2.7 bio gene expression

gene definition

A gene is a section of DNA that contains the base sequence coding for a specific polypeptide chain.

triplet definition

A triplet is a sequence of three consecutive nucleotides on the DNA strand, and each triplet codes for a specific amino acid during protein synthesis.

Transcription

Transcription is the first step in protein synthesis, and it occurs in the nucleus. The purpose of transcription is to produce an mRNA copy of the gene so that the genetic information can leave the nucleus and be directly used in translation to make a protein. This ensures that the original DNA does not get damaged by leaving the nucleus.

Transcription begins when the RNA polymerase enzyme binds to a gene and unzips the DNA double helix strands to expose the bases of the gene. One strand of DNA is used as a template, where free RNA nucleotides join the strand using complementary base-pairing rule (A—U, C—G), producing a single mRNA strand. Each three consecutive bases on the mRNA strand is called a codon, and each codon codes for a specific amino acid. Each codon is complementary to a triplet on the template DNA strand (ensure you defined triplet before). When the gene is fully transcribed, the mRNA detaches and moves out of the nucleus into the cytoplasm and attaches to a ribosome in preparation for translation.

Translation

The purpose of translation is to decode the mRNA strand produced during transcription to form a specific sequence of amino acids in a polypeptide.

Translation happens at the ribosome after it attaches to the mRNA in the cytoplasm. The ribosome reads the mRNA strand in sets of three bases (codons). When the ribosome reads the START codon (AUG), a tRNA with the complementary anticodon (UAC) temporarily binds to the codon and brings the amino acid methionine (MET). The tRNA is then released without its amino acid. As the ribosome moves along the mRNA to the next codon, another tRNA with the complementary anticodon binds to the codon and delivers the corresponding amino acid. The amino acids are joined together by peptide bonds as each new amino acid is added to the chain, causing the polypeptide chain to grow. Translation continues until a STOP codon (UAA / UAG / UGA) is reached, causing the ribosome to detach from the mRNA and release the completed polypeptide chain. The polypeptide chain is now ready to be folded into a functional protein used for cellular processes.

• define anticodon before this

Mutation

A mutation is a random permanent change in the DNA base sequence.

Spontaneous mutations

A spontaneous mutation occurs naturally when there is a failure during DNA replication

Induced mutations

An induced mutation occurs as a result of exposure to mutagens.

Redundancy

The genetic code has redundancy due to the fact that two or more codons can specify the same amino acid (degeneracy).

For example, codons GAA and GAG both specify glutamic acid (GLU). [Any example can be given.] This means that there are more codons than amino acids so in any given translation, some codons will be redundant.

Base substitution mutation

Same sense mutation: if the substituted base does not cause a change in the amino acids sequence, it is a same sense mutation.

Missense mutation: if the substituted base does change the amino acids sequence, it is a missense mutation (can still produce a non-functional protein). The different amino acid may cause the final protein to fold slightly differently, and therefore not function correctly.

Nonsense mutation: if the substituted base results in a premature STOP codon, it will have a severe impact on protein synthesis as the protein is cut short.

Base deletion/insertion

When a mutation results in the deletion or insertion of a base on the template DNA strand, it causes a reading frame shift because bases are read in groups of three (triplets). This frameshift changes how each subsequent triplet is read, altering the amino acid sequence and therefore the final protein.

Point mutation

mutations that only involve a single nucleotide (one base).

mutation question structure

1. This disease is caused by a __ mutation, where [number] bases are deleted/inserted/substituted in the DNA sequence.

2. When this mutated DNA is transcribed, the mRNA contains the corresponding bases (__), which alters the codons read during translation.

3. describe mutated bases:

• if three bases are inserted: ‘the first three inserted/deleted bases form an extra codon, meaning an additional amino acid is added to the polypeptide chain’.

• If under three: “The __ inserted/deleted base causes a reading-frameshift because bases are read in groups of three. This frameshift changes how each subsequent codon is read, so every amino acid added after this point is likely to be different from the sequence coded for on the normal gene, therefore affecting how the final protein folds.”

4. The order of amino acids in a protein is important because it determines how the polypeptide folds and how different parts of the chain interact with each other. The folding of the polypeptide is essential for the protein to form the correct 3D shape needed for proper function.

5. Because the mutation changes the amino acid sequence, the enzyme’s active site shape is altered, meaning the enzyme can no longer carry out its function of ______.

6. This loss of protein function disrupts normal cellular processes, leading to symptoms such as [context]. As a result, the individual may experience [context/disease], which affects their daily life by causing [context].

metabolic pathway question structure

1. A metabolic pathway is a series of enzyme-controlled reactions, where the product of one reaction becomes the substrate for the next reaction.

2. Under normal function, the __ gene produces the enzyme __, which catalyses the first step of breaking down/converting [metabolite 1] into [metabolite 2].

3. A second gene produces a second enzyme [enzyme 2], which then breaks down [metabolite 2] into [metabolite 3].

4. Since there is a mutation in the __ gene in [some context idk] a non-functioning __ enzyme is produced. This blocks the [number] step of the metabolic pathway, meaning [metabolite #] cannot be broken down and instead builds up to toxic levels. Even though enzyme 2 still functions normally, it has no substrate to act on, so [metabolite 3] is not produced.

5. The very first metabolite production may also slow down (because the others are not functioning or wtv) - optional add

6. The buildup of toxic substances and the lack of [essential product] disrupts normal cell function [give more context as to why if stated in description], leading to symptoms such as [disease symptons]. As a result, the individual experiences [disease], which affects their daily life by [context].

Phenotype

The physical expression of an individual resulting from the interaction of its genotype with the environment.

Genotype + environment —> phenotype

Genotype

The set of alleles that determine the expression of an organism’s particular trait.

Explaining what affects the phenotype

The phenotype [wtv] was caused by [what you think e.g. constant wind]. Environment is determining the phenotype of the organism.

Or

The phenotype [wtv] is due to its inherited gene (genotype).

Environmental factor

An environmental factor is an internal/external factor that affects the organism’s phenotype without altering its genotype e.g. trees growing in persistent windy conditions may grow sideways.

Mutagen

A mutagen is a physical/chemical factor that changes an organism’s genotype e.g. UV radiation can cause mutations that lead to skin cancer.

Examples of mutagen: alcohol, drugs, UV radiation/light

Environment affecting genotype example structure answer

1. environmental factor definition + example

2. mutation definition + example

3. Phenotype is the physical expression of the genes, and it can be influenced by environmental conditions.

4. The phenotype results from the interaction between the genotype and environment e.g. [context from question]

5. The __ acts as an environmental factor that changes the __’s physical expression without changing the actual DNA sequence, allowing [context] even though its genotype remains unchanged. It is not a mutagen.

   1. or other way around if it is.

DNA structure

1. double stranded polymer made of nucleotides.

2. Found in cell nucleus (cannot leave)

3. nucleotides are made of phosphate group bonded to deoxyribose sugar, which is bonded to one of the four nitrogen bases: adenine (A), guanine (G), thymine (T), and cytosine (C).

4. only one form

5. Stores the entire genetic code for the organism

6. Much more longer-lived and more stable

7. Used as the template during transcription.

8. triplets are called triplets

mRNA structure

• single-stranded polymer made of a smaller strand of nucleotides

• mRNA is made in the nucleus but leaves to the cytoplasm

• mRNA nucleotide is made of phosphate group bonded to ribose sugar, which is bonded to a nitrogenous base (like DNA). However, mRNA has a nitrogen base uracil that replaces the base thymine found in DNA nucleotide. (say mRNA if talking about mRNA) Shares the rest of the same bases as DNA.

• Carries the code for one gene to the ribosome

• Short-lived; broken down after translation

• Triplets on mRNA are called codons

• Used as the template strand during translation

• three different forms - say for RNA only

  • mRNA - carrier molecule, takes the copy of genetic info from nucleus to ribosome.

  • tRNA - attaches to amino acids in cytoplasm, carries correct amino acid to ribosome for protein synthesis.

  • rRNA - help make up the ribosome that are site of protein synthesis

Protein

Proteins are large polymer molecules made up of many smaller repeating units called amino acids. The amino acids are joined together by peptide bonds, forming a polypeptide chain. 

functional protein structure

primary structure - sequence of amino acids bonded together in a polypeptide chain

secondary structure - folding of polypeptide chain (primary) into stable structures such as alpha helices and beta sheets by H bonding between residues (r groups).

• alpha helix = polypeptide backbone FOLLOWS a helical path, helical shape held in place by H bonds.

• beta sheet = strands of protein lie adjacent to one another and are held by H bonds BETWEEN the peptide backbone.

tertiary structure - complete 3d folding of polypeptide chain into a specific shape to form a protein. held in place by salt bridges, H bonds, and disulfide bonds.

quaternary structure - when two or more proteins (tertiary units) fit together to form a FUNCTIONAL protein.

fibrous proteins

structural proteins. composed of long protein filaments which are inert, water insoluble, and used in structural support and movement. examples include: keratin, collagen, and elastin. they are usually used in the body to make bones, muscle fibres, and connective tissues.

globular protein

large, round molecules that are composed of folded polypeptide chains. they are water soluble, unstable, and sensitive to pH and the environment. Globular proteins include enzymes and hormones.

importance of proteins

Proteins are important because they constitute enzymes which catalyse many important reactions in the cell. They are also involved in transporting chemicals, regulation and protection, and providing structure for the cell. Proteins are vital for maintaining essential life processes.

anticodon definition

An anticodon is a sequence of three nucleotides on a tRNA molecule that matches with a specific codon on a strand of mRNA during translation.

base insertion/deletion vs base substitution (which is worse)

Base insertion or deletion causes a frameshift, altering every triplet after the mutation and usually producing a completely non‑functional protein. Whereas, base substitution typically affects only one codon and may have little or no effect on the final protein; even if the amino acid changes, the protein may still fold correctly enough to function (though sometimes at a reduced level).

mRNA vs tRNA

similarity:

• share same base

• type of RNA molecule

mRNA:

• made during transcription

• Carries genetic code from DNA (nucleus) to ribosome

• each three bases = codon

• Codons determine which amino acid is added during translation

• used as a template strand for translation that the ribosome reads

• Short lived; broken down after translation.

tRNA (Transfer RNA)

• Each tRNA carries one specific amino acid

• Has an anticodon that is complementary to an mRNA codon

• Anticodon–codon pairing ensures the correct amino acid is added

• Transfers amino acids to the ribosome during translation

• Reused many times; not destroyed after one use

why DNA cannot be directly translated

DNA cannot be directly translated because it is double‑stranded, cannot leave the nucleus, and uses bases that ribosomes cannot read.

• DNA is too large, too stable, and too valuable to risk damage in the cytoplasm. Translation happens at the ribosome which is in the cytoplasm, therefore DNA could be easily damaged if it left the nucleus.

• The ribosomes can also only read single-stranded sequences, however DNA is double-stranded. DNA also uses bases that the ribosomes cannot read. tRNA anticodons pair with AUCG, however DNA contains the bases ATCG.

• Translation must only use the instructions for one protein at a time. DNA contains all genes, so translating it directly would be chaotic.

• mRNA is the correct format for ribosomes.

accuracy of transcription and translation

Transcription and translation are both highly accurate processes.

During transcription, RNA polymerase matches RNA nucleotides to the DNA template strand using precise complementary base‑pairing (A–U and C–G), producing an mRNA sequence that is an exact copy of the gene. RNA polymerase reduces errors and ensures the codons on the mRNA accurately represent the DNA triplets.

During translation, each tRNA carries only one specific amino acid and its anticodon must accurately match the mRNA codon before the ribosome forms a peptide bond.

This ensures that the correct amino acid sequence is produced, allowing the polypeptide to fold into its proper 3D shape and carry out its specific function.