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Questions and Answers
What is the main function of ribosomal RNA (rRNA)?
What is the role of transfer RNA (tRNA) in protein synthesis?
What does the term 'degenerate' refer to in the context of the genetic code?
In which cellular process does transcription occur?
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What is the function of the anticodon in tRNA?
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Where does the process of transcription take place?
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What is the first step in the transcription process?
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Which statement about the genetic code is true?
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What is the primary role of Taq polymerase in the PCR process?
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During which step of PCR does the DNA double helix separate into single strands?
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What purpose do the forward and reverse primers serve in PCR?
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What temperature is optimal for the elongation step of PCR when Taq polymerase works best?
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What technique is used to separate DNA fragments based on their molecular size?
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What aspect of DNA fingerprinting allows for the identification of different individuals?
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What does DNA sequencing determine about a DNA strand?
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What is the result of repeating the PCR process multiple times?
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What is the primary function of the regulatory gene in the trp operon?
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In the context of the trp operon, what occurs when tryptophan is in low supply?
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What role does the operator play in the trp operon?
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Which of the following components is NOT part of the trp operon?
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How does the formation of the antiterminator hairpin affect transcription in the trp operon?
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What happens during high levels of tryptophan in the trp operon?
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What is the primary purpose of the polymerase chain reaction (PCR)?
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Which component of PCR is responsible for adding free nucleotides to synthesize new DNA strands?
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What is a structural gene in the context of the trp operon?
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What is the function of the leader region in the trp operon?
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What is a major ethical concern regarding the use of CRISPR technology?
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What does a buffer do in the PCR process?
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How does the amount of DNA present after each cycle of PCR relate to the number of cycles?
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What issue arises from the inability to obtain informed consent from embryos in genetic research?
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What is a concern related to off-target cleavages in CRISPR usage?
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Which of the following best describes the role of primers in PCR?
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What describes the process of photosynthesis in relation to energy?
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What role do enzymes play in biochemical reactions?
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What is the function of coenzymes in cellular respiration?
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How do coenzymes inter-convert between their forms?
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In which situation would NAD+ be acting as a coenzyme?
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What is an enzyme-substrate complex?
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What is true about the activation energy of an enzyme-catalyzed reaction compared to an uncatalyzed reaction?
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What type of pathway is cellular respiration categorized as?
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What is a cofactor?
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Which best describes the action of NAD during its transition from NAD+ to NADH?
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Study Notes
Ribosomal RNA (rRNA)
- rRNA is a stable form of RNA found in ribosomes.
- rRNA combines with proteins and enzymes in the cytoplasm to form ribosomes.
- Ribosomes are the site of protein synthesis.
Transfer RNA (tRNA)
- tRNA is a form of RNA that can attach to specific amino acids and carry them to a ribosome during translation.
- tRNA molecules carry amino acids to ribosomes in the cytoplasm, where they are used to construct proteins.
- An anticodon (three nucleotides) on tRNA binds to the complementary codon on mRNA.
The Genetic Code
- The genetic code is a representation of genetic information using non-overlapping groups of three bases (triplets) in a DNA template chain.
- Each genetic instruction consists of a triplet of bases (e.g., AAT or GCT).
- The genetic code is universal, meaning the same sequence of nucleotides codes for the same amino acid in bacteria, plants, and animals.
- The genetic code is degenerate or redundant, meaning more than one triplet of bases can code for the same amino acid.
- Degeneracy allows for tolerance to mutations.
- The genetic code is unambiguous, meaning each codon codes for only one amino acid.
Gene Expression
- Gene expression involves the processes of transcription and translation.
Transcription
- Transcription is the process of copying genetic instructions from DNA to messenger RNA (mRNA).
- Transcription occurs in the nucleus.
- During transcription, thymine (T) in DNA is replaced with uracil (U) in mRNA.
- Transcription has three steps: initiation, elongation, and termination.
- Initiation: RNA polymerase binds to the promoter sequence of DNA, causing the double-stranded DNA to unwind and unzip, exposing the bases of each strand.
- Elongation: RNA polymerase catalyses transcription by joining complementary nucleotides onto the growing 3’ end of the mRNA strand.
- Termination: After the RNA polymerase moves to the downstream region of the gene, transcription stops, and the pre-mRNA is released from the template.
Regulator Genes
- Regulator genes produce proteins that control the activity of other genes.
- Regulator genes help organisms conserve energy and ensure cells produce the appropriate proteins.
Trp Operon
- The Trp operon is a series of genes in certain bacteria that encode for the production of the amino acid tryptophan.
- An operon is a group of linked structural genes with a common promoter and operator that are transcribed as a single unit.
- The Trp operon is composed of:
- Structural genes: code for RNA or protein products other than a regulator (e.g., trpA, trpB, trpC, trpD, and trpE, which encodes tryptophan synthetase)
- Regulatory gene: codes for a product (usually protein) that controls the expression of other genes (e.g., a repressor, which when active, binds to DNA and regulates gene expression by decreasing transcription).
- Promoter (Ptrp): Short DNA segment where RNA polymerase attaches and starts transcription of structural genes.
- Operator (O): Short DNA segment that provides a binding site for a repressor, preventing transcription.
- Leader: Contains the trpL gene (for the leader peptide) and attenuator section that further regulates transcription.
Attenuation
- Attenuation further regulates transcription in the Trp operon.
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Low levels of tryptophan (or absence):
- The ribosome pauses at the trp codon, waiting for enough tryptophan to produce the leader polypeptide.
- This pausing prevents a hairpin loop from forming between mRNA regions 1 and 2.
- A hairpin loop forms between regions 2 and 3, which does not cause the RNA polymerase to detach and prevents the terminator hairpin of regions 3 and 4 from forming.
CRISPR-Cas9 Technology
- CRISPR-Cas9 is a powerful gene-editing tool that allows for precise changes in DNA sequences.
- CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats.
- Cas9 is a CRISPR-associated protein 9.
- The CRISPR-Cas9 system involves a guide RNA (gRNA) that directs the Cas9 enzyme to a specific DNA sequence.
- Cas9 then cuts the DNA at the target site, allowing for the insertion or deletion of genetic material.
Ethical Concerns Regarding CRISPR-Cas9
- Scientists are hesitant to use CRISPR outside of research due to safety concerns, including potential off-target cleavages and mosaics.
- Ethical concerns surrounding CRISPR include:
- Informed consent: It is impossible to obtain informed consent from embryos.
- Inequality: The cost of CRISPR technology could potentially create inequalities in access.
- Discrimination: CRISPR could be used to discriminate against individuals based on perceived biological inferiority.
Polymerase Chain Reaction (PCR)
- PCR is a laboratory technique that produces many identical copies of DNA from a small initial sample.
- PCR amplifies DNA by making multiple identical copies.
- Taq polymerase is an enzyme used in PCR that adds free nucleotides to single-stranded DNA to synthesize a new strand.
- PCR amplifies a DNA sample to increase the quantity of DNA available.
- After each cycle of PCR, the amount of DNA doubles (2^n, where n is the number of cycles).
PCR Ingredients
- Taq polymerase
- Buffer
- DNA sample
- Primers
- Free nucleotides
- PCR tube
PCR Steps
- Denaturing: DNA is heated to approximately 90–95 °C to separate the strands, forming single-stranded DNA. (occurs for 1 minute)
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Annealing: The single-stranded DNA is cooled to approximately 50–55 °C to allow primers to bind to complementary sequences on the single-stranded DNA. (occurs for 2 minutes)
- Forward primer: binds to the 3’ end of the template strand and reads DNA in the same direction as RNA polymerase.
- Reverse primer: binds to the 3’ end of the coding strand and reads DNA in the reverse direction to RNA polymerase.
- Elongation: DNA is heated to 72 °C, allowing Taq polymerase to work optimally. Taq polymerase binds to the primer and uses free nucleotides to synthesize new complementary strands to each template strand. (occurs for 1 minute)
Gel Electrophoresis
- Gel electrophoresis separates DNA fragments based on their molecular size through an electric field.
- DNA fingerprinting identifies DNA from different individuals based on variable numbers of tandem repeats of short DNA segments near the ends of chromosomes.
- DNA sequencing identifies the order or sequence of bases along a DNA strand.
- Gel Electrophoresis is typically used after a DNA sample has been cut up using restriction endonucleases or after a short sequence of DNA has been amplified using PCR.
Gel Electrophoresis Steps
- DNA samples are loaded into wells on a gel.
- An electric current is applied to the gel.
- DNA fragments migrate through the gel towards the positive electrode.
- Smaller fragments move faster and farther than larger fragments.
- The separated DNA fragments can be visualized using dyes or other methods.
Metabolism
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Anabolism: Building complex molecules from simple ones. Energy-requiring or endergonic.
- Example: Photosynthesis.
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Catabolism: Breaking down complex molecules into simpler ones. Energy-releasing or exergonic.
- Example: Cellular respiration.
Enzymes
- Enzymes speed up the rate of reactions by lowering the activation energy needed for reactions.
- Enzymes consist of one or more polypeptide chains.
- When a substrate joins to an active site of an enzyme, it temporarily forms an enzyme-substrate complex.
- The shape of the active site is not rigid and can adjust to the shape of the substrate.
Enzymes in Photosynthesis and Cellular Respiration
- Enzymes regulate each step in photosynthesis and cellular respiration to speed up and control reactions, ensuring efficient metabolism.
Coenzymes
- Coenzymes are organic molecules that act with enzymes to alter the rate of a reaction.
- Coenzymes are a subset of cofactors.
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Cofactors: Non-protein molecules or ions that are essential for the normal functioning of some enzymes.
- Inorganic cofactors: Do not contain carbon and include metal ions.
- Organic cofactors: Small non-protein organic molecules needed for function of specific enzymes.
- During reactions, coenzymes bind to the active site, donate energy or molecules, and cannot be immediately reused.
- Coenzymes leave the enzyme and are recycled by accepting more energy to assist in more reactions, known as the cycling of coenzymes.
- Coenzymes are essential for certain biochemical processes.
Coenzymes in Cellular Respiration
- Coenzymes are non-protein organic molecules.
NAD
- NAD+ is the unloaded form of NADH, which can accept hydrogen ions and electrons during cellular respiration.
- When a substrate needs to give up electrons and hydrogen ions (is 'oxidised'), NAD+ accepts these and becomes NADH.
- As NAD transitions between loaded and unloaded forms, it switches from helping enzymes catalyse reactions where electrons are lost ('reduction') to helping those enzymes that catalyse reactions where electrons are gained ('oxidation').
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