Mutations, Epigenetics, and Genes

Mutations

• A mutation involves a change in the structure of a nucleic acid.

Epigenetic Mechanisms

• Epigenetic mechanisms lead to heritable alterations in gene expression.
• These are due to non-coding events that change phenotype/gene expression.

Types of Mutations

• Deletion: A gene is removed from the sequence.
• Duplication: A gene is put in twice or repeated.
• Inversion: A gene is flipped in the sequence.
• Translocation: Part of a gene from one sequence switches with a part of another sequence.
• Insertion: A gene sequence is inserted into another gene sequence.

Genome Definition

• Genome is the collective term for all DNA molecules within a cell or organism.
• This includes chromosomes and genes.

Types of Genes

• There are two types of genes: introns and exons.
• Exons: Genes that are expressed.
• Introns: Genes that are removed, but variants of a gene can arise depending on how they are removed.

DNA Molecules in Males

• Males have 25 different types of DNA molecules.
• These are comprised of 22 autosomal, 2 sex chromosomes (X and Y), and 1 mitochondria.

DNA Molecules in Females

• Females have 24 different types of DNA molecules.
• These are comprised of 22 autosomal, 1 sex chromosome (X), and 1 mitochondria.

Point Mutations

• Silent: There's a change in the nucleotide sequence, but no change in the amino acid.
• Nonsense: There's a change in nucleotide sequence which results in the creation of a termination codon.
• Missense: There's a change in nucleotide sequence which results in a different amino acid.
• The first two, conservation and non-conservation, both result in a change in the amino acid.
• Conservative: the amino acid is similar to the non-mutation, either in charge, polarity, etc. and hence functions similarly.
• Non-conservative: the amino acid is not similar to the non-mutation and hence functions significantly differently.

Epigenetic Mechanisms

• DNA methylation adds a methyl group to one of the existing bases in the original sequence.
• DNA methylation may stop gene transcription if it occurs on a promoter.
• Histone modification involves any change to the histone protein.
• This can ultimately alter chromatin structure.
• Both DNA methylation and histone modification result in genes still being present, but with attachments that prevent them from being expressed.

Triggers for Epigenetic Mechanisms

• Common environmental factors can trigger epigenetic mechanisms.
• Diet, exercise, pollutants, stress, and alcohol etc can affect the mechanisms.

Effects of Epigenetic Alterations

• Epigenetic alternations can result in diseases like cancer.

DNA vs RNA structure

• DNA does not have an -OH group on the 2' carbon, it has deoxy.
• RNA has an -OH group on the 2' carbon.

Purine vs Pyrimidine bases.

• Purines are double ringed.
• Pyrimidines are single ringed.

Adenine vs Guanine

• Guanine has an oxygen
• Adenine does not contain oxygen

Cytosine vs Thymine vs Uracil

• Cytosine has only 1 oxygen atom.
• Thymine and Uracil have two oxygen atoms.
• Thymine has a methyl group attached and is bigger than the other base pairs,
• Uracil does not have a methyl group attached and is smaller than the other base pairs.

ssDNA Structure

• Single stranded DNA has a phosphate group attached at the 5' end.
• Single stranded DNA has a hydroxide group attached at the 3' end.

ssDNA Structure Considerations

• If one were to read a molecule from top to bottom, one strand runs from 5' to 3' while the other runs from 3' to 5'.

Hydrogen Bonds - True or False

• Hydrogen bonds are stronger than covalent bonds = FALSE
• H bonds are weaker than covalent bonds.

Hydrogen Bonds between base pairs

• There are 2 hydrogen bonds between A and T/U.
• There are 3 hydrogen bonds between C and G.

Breaking Hydrogen Bonds

• DNA polymerase breaks the H bonds between A with T/U and C with G.

DNA Transcription - True or False

• DNA transcription is a semi-conservative process = FALSE
• DNA REPLICATION is semiconservative because both parental strands are kept and are instead paired with a daughter strand

DNA Synthesis

• DNA is synthesized in the 5' to 3' direction.

DNA Template Assumptions

Template is 3' to 5', which means that the template stops at the 5' end, the opposite would be the new synthesized strand, which would hence start at the 3' end

• Replication process would be discontinuous
• Template is 5' to 3’ which means that the bottom of the template is 3’ The newly synthesized strand would start with 5
• Replication process would be continuous

Types of DNA Polymerases - True or False

• There are two types of DNA polymerases: DNA-dependent and RNA-dependent = TRUE
• Dependency relates to what the DNA polymerase focuses on

Types of DNA-dependent polymerases

• The types of DNA-dependent polymerases are: alpha, delta & epsilon, beta, gamma

Role of alpha polymerase

• Initiates DNA replication at the origin.
• Initiates DNA replication at the beginning of each Okazaki fragment

Role of delta and epsilon polymerases

• DNA repair is the major function of delta and epsilon polymerases.

Role of beta polymerase

• Beta polymerase plays a role in base excision repair.

Role of gamma polymerase

• It is repsonsible for mithcondiral DNA synthesis and repair

Types of RNA-dependent polymerases?

• Transposon reverse transcriptase
• Telomerase reverse transcriptase (TERT)

Role of transposon reverse transcriptase?

• Converts RNA to complementary DNA to integrate into the genome.
• Gives rise to new exons.

Role of telomerase reverse transcriptase

• Uses an RNA template to replicate DNA at the ends of linear chromosomes (telomeres).

DNA Polymerase Replication - True or False

• DNA polymerase is involved in both DNA replication and transcription = FALSE
• DNA polymerase is only involved in DNA replication because a new DNA strand is being formed
• RNA transcriptase is involved in RNA replication because a new RNA strand is being formed

Sense vs Antisense DNA strands

• During transcription, the sense strand is the exact sequence that would appear in the transcribed RNA.
• In the sense strand, Uracil replaces Thymine.
• The anti-sense strand is the template strand that transcription occurs from.
• It has the opposite base pairs from the sense strand and the RNA formed (switching U and T).

Definite Sense Strand - True or False

• There is a definite sense strand in every DNA molecule = FALSE, varies

Chromatin

• Is the unravelled condensed structure of DNA for the purpose of packaging into the nucleus.
• It is NOT condensed into chromosomes.

Protein DNA complex of chromatin

• DNA molecules are coiled tightly around proteins called histones.

Organization of chromatin

• An average sized chromatin is 4.8cm long with 140 million base pairs.
• It needs to be tightly coiled so that it fits in the nucleus/cell.

Chromatin structure

• It supports rapid DNA replication, but is not bound into chromosomes so is still coiled.
• It aids in proper segregation of replicated DNA during cell division, making it more coiled so that it can be efficiently separated
• Aids in transcriptional regulation, being able to uncoil to transcribe a particular gene

Unit of chromatin

• The smallest unit of chromatin is nucleosomes.

Nucleosome definition

• A nucleosome is DNA wrapped around a histone protein.

In relation to size

• DNA is 2 nm and wraps around a nucleosome (10 nm).
• Nucleosomes are then arranged into chromatin fibers, which are a thickness of 30 nm.

Looped structures

• Are chromatin fibers looped and kept in shape by scaffolds of non-histone proteins.

Differentiate euchromatin and heterochromatin

• Euchromatin is very relaxed and allows for proper transcription.
• Heterochromatin is highly condensed, not good for transcription but good for cell division.

Transcription

• Transcription can effectively occur with heterochromatin = FALSE, heterochromatin is highly condensed and hence cannot be used for transcription

Specialized chromosome regions

• Centromeres
• Replication origins
• Telomeres

Centromeres

• centromeres are a specific sequence of DNA located at the midsection of the chromosome
• Centromeres are bound by kinetochore fibers during DNA segregation
• Centromeres are essential for proper segregation of chromosomes during cell division

Chromotere terms

• centromere is in the center of the chromosome
• kinetochores are the regions on a centromere during cell division where microtubules attach

conservation of cetromeres

• There is high conservation of the sequence of centromeres = FALSE
• Fspecially in mammalian DNA where heterochromatic regions are dominated by highly repetitive DNA sequences that extend over many bases

Origin of replication description

• It is a specific sequence of DNA that commences the replication of chromosomes.
• In eukaryotes, multiple sites of origin are necessary

Multiple origins for replication

• If there was only 1 origin of replication the replication would take way too long.
• Having multiple origins of replication allows for the replication to occur more quickly so that multiple proteins can commence the replication.

Conservation of Replication Origins - True or False

• Origins of replication are highly conserved in nature = FALSE
• Origins of replication have no special way of being conserved

Telomeres

• Telomeres are specialized sequences at the ends of chromosomes.

Telomere functions

• Stability of chromosomes ends
• Replication of chromosomes ends (TERT)

Highly conserved telomeres - True or False

• Telomeres are highly conserved throughout nature = TRUE as a result of the T-loop

T-loop description

• The T-loop (telomerase loop) is a loop of G-rich strands bonded with C-rich strands to create a loop shaped to conserve the telomerase through nature.
• The shape of this loop is a great way to protect it from nucleases and ligases

G-rich strand

• The DNA of telomeres has a lot of G-rich strands where telomeric proteins bind
• It has about 2000 ds repeats and about 30 ss repeats so that the DNA can loop around and fold back onto the C-rich strand; in between the folding and the ds repeats are the ss repeats, resembling a circular velcro on sneakers

DNA copies

• the number copies of DNA are represented as C

Haploid number of DNA copies

• The haploid number copies of DNA aare represented as 1c

What's it called when there are no copies of DNA?

• When there are no copies of DNA we call it nulliploid.
• This state has no nucleus (such as in erythrocytes and some keratinocytes).

mtDNA copies

• There can be anywhere from 100-1000’s mitochondria.

Mitochondrial DNA in Gametes

• There are 100 copies of mitochondrial DNA in sperm.
• There are 250,000 copies of mitochondrial DNA in eggs.

Gamete Cells - Tru or False

• Sperm and egg cells are diploid = FALSE.
• They are haploid because each only has one set of chromosomes from each parent.

What Chromosomes do gametes contain?

• Gametes contain 22 autosomal (non-sex) and 1 sex (X or Y) chromosomes

X chromosome - True of False

• The X chromosome only comes from females = FALSE
• It can also come from males

Egg Sex Chromosome - True of False

• The only sex chromosome that an egg cell would contain is an X = TRUE

Types of Sperm Cells - True or False

• Sperm cells can only contain the Y sex chromosome = FALSE
• Sperm cells can contain either the X or Y chromosome

Chromosome content changes

• Early S: cell has undergone the M phase, 2n, 2c
• Middle S: cohesins are used to hold copies of newly synthesized DNA together, 2n, 4c (same number chromosomes, twice as much DNA)
• Late S: cohesins removed except for centromeres, 2n, 4c

Gap phases.

• They are phases between M and S, typically labelled G1 or G2
• Specifically, G1 is between M and S while G2 is between S and M

GO Phase description

• If the cell does not receive the go ahead signal for G1, it goes to GO where it does not replicate until suitable conditions allow

M phase changes

• prophase: chromatids are still paired together in a typical cell, 4c, 2n
• anaphase: cells are still together but chromatids are separated, 4c, 4n
• cytokinesis: daughter cells separated with half the chromatids in each, 2c, 2n

Mitosis and Meiosis - True or False

• Mitosis and meiosis both result in 2n = FALSE
• Mitosis results in 2n but meiosis results in n

Mitochondrial Mass - True of False

• The amount of mtDNA is unaffected by the mass of the mitochondrion = FALSE
• The greater the mass of the mitochondrion, the greater the amount of mtDNA

Equal replication

• True or False - Just like in mitosis of typical cells - mtDNA is replicated evenly = FALSE, some may be replicated a lot and some not at all.

Equal Segregation - True or False

• The segregation of mtDNA must be equal in daughter cells, just like with typical cells in mitosis = FALSE, neither evenly replicated nor segregated

Heteroplasmy related to mtDNA

• Heteroplasmy is the presence of more than one type of organellar genome (mitochondrion).
• Variants can arise to give a mixed population of mtDNA

List of the five mitosis phases,

• Prophase
• Prometaphase
• Metaphase
• Anaphase
• Telophase

Events during prophase.

• The centrioles separate and migrate to opposite poles of the cell.
• The chromatin is condensed into chromosomes.

prometaphase description

• The nuclear envelope is broken down, and the kinetochore microtubules attach to the kinetochores of the centromeres.

What happens during metaphase?

• The chromosomes are lined up in the middle of the cell (mitotic spindle?).

What happens during anaphase?

• The centromeres are pulled towards opposite ends, breaking the sister chromatids from each other.

Events during telophase .

• New nuclear envelopes form around each of the two sets chromosomes that begin to unwind.

Cytokinesis Description

• Cytokinesis is when the daughter cells from mitosis are cleaved from one another.

Interphase Description

• Interphase is the period of the cell cycle between cell divisions, everything except for the M phase

Meiosis description

• The is reductive division undergone by primordial spermatocytes and oocytes

Meisosis vs spermatocytes and oocytes

• For spermatocytes, the primary one divides into four spermatozoa
• For oocytes, the primary one results in one mature egg and a polar body that does not develop into an egg

Synapsis description

• Maternal and paternal homologs are paired and crossover occurs.

Homologs random Description

• Homologs are randomly positioned but with matching locations
• Homologs produce the crossing physical breakage of DNA in one maternal and one paternal and subsequently joining the fragments

Goal of traits

• The goal being is to produce novel variants of gametes

Gametes

• Every sperm and egg is genetically different. True, hence the zygote is unique

Homologous

• With 23 pairs of homologous chromosomes, there are 2^23 possibilities for which of the two daughter cells the homologs will end up
• Homologs are independent because the homologs do not affect one another's migration

Recombinational

• This is a crossing over results between maternal and paternal homolog genes, which on top of independent assortment means a virtually an infinite number of combinations for the resulting chromosomes.