3/4 Bio, AOS 1

What is the relationship between nucleic acids and proteins?

• DNA (a nucleic acid) stores genetic information in its base sequence

• This information is transcribed into RNA and translated into proteins

• Proteins determine cell structure and function, ultimately producing traits

• Therefore: DNA → RNA → Protein → Phenotype

Why are proteins important in cells?

• They are a primary structural component and allow most processes within a cell

Describe the structure of DNA in detail.

• DNA is a double-stranded helix

• Strands are antiparallel (one 5'→3', other 3'→5')

• Backbone = alternating deoxyribose sugar + phosphate

• Bases point inward and pair via hydrogen bonds

What do nucleotides do.

• they store genetic information enabling proteins synthesis

Explain complementary base pairing.

• Adenine (A) pairs with Thymine (T) → 2 hydrogen bonds

• Cytosine (C) pairs with Guanine (G) → 3 hydrogen bonds

• Ensures accurate replication and transcription

Why is DNA structure important for its function?

• Base sequence stores information

• Complementary pairing ensures accuracy

• Double helix protects genetic material

• Antiparallel strands allow enzyme function

What is the genetic code?

• A set of rules mapping mRNA codons → amino acids

• Each codon = 3 bases

What are the key properties of the genetic code?

• Triplet: 3 bases per codon

• Universal: same across most organisms

• Degenerate: multiple codons → same amino acid

• Non-overlapping: each base read once

What are start and stop codons?

• specific three-nucleotide sequences in mRNA that signal the beginning and end of protein synthesis

What is a gene?

A sequence of DNA that codes for a functional protein or RNA

Describe the structure of a eukaryotic gene.

• Promoter: RNA polymerase binding site

• Exons: coding regions

• Introns: non-coding regions

• Terminator: signals end of transcription

What is the difference between exons and introns?

• Exons → expressed (translated into protein)

• Introns → removed during RNA processing

What is transcription?

The process of copying DNA into pre-mRNA

Where does transcription occur?

• Eukaryotes: nucleus

• Prokaryotes: cytoplasm

Outline transcription step-by-step.

1. Initiation:

• RNA polymerase binds promoter

• DNA unwinds

2. Elongation:

• RNA polymerase reads template strand (3'→5')

• Builds mRNA (5'→3') using complementary pairing

3. Termination:

• Reaches terminator

• mRNA released

What base pairing occurs in transcription?

• A → U

• T → A

• C → G

• G → C

What is the template strand?

The DNA strand used by RNA polymerase to build mRNA

What is RNA processing?

Modification of pre-mRNA to produce mature mRNA

What happens during RNA splicing?

• Introns removed

• Exons joined

What is translation?

The process of converting mRNA into a polypeptide (protein)

Where does translation occur?

At ribosomes in the cytoplasm

Outline translation step-by-step.

1. Initiation:

• Ribosome binds mRNA

• Start codon recognised

2. Elongation:

• tRNA anticodon pairs with codon

• Amino acids joined via peptide bonds

3. Termination:

• Stop codon reached

• Protein released

What is a codon and anticodon?

• Codon → 3 bases on mRNA

• Anticodon → complementary 3 bases on tRNA

What is gene regulation?

Control of gene expression — when and how much protein is produced

What is the trp operon?

A repressible operon controlling tryptophan production in bacteria

What happens when tryptophan levels are LOW?

• Repressor inactive

• Cannot bind operator

• Transcription occurs

• Tryptophan produced

What happens when tryptophan levels are HIGH?

• Tryptophan binds repressor

• Repressor activated

• Binds operator

• Blocks transcription

What is DNA manipulation?

The process of cutting, joining, or copying DNA

What do restriction enzymes do?

• Cut DNA at specific sequences

• Produce sticky or blunt ends

Why are sticky ends useful?

• Overhangs allow easier base pairing

• Makes joining DNA fragments easier

What does DNA ligase do?

• Joins DNA fragments

• Forms phosphodiester bonds

What does DNA polymerase do?

• Synthesises new DNA strands

• Adds nucleotides in 5' → 3' direction

How are these enzymes used together?

• Restriction enzymes cut DNA

• Ligase joins fragments

• Polymerase copies DNA

What is CRISPR-Cas9?

A gene-editing technology adapted from a bacterial immune system that allows targeted modification of DNA sequences

What is Cas9?

An endonuclease enzyme that cuts DNA at a specific location

What is the natural function of CRISPR-Cas9 in bacteria?

• Acts as an adaptive immune system

• Stores viral DNA sequences

• Recognises and destroys matching viral DNA in future infections

What are the key components of CRISPR-Cas9?

• Guide RNA (gRNA): matches target DNA sequence

• Cas9 enzyme: cuts DNA

• Target DNA: sequence being edited

How does CRISPR-Cas9 edit DNA step-by-step?

1. Guide RNA binds complementary DNA sequence

2. Cas9 binds and scans DNA

3. Cas9 makes a double-strand break

4. Cell repairs DNA via:

   • NHEJ (non-homologous end joining) → random mutations

   • HDR (homology-directed repair) → precise insertion using template

What is a PAM sequence and why is it important?

• Protospacer Adjacent Motif (PAM)

• Short DNA sequence required for Cas9 binding

• Ensures Cas9 cuts only at correct locations

Applications of CRISPR-Cas9?

• Gene therapy

• Treat genetic diseases

• Improve crops

• Create model organisms

What is PCR?

A technique used to amplify a specific DNA sequence, producing millions of copies

What are the requirements for PCR?

• Template DNA

• Primers

• DNA polymerase (Taq polymerase)

• Free nucleotides

• Thermal cycler

Why is Taq polymerase used?

• Heat-stable enzyme from bacteria

• Does not denature at high temperatures

What are primers?

• Short DNA sequences

• Bind to target DNA

• Provide starting point for DNA synthesis

Outline the PCR cycle.

1. Denaturation (~95°C):

• DNA strands separate

2. Annealing (~50–65°C):

• Primers bind to target sequence

3. Extension (72°C):

• DNA polymerase synthesises new strand

Why is PCR exponential?

• Each cycle doubles DNA

• After n cycles → 2ⁿ copies

What is gel electrophoresis?

A technique used to separate DNA fragments based on size

Why does DNA move in gel electrophoresis?

• DNA is negatively charged (phosphate backbone)

• Moves toward positive electrode

How are DNA fragments separated?

• Smaller fragments move faster and further

• Larger fragments move slower

What is the role of the gel?

• Acts as a sieve

• Slows movement based on size

What is a DNA ladder?

• Set of fragments of known sizes

• Used to estimate fragment length

How do you interpret gel electrophoresis results?

• Compare band positions

• Same pattern = same DNA

• Different pattern = different DNA

Define gene.

sequence of DNA that codes for a functional protein or RNA

Define genome.

The complete set of genetic material in an organism

Define proteome.

The full set of proteins expressed by a cell at a given time

Define enzyme.

A biological catalyst that speeds up chemical reactions

Define plasmid.

Small circular DNA molecule in bacteria used as a vector

Define transgenic organism.

An organism that contains DNA from another species

Define genetically modified organism (GMO).

An organism whose DNA has been altered using biotechnology

Define RNA.

A single-stranded nucleic acid involved in gene expression that carries genetic information from DNA to ribosomes

Define codon.

A sequence of three nucleotides on mRNA that codes for a specific amino acid or stop signal

Define anticodon.

A sequence of three nucleotides on tRNA that is complementary to an mRNA codon

Define polypeptide.

A chain of amino acids linked by peptide bonds that folds to form a protein

Define promoter.

A DNA sequence where RNA polymerase binds to initiate transcription

Define tRNA.

A type of RNA that carries specific amino acids to the ribosome and matches anticodons to codons

Define restriction enzyme (endonuclease).

An enzyme that cuts DNA at specific recognition sequences

Define autonomy.

The right of individuals to make informed decisions about their own lives

Define beneficence.

The obligation to act in ways that promote good and benefit others

Define non-maleficence.

The obligation to avoid causing harm

Define justice.

Fair and equitable distribution of benefits and risks

Define utilitarianism.

An ethical framework that judges actions based on the greatest good for the greatest number

Define rights-based ethics.

An approach focusing on protecting individual rights and freedoms

Define virtue ethics.

An approach based on moral character and virtues rather than rules or consequences

What are social factors in bioethics?

Impacts on society, cultural values, and public acceptance

What are economic factors?

Costs, affordability, and access to technologies

What are legal factors?

Laws and regulations governing the use of biological technologies

What are political factors?

Government policies and decision-making influencing biotechnology use