Biology 1002B Lecture Notes - Lecture 9: Hox Gene, Reading Frame, Point Mutation

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13 Jun 2018

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Lecture 18 Outcomes

Main mechanisms of epigenetic regulation

- heritable changes in gene activity and expression that occur without alteration in DNA

sequence

- either DNA methylation or DNA histone modifications

- feedback loops (when a positive regulator binds to its own promoter, and stimulates itself)

Different types of mutations in protein coding genes

Likely effect of various types of mutations on gene expression

- Silent Mutation: since the genetic code is redundant there are many amino acids that can

code for the same codon  DNA is different (genetic variation) but not protein variation

- Missense Mutation: point mutation that causes a change in amino acid and therefore a

change in the protein formed

- Nonsense Mutation: point mutation that creates a stop codon, which will end transcription

prematurely, therefore the protein will be way too small, and probably not carry out function

- Frameshift Mutation: caused by an in/del mutation

- if insertion, the extra base appears in the RNA because also in the DNA

- everything downstream of the addition or deletion will be read incorrectly because the

reading frame is shifted

- inserting a base into the exon will have no effect to the splicing but the protein can either

be too long or too short because the reading

frame is shifted so the stop codon could be

missed or a new one could be made

Characteristics that make Drosophila an

attractive model system.

- lead to a search for Hox genes in other organisms

- similar function in humans

Main stages in Drosophila embryonic

development

- all mothers that make eggs, pack the eggs with

organelles (organelles come from our moms),

moms also pack the eggs with proteins and mRNA

that will facilitate its development after fertilization

- generally when the nucleus divided in cell division,

so did the cell but in this case, the nucleus divides

but the cell does not, therefore you end up with

MANY nuclei in one cell called multinucleated

cells

- nucleated cells move to the outer wall, and you

end up with an empty cell with nuclei around the

edges

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Main role of maternal effect, segmentation and homeotic genes in

Drosophila development.

- maternal effect genes control egg polarity (embryo polarity), transcribed in the mother but

translated in the egg (first genes to be translated)

- bicoid is a maternal effect gene responsible for the development of the head and the thorax

due to the concentration gradient of the bicoid protein that is greater near the anterior

(head) end than the posterior (back) end

- nanos is a maternal effect gene that is responsible for the development of the posterior

structures

- gurken: establishes top and bottom

- segmentation genes are responsible for subdividing the embryo into regions, maternal effect

proteins regulate the expression of the segmentation genes to be expressed at different times

and locations during embryogenesis

- Gap genes are activated based on their position in the embryo relative to the maternally

determined anterior-posterior axis (concentration gradient), the products of gap genes

(proteins) control subdivision of the embryo

- mutations in gap genes can cause: (1) gap gene mutants are missing 1/more segments,

(2) pair-rule gene mutants are missing every other segment, (3) segment polarity genes

are missing one part and have another duplicated as a mirror image

- products of gap genes are transcription factors that activate pair rule genes, and products

of pair rule genes regulate the expression of segment polarity genes, and the products of

segment polarity genes are responsible for the creating the pattern of the embryo

- homeotic genes determine the structure and specify what each segment will be after

metamorphosis, they encode transcription factors that regulate expression of genes

responsible for developing adult structures

structure/function of the "homeobox" in homeotic genes

- Each homeotic gene (responsible for controlling expression/binding of DNA) has a common

region called a homeobox that is key to its function

- Eight homeobox (Hox) genes in Drosophila are organized along a chromosome in the same

order as they are expressed along the anteriorposterior body axis

- homeobox genes are 180 bp sequence coding for a DNA-binding domain

- A homeobox corresponds to an amino acid section of the encoded transcription factor called

the homeodomain

- Hox genes control the development of segments or regions of the body and are arranged in

order in the genome

Significance of evolutionary conservation of Hox genes

- Homeobox sequences in Hox genes are highly conserved, indicating common function in the

wide range of animals in which they occur

- strong evolution of hox genes give rise to segmentation

mechanism of plasmid toxin/antitoxin system as a possible origin for cell death genes.

- bacterial plasmids (small circular, double stranded DNA molecules) can code for their own

transfer

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Document Summary

Heritable changes in gene activity and expression that occur without alteration in dna sequence. Either dna methylation or dna histone modifications. Feedback loops (when a positive regulator binds to its own promoter, and stimulates itself) Different types of mutations in protein coding genes. Likely effect of various types of mutations on gene expression. Silent mutation: since the genetic code is redundant there are many amino acids that can code for the same codon (cid:1680) dna is different (genetic variation) but not protein variation. Missense mutation: point mutation that causes a change in amino acid and therefore a change in the protein formed. Nonsense mutation: point mutation that creates a stop codon, which will end transcription prematurely, therefore the protein will be way too small, and probably not carry out function. Frameshift mutation: caused by an in/del mutation. If insertion, the extra base appears in the rna because also in the dna.

Related Questions

Part B

Think about the DNA coding sequence of a gene. If an A were swapped for a T, what kind of mutation could it cause and why?

a) It could cause a frameshift nonsense or frameshift missense mutation because it would change the reading frame of the codon triplet.

b) It could cause a silent, missense, or nonsense mutation because those are the types that can be caused by a nucleotide-pair substitution like this one.

c) It could cause a nonsense mutation because the sequence would no longer be the same, so the protein would be shorter and non-functional.

d) It could cause a silent mutation because A and T are complementary to each other so it is not really a substitution mutation.

Part C

Why is a frameshift missense mutation more likely to have a severe effect on phenotype than a nucleotide-pair substitution missense mutation in the same protein?

a) A substitution missense mutation causes the protein to be shorter and thus non-functional.

b) A frameshift missense will cause the codons to be out of order, but a substitution missense does not change the order of the codons.

c) A frameshift missense mutation will cause an early Stop codon, but a substitution missense might be silent.

d) A substitution missense affects only one codon, but a frameshift missense affects all codons downstream of the frameshift.

Part D

Which of the following sequences shows a frameshift mutation compared to the wild-type mRNA sequence?

a) wild-type	5â-AUGCAUACAUUGGAGUGA-3â
mutant	5â-AUGCAUACAGAGUGA-3â

b) wild-type	5â-AUGCAUACAUUGGAGUGA-3â
mutant	5â-AUGCAUACGUUGGAGUGA-3â

c) wild-type	5â-AUGCAUACAUUGGAGUGA-3â
mutant	5â-AUGCAUACAUCUGGAGUGA-3â

d) wild-type	5â-AUGCAUACAUUGGAGUGA-3â
mutant	5â-AUGCAUGUGACAUUGGAGUGA-3â

Part F

Suppose that the triplet of nucleotides indicated in bold (AGC) spans two codons, that is, CTA and GCC. If the triplet AGC were deleted from this DNA coding sequence, what effect would it have on the resulting protein?

5â-ATGCTAGCCTATCGTAAC-3â

a) The two flanking codons would be altered, but the rest of the amino acid sequence would be the same because there would be no frameshift.

b) The entire amino acid sequence would be altered due to the frameshift.

c) All of the amino acids after the deletion would be altered due to the frameshift.

d) All of the amino acids up to the deletion would be altered due to the frameshift.

mauvetrout554

1. An occurrence of a gene made larger by trinucleotide repeats is:

Allelic expansion

Nucleotide expansion

Translocation mutation

Transformation

2. a chemical that can damage and/or change DNA is called a/an:

Allele

Endonuclease

Vector

Mutagen

3. An occurrence when a section of a chromosome relocates itself to an entirely different (non-homologous) chromosome is called a/an:

Inversion mutation

Translocation mutation

Transformation mutation

Duplication mutation

4. The tandem repeat in the sequence GGGAAGGGAAGGGAAGGGAAGGGAAG is:

GGA

GGGAA

GGAAG

GGAAGGG

A disease characterized by abnormally shaped hemoglobin is called:

Cystic Fibrosis

Sickle Cell Anemia

Marfan Syndrome

Leukemia

5. A point mutation that causes a substitution of a stop codon with an amino acid and leads to the formation of a longer protein is a:

Nonsense mutation

Missense mutation

Sense mutation

Frameshift mutation

6. Addition or deletion of nucleotides in a DNA sequence is known as a:

Nonsense mutation

Missense mutation

Sense mutation

Frameshift mutation

7. The least severe type of chromosomal mutation is:

Point

Frameshift

Inversion

Translocation

8. Chemicals inserting themselves into DNA can cause a:

Missense mutation

Nonsense mutation

Sense mutation

Frameshift mutation

9. A genetic condition caused by allelic expansion is:

Familial hypercholesterolemia

Fragile X syndrome

Alkaptonuria

Galactosemia

10. Which of the following is most likely the original DNA strand if the mutated DNA strand is ATAGUUGATGUA ?

ATAGAAGATGAA

ATAGCCGATGCA

ATAGGGGATGGA

ATAGTTGATGTA

11. An unbalanced chromosomal mutation would include a/an:

duplication (insertion)

inversion

translocation

denaturation

12. Many translocation mutations are found to be involved with:

cancers

sickle cell anemia

Huntington disease

cystic fibrosis

13. A common repeat throughout the human genome that is approximately 300 bases in length is called a/an:

EcoRI repeat

Hind repeat

Exo repeat

Alu repeat

14. A balanced chromosomal mutation includes:

imprintation

denaturation

inversion

deletion

salmondinosaur263

QUESTION 3

What is the purpose of chromatin-remodeling enzymes in human cells?

The enzymes control the rate of translation of an mRNA transcript

The enzymes add phosphate or methyl groups to histone tails

The enzymes slide nucleosomes farther apart or closer to each other

The enzymes send damaged proteins to the proteasome for degradation

The enzymes cause DNA looping to occur

QUESTION 10

If you can drink milk as an adult, it means that you have inherited a mutation in the an enhancer for your lactase gene (the gene that encodes the enzyme you need to break down lactose). Predict the effect of this mutation:

The mutation changes the number of domains in the enzyme, which makes it work more efficiently

The mutation changes the amino acid sequence of the lactase protein

The mutation increases the number of copies of the lactase gene that will be found in your genome

The mutation changes whether the lactase sequence is found in an intron or exon

The mutation affects the expression of the lactase gene

QUESTION 12

What determines where in the genome a transcription regulator will bind?

Transcription regulators bind to the 5' UTR region of a gene

Regulators bind via complementary base-pairing to certain DNA molecules

Covalent bonds form between the transcription regulator and the atoms of the DNA backbone

Every eukaryotic gene has a different transcription regulator that will bind to the 5' end of the gene

Transcription regulators bind to specific DNA sequences via multiple weak non-covalent interactions

QUESTION 15

What is the histone code used for?

		Phosphorylation and acetylation of DNA affect its ability to be compacted
		Changes to the sequence of DNA change whether DNA will wrap around histone proteins
		Covalent modifications of histones affect the ability of the transcription initiation complex to form
		Histones provide the codon sequences needed for translation to occur
		The histone code affects which amino acids will get added to a polypeptide

Biology 1002B Lecture Notes - Lecture 9: Hox Gene, Reading Frame, Point Mutation

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