lecture 1

Question 1

explain and detail the learning outcomes

Answer 1

2. Explain why there is a need to maintain high sequence similarity during replication:
   Maintaining high sequence similarity during DNA replication is essential because:

Genetic Fidelity: Accurate replication ensures that the genetic information passed from one cell generation to the next remains consistent. This is vital for preserving the structure and function of proteins encoded by the DNA.
Prevention of Mutations: Errors in replication can introduce mutations, which may lead to nonfunctional or harmful proteins, potentially causing diseases such as cancer.
Evolutionary Conservation: Many DNA sequences are conserved due to their critical biological functions. High-fidelity replication ensures these important sequences are preserved across generations and species.

3. Identify key enzymes needed for replication that are common to both eukaryotes and prokaryotes and explain their function:
   DNA Helicase: Unwinds the DNA double helix by breaking the hydrogen bonds between the complementary strands, creating the replication fork.
   DNA Polymerase: Synthesizes the new DNA strand by adding nucleotides to the 3’ end of the growing strand, using the original strand as a template. It also proofreads to ensure accuracy.
   Primase: Synthesizes short RNA primers to provide a starting point for DNA polymerase to begin replication.
   Ligase: Joins Okazaki fragments on the lagging strand by sealing nicks in the sugar-phosphate backbone.
   Single-Strand Binding Proteins (SSBs): Bind to single-stranded DNA to prevent reannealing and protect the strands during replication.
   Topoisomerase: Relieves supercoiling and tension ahead of the replication fork by cutting and rejoining DNA strands.
   These enzymes ensure the process of replication is fast, efficient, and accurate across both prokaryotic and eukaryotic organisms.
4. Describe the steps of replication and explain where in this process there is an opportunity for a loss of sequence conservation:
   Steps of Replication:
   Initiation:
   Helicase unwinds the DNA, and primase lays down RNA primers.
   Elongation:
   DNA polymerase extends the new strand by adding complementary nucleotides to the template strand.
   Leading strand is synthesized continuously, while the lagging strand is synthesized in Okazaki fragments.
   Termination:
   Replication is completed when DNA polymerase reaches the end of the template or when two replication forks meet.
   Opportunities for Loss of Sequence Conservation:
   Errors in DNA Polymerase Activity: Despite proofreading, DNA polymerase can make errors, leading to mismatches that can introduce mutations if not corrected.
   Replication of Repetitive Sequences: Repetitive sequences (e.g., microsatellites) are prone to slippage, leading to insertions or deletions.
   Mutagenic Factors: Environmental mutagens or internal factors like reactive oxygen species (ROS) can damage DNA during replication, leading to incorrect base pairing.
5. Apply principles of biochemistry to explain under what circumstances DNA sequences can be good and when it can be bad (using examples might help you):
   Beneficial DNA Sequences:
   Functional Genes: DNA sequences that encode functional proteins, such as the insulin gene, are crucial for health and proper cellular function.
   Evolutionary Adaptations: Mutations that provide a survival advantage can be beneficial. For example, a mutation that leads to antibiotic resistance in bacteria may be advantageous in the presence of antibiotics.
   Harmful DNA Sequences:
   Harmful Mutations: DNA mutations that alter the function of important proteins can lead to diseases. For instance, a single nucleotide mutation in the beta-globin gene can cause sickle cell anemia.
   Oncogenes: Mutations in certain genes (e.g., RAS or TP53) can lead to uncontrolled cell growth, resulting in cancer.

Summary:
High Sequence Similarity: Necessary for the accurate transfer of genetic information.
Common Enzymes: DNA polymerase, helicase, and primase are key in both prokaryotic and eukaryotic replication.
Replication Process: Initiation, elongation, and termination stages provide opportunities for errors.
Biochemistry and DNA: DNA sequences are “good” when they contribute to normal function and “bad” when they lead to detrimental mutations or diseases

Question 2

What do you remember about DNA replication?, detail the fundamentals

Answer 2

• during semi conservative replication the 2 new DNA strands both contain half of the original DNA (in the form of half the original strand)
• DNA replication occurs during the S phase of the cell cycle
• DNA replication is carried out by sigma factors in prokaryotes- Sigma factors recognize specific
  DNA sequences called promoters, typically located just upstream of the genes they control. Different sigma factors recognize different promoter sequences, ensuring that the right set of genes is expressed under specific conditions.
  Sigma factors are proteins that are part of bacterial RNA polymerase (RNAP) and are responsible for the initiation of transcription:
  Function
  Sigma factors help RNAP recognize promoters, open them, and separate DNA strands. They also help with the first steps of RNA synthesis.
  Specificity
  Sigma factors determine which promoter DNA binds to, which allows for the efficient initiation of transcription

-there are similar enzymes required to carry out DNA replication in prokaryotes and eukaryotes

Question 3

Why do eukaryotes use semi-conservative replication?

Answer 3

in order to maintain integrity, and high fidelity of the DNA sequence- eukaryotes have very large genomes with lots of regions of non-coding DNA which is important for the regulation of transcription- low fidelity can be fatal

Question 4

Why Integrity of the DNA is essential

Answer 4

Inheritance of germline sequences helps to introduce genetic variation among a population while there are also mechanisms in place to limit errors in replication that lead to a change in the germline DNA

-changes in nuclei acid sequence can result in changes of the amino acid sequence- this can affect the formation of proteins and their shapes
–changes in amino acid sequence may not affect the type of protein formed

–however changes in amino acid sequence may also result in a change to the shape of the protein, change in the protein function or change in the expression of the protein

• a possible change that can occur to change the shape of a protein is a change from a specific amino acid to one with a different charge within the amino acid sequence- this can for example result in amino acids repelling or attracting one another in the sequence which can ultimately affect the proteins shape as a result the formed protein may no longer be able to bind to a substrate that it was required to bind to
• ergo the change in amino acid sequence can mean the function of the protein is to be affected or the level of expression of the protein is affected because if it cannot fold properly the protein will be exported from the ER and degraded
• these potential changes can be passed down through generations if not fixed and result in diseases when expressed as a potential phenotype

potential changes in the DNA sequences at the gamete and zygote level can create detrimental effects as potential diseases may be passed on to the next generation

Question 5

Mechanisms for the preservation of DNA integrity

Answer 5

*Presence of a nuclear envelope
*Condensation of chromatin when genes are not active- prevents unwanted things from accessing DNA due to high level of compacting around histones
*Semi-conservative replication mechanism- reduces the likelihood of changes to base pairing of DNA

*-Presence of chromosomal structures such as:
*Telomeres –repeating sequences of DNA that are shortened with age, they are replicated by a different mechanism to other parts of the chromosome
*Centromere –repetitive sequences of DNA that are highly packaged to provide a robust attachment site to the mitotic spindleAlberts

Question 6

why may changes to the amino acid sequence have no affect on the protein formation?

Answer 6

Changes to the amino acid sequence of a protein, known as mutations, do not always affect protein formation or function due to several factors:

1. Genetic Code Degeneracy (Redundancy)
   The genetic code is degenerate, meaning that multiple codons (three-nucleotide sequences in DNA or RNA) can code for the same amino acid.
   For example, the amino acids leucine, serine, and arginine each have six different codons that encode them.
   If a mutation occurs in the DNA sequence that changes a codon to another codon for the same amino acid (a synonymous mutation or silent mutation), the amino acid sequence of the protein remains unchanged, and the protein’s structure and function are not affected.
2. Similar Amino Acid Properties (Conservative Substitution)
   Even when a mutation changes an amino acid, the substituted amino acid may have similar properties to the original one.
   For example, if a hydrophobic amino acid like valine is replaced by another hydrophobic amino acid like leucine, the overall structure and function of the protein may remain largely unaffected because both amino acids have similar chemical properties.
   These types of substitutions are called conservative substitutions, as they do not significantly disrupt the protein’s folding or activity.
3. Location of the Mutation
   The effect of a mutation depends on where in the protein the change occurs:
   Non-critical regions: If the mutation occurs in a non-essential part of the protein, such as a loop or an area that is not directly involved in the protein’s function, the protein might still fold and function normally.
   Active or binding sites: Mutations in the active site of an enzyme or a binding site of a receptor are more likely to have a significant impact on protein function.
4. Protein Folding and Structure
   Proteins have a robust ability to fold into their functional structures due to the thermodynamic stability of their native state.
   Small changes in the amino acid sequence might not be enough to destabilize the protein’s 3D structure, allowing it to fold properly and maintain its function.
   Chaperone proteins in cells also assist in the correct folding of proteins, helping to prevent potential issues caused by minor mutations.
5. Redundant and Compensatory Pathways
   Some proteins are part of larger protein families or biochemical pathways with redundant functions.
   If a mutation affects one protein’s function, other proteins or pathways might compensate for its loss or reduced activity, minimizing the impact of the mutation on cellular functions.
   Summary
   Changes to the amino acid sequence may have no effect on protein formation or function due to the degeneracy of the genetic code, conservative amino acid substitutions, the mutation’s location within the protein, the protein’s inherent stability, and compensatory cellular mechanisms. These factors allow proteins to tolerate some level of variation without compromising their structure or activity.

Question 7

what is The Nuclear Envelope made up of?

Answer 7

➢Consists of two concentric membranes
➢Contiguous with one another but are functionally distinct
➢To gain entry into the nucleus proteins and nucleic acids must be transported through the nuclear pore comple

Question 8

how does the nuclear pore complex work?

Answer 8

how does the nuclear pore complex

The nuclear pore complex (NPC) is a large protein structure embedded in the nuclear envelope that regulates the transport of molecules between the nucleus and the cytoplasm in eukaryotic cells. The NPC acts as a gateway, controlling the exchange of materials, such as RNA, proteins, ions, and signaling molecules, to ensure that only the appropriate molecules move in and out of the nucleus.

Structure of the Nuclear Pore Complex
The NPC is a large protein assembly made up of multiple nucleoporins (proteins that make up the pore).
It has a symmetrical structure with eightfold radial symmetry and consists of multiple parts:
Cytoplasmic filaments: Extend into the cytoplasm and play a role in recognizing and interacting with transport molecules.
Central channel: The main pore through which molecules pass.
Nuclear basket: Extends into the nucleus and aids in the selective transport of cargo.
Ring structures: Found on both the nuclear and cytoplasmic sides, providing the framework for the NPC.
How the NPC Works: Transport Mechanisms
The transport through the NPC can be classified into two types: passive diffusion and active transport.

Passive Diffusion:

Small molecules and ions (less than 40 kDa in size) can passively diffuse through the NPC without the need for energy or specific transport signals.
This process is non-selective, allowing molecules to move through the central channel freely based on their size and concentration gradient.
Active Transport:

Large molecules like RNA, proteins, and ribonucleoprotein complexes (greater than 40 kDa) require active transport mechanisms to pass through the NPC.
Active transport requires:
Nuclear Localization Signals (NLS): For proteins that need to be imported into the nucleus. NLS is a specific sequence of amino acids on the cargo protein that signals it should be transported into the nucleus.
Nuclear Export Signals (NES): For molecules that need to be exported out of the nucleus to the cytoplasm.
Transport receptors (importins and exportins) recognize these signals and bind to the cargo molecules to facilitate their movement through the NPC.

Steps of Active Transport through the NPC

1. Cargo Recognition:

In the cytoplasm, transport receptors like importins bind to the cargo protein containing an NLS.
This binding forms a cargo-receptor complex.

2. Translocation through the NPC:

The cargo-receptor complex moves through the NPC, interacting with the nucleoporins that line the channel.
These interactions are facilitated by FG repeats (phenylalanine-glycine-rich regions) present in the nucleoporins, which act as binding sites for transport receptors.

3. Release and Cargo Delivery:

Once inside the nucleus, the complex encounters Ran-GTP, a small GTPase that triggers the release of the cargo from the receptor.
The receptor, now bound to Ran-GTP, is transported back to the cytoplasm.
In the cytoplasm, Ran-GTP is converted to Ran-GDP, causing the receptor to release Ran and become ready to bind to new cargo.

4. Recycling:

The transport receptors are continuously recycled between the nucleus and the cytoplasm, making the process efficient and energy-effective.

Regulation of Transport through the NPC

Ran-GTP gradient: The asymmetric distribution of Ran-GTP in the nucleus and Ran-GDP in the cytoplasm is critical for the directionality of transport.
Post-translational modifications: Changes in the state of nucleoporins or cargo proteins can regulate transport rates.
Cell cycle control: During different phases of the cell cycle, the activity and number of NPCs can change, affecting nuclear transport.

Importance of the Nuclear Pore Complex

Gene expression regulation: NPCs control the export of mRNA from the nucleus to the cytoplasm, which is essential for protein synthesis.
Signal transduction: They allow signaling molecules to enter the nucleus and affect gene regulation.
Protection of genetic material: By controlling what enters and leaves the nucleus, the NPC ensures the integrity and proper functioning of the cell’s genetic material.

Summary
The nuclear pore complex acts as a selective gatekeeper for the movement of molecules between the nucleus and cytoplasm. It uses passive diffusion for small molecules and active transport for larger molecules through the interaction of transport receptors with specific nuclear localization and export signals. This mechanism is crucial for maintaining cellular functions such as gene expression, signal transduction, and the overall integrity of the cell’s genome.

Question 9

what are the components of chromatin?

Answer 9

Components of chromatin
*Two molecules of each of four histone (H2A, H2B, H3and H4) make an octamer.
*Histones are very well conserved between species
*146 ntof DNA winds 1.65 times around histone core to form the nucleosome.
*Hydrogen bonds form between the DNA and the histone octamer
*Each nucleosome is separated from the next by up to 80 ntof linker DNA
*Histone H1 works as a clamp

linker DNA is The double-stranded DNA that joins the DNA of one nucleosome to the next. Linker DNA is usually about 20 base pairs in length, but can vary between organisms and cell types. It helps to stabilize the structure of chromatin by associating with a linker histone H1.

Question 10

why can DNA packaging prevent enzymes from gaining access to it?

Answer 10

As packaging gets more complex the “room” taken up by DNA gets smaller and it is harder for proteins to gain access to the DNA to “read” it (transcription) or replicate it (replication)

Question 11

how is Replication is based upon the formation of base-pairs

Answer 11

Replication is based upon the formation of base-pairs

*Replication must occur before cell division starts.
*The original copy is used as a template to complimentary copy of genomic DNA.

*This occurs in a stepwise manner:
1.The double helix must be separated into 2 strands, generating the replication fork (separation).

2.DNA Primase makes short RNAs (primers) acting as a platform for DNA polymerase (Initiation –leading strand only).

3.The template strand bases are recognised by free bases and then joined together by DNA polymerase (polymerization)

4.On the lagging strand DNA primase creates primers every 100-200 bp, which are extended by DNA polymerase and joined together by DNA ligase

Question 11

what enzymes are involed in DNA replication?

Answer 11

DNA helicase
DNA primase
DNA ligase
DNA polymerase
Topoisomerase

Question 12

Step 1a: Separation

Answer 12

Before replication can begin, the helix needs to be separated into 2 template strands by DNA helicase.

DNA helicase binds to a single strand of DNA and spins around it, propelled by the hydrolysis of ATP, physically breaking the hydrogen bonds between bases.

Question 13

Step 1b: Separation

Answer 13

Once separated the single stranded DNA is bound by single stranded binding (SSB) proteins to prevent secondary structures forming

Question 14

Step 2: Initiation

Answer 14

Once the replication fork is formed DNA Primasemakes short RNA primers of around 10nt in length which recognise bases at the replication fork

Question 15

Step 3: Polymerisation

Answer 15

This presents DNA Polymerase with the template that is needed to initiate its action, nucleotides are added by phosphodiester bonds in a 5’ to 3’ direction

Question 16

what is cooperatove binding?

Answer 16

Cooperative binding is a phenomenon in which the binding of a ligand to one site on a protein affects the binding affinity of additional ligand molecules to other binding sites on the same protein. This type of binding typically occurs in proteins with multiple binding sites and is common in multi-subunit proteins, such as enzymes and hemoglobin.

Key Features of Cooperative Binding
Positive Cooperativity:

When the binding of a ligand to one site increases the affinity of the other binding sites for additional ligand molecules.
This results in a sigmoidal (S-shaped) binding curve rather than a hyperbolic curve, indicating that once one ligand binds, subsequent ligands bind more easily.
An example of positive cooperativity is hemoglobin, where the binding of one oxygen molecule increases the likelihood that additional oxygen molecules will bind to the other subunits.
Negative Cooperativity:

When the binding of a ligand to one site decreases the affinity of other sites for additional ligand molecules.
This type of cooperativity leads to a decrease in the protein’s ability to bind more ligand molecules after the first binding event.
Negative cooperativity is less common but can occur in certain enzymes and receptor systems.
Examples of Cooperative Binding
Hemoglobin and Oxygen Binding:

Hemoglobin, the oxygen-carrying protein in red blood cells, exhibits positive cooperativity.
Hemoglobin has four subunits, each capable of binding one oxygen molecule. When one oxygen molecule binds, it induces a conformational change that increases the affinity of the remaining subunits for oxygen.
This cooperative binding is essential for efficient oxygen uptake in the lungs and release in tissues.
Enzyme Regulation:

Many enzymes exhibit cooperative binding to their substrates or regulatory molecules.
Allosteric enzymes, which are regulated by molecules binding to sites other than their active site, often show cooperative binding. This allows for fine-tuning of enzyme activity in response to changes in cellular conditions.
Mechanism of Cooperative Binding
Conformational Changes: Cooperative binding often involves conformational changes in the protein structure. When a ligand binds to one site, it alters the shape of the protein, making other binding sites more (or less) accessible for the ligand.
Allosteric Sites: The binding of a ligand at one site can affect the binding affinity at another site through allosteric effects, where the interaction is not directly at the active site but elsewhere on the protein.
Importance of Cooperative Binding
Efficient Regulation: Cooperative binding allows for more precise regulation of biological processes. For example, in hemoglobin, it ensures that oxygen is easily picked up in the lungs and readily released in tissues where it is needed.
Sensitivity to Changes: Cooperative binding can make proteins highly sensitive to small changes in ligand concentration, which is crucial in processes like enzyme catalysis and signal transduction.
Allosteric Regulation: Many biological pathways depend on cooperative binding to regulate enzyme activities, allowing cells to respond dynamically to changes in the environment or metabolic demands.
Summary
Cooperative binding is a mechanism in which the binding of a ligand to one site on a multi-subunit protein influences the binding affinity of additional ligands to other sites. This phenomenon can either increase (positive cooperativity) or decrease (negative cooperativity) the affinity of subsequent ligand binding. It plays a vital role in processes such as oxygen transport by hemoglobin, enzyme regulation, and cellular signaling, enhancing the efficiency and sensitivity of biological responses.

Question 17

what is the proofreading that polymerase has?

Answer 17

DNA polymerase has a built-in proofreading mechanism that helps ensure the accuracy of DNA replication. During the replication process, DNA polymerase adds nucleotides to a growing DNA strand based on the complementary sequence of the template strand. However, sometimes errors occur when the wrong nucleotide is incorporated. Here’s how the proofreading process works:

Proofreading Mechanism of DNA Polymerase

1. 3’ to 5’ Exonuclease Activity:

DNA polymerase has an inherent 3’ to 5’ exonuclease activity, which allows it to remove incorrectly paired nucleotides.
If the enzyme detects that a newly added nucleotide does not correctly pair with the template strand, it temporarily stops adding new nucleotides.

2. Error Detection:

DNA polymerase recognizes that the DNA structure is distorted due to the incorrect base pairing. This recognition signals the enzyme to switch from its polymerization mode (adding nucleotides) to its exonuclease mode (removing nucleotides).

3. Removal of the Mismatched Nucleotide:

The enzyme moves backward by one nucleotide position in the 3’ to 5’ direction and removes the incorrect nucleotide.
Once the incorrect nucleotide is excised, the polymerase resumes its 5’ to 3’ polymerization activity and adds the correct nucleotide in its place.

4. Resumption of DNA Synthesis:

After correcting the mistake, DNA polymerase continues to synthesize the new strand in the 5’ to 3’ direction, with the accuracy of the process greatly improved by this proofreading capability.
Importance of Proofreading
Increases Fidelity: Proofreading by DNA polymerase significantly increases the fidelity (accuracy) of DNA replication, reducing the number of errors or mutations that can occur.
Error Rate Reduction: Without proofreading, the error rate during DNA replication would be about 1 in 10,000 nucleotides. With proofreading, this error rate is reduced to about 1 in 10 million nucleotides.
Prevention of Mutations: Proofreading helps prevent the accumulation of mutations, which can lead to genetic disorders, cancers, or cell dysfunction.

Types of DNA Polymerases with Proofreading
Prokaryotic DNA Polymerases: In bacteria, DNA polymerase III is the main enzyme involved in replication and has proofreading activity. DNA polymerase I also has exonuclease activity and participates in DNA repair.
Eukaryotic DNA Polymerases: In eukaryotic cells, polymerases like DNA polymerase δ (delta) and DNA polymerase ε (epsilon) are responsible for synthesizing the leading and lagging strands and have proofreading capabilities.
Limitations of Proofreading
Although proofreading is a highly effective mechanism for error correction, it is not foolproof. Some errors still go undetected or occur later during replication or repair processes.
Additional repair mechanisms, such as mismatch repair, work alongside DNA polymerase to further correct any errors missed during the proofreading process.

Summary
The proofreading function of DNA polymerase, with its 3’ to 5’ exonuclease activity, is a critical component of the replication process. It ensures that DNA synthesis proceeds with high fidelity, preventing errors that could lead to mutations and maintaining the integrity of the genetic code

Question 18

Step 4: …and on the lagging strand

Answer 18

DNA Polymerasecannot generate a long polymer in the 3’ to 5’ direction so instead DNA primase has tohelp out…

Short Okazaki Fragments are generated by DNA polymerase using the primers as a starting point. This creates short sections of complementary, double stranded (ds) DNA which are then extended to replace the next primer in a 5’ to 3’ direction.

The sections of DNA are stuck together by DNA ligaseto form the second complimentary copy

Question 19

DNA polymerase

Answer 19

*To generate an exact copy of the original DNA the DNA polymerase must have proofreadingability.

*DNA polymerases have 2 discrete sites; P is for polymerisation and E is for editing (right).

*The incorrectly paired nucleotide is removed by the E site, which has exonucleaseactivity and breaks the phosphodiester bond, enabling a new base to be added when the backbone is translocated back to the P site.

Question 20

What effect could this have on the protein sequence? (select any that apply

Answer 20

c)Frameshift “mutation”
d)Premature stop to translation
e)Changed splicing

When depurination occurs, there is no change in the base pair sequence, however there is a deletion of a base. This cannot be repaired, instead we lose a base of the sequence

Question 21

What happens when the sugar phosphate backbone is broken?

Answer 21

When the break is in a single strand of the double helix then Single Strand Break Repair is initiated

When both strands of the double helix break Double Strand Break Repair is initiated

*Non-Homologous End Joining -more error prone, often occurs outside S-phase

*Homologous Recombination –uses the second, homologous, chromosome as a template, no loss of nucleotides

Question 22

Double Strand Breaks are also normal…can you remember where?

Answer 22

Double strand breaks (DSBs) in DNA are a normal part of several cellular processes, especially during specific events in the cell cycle and in certain biological processes. Here are some contexts where DSBs naturally occur:

1. Meiosis (Crossing Over):
   During meiosis, DSBs are intentionally created in the DNA to facilitate the process of homologous recombination (or crossing over), where genetic material is exchanged between homologous chromosomes. This is critical for genetic diversity in gametes (sperm and egg cells).
2. V(D)J Recombination in Immune Cells:
   In the development of B-cells and T-cells in the immune system, DSBs are part of the process known as V(D)J recombination. This is essential for generating the diverse repertoire of antibodies and T-cell receptors that can recognize a vast array of antigens.
3. DNA Repair (Homologous Recombination):
   DSBs are a common form of DNA damage, and while not initially “normal,” they are often repaired by the cell using homologous recombination or non-homologous end joining (NHEJ). Cells have specialized repair pathways to handle DSBs caused by replication errors or external factors like ionizing radiation.
4. Replication Fork Collisions:
   During DNA replication, if the replication machinery encounters a problem (such as a tightly bound protein or a nick in the template strand), it can result in a DSB. These replication-induced breaks are part of the cell’s regular cycle and are repaired promptly.
   Summary:
   DSBs are a natural part of biological processes like meiosis and immune cell development, and also occur during DNA replication and repair. While DSBs can be dangerous if left unrepaired, cells have sophisticated mechanisms to ensure these breaks are properly fixed.

Question 23

Crossing over occurs to generate diversity

Answer 23

Crossing over occurs during Prophase I in meiosis

Double stranded breaks allow the translocation of DNA from one homologous chromosome to the other to generate chiasma.

When gametes are formed, chiasma have genetic sequences from both parents.

Crossing over between chromosomes does not have to occur at the end of a gene, although this is more likely.

Question 24

Inheritance of genes (genetics

Answer 24

Some genes that we are following can be on different chromosomes, therefore when we follow the traits across generations/the population the traits do not influence the inheritance of one another. This principle is known as independent assortment

Question 25

Crossing over allows linked genes to be separated

Answer 25

Linked genes are located physically close to one another on a chromosome, they are part of a linkage group.

The closer genes are to one another the lower the chance they will be separated during crossing over.

When genes are part of a linkage group they are inherited together and Mendels principles of inheritance do not apply.

Crossing over can allow linked genes to be separated from one another and inherited in a different pattern to one another

Question 26

Inheritance of genes in linkage groups

Answer 26

Genes that are on the same chromosome may be separated by crossing over events, also called recombination events. Letssee how this affects the inheritance of genes.

Terminologies to remember P=parentalgeneration
F1 = First progeny

Genes that are on the same chromosome may be separated by crossing over events, also called recombination events. Letssee how this affects the inheritance of genes

Question 27

Inheritance of genes in linkage groupsWhat will the phenotypes be of the 2 gametes shown?

Answer 27

The image you uploaded is about the inheritance of genes in linkage groups, with a focus on gametes and their possible combinations. Here’s an interpretation of the questions in the image:

1. Phenotypes of the 2 gametes shown:The two gametes appear to show different combinations of alleles for two linked genes (likely “B/b” and “A/a”). In the first gamete, the alleles seem to be “B” and “a”, and in the second gamete, they seem to be “b” and “A”.Assuming no recombination, the gametes will have the following phenotypes based on the alleles:Gamete 1: “B” (dominant) and “a” (recessive).Gamete 2: “b” (recessive) and “A” (dominant).
2. How many other combinations could there be?In the case of linked genes, the combinations depend on recombination during meiosis. Without recombination, the two genes would assort together as seen in the two gametes shown. If recombination occurs, the alleles could be mixed, leading to four potential combinations: B-A, B-a, b-A, and b-a.
3. Difference if genes were on different chromosomes:If the genes were on different chromosomes, independent assortment would occur, leading to all possible allele combinations being equally likely. This is in contrast to linked genes, where recombination between the two loci is less frequent, and the parental combinations (those originally found on the same chromosome) are more common.

Question 28

Other outcomes of double stranded breaks

Answer 28

Double stranded breaks allow chunks of chromosomes to move around and attach to other chromosomes, this is known as translocation.This can cause a number ofgenetic diseases

✓t(8;14)(q24;q32) –Involves moving the MYCgene to cause Burkitt’s Lymphoma

✓Part of chromosome 21 attaches to chromosome 14 -causes a form of Down Syndrome.

Note: Human Gene names formatted in capital letters and in italics

Question 29

For extra help

Answer 29

For extra help

*Alberts, B., Wilson, JH., & Hunt, T. (2014) Molecular Biology of the Cell. 6thedition, W. W. Norton & Company, USA. Available as an ebook

*Lodish, H. (2016) Molecular Cell Biology, 8th Ed. W. H. Freeman and Company, copies in the Library

*CaladoRT, Young NS. Telomere diseases. N Engl J Med. 2009 Dec 10;361(24):2353-65. doi: 10.1056/NEJMra0903373. PMID: 20007561; PMCID: PMC3401586.

*Hawkins, M., Dimude, J.U., Howard, J.A.L., Smith, A.J., Dillingham, M.S., Savery, N.J., Rudolph, C.J., & McGlynn, P. (2019) Direct removal of RNA polymerase barriers to replication by accessory replicative helicases,Nucleic Acids Research, 47(10):5100–5113

*Li, GM. Mechanisms and functions of DNA mismatch repair.Cell Res18, 85–98 (2008).

*Church, J.M. (2014) “Polymerase proofreading-associated polyposis: a new, dominantly inherited syndrome of hereditary colorectal cancer predisposition.”Diseases of the colon and rectumvol. 57(3): 396-7

Question 30

Replication is based upon the formation of base-pairs

Answer 30

Question 31

Single stranded binding proteins maintain the open structure

Answer 31