Coding Region Variations and Phenotypic Differences
Gene Structure and Expression
Learning Objective: Explain how variations in DNA sequences within the coding region of the huntingtin gene in humans and keratin genes in sheep lead to phenotypic differences among individuals.
Gene Components
A gene is a transcribed DNA sequence on a chromosome.
Coding Region (Coding DNA): Contains information used for protein production.
Non-Coding Region (Non-Coding DNA): Important for determining when and where a gene is expressed.
Alleles and Expression
Each individual has two alleles for each gene.
Alleles may have DNA sequence differences (represented by asterisks).
Both alleles are expressed in cells.
Both alleles are transcribed.
mRNAs are translated.
Both protein versions are produced.
Coding Region Differences
Alleles of protein-coding genes often differ in the DNA sequence of their coding regions.
Some differences don't alter the amino acid sequence due to the redundancy of codons. (e.g., CAC and CAT both code for histidine).
Some DNA sequence differences between alleles cause changes in the amino acid sequence of the encoded proteins.
Example
CAC encodes histidine.
CAG now encodes glutamine.
Differences can affect the number of amino acids encoded.
Question
Differences between alleles in which part of the gene can cause differences in the structure and function of proteins encoded by the alleles?
A. The coding region of the gene.
B. The noncoding region of the gene.
The correct answer is A, the coding region of the gene
Case Studies
Huntington's Disease (HD)
Inherited disease in humans.
Hair and Fur Differences
Differences in hair and fur among mammals (especially sheep) due to variations in keratin genes.
Huntington's Disease (HD) Detailed Explanation
HTT gene on chromosome 4 contains a triplet repeat (CAG).
Normal individuals: 10-35 repeats.
HD patients: 36 or more repeats.
CAG codes for glutamine, leading to a polyglutamine disease.
Mutated protein aggregates in neuronal cells of the caudate and putamen, causing cell death.
Genotype-Phenotype Relationship
The Huntington gene is transcribed into mRNA.
mRNA is translated into the Huntington protein.
Every person has two alleles of the Huntington gene.
Both alleles are transcribed and translated.
Both contribute to Huntington function in the brain's phenotype.
Typical type encodes a protein with <36 glutamines.
HD-associated type encodes a protein with ≥36 glutamines.
Both allele types are transcribed at the same level.
Same amount of protein is produced for both allele types.
Malformed protein in HD leads to neuron death, altering brain structure and causing neurologic and behavioral changes.
Keratin Genes and Wool Type Differences
Hair, fur, horns, and nails are made of keratin.
Variation among keratin genes results in different amino acid sequences.
Keratin proteins form helical structures.
Higher cysteine content leads to more disulfide bonds, making filaments stronger.
Differences in DNA sequence lead to differences in amino acids present in the protein.
Alleles
Three common alleles: a, b, and c.
Nucleotide positions 215 and 277 vary among alleles.
Resulting in differences in cysteine, glycine, and tyrosine content of the keratin proteins.
*Changing DNA codons in keratin genes from other amino acids to cysteine, glycine, and tyrosine (or conversely) causes hair and fur fibers to have different structural properties.
Genetic Code Table
Used to determine how changes in nucleotide sequences affect amino acid sequences.
Remember that U in mRNA corresponds to T in DNA.
Changing the nucleotide in the third position of any of the glycine codons will simply change to another glycine codon.
Important Realization
Not all DNA sequence changes in a coding part of a gene result in amino acid sequence changes in the encoded protein.
For the alleles, it turns out that two of the positions, nucleotide 215 and nucleotide 277, involve differences among the alleles that result in protein sequence differences involving those critical free amino acids among the keratin alleles.
Keratin Production Process
Each cell has two alleles of keratin, both expressed.
Keratin gene is transcribed in skin cells.
Coding part of the gene (codons) codes for the amino acid sequence.
Information is transferred to mRNA via transcription.
mRNA is translated by ribosomes into keratin amino acid chains.
Amino acid chain folds into its final shape.
Protein becomes part of the animal's hair or fur.
Wool Phenotype
Sheep with different keratin alleles have different wool properties.
Differences in amino acid sequences cause proteins to have different structural properties.
Amounts of keratin protein produced are about the same due to similar mRNA levels.
There are no meaningful differences in DNA sequence in the noncoding parts of the gene.
Model for Wool Type Variation
Concepts
Variation in wool type between different individual sheep.
Genes
A keratin gene is a sequence of DNA on a chromosome.
Each individual has two copies or versions of that chromosome, one inherited from each parent, contains an allele of the gene.
Different alleles represent variation in the form of DNA sequence differences, and thus each individual's genome has two alleles of the keratin gene, which may be the same or different from each other.
Like all protein coding genes, the keratin gene contains both coding DNA and noncoding DNA.
Different alleles have different DNA sequences in their coding DNA and or their noncoding DNA.
The critical DNA sequence differences between alleles are in the coding DNA.
Transcription
The noncoding DNA contains the promoter sequence, which is adjacent to the site where transcription of the gene starts.
The coding DNA undergoes transcription, which begins when RNA polymerase binds to the promoter and begins to transcribe the gene, resulting in the production of the keratin messenger RNA or mRNA.
*Many, many copies of the mRNA may be made, but this depends on the cell and other factors.
Protein Synthesis
Transcription of the keratin genes and production of the keratin proteins take place in certain kinds of skin cells.
Protein and Phenotype
The keratin becomes part of the wool phenotype.
In this case, the structure of the keratin influences the texture of the wool.
Protein influences the phenotype, which in this case is wool type.
One version of the keratin protein results in the individual having wool of one type, and another version of the keratin protein results in individuals having wool of a different type.
Alleles determine the wool type
General Model
Many phenotypic differences can be explained by DNA sequence differences in the coding region of genes.
The next lecture will focus on the role of non-coding DNA.
Gene Structure and Expression
Learning Objective: Explain how variations in DNA sequences within the coding region of the huntingtin gene in humans and keratin genes in sheep lead to phenotypic differences among individuals.
Gene Components
A gene is a transcribed DNA sequence on a chromosome.
Coding Region (Coding DNA): Contains information used for protein production.
Exons are coding regions that are transcribed and translated.
Determines the amino acid sequence of the protein.
Non-Coding Region (Non-Coding DNA): Important for determining when and where a gene is expressed.
Includes promoters, enhancers, and silencers.
Regulates gene expression by influencing transcription rates.
Alleles and Expression
Each individual has two alleles for each gene.
One allele inherited from each parent.
Alleles may have DNA sequence differences (represented by asterisks).
Both alleles are expressed in cells.
Both alleles are transcribed.
mRNAs are translated.
Both protein versions are produced.
Coding Region Differences
Alleles of protein-coding genes often differ in the DNA sequence of their coding regions.
These differences can lead to variations in protein structure and function.
Some differences don't alter the amino acid sequence due to the redundancy of codons. (e.g., CAC and CAT both code for histidine).
Silent mutations do not change the amino acid sequence.
Some DNA sequence differences between alleles cause changes in the amino acid sequence of the encoded proteins.
Missense mutations result in a different amino acid being incorporated into the protein.
Nonsense mutations introduce a premature stop codon, leading to a truncated protein.
Example
CAC encodes histidine.
CAG now encodes glutamine.
Differences can affect the number of amino acids encoded.
Insertions or deletions can cause frameshift mutations, altering the entire amino acid sequence downstream of the mutation.
Question
Differences between alleles in which part of the gene can cause differences in the structure and function of proteins encoded by the alleles?
A. The coding region of the gene.
B. The noncoding region of the gene.
The correct answer is A, the coding region of the gene
Case Studies
Huntington's Disease (HD)
Inherited disease in humans.
Caused by an expansion of a CAG repeat in the HTT gene.
Hair and Fur Differences
Differences in hair and fur among mammals (especially sheep) due to variations in keratin genes.
Keratin genes determine the structure and properties of hair and fur fibers.
Huntington's Disease (HD) Detailed Explanation
HTT gene on chromosome 4 contains a triplet repeat (CAG).
Normal individuals: 10-35 repeats.
HD patients: 36 or more repeats.
CAG codes for glutamine, leading to a polyglutamine disease.
Mutated protein aggregates in neuronal cells of the caudate and putamen, causing cell death.
The polyglutamine expansion causes the protein to misfold and form aggregates.
Genotype-Phenotype Relationship
The Huntington gene is transcribed into mRNA.
mRNA is translated into the Huntington protein.
Every person has two alleles of the Huntington gene.
Both alleles are transcribed and translated.
Both contribute to Huntington function in the brain's phenotype.
Typical type encodes a protein with <36 glutamines.
HD-associated type encodes a protein with ≥36 glutamines.
Both allele types are transcribed at the same level.
Same amount of protein is produced for both allele types.
Malformed protein in HD leads to neuron death, altering brain structure and causing neurologic and behavioral changes.
Symptoms include motor, cognitive, and psychiatric disturbances.
Keratin Genes and Wool Type Differences
Hair, fur, horns, and nails are made of keratin.
Variation among keratin genes results in different amino acid sequences.
Keratin proteins form helical structures.
Higher cysteine content leads to more disulfide bonds, making filaments stronger.
Differences in DNA sequence lead to differences in amino acids present in the protein.
Alleles
Three common alleles: a, b, and c.
Nucleotide positions 215 and 277 vary among alleles.
Resulting in differences in cysteine, glycine, and tyrosine content of the keratin proteins.
Changing DNA codons in keratin genes from other amino acids to cysteine, glycine, and tyrosine (or conversely) causes hair and fur fibers to have different structural properties.
Cysteine forms disulfide bonds, which increase the strength and stiffness of the fiber.
Glycine provides flexibility to the fiber.
Tyrosine affects the fiber's ability to absorb water and dyes.
Genetic Code Table
Used to determine how changes in nucleotide sequences affect amino acid sequences.
Remember that U in mRNA corresponds to T in DNA.
Changing the nucleotide in the third position of any of the glycine codons will simply change to another glycine codon.
Due to the degeneracy of the genetic code.
Important Realization
Not all DNA sequence changes in a coding part of a gene result in amino acid sequence changes in the encoded protein.
For the alleles, it turns out that two of the positions, nucleotide 215 and nucleotide 277, involve differences among the alleles that result in protein sequence differences involving those critical free amino acids among the keratin alleles.
These specific amino acid differences significantly influence the properties of keratin fibers.
Keratin Production Process
Each cell has two alleles of keratin, both expressed.
Keratin gene is transcribed in skin cells.
Coding part of the gene (codons) codes for the amino acid sequence.
Information is transferred to mRNA via transcription.
mRNA is translated by ribosomes into keratin amino acid chains.
Amino acid chain folds into its final shape.
Protein becomes part of the animal's hair or fur.
The folding process is influenced by the amino acid sequence and post-translational modifications.
Wool Phenotype
Sheep with different keratin alleles have different wool properties.
Differences in amino acid sequences cause proteins to have different structural properties.
Amounts of keratin protein produced are about the same due to similar mRNA levels.
There are no meaningful differences in DNA sequence in the noncoding parts of the gene.
The coding region is primarily responsible for the observed phenotypic differences.
Model for Wool Type Variation
Concepts
Variation in wool type between different individual sheep.
Wool type is determined by the structure and properties of keratin fibers.
Genes
A keratin gene is a sequence of DNA on a chromosome.
Each individual has two copies or versions of that chromosome, one inherited from each parent, contains an allele of the gene.
Different alleles represent variation in the form of DNA sequence differences, and thus each individual's genome has two alleles of the keratin gene, which may be the same or different from each other.
Like all protein coding genes, the keratin gene contains both coding DNA and noncoding DNA.
Different alleles have different DNA sequences in their coding DNA and or their noncoding DNA.
The critical DNA sequence differences between alleles are in the coding DNA.
These differences lead to variations in the amino acid sequence of the keratin protein.
Transcription
The noncoding DNA contains the promoter sequence, which is adjacent to the site where transcription of the gene starts.
The coding DNA undergoes transcription, which begins when RNA polymerase binds to the promoter and begins to transcribe the gene, resulting in the production of the keratin messenger RNA or mRNA.
*Many, many copies of the mRNA may be made, but this depends on the cell and other factors.
The rate of transcription is influenced by the promoter sequence and other regulatory elements.
Protein Synthesis
Transcription of the keratin genes and production of the keratin proteins take place in certain kinds of skin cells.
Ribosomes in these cells translate the mRNA into keratin protein.
Protein and Phenotype
The keratin becomes part of the wool phenotype.
In this case, the structure of the keratin influences the texture of the wool.
Protein influences the phenotype, which in this case is wool type.
One version of the keratin protein results in the individual having wool of one type, and another version of the keratin protein results in individuals having wool of a different type.
Alleles determine the wool type
Different alleles lead to different protein structures, resulting in different wool types.
General Model
Many phenotypic differences can be explained by DNA sequence differences in the coding region of genes.
The next lecture will focus on the role of non-coding DNA.