_2O$).

What chemical groups define the two distinct ends of a polypeptide, and in what direction is it synthesized?

A polypeptide has a free amino group at the N-terminus and a free carboxyl group at the C-terminus. It is synthesized from the N-terminus to the C-terminus.

What chemical groups define the two ends of a nucleic acid strand, and in what direction is it synthesized?

The $5'$ end has a free phosphate group on the $5'$ carbon, and the $3'$ end has a free hydroxyl group ($-OH$) on the $3'$ carbon. Strands are read and synthesized in the $5' \rightarrow 3'$ direction.

Why does a cell need to couple polymerization reactions to ATP hydrolysis?

Polymerization is anabolic and builds order from free monomers, decreasing entropy and yielding a positive $\Delta G$ (non-spontaneous). Coupling to favorable ATP hydrolysis ($\Delta G \approx -7.3\,\text{kcal/mol}$ or $-30.5\,\text{kJ/mol}$) makes the overall process net negative.

How do saturated fatty acid tails differ from unsaturated fatty acid tails in structure and packing?

Saturated tails contain no $C=C$ double bonds and pack tightly together. Unsaturated tails have double bonds (often cis) that create kinks, preventing tight packing.

What does it mean that a phospholipid is amphipathic?

It possesses both a hydrophilic region (a polar, often charged head group) and a hydrophobic region (two nonpolar hydrocarbon tails).

Why do free fatty acids form micelles in water while phospholipids form bilayers?

Single-tailed lipids like free fatty acids are wedge- or cone-shaped and pack into spherical micelles, whereas phospholipids have two bulky tails giving them a cylindrical shape that packs into two-layered sheets (bilayers).

Why does a planar lipid bilayer spontaneously close to form a sealed vesicle?

A flat bilayer has exposed edges where hydrophobic tails meet water, which is energetically unfavorable. Sealing into a sphere eliminates exposed edges.

What types of amino acid side chains face the lipid tails in a transmembrane protein segment?

Nonpolar, hydrophobic side chains (such as Leu, Ile, Val, and Phe) that interact favorably with the hydrocarbon tails via van der Waals forces.

What structural factors maintain membrane fluidity at lower temperatures?

Unsaturated fatty acid tails (kinks prevent tight packing) and cholesterol (which sits between phospholipids).

Rank small nonpolar molecules, small uncharged polar molecules, large uncharged polar molecules, and charged ions by their permeability across a pure lipid bilayer.

Small nonpolar ($O_2$, $CO_2$, $N_2$) $>$ small uncharged polar (water, ethanol, urea) $>$ large uncharged polar (glucose) $>$ charged ions ($Na^+$, $K^+$, $Cl^-$, $H^+$).

What are two structural and functional differences between channels and carriers (transporters)?

1. Channels form continuous pores that move ions rapidly (millions per second) by size and charge; carriers bind substrates, undergo shape changes, and move solutes slower (hundreds to thousands per second). 2. Carriers exhibit saturation with limited binding sites and can perform active transport when coupled to energy, whereas channels cannot move solutes uphill.

How does a rate-versus-concentration graph distinguish simple diffusion from facilitated diffusion?

Simple diffusion produces a straight line that rises continuously in proportion to concentration with no plateau, whereas facilitated diffusion produces a curve that levels off (plateaus) as membrane transport proteins saturate.

On a graph of concentration ratio (inside/outside) over time, what indicates active transport?

The internal-to-external concentration ratio rises above $1$ and remains there, showing that solute is pumped against its concentration gradient.

How does osmosis differ from simple diffusion?

Diffusion refers to the movement of any solute down its concentration gradient, whereas osmosis is specifically the diffusion of water across a semipermeable membrane toward higher solute concentration.

What are the four components bonded to the central $\alpha$-carbon of an amino acid?

1. An amino group ($-NH_3^+$). 2. A carboxyl group ($-COO^-$). 3. A hydrogen atom. 4. A variable R-group (side chain).

What unique structural roles are played by cysteine, glycine, and proline in protein conformation?

Cysteine can form covalent disulfide bonds ($-S-S-$) with another cysteine; glycine has a single hydrogen as its R-group, providing structural flexibility; proline contains a ring bonded to the backbone, introducing rigid kinks.

What interactions stabilize protein secondary structure compared to tertiary structure?

Secondary structure ($\alpha$-helices and $\beta$-sheets) is stabilized by hydrogen bonds between backbone $C=O$ and $N-H$ groups. Tertiary structure is stabilized by interactions between side chains (R-groups), including hydrophobic clustering, H-bonds, ionic bonds, van der Waals forces, and disulfide bonds.

What happens during protein denaturation, and what level of structure is preserved?

Denaturation disrupts non-covalent interactions and unfolds secondary, tertiary, and quaternary structures, causing loss of function. Primary structure remains intact because covalent peptide bonds are not broken.

What is allosteric regulation of a protein?

A regulatory mechanism where an effector molecule binds reversibly to a site other than the active site, inducing a conformational change that alters the protein's activity.

What are the three components of a nucleotide, and to which sugar carbons are the functional units attached?

A pentose sugar (deoxyribose or ribose), a nitrogenous base attached to the $1'$ carbon, and a phosphate group attached to the $5'$ carbon.

What physical interaction contributes the largest amount of stability to the DNA double helix?

Base stacking, driven by van der Waals interactions and the hydrophobic effect among the flat nitrogenous bases in the helix interior.

According to Chargaff's rules, if a double-stranded DNA molecule contains $30\%$ adenine ($A$), what are the percentages of thymine ($T$), guanine ($G$), and cytosine ($C$)?

$T = 30\%$, $G = 20\%$, and $C = 20\%$ (since $\text{\%}A = \text{\%}T = 30\%$, leaving $40\%$ divided equally between $G$ and $C$).

What are two fundamental chemical differences that distinguish RNA from DNA?

1. RNA contains ribose sugar with a $2'$ $-OH$ group, whereas DNA contains deoxyribose lacking an $O$ at the $2'$ carbon. 2. RNA utilizes the base uracil ($U$) in place of thymine ($T$).

How do bacteria and eukaryotes differ regarding the spatial and temporal coupling of transcription and translation?

Bacteria lack a nucleus, allowing translation to begin on an mRNA while it is still being transcribed in the cytoplasm. Eukaryotes transcribe and process mRNA inside the nucleus before exporting it to the cytoplasm for translation.

How does the template strand differ from the coding strand during transcription?

The template (non-coding) strand is read $3' \rightarrow 5'$ by RNA polymerase to synthesize RNA. The coding (non-template) strand matches the sequence of the resulting RNA ($5' \rightarrow 3'$), with $T$ in DNA corresponding to $U$ in RNA.

What is the function of the sigma factor in bacterial transcription?

The sigma factor binds to bacterial core RNA polymerase to form the holoenzyme, directing it to recognize specific promoter sequences at the $-10$ and $-35$ regions.

What are two structural differences between bacterial mRNA and eukaryotic mRNA?

Bacterial mRNA is often polycistronic (carrying multiple open reading frames) and is unprocessed; eukaryotic mRNA is monocistronic and undergoes $5'$ capping, $3'$ polyadenylation, and splicing.

Why is aminoacyl-tRNA synthetase considered the real translator of the genetic code?

It pairs a specific amino acid with its cognate tRNA using ATP. The ribosome only checks codon-anticodon pairing and cannot verify if the correct amino acid is loaded onto the tRNA.

What events occur at the A, P, and E sites of a ribosome during translational elongation?

An incoming charged aminoacyl-tRNA enters the A site; peptide bond formation occurs between the chain on the tRNA at the P site and the amino acid at the A site; after translocation, the uncharged tRNA exits from the E site.

What is meant by the terms 'redundant' and 'non-overlapping' when applied to the genetic code?

Redundant (degenerate) means multiple codons can code for the same amino acid ($64$ codons for $20$ amino acids). Non-overlapping means each nucleotide is part of only one triplet codon, read in sequence from a fixed start point.

How can the direction of transcription be determined in an electron micrograph of coupled bacterial gene expression?

RNA polymerase moves along the DNA toward the end where nascent mRNA transcripts are longest.

What are the three tenets of cell theory?

1. All living organisms are composed of one or more cells. 2. The cell is the smallest unit of life. 3. All cells arise from pre-existing cells by cell division.

How do bacterial chromosomes differ from eukaryotic chromosomes in shape, copy number, and packaging?

Bacterial genomes typically consist of a single circular chromosome located in the nucleoid compacted by DNA-binding proteins. Eukaryotic genomes consist of multiple linear chromosomes enclosed in a nucleus and wrapped around histones into chromatin.

What four key observations support the endosymbiotic theory for the origin of mitochondria and chloroplasts?

They possess a double membrane, contain their own circular DNA, have $70\text{S}$ ribosomes, and divide autonomously by binary fission.

A scale bar representing $2\,\mu m$ measures $8\,\text{mm}$ on a diagram. If a cell measures $20\,\text{mm}$, what is its actual length?

$5\,\mu m$ (Calculation: $\frac{2\,\mu m}{8\,\text{mm}} = 0.25\,\mu m/\text{mm}$; $20\,\text{mm} \times 0.25\,\mu m/\text{mm} = 5\,\mu m$).

What are the four phases of a bacterial population growth curve in order?

Lag phase, exponential (log) phase, stationary phase, and death (decline) phase.

What biological processes occur during the lag phase of bacterial growth?

Cells do not divide; instead, they adapt to the medium, increase in size, and synthesize the specific RNA, enzymes, and proteins required to metabolize available nutrients.

Why does the population cell count stay constant in the stationary phase of a growth curve?

The rate of cell division equals the rate of cell death because nutrients are depleted and toxic metabolic wastes accumulate.