VCE Biology: Enzymes, Nucleic Acids, Photosynthesis, Cellular Respiration, and DNA Manipulation

Comprehensive flashcards covering key topics from Chapter 3 (Enzymes), Chapter 5 (Photosynthesis), Chapter 2 (Nucleic Acids and Proteins), Chapter 6 (Cellular Respiration), and Chapter 4 (DNA Manipulation).

What is an enzyme and what is its primary function in biological systems?

An enzyme is an organic molecule, typically a protein, that acts as a catalyst to speed up specific chemical reactions without being used up, broken down, or turned into a product by lowering the activation energy of the reaction.

What occurs when a substrate binds to an enzyme's active site according to the induced fit model?

The active site and substrate undergo a conformational change (a slight adjustment in three-dimensional shape) to form a tighter, complementary connection within the enzyme-substrate complex.

In the temperature response graph shown, what do points X, Y, and Z represent regarding enzyme activity?

Point X represents the enzyme's optimal temperature where activity is highest. Point Y represents a low temperature limit where kinetic energy is reduced causing loss of function (reversible freezing). Point Z represents a high temperature limit where the enzyme irreversibly denatures.

How does denaturation affect an enzyme's structure and catalytic function?

Denaturation breaks the bonds forming the tertiary and quaternary structures of the enzyme, inducing an irreversible conformational change in its active site so the substrate can no longer fit or bind.

What is the difference between competitive and non-competitive enzyme inhibition?

Competitive inhibitors bind directly to the enzyme's active site and block substrate binding. Non-competitive (allosteric) inhibitors bind to an allosteric site, causing a conformational change in the active site that prevents substrate binding.

How can reversible competitive inhibition be overcome in a reaction?

Reversible competitive inhibition can be overcome by increasing the concentration of the substrate, which increases the likelihood of a substrate molecule binding to the active site rather than the inhibitor.

What is a coenzyme and how does it function during enzymatic reactions?

A coenzyme is a non-protein organic cofactor that assists enzyme function by donating energy or molecules. Unlike the enzyme, its structure is changed during the reaction, requiring it to be recycled (reloaded) afterwards.

What is the proteome?

The proteome refers to the entire set of proteins expressed by a cell, tissue, or organism at a given time.

Based on the generalized diagram, what four functional groups or atoms are attached to the central carbon of an amino acid monomer?

The central carbon is bonded to an amino group ($-\text{NH}_2$), a carboxyl group ($-\text{COOH}$), a hydrogen atom ($\text{H}$), and a variable R-group.

How are amino acid monomers joined together to form a polypeptide, and what bond is created?

Amino acids are joined together at ribosomes via a condensation reaction, producing a molecule of water as a by-product and forming a peptide bond between adjacent amino acids.

What characterizes the four hierarchical levels of protein structure?

Primary: sequence of amino acids. Secondary: folding into $\alpha$-helices, $\beta$-pleated sheets, or random coils via hydrogen bonds. Tertiary: functional 3D shape formed by R-group interactions. Quaternary: bonding of two or more polypeptide chains or addition of prosthetic groups.

What are the three structural components of a nucleotide monomer?

A phosphate group, a five-carbon (pentose) sugar, and a nitrogen-containing base.

What are the key structural differences between DNA and RNA?

DNA contains a deoxyribose sugar, the base thymine ($\text{T}$), and is double-stranded and long-term/inherited. RNA contains a ribose sugar, the base uracil ($\text{U}$), and is single-stranded and temporary/short-lived.

What do the terms universal, unambiguous, degenerate, and non-overlapping mean regarding the genetic code?

Universal: nearly all organisms use the same codons for amino acids. Unambiguous: each codon codes for only one specific amino acid. Degenerate: an amino acid can be coded for by multiple different codons. Non-overlapping: triplets/codons are read sequentially without sharing nucleotides.

What are the key steps of transcription in eukaryotic cells?

RNA polymerase binds to the promoter region with transcription factors, unwinds and unzips the DNA double helix, reads the template strand ($3' \rightarrow 5'$), and joins complementary RNA nucleotides to synthesize a pre-mRNA strand ($5' \rightarrow 3'$) until a termination sequence is reached.

What three modifications occur during RNA processing in eukaryotic cells?

The addition of a $5'$ methyl-G cap, the addition of a $3'$ poly-A tail, and splicing via a spliceosome to remove non-coding introns and join coding exons together.

What are the key steps of translation during protein synthesis at the ribosome?

The ribosome binds to the $5'$ end of mRNA and reads codons until the start codon ($\text{AUG}$) is reached. Complementary tRNA anticodons deliver corresponding amino acids to the ribosome, where adjacent amino acids are joined by peptide bonds via condensation reactions until a stop codon terminates translation.

How does repression regulate the trp operon when intracellular tryptophan levels are high?

Tryptophan binds to the repressor protein, inducing a conformational change to its active form. The active repressor binds to the operator region, physically blocking RNA polymerase from transcribing the structural genes ($\textit{trpE--A}$).

How does attenuation regulate the trp operon when tRNA-bound tryptophan levels are high?

The ribosome translates the leader region without pausing at the two $\textit{trp}$ codons. This causes the mRNA strand to fold into a terminator hairpin loop, causing the mRNA to detach from the DNA template strand and terminating transcription before structural genes are reached.

What pathway do secreted proteins follow through the cell organelles before exiting via exocytosis?

Synthesized at ribosomes attached to the rough endoplasmic reticulum (where they are folded), transported via transport vesicles to the Golgi apparatus (where they are modified and packaged), and carried in secretory vesicles to fuse with the plasma membrane for release.

What is the simplified chemical equation for C3 photosynthesis?

$$6\text{CO}_2 + 6\text{H}_2\text{O} \xrightarrow{\text{sunlight}} \text{C}_6\text{H}_{12}\text{O}_6 + 6\text{O}_2$$

What are the location, inputs, and outputs of the light-dependent stage of photosynthesis?

Location: thylakoid membranes/grana. Inputs: $12\text{H}_2\text{O}$, $12\text{NADP}^+$, $18\text{ADP} + \text{P}_i$. Outputs: $6\text{O}_2$, $12\text{NADPH}$, $18\text{ATP}$.

What are the location, inputs, and outputs of the light-independent stage (Calvin cycle) of photosynthesis?

Location: stroma. Inputs: $6\text{CO}_2$, $12\text{NADPH}$, $18\text{ATP}$. Outputs: $\text{C}_6\text{H}_{12}\text{O}_6$, $6\text{H}_2\text{O}$, $12\text{NADP}^+$, $18\text{ADP} + \text{P}_i$.

What is the primary function of Rubisco in photosynthesis, and what is its major flaw?

Rubisco fixes carbon from inorganic $\text{CO}_2$ into organic $3\text{-PGA}$ in the Calvin cycle. Its flaw is that it can also bind to $\text{O}_2$ as a substrate, initiating the wasteful process of photorespiration.

How do C4 plants minimize photorespiration compared to C3 plants?

C4 plants separate initial carbon fixation and the Calvin cycle spatially across different cells. Initial $\text{CO}_2$ fixation occurs in mesophyll cells via PEP carboxylase to form a 4-carbon compound (malate), which is transported to bundle-sheath cells where it releases $\text{CO}_2$ to maintain high $\text{CO}_2$ concentrations around Rubisco.

How do CAM plants minimize photorespiration and water loss compared to C3 plants?

CAM plants separate initial carbon fixation and the Calvin cycle temporally over time. Stomata open at night to fix $\text{CO}_2$ into 4-carbon malate stored in vacuoles. During the day, stomata close to prevent water loss and malate releases $\text{CO}_2$ inside mesophyll cells for the Calvin cycle.

How does light intensity affect the rate of photosynthesis?

Increasing light intensity increases the rate of photosynthesis by exciting more electrons in chlorophyll until a light-saturation point is reached, after which the rate plateaus due to another limiting factor or enzyme saturation.

What is the overall chemical equation and total ATP yield for aerobic cellular respiration?

$\text{C}_6\text{H}_{12}\text{O}_6 + 6\text{O}_2 \rightarrow 6\text{CO}_2 + 6\text{H}_2\text{O} + 30\text{ or } 32\,\text{ATP}$. It yields $30$ or $32\,\text{ATP}$ per glucose molecule.

What are the location, inputs, and outputs of glycolysis?

Location: cytosol. Inputs: $1\text{ glucose (C}_6\text{H}_{12}\text{O}_6\text{)}$, $2\text{ADP} + 2\text{P}_i$, $2\text{NAD}^+ + 2\text{H}^+$. Outputs: $2\text{ pyruvate}$, $2\text{ ATP}$, $2\text{ NADH}$.

What are the location, inputs, and outputs of the Krebs cycle (per glucose molecule)?

Location: mitochondrial matrix. Inputs: $2\text{ acetyl-CoA}$, $2\text{ADP} + 2\text{P}_i$, $6\text{NAD}^+ + 6\text{H}^+$, $2\text{FAD} + 4\text{H}^+$. Outputs: $4\text{CO}_2$, $2\text{ ATP}$, $6\text{ NADH}$, $2\text{ FADH}_2$.

What are the location, inputs, and outputs of the electron transport chain in aerobic cellular respiration?

Location: cristae of the inner mitochondrial membrane. Inputs: $6\text{O}_2$, $26\text{ or } 28\text{ ADP} + \text{P}_i$, $10\text{ NADH}$, $2\text{ FADH}_2$. Outputs: $6\text{H}_2\text{O}$, $26\text{ or } 28\text{ ATP}$, $10\text{NAD}^+ + 10\text{H}^+$, $2\text{FAD} + 4\text{H}^+$.

What is the role of oxygen in the electron transport chain?

Oxygen acts as the terminal electron and proton acceptor, binding free $\text{H}^+$ and $e^-$ at the end of the electron transport chain to form harmless $\text{H}_2\text{O}$, preventing toxic buildup.

What are the word equations and ATP yields for anaerobic fermentation in animals versus yeast?

Animals: $\text{Glucose} \rightarrow \text{Lactic acid} + 2\,\text{ATP}$. Yeast: $\text{Glucose} \rightarrow \text{Ethanol} + \text{Carbon dioxide} + 2\,\text{ATP}$. Both yield $2\,\text{ATP}$ per glucose molecule.

What are the four main steps involved in producing bioethanol from plant biomass?

1. Deconstruction (breaking down biomass/cell walls physically, chemically, or thermally). 2. Enzymatic hydrolysis (enzymes break down starch/cellulose to glucose using water). 3. Ethanol fermentation (yeast anaerobically ferments glucose into ethanol and $\text{CO}_2$). 4. Purification and dehydration (distillation of ethanol).

How do first-generation biofuels differ from second-generation biofuels?

First-generation biofuels are produced from edible food crops (e.g. corn, sugarcane) and compete with agriculture/food production. Second-generation biofuels are produced from non-edible crops or waste residues (e.g. wood waste, agricultural residue) and do not compete directly with food crops.

What are restriction endonucleases and how do sticky ends differ from blunt ends?

Restriction endonucleases are bacterial enzymes that cut double-stranded DNA at specific palindromic recognition sites. Sticky ends are staggered cuts with overhanging unpaired nucleotides; blunt ends are straight cuts across the DNA with no overhanging nucleotides.

What is the function of DNA ligase in DNA manipulation?

DNA ligase joins two DNA fragments together by catalysing the formation of phosphodiester bonds in the sugar-phosphate backbone.

What is the natural function of the CRISPR-Cas9 system in prokaryotes?

CRISPR-Cas9 acts as an adaptive immune system in bacteria to defend against viral invasion by bacteriophages by capturing viral DNA fragments and using gRNA to direct Cas9 to cut invading viral DNA.

What are the three steps in the natural bacterial CRISPR-Cas9 immune response?

1. Exposure: Cas1 and Cas2 cut a protospacer from invading viral DNA and insert it as a spacer into the bacterial CRISPR locus. 2. Expression: CRISPR spacers are transcribed into gRNA which binds to Cas9. 3. Extermination: gRNA directs Cas9 to complementary foreign viral DNA adjacent to a PAM sequence, where Cas9 cleaves both strands creating a blunt end cut.

What is a Protospacer Adjacent Motif (PAM) and why is it important?

A PAM is a short sequence ($2\text{--}6$ nucleotides, e.g. NGG) found immediately next to target viral DNA. It signals Cas1/Cas2 to extract protospacers and enables Cas9 to rapidly bind and cut target DNA without destroying the bacterium's own CRISPR locus (which lacks PAMs).

What are the three temperature-controlled steps in a cycle of the Polymerase Chain Reaction (PCR)?

1. Denaturation ($90\text{--}95\,^{\circ}\text{C}$): breaks hydrogen bonds to separate double-stranded DNA into single strands. 2. Annealing ($50\text{--}55\,^{\circ}\text{C}$): allows DNA primers to bind to complementary $3'$ ends. 3. Elongation ($72\,^{\circ}\text{C}$): Taq polymerase synthesizes a complementary DNA strand $\text{in } 5' \rightarrow 3'$ direction.

How does gel electrophoresis separate DNA fragments, and how do smaller fragments behave compared to larger ones?

Gel electrophoresis uses an electric current to pull negatively charged DNA fragments through pores in an agarose gel toward the positive electrode. Smaller fragments move faster and travel further down the gel lane than larger fragments.

What is a standard ladder in gel electrophoresis and why is it used?

A standard ladder is a sample containing DNA fragments of known molecular sizes (in bp or kb) run alongside experimental samples to estimate the size of unknown DNA fragments.

What essential components must a plasmid vector contain for gene cloning?

A restriction endonuclease site (for gene insertion), an antibiotic resistance gene (e.g. $amp^R$ for selection), an origin of replication (ORI, for self-replication), and a reporter gene (e.g. $gfp$ or $lacZ$ to distinguish recombinant from non-recombinant plasmids).

How does heat shock facilitate bacterial transformation?

Chilling bacteria and plasmids in a $\text{Ca}^{2+}$ solution on ice then rapidly heating them to $37\text{--}42\,^{\circ}\text{C}$ increases the permeability of the bacterial plasma membrane, allowing recombinant plasmids to enter the cytoplasm.

How is recombinant human insulin produced using transformed E. coli bacteria?

Insulin A and B subunit genes (without introns) are inserted into separate plasmids attached to the $lacZ$ gene (producing a $\beta$-galactosidase fusion protein). Recombinant plasmids are transformed into $E. coli$, selected, and expressed. The fusion proteins are extracted, cyanogen bromide cleaves off $\beta$-galactosidase, and purified A and B chains are mixed to form disulphide bonds.

What is the difference between a Genetically Modified Organism (GMO), a cisgenic organism, and a Transgenic Organism (TGO)?

GMO: any organism whose genome has been altered using genetic engineering. Cisgenic organism: a GMO containing foreign DNA from the same or sexually compatible species. Transgenic organism (TGO): a GMO containing foreign DNA from a different species.