Gene Expression Flashcards
Define DNA
> DNA (Deoxyribonucleic Acid):
- Double-stranded molecule carrying genetic instructions for the growth, development, and reproduction of organisms.
- Consists of long chains of nucleotides.
> Nucleotide Composition:
Each nucleotide contains:
- Sugar (deoxyribose).
- Phosphate group.
- One of four nitrogenous bases:
*Adenine (A).
*Thymine (T).
*Cytosine (C).
*Guanine (G).
> DNA Structure:
- Two strands are complementary and run antiparallel (in opposite directions), forming a double helix structure.
> Base pairing rules:
- Adenine (A) pairs with Thymine (T), in a double bond.
- Cytosine (C) pairs with Guanine (G), in a triple bond.
- The pairs are linked together by hydrogen bonds.
> Function:
- Encodes genetic information organised into units called genes.
- Genes serve as instructions for synthesising proteins, which perform vital cellular functions.
> Location:
- Found in the nucleus of eukaryotic cells.
> DNA Replication:
The base-pairing rule ensures accurate replication during cell division.
> Mutation and Variation:
DNA can undergo mutations (changes in base sequences), leading to genetic variation or, in some cases, disease.
Define Chromosome
> Chromosome:
- A long, thread-like structure made of tightly coiled DNA wrapped around histone proteins.
- Contains genetic information in the form of genes.
> Chromosome Structure:
- DNA wrapped around histones forms a complex called chromatin.
- Allows large amounts of DNA to fit within the nucleus.
> Function:
- Ensure accurate replication and distribution of DNA during cell division (mitosis and meiosis).
- Facilitate the transmission of genetic information to offspring.
> Location:
- Found in the nucleus of every cell of our body.
> Human Chromosome Number:
-Humans have 46 chromosomes arranged in 23 pairs.
- Offspring inherit 23 chromosomes from each parent.
> Homologous Chromosomes:
- Chromosomes exist in pairs in diploid organisms.
- Each pair carries the same genes but may have different alleles (versions of the gene).
Define Genes
> Gene:
- A sequence of DNA that provides instructions for making specific proteins.
- The fundamental unit of heredity, passing traits from parents to offspring.
> Location:
Genes are found on chromosomes inside the cell’s nucleus, containing the organism’s entire genome.
> Function of Genes:
Encode information to produce proteins, which:
- Catalyse reactions
- Provide structure
- Regulate processes
Define an Allele
> Allele:
- A specific version of a gene that can vary due to mutations.
- Found at a specific location on a chromosome.
- Contributes to genetic diversity within a population.
> Homozygous:
An organism has two identical alleles for a gene (e.g., AA or aa).
> Heterozygous:
An organism has two different alleles for a gene (e.g., Aa).
> Dominant Allele:
Expressed in the phenotype even if only one copy is present (e.g., Aa or AA = dominant trait).
> Recessive Allele:
- Only expressed in the phenotype if two copies are present (e.g., aa).
- Example:
For eye color:
B (brown) = dominant
b (blue) = recessive
BB or Bb = brown eyes, bb = blue eyes.
Explain the difference between genotype and phenotype
> Genotype:
-The genetic makeup of an organism, consisting of the alleles inherited from both parents.
- Represented by symbols, e.g., BB, Bb, bb for a single gene.
- Determines the potential traits but does not always predict the visible expression.
> Phenotype:
- The observable characteristics of an organism, resulting from the interaction of the genotype with the environment.
- Includes traits like eye colour, height, and metabolic efficiency.
- What is actually seen or measured, e.g., brown eyes.
Define RNA
> Definition:
RNA is a single-stranded nucleic acid that plays key roles in coding, decoding, regulation, and expression of genes.
> Structure:
- Single-stranded molecule.
- Backbone: Composed of ribose sugar and a phosphate group.
- Nitrogenous Bases: Adenine (A), Uracil (U), Cytosine (C), Guanine (G).
Uracil (U) replaces Thymine (T) found in DNA.
> Types of RNA and Functions:
- mRNA (Messenger RNA):
Made from the DNA template strand. It carries genetic information from DNA to the ribosome. Serves as a template for protein synthesis. - tRNA (Transfer RNA):
Brings amino acids to the ribosome during protein synthesis.
Matches amino acids to the coded mRNA message via its anticodon. - rRNA (Ribosomal RNA):
Combines with proteins to form ribosomes, the site of protein synthesis.
Ribosome
The Ribosome is the organelle that “reads” the mRNA and, with help from tRNA, adds amino acids to a polypeptide chain that correspond to each codon on the mRNA until a stop codon is reached.
Explain the differences
between DNA and RNA
> DNA (Deoxyribonucleic Acid):
- Structure: Double-stranded molecule with a long chain of nucleotides.
- Function: Carries the genetic information for the development, functioning, and reproduction of all living organisms.
- Replication: Self-replicating, meaning it can make copies of itself.
- Length: Longer and more stable.
> RNA (Ribonucleic Acid):
- Structure: Single-stranded molecule with a shorter chain of nucleotides.
- Function: Transmits genetic information from DNA to the ribosomes for protein synthesis.
- Replication: Not self-replicating, synthesised from DNA when needed via transcription.
- Length: Shorter, less stable than DNA.
Explain the connection between DNA and proteins
> DNA Function:
DNA contains nucleotides that encode the necessary information to make amino acids, which form proteins. While DNA stores the genetic blueprint, it does not directly produce proteins.
> RNA Function:
RNA acts as the messenger between DNA and the machinery that produces proteins.
What are Codons & Anti-codons
> Codon Definition:
A codon is a sequence of three nucleotides (bases) on mRNA that corresponds to a specific amino acid or a stop signal during translation in protein synthesis.
> Genetic Code:
The genetic code consists of 64 codons, of which 61 code for amino acids, while the remaining three (UAA, UAG, UGA) act as stop signals.
> Start Codon (AUG):
AUG serves a dual role: it codes for methionine and signals the start of translation.
> Anti-codon Definition:
- An anti-codon is a sequence of three nucleotides on a tRNA molecule that is complementary to a specific codon on the mRNA. It ensures the correct amino acid is added during translation.
Complimentary (biology meaning)
Opposite to, as in looking into a mirror.
Explain DNA triplets
> Definition:
A DNA triplet, also referred to as a codon, is a sequence of three nucleotide bases in a DNA molecule that codes for a specific amino acid or a stop signal during protein synthesis. The arrangement of these bases in DNA dictates the sequence of amino acids that will form a protein.
> Key Details:
- Start Codon (AUG):
On the mRNA, the triplet AUG (which corresponds to TAC on the DNA) functions as the start signal for translation and codes for the amino acid methionine.
- Stop Codons (UAA, UAG, UGA):
The mRNA triplets UAA, UAG, and UGA do not correspond to any amino acids. Instead, they act as stop signals, indicating the end of the protein synthesis process.
Define transcription + explain its process
> Transcription Overview:
Transcription is the process of converting a segment of DNA into messenger RNA (mRNA), which is later translated into proteins.
> Steps of Transcription:
*Step 1: Initiation…
- Transcription begins in the nucleus.
- RNA polymerase binds to the the template strand of DNA.
- RNA polymerase unwinds the DNA double helix, exposing the template strand that will be transcribed into RNA.
*Step 2: Elongation…
- RNA polymerase moves along the template strand, reading its base sequences.
- As RNA polymerase moves forward, it matches complementary RNA nucleotides to the exposed DNA bases:
Adenine (A) pairs with uracil (U) in RNA.
Cytosine (C) pairs with guanine (G).
- The growing RNA strand (called pre-mRNA) detaches from the DNA as RNA polymerase moves forward. The DNA strands rejoin after RNA polymerase passes.
*Step 3: Termination…
- Transcription continues until RNA polymerase reaches a specific terminator sequence on the DNA, signalling the end of transcription.
- RNA polymerase releases the newly synthesised pre-mRNA and detaches from the DNA template.
- The DNA rewinds, and the mRNA moves out from the nucleus via the nuclear pore, to the cytoplasm for translation.
Define translation + explain its process
> Translation Overview:
Translation is the process of decoding mRNA into a polypeptide chain of amino acids, forming proteins essential for life functions.
- Step 1: Initiation
- In the cytoplasm, the small ribosomal subunit binds to the mRNA strand at the start codon (AUG).
- A tRNA molecule with the anticodon UAC binds to the start codon, bringing the amino acid methionine to the ribosome.
- The large ribosomal subunit then attaches to the small subunit, forming a complete ribosome, ready to begin translation.
*Step 2: Elongation
- The ribosome moves along the mRNA, exposing the next codon.
- A tRNA molecule with a complementary anticodon binds to the new codon, bringing the corresponding amino acid to the ribosome.
- The ribosome catalyses the formation of a peptide bond between the existing amino acid and the new one, extending the growing polypeptide chain.
*Step 3: Termination
- When the ribosome reaches a stop codon (UAA, UAG, or UGA), there is no corresponding tRNA for these codons.
- This signals the end of translation, and the ribosome releases the completed polypeptide chain.
- The new protein detaches, ready for folding and modifications.
- The ribosome, tRNA, and mRNA disassemble, allowing them to be reused for another round of translation.
Define Mutation
A mutation is a permanent change in the DNA sequence of an organism.
It can occur as a single nucleotide change (point mutation) or involve larger DNA segments (frame shift mutation).
> Causes of Mutations:
- Spontaneous Mutations: Arise from errors during DNA replication.
- Induced Mutations: Caused by external factors, known as mutagens, such as radiation or chemicals (environmental factors).
> Effects on Genotype and Phenotype:
- Genotype: Mutation alters the organism’s genetic information.
- Phenotype: Not all mutations have visible effects on the organism’s traits. Some may cause disease or impair function. Or some can enhance survival or reproduction, contributing to evolution.
Point mutations verses Frame shift mutations
> Point Mutation: Point mutations are changes in a single nucleotide base in the DNA sequence. These mutations are: Substitution, Silent, Missense, Nonsense.
> Frameshift Mutation: Frameshift mutations are where multiple nucleotides are added or deleted from the DNA sequence, altering the reading frame of codons in translation, thus the genetic code. These mutations are: Insertion, Deletion, Duplication.
Three types of frame shift mutations:
- Insertion Mutation:
- A frameshift mutation where one or more nucleotide base pairs are added into the DNA sequence.
- This alters the reading frame as the nucleotide base pairs are not in multiples of three, which alters every sequence of triplets downstream of the mutation, causing significant changes in the resulting protein.
- While insertion mutations often lead to genetic disorders, they can also contribute to genetic diversity, sometimes providing evolutionary advantages. - Deletion Mutation:
- A frame shift mutation where one or more nucleotides are removed from the DNA sequence.
- Can affect a single nucleotide or large sections of DNA, sometimes deleting entire genes.
- A small deletion leads to incorrect codon reading downstream. And thus produces nonfunctional or entirely different proteins.
- Large deletions that lead to the loss of entire genes or multiple genes can result in the loss of essential proteins, with severe consequences, like genetic disorders or diseases.
- The severity ranges from benign to severe, and depends on the function of the affected gene and whether the mutation is homozygous (both gene copies mutated) or heterozygous (one mutated copy). - Duplication Mutation:
- A segment of the DNA is copied and inserted into the sequence, leading to the repetition of that segment.
- This extra copy may be located directly next to the original sequence or elsewhere in the genome.
- Arises from replication errors, unequal crossing over, or repair errors.
- Can occur in coding or noncoding regions.
- Affects gene dosage, can contribute to evolution, and is sometimes linked to genetic disorders.
Four types of point mutations:
- Substitution Mutation:
- A point mutation where a single nucleotide in the DNA sequence is replaced by a different nucleotide.
- Can alter the genetic code and affect protein synthesis. But also may have no effect on the amino acid that is coded for, due to the redundancy of the genetic code. - Silent Mutation:
- Results in a codon that codes for the same amino acid due to the redundancy in the genetic code.
- No effect on protein structure or function.
- Example: Protein synthesis remains unchanged; has little or no effect on the organism. - Missense Mutation:
- Changes the codon to one that codes for a different amino acid.
- Impact on protein synthesis: May alter the protein’s structure and function, sometimes leading to disease.
- In rare cases, a missense mutation may improve protein function, offering an advantage. - Nonsense Mutation:
- Creates a premature stop codon, shortening the protein.
- Results in a nonfunctional or incomplete protein, often leading to severe consequences.
Explain how a mutation
can be beneficial
> Definition of Beneficial Mutation:
A mutation that improves an organism’s ability to survive or reproduce in its environment.
> How Beneficial Mutations Work:
Enhancing Proteins: A mutation may alter the structure of a protein (e.g., an enzyme) to make it more efficient or allow the organism to exploit new resources.
> Evolutionary Importance:
- Beneficial mutations contribute to genetic variation, which is essential for natural selection.
- Over time, these mutations enable populations to adapt to changing environments and may lead to the emergence of new species.
Explain why some mutations can have no effect
Because they are a neutral mutation. Which means it is a mutation that has no effect on the organism’s phenotype.
> Causes of Neutral Mutations:
1. Non-functional DNA: Mutation occurs in a region of DNA that doesn’t code for proteins or serve any regulatory function.
2. Silent Mutation: Mutation occurs in a protein-coding region but does not change the amino acid sequence due to the redundancy of the genetic code.
Explain what proteins are made of
> Proteins:
- Large molecules composed of long chains of amino acids.
- Each protein consists of hundreds or thousands of amino acids.
> Amino Acids:
- The building blocks of proteins.
- There are 20 different types of amino acids that can combine in various sequences to form proteins.
Define Enzymes
> Definition of Enzymes:
- Biological catalysts that speed up chemical reactions without being consumed.
- Most enzymes are proteins, though some RNA molecules (ribozymes) also act as enzymes.
> How Enzymes Work:
- Lower Activation Energy: Enzymes reduce the energy required for a reaction to proceed, forming an enzyme-substrate complex.
- They may bring substrates closer, orient them correctly, or alter the chemical environment to favour the reaction, enabling faster and more efficient reactions under cellular conditions.
> Enzyme Specificity:
- Each enzyme has a unique three-dimensional structure, particularly in its active site, which binds specific substrates.
- Described by the “lock and key” or “induced fit” models, where only particular substrates fit the enzyme’s active site.
Define Substrate
> Substrate Definition:
- The specific reactant that an enzyme acts upon during a biochemical reaction.
> Enzyme-Substrate Interaction:
- Enzymes lower the activation energy, speeding up reactions.
- The substrate binds to the active site of the enzyme, forming an enzyme-substrate complex.
> Specificity:
Interaction models like “lock and key” or “induced fit” ensure that enzymes only catalyse reactions with specific substrates.
> Reaction Process:
1. Substrate binds to the enzyme’s active site.
2. The enzyme-substrate complex lowers activation energy.
3. Substrate is converted into products, which are released from the enzyme.
Define Metabolic Pathway + explain how metabolic pathways function
> Metabolic Pathway Definition:
- A series of interconnected biochemical reactions within a cell, where each product of a reaction becomes the substrate for the next step.
> Function of Enzymes in Pathways:
- Enzymes: Each step is catalysed by a specific enzyme, ensuring the reaction proceeds at a controlled rate.
- Enzyme Specificity: Enzymes catalyse only specific reactions or types of reactions.
> Importance of Metabolic Pathways:
- Maintain homeostasis by regulating cellular processes.
- Enable essential cellular functions like energy production, growth, and repair.
Primary, Secondary, Tertiary, Quaternary Structures
> Primary Structure: The sequence of amino acids in a polypeptide chain.
> Secondary Structure: Shape of the polypeptide chain. This occurs when amino acids are linked together by hydrogen bonds into an alpha helix or beta-pleated sheet.
> Tertiary Structure: Shape of the polypeptide chain once it has been folded. This involves the protein folding into complex shapes due to attractions and repulsions of different amino acids. These are held together by di-sulphide bonds.
> Quaternary Structure: Two or more polypeptide chains bonded together.
Explain the effect of disrupting a step in a metabolic pathway
> Enzyme Specificity:
- Each enzyme is responsible for catalysing a specific reaction in a metabolic pathway.
- If disrupted: The reaction slows down or stops, impacting the entire pathway and cellular function.
> Consequences of Enzyme Disruption:
- Substrate Accumulation: The unconverted substrate builds up, potentially reaching toxic levels.
- Reduced/Absent Final Product: The final product, essential for cellular functions like energy production or synthesis of molecules, becomes deficient.
> Impact on Health:
- The buildup of substrates and lack of essential products can lead to metabolic disorders with symptoms ranging from intellectual disabilities to systemic health issues if untreated.
Explain what happens when a metabolic pathway doesn’t function properly
> What Happens When a Pathway Fails?
- Enzyme Deficiency or Malfunction: Leads to accumulation of substrates or a shortage of essential products.
> Consequences of Dysfunction:
- Cellular Malfunction: Insufficient final products impair processes like energy production or the synthesis of crucial molecules.
- Symptoms: Can range from mild to severe, affecting multiple organs depending on the pathway.
> Compensation by Alternative Pathways:
- Cells may use alternative metabolic pathways to bypass the defective one.
- Partial Compensation: Can reduce the impact but may not fully restore normal function.
- Additional Stress: Reliance on alternative pathways may cause imbalances and cellular stress.
Explain how DNA and environment result in the phenotype of an organism
> Phenotype: The physical expression of traits in an organism.
> Genotype vs. Phenotype:
- Genotype: The genetic code (alleles) inherited from parents.
- Phenotype: The observable traits resulting from both genotype and environmental factors.
- Example: Different alleles for eye colour lead to blue, green, or brown eyes.
> Environmental Influence on Phenotype:
- Environmental factors (e.g., diet, climate, UV exposure) can affect gene expression.
- Example: Skin pigmentation changes with sunlight exposure, even though pigmentation is genetically controlled.
> Key Examples of Gene-Environment Interaction:
1. Height:
- Genetics determine potential height.
Environmental factors like nutrition during childhood play a critical role in actual height.
- Disease Susceptibility:
- Genetic predisposition can increase disease risk.
- Lifestyle, stress, and exposure to pathogens influence whether the disease manifests.
Redundancy and Degeneracy
Degeneracy: More codons than amino acids.
Redundancy: Codons that code for the same amino acid.
What is gene expression
Gene expression is the process by which the information encoded in a gene is turned into a function via protein synthesis
