Cell and metabolism
What are cristae?
The folded structures of the inner mitochondrial membrane that provide a large surface area for cellular respiration.
What are enzymes?
Biological catalysts that speed up reactions by lowering activation energy, typically ending in "-ase".
What is the name for a virus that specifically infects bacteria?
Bacteriophage (or "phage" for short).
What is the name of the process where a cell divides to form two identical daughter cells?
mitosis
What enzyme makes mRNA from DNA?
RNA polymerase
What is glycolysis? (2 pts)
The process that occurs in the cytoplasm, breaking down glucose into pyruvate and producing a small amount of ATP.
This class of organic molecules includes sugars and starches, serving as primary energy sources and structural components. Name the category and give one example of a structural polysaccharide in plants.
Carbohydrates. Example: Cellulose (plant cell walls).
Name two structural components that all viruses must have to be functional, and briefly state the role of each component.
Genetic material (either DNA or RNA) – Contains the instructions (genes) needed to make new virus particles.
Protein capsid – A protective coat made of protein subunits that surrounds and protects the genetic material.
Name the four main phases of the eukaryotic cell cycle in order, and briefly state what happens in one of them.
G1 (cell growth), S (DNA synthesis/replication), G2 (preparation for division), M (mitosis and cytokinesis).
What is removed from pre-mRNA during RNA processing in eukaryotes?
Introns (non-coding regions)
Compare and contrast facilitated diffusion and active transport across cell membranes. (4pt)
Direction relative to concentration gradient:
Facilitated diffusion moves substances down their concentration gradient (high to low).
Active transport moves substances against their concentration gradient (low to high).
Energy requirement:
Facilitated diffusion is a passive process and does not require energy input (e.g., ATP).
Active transport is an active process and requires energy, typically from ATP hydrolysis. (Note: Secondary active transport uses an established electrochemical gradient.)
Role of transport proteins:
Both processes require specific integral membrane proteins.
Facilitated diffusion uses channel proteins (e.g., ion channels, aquaporins) or carrier proteins (uniporters).
Active transport uses carrier proteins that function as pumps (e.g., ATPases like the sodium-potassium pump).
Saturation kinetics:
Both processes exhibit saturation kinetics: The rate of transport plateaus at high solute concentrations as all available protein binding sites are occupied.
Specificity:
Both processes show specificity: Transport proteins bind to specific molecules/ions based on shape, size, and charge.
Regulation:
Facilitated diffusion channels can be regulated (e.g., voltage-gated, ligand-gated).
Active transport pumps are often regulated by cellular signals (e.g., hormones, phosphorylation).
Primary biological function:
Facilitated diffusion allows efficient passive uptake or release of essential polar molecules/ions (e.g., glucose via GLUT proteins, water via aquaporins).
Active transport is essential for creating and maintaining concentration gradients, absorbing nutrients against gradients, expelling wastes, and establishing membrane potentials (e.g., Na⁺/K⁺ pump maintains resting potential).
Additional contrast:
Active transport can be classified as primary (direct ATP use) or secondary (uses energy from an ion gradient created by primary transport, e.g., symporters, antiporters).
Facilitated diffusion involves only downhill movement and cannot create a net concentration gradient.
Compare saturated and unsaturated fatty acids in terms of their chemical structure, physical properties at room temperature, and effects on membrane fluidity.
Saturated: No double bonds, straight chains, solid at room temp, decreases membrane fluidity. Unsaturated: One or more double bonds (causing kinks), liquid at room temp, increases membrane fluidity.
HIV is a retrovirus. Explain what makes retroviruses unique compared to other viruses, focusing on their replication strategy.
Unique feature: Use reverse transcriptase to convert their RNA genome into DNA
Replication strategy: RNA → DNA (reverse transcription) → DNA integrates into host chromosome (provirus) → host cell transcribes viral genes → new viral particles assemble
Consequence: Integrated viral DNA can remain latent for years, making HIV infection permanent
During DNA replication, several key enzymes work together.
What enzyme is responsible for unwinding the DNA double helix?
What enzyme synthesizes the new DNA strand by adding nucleotides?
Why are RNA primers necessary to start DNA synthesis?
DNA helicase – unwinds and separates the two DNA strands at the replication fork.
DNA polymerase (specifically DNA polymerase III in prokaryotes) – adds nucleotides to the growing DNA strand.
DNA polymerase can only add nucleotides to an existing 3'-OH end. RNA primers (made by primase) provide this starting point.
Name three key properties of the genetic code.
Universal: Same in most organisms
Degenerate: Multiple codons for most amino acids
Non-overlapping: Each base part of only one codon
Specific start/stop codons: AUG starts, UAA/UAG/UGA stop
Eukaryotic cells are characterized by extensive compartmentalization. Explain two distinct advantages this provides for cellular function, and for one of these advantages, provide a specific example involving a named organelle. (4 pts, 2 for features and 2 for examples)
Localised enzymes and substrate: higher concentration and higher rate of reaction (e.g. mitochondria)
Keep incompatible biochemicals separated (digestive enzymes in lysosomes)
Keep optimum condition for certain process (optimum pH for digesti ve enzymes)
In the early 1950s, Erwin Chargaff's quantitative analysis of DNA composition provided crucial evidence for understanding its structure.
State the two main conclusions known as "Chargaff's Rules" based on his analysis of DNA from different organisms.
Rule of Base Pair Equivalence: In double-stranded DNA from any species, the amount of adenine (A) equals the amount of thymine (T), and the amount of guanine (G) equals the amount of cytosine (C).
(A = T, G = C)
Rule of Species Specificity: The total purine content (A + G) equals the total pyrimidine content (T + C), but the ratio of A+T to G+C varies between different species and is characteristic of that species.
A virus can have either a lytic or lysogenic life cycle. Compare these two strategies and explain one evolutionary advantage of each for viral survival and reproduction.
Lytic Cycle: Immediate replication → cell lysis → rapid spread. Advantage: Quick production of many virions during optimal conditions.
Lysogenic Cycle: Viral DNA integrates into host genome (prophage) → replicates with host → may activate later. Advantage: Viral genome persists during unfavorable conditions; spreads vertically to host offspring.
Explain how mutations in two different types of genes can lead to cancer?
Proto-oncogenes → when mutated become oncogenes (e.g., growth factor genes that are always "ON") → excessive cell division.
Tumor suppressor genes → when mutated become inactive (e.g., p53 which normally stops damaged cells from dividing) → damaged cells keep dividing.
How does the ubiquitin-proteasome system control protein levels in cells?
Ubiquitination: Target protein tagged with ubiquitin molecules
Recognition: Proteasome recognizes ubiquitin tag
Degradation: Protein unfolded and broken into peptides
Recycling: Amino acids reused
Function: Quality control, regulation, removal of damaged/misfolded proteins
Compare and contrast the specific mechanisms of chemiosmosis in mitochondria (cellular respiration) versus chloroplasts (photosynthesis). Include details on where protons are pumped and where ATP is synthesized.
Similarities: Both use electron transport chains to pump protons, creating a proton gradient. Both use ATP synthase to produce ATP as protons flow back across the membrane.
Differences:
Mitochondria: Protons are pumped from the matrix to the intermembrane space during cellular respiration. ATP is made in the matrix as protons flow back through ATP synthase.
Chloroplasts: During the light reactions, protons are pumped from the stroma into the thylakoid space. ATP is made in the stroma as protons flow back out through ATP synthase.
You discover an enzyme that works best at 70°C and pH2 . Propose 2 structural features this enzyme likely has that allow it to function under these extreme conditions.
1) More disulfide bridges between cysteine residues for thermal stability.
2）Tight internal packing. More hydrophobic interactions in the protein's core.Closer packing of amino acids with nonpolar side chains.Creates a more rigid, stable structure that resists unfolding
3) less ionic bonds
Evaluate the evidence supporting the "RNA World Hypothesis" for the origin of life. Include the significance of ribozymes and how this hypothesis explains the transition to DNA/protein systems.
Evidence includes: 1) Ribozymes - RNA molecules that can act as enzymes, showing RNA can both store information and catalyze reactions. 2) RNA can self-replicate in laboratory conditions. 3) ATP and other nucleotides are RNA components, suggesting ancient metabolic pathways. The hypothesis suggests RNA-based life preceded DNA/protein systems, with DNA evolving later for more stable storage and proteins for more diverse catalysis.
During mitosis, a cell fails to properly attach one chromosome to the spindle fibers.
What checkpoint in mitosis should catch this error?
What happens if this checkpoint fails and the cell proceeds?
The spindle assembly checkpoint (metaphase checkpoint).
The chromosome may not separate properly → daughter cells receive wrong number of chromosomes.
In the trp operon of E. coli, what happens when tryptophan levels are high versus low? How does this differ from the lac operon's logic?
High tryptophan: Tryptophan binds repressor → active repressor binds operator → transcription OFF (repressible system)
Low tryptophan: No tryptophan to bind repressor → inactive repressor → transcription ON
Difference: trp operon is repressible (default ON, turned OFF by product); lac operon is inducible (default OFF, turned ON by substrate)