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Chapter 1 - Introduction to Genetics
The Genetics Essentials Concepts and Connections Fourth Edition of Biology 2416 by Benjamin Pierce is the textbook for this semester. The first chapter, an introduction to genetics, covers the history of genetics and the fundamental terms and principles of genetics.
Each chromosome houses thousands of genes. For instance, the diastrophic dysplasia gene lives on chromosome 5. A gene is a segment of a chromosome. When a gene is mutated, it is not created or functioning correctly, leading to deformities.
In agriculture, people have been selecting for better crops for generations, leading to bigger and better fruits. A modern apple, for instance, is not what our ancestors ate, but selective breeding has created crops that can grow in previously inhospitable locations.
Genetics is the fundamental reason why Pfizer, Moderna, and Johnson & Johnson vaccines work.
The mRNA vaccine is unique in that it requires genetics to function. The vaccine injects actual protein into the body, which is translated from the S protein gene using chick eggs. The reason why a fruit fly becomes a fruit fly and why you become you is genetics. The image below shows a fruit fly embryo expressing a gene in green.
The main cause of cancer is gene mutations, and genetics plays a significant role in human development. All life forms have genetic similarities, such as the same codons and triplet codes in genes. Research on the function of one organism's genes may apply to other organisms. The genes of one organism may exist and thrive in another organism.
Molecular genetics is where modern-day discoveries are happening. It involves looking at the gene molecule itself to figure out how it works and how proteins transcribe and translate the genes.
Population genetics, on the other hand, looks at populations of the same species of individuals. These populations are studied to gain a better understanding of genetics in biology.
Model genetic organisms are organisms that are useful for genetic analysis due to their short generation time. For example, a mouse has a 19-day gestation period compared to a human's nine-month gestation period. Moreover, a human may only have one or two offspring, whereas a fruit fly is one of the most intensely studied organisms and typically produces many offspring.
Different model organisms are currently being used in genetics labs across the planet. The most significant discoveries in genetics have been found through the study of these model organisms because the same genes usually perform the same biological functions in all organisms.
Fruit fly is one of the most intensely studied model organisms found in different genetics labs globally. For instance, some labs at UT Southwestern and a postdoctoral fellowship at UCLA focus on fruit fly genetics research.
All of these animals proliferate quickly and have great litter big litters, making them useful in the lab setting. For example, zebrafish can be used to study pigmentation when studying skin conditions. However, horses are expensive to house, feed, and propagate due to their few progenies and long generation time. Humans have been using genetics for thousands of years, and it's not a new concept to take organisms with beneficial traits and try to proliferate them.
Early on, there were many misconceptions about heredity, but as people turned their attention to how genes are inherited, they naturally made several errors. The rise of the science of genetics brought some pioneers, such as Weisman, Fleming, Darwin, Weissmann, Schleiden, and Schwann, who showed us the cell
Chapter 2 - Chromosome and Cellular Reproduction
Prokaryotes are single-celled creatures that have a plasma membrane, and they make up the domains of life, including bacteria and archaea. On the other hand, eukaryotic cells are much bigger than prokaryotic cells and can be unicellular or multicellular creatures that have membrane-bound organelles.
In prokaryotic cells, the whole creature is one cell, and the nucleus is considered a membrane-bound organelle. The chromosomes are inside this double membrane called the nuclear envelope.
In eukaryotes, the unifying feature is the nucleus, and the nucleus itself is closely associated with histones. Histones are proteins that wrap around DNA to give structure to the chromosomes. Unlike eukaryotes, prokaryotes do not have histones, but they have histone-like proteins instead.
If you want to learn more about eukaryotic and prokaryotic cells, Dr. D has a nice video on biology 1406 chapter 4 on YouTube.
A virus is a genetic material encapsulated in a protein coat. Some viruses have a DNA genome, while others have an RNA genome. Some viruses may also have proteins like spike proteins on their protein coat.
Homologous chromosomes and sister chromatids are explained thoroughly in a video. The cell cycle involves interphase, mitosis, and meiosis. Humans have 46 chromosomes, 23 from mom and 23 from dad. The chromosomes are not identical in content, but only in number and gene types. Haploid cells carry only one set of genetic information. The egg and sperm are haploid, but when fertilization occurs, the resulting zygote has two sets of chromosomes.
Having four chromosomes is too many, as ideally, a zygote should have only two sets.
Chapter 3 - Basic Principles of Heredity
The Genetics Essentials Concepts and Connections Fourth Edition textbook delves into the basic principles of heredity and the concept of dominant and recessive alleles. In this refresher video from Biology 1406, what you need to know about genetics.
Gregor Mendel, who studied at the University of Vienna, analyzed his results mathematically. He used his understanding of statistics to study easily differentiated characteristics, such as yellow or green pods. A locus is the position of the allele on the chromosome, while an allele is an alternative version of the gene.
A characteristic is an attribute or feature possessed by an organism. For example, if an organism has brown eyes, that is their phenotype, even if they carry a blue eye allele. This is because brown eye color is dominant over the recessive version.
Sometimes an organism's genotype can be determined by observing its phenotype, but only if it is showing the recessive phenotype. For example, if I have blue eyes, you could guess that my alleles are blue/blue because they are recessive, and the only way I would show blue eyes is if I have two recessive alleles. However, sometimes an organism's genotype cannot be determined from its phenotype.
In Mendel's experiments, each pea served as an embryo which could then be planted to grow a new plant. Male flowers contribute pollen to the female flower's anther, and each embryo grows into a new plant. By studying the peas from these plants, Mendel discovered that each organism has two pieces of information for any one trait, which we now know as two alleles for every gene. Mendel would have called it two varieties of every characteristic. Mendel's monohybrid cross taught us the principle of segregation of alleles and the concept of dominant and recessive alleles.
X+ sperm, red-eyed females with XW X+ offspring are produced. If the XW egg meets the Y sperm, white-eyed males, and red-eyed males are produced.
Chapter 5 - Linkage, Recombination, and Eukaryotic
Gene Mapping
In the Genetics Essentials Concepts and Connections Fourth Edition textbook, Dr. D explains the concept of gene linkage. Gene linkage occurs when genes are on the same chromosome. During meiosis, genetic variability is caused by gene linkage recombination.
In 1905, William Bateson, Edith Sanders, and Reginald Punnett of Pundit Square fame demonstrated an exception to Mendel's experiment. They were studying another flowering plant and noticed that when crossing a true-breeding purple flower with long pollen with a true-breeding red flower with round pollen, the F2 generation did not follow the expected 9:3:3:1 ratio for a dihybrid cross of flower color and pollen shape. This is because independent assortment, which shuffles different chromosomes, is not shuffling linked genes.
The only way to get recombinants of linked genes is through crossing over. This expands on Mendel's concepts rather than disproving them.
About linked alleles, they refer to different alleles on the same chromosome. The only way to break up those combinations is through crossing over between those two alleles.
When genes are really close together on the chromosome, they tend to be completely linked. After fertilization, you will end up with non-recombinant progeny (offspring that look like the parents) and an equal proportion of recombinant progeny.
Mendel's studies with the pea plants were all about independent assortment, but he got really lucky with that. The further alleles are on a chromosome, the more likely they'll get recombined. On the other hand, the closer those alleles are on the chromosome, the less likely it is to see a recombination – it's even rare.
Chapter6 - Chromosome Variation
The Genetics Essentials Concepts and Connections 4th edition textbook is discussing chromosome variation. Chromosomes have varying morphology, with centromeres located differently on different chromosomes, resulting in two arms of equal length. Telomeres are located at the very ends of the eukaryotic chromosomes. Mitotic chromosomes can be stained to reveal their banding; this staining technique can highlight rich regions called G-banding. Another technique highlighting the C and G rich areas is called R-banding. Chromosome rearrangements can occur, such as duplications, deletions, inversions, and translocations. For example, part of the chromosome with the alleles C, D, and E could be duplicated or lost with deletions, with inversions and translocations involving the movement of a part of a chromosome to another chromosome.
To understand the impact of mutations or rearrangements on an organism, it's important to understand the role of alleles. Let's take a gene with alleles a, b, and c, which produce gene products such as enzymes.
Various duplications or deletions of these alleles can result in a myriad of human symptoms as they alter gene expression. Extra copies of a gene can lead to developmental defects due to varying amounts of the protein produced from that gene.
There are two types of inversions - one involving the centromere and the other not. Flipping the chromosome in inversions can break a gene apart, resulting in position effect where a part of the chromosome may not be read as easily by the cell machinery.
Chapter 7 - Bacterial and Viral Genetic Systems
We will be discussing Chapter 7 from Genetics Essentials: Concepts and Connections, 4th Edition, which talks about bacterial and viral genetic systems.
One of the advantages of using bacteria and viruses for genetic studies is their rapid reproduction and growth. Viruses can also be cultured and infect cells in culture to reproduce themselves.
Culturing bacteria is easy and simple, especially if you have taken microbiology. All you need to do is take a sterile tube with sterile broth inside, add the bacterial medium, and incubate it for a few days, and you will have millions or billions of bacteria within that vial.
Bacteria have plasmids - small, extra chromosomal, circular DNAs that replicate independently of the genomic DNA. These plasmids contain their own genes, which can be useful, such as genes that code for antibiotic resistance.
Plasmids are composed of RNA and normally exist inside bacteria cells possessing only a single strand of DNA. They replicate independently of the genomic DNA and have a specific origin of replication where replication begins in both directions. The plasmid replicates much faster than the bacterial cell, leading to some degree of genetic variation. There is a "pseudomating" process with plasmids, but it is not a vertical transmission of genes (meaning it is not passed from parent to child). Instead, plasmids shuffle genes around and can be found in F plus cells - these are cells that have the F factor plasmid or epi episome. The F factor integrates itself into the donor chromosome by incorporating itself with the insertion sequence it has.
Chapter 9 DNA Replication and Recombination
Eukaryotic cells undergo DNA replication differently than prokaryotic cells.
Prokaryotes have one circularized chromosome with a single origin of replication. At each origin, the DNA unwinds and produces a replication bubble. Replication occurs in both directions within each bubble.
The polymerase enzyme links nucleotides together with phosphodiester bonds to form DNA strands in a 5' to 3' direction with respect to the daughter strand. The leading strand undergoes continuous replication, whereas the lagging strand undergoes discontinuous replication. On the lagging strand, DNA is synthesized in the 5' to 3' direction, and these short DNA fragments are known as Okazaki fragments.
The antiparallel nature of DNA strands means that the DNA must unwind more before a new fragment can form on the top strand.
Bacteria DNA Replication
In bacteria, DNA replication happens quite differently than in eukaryotes. The process starts with the initiation of replication at a single origin called Rec. This requires the initiation protein DNA A to bind to the origin of replication to recruit helicase. DNA helicase is necessary to unwind the DNA, which is an essential part of the process.
Initiator proteins initiate replication by recruiting helicase. Helicase is responsible for unwinding the DNA, while single-strand binding proteins keep the DNA strands apart. Gyrase plays a role in making sure that DNA doesn't get too tangled up.
RNA primers are necessary for DNA replication to occur. The leading strand requires only one primer, and the rest is synthesized by DNA polymerase. However, on the lagging strand, each time DNA is unwound, a new primer must
be laid down with new polymerase or primase. The result of this process is called the Okazaki fragments.
The two replication forks meet when they meet again, and termination occurs.
Chapter 11 - Translation
"Genetics Essentials Textbook: Concepts and Connections" Fourth Edition by Dr. D
In this edition, Dr. D talks about how the ribosome uses tRNA to read codons specifically on mRNA during the process of initiation, elongation, and termination. Additionally, he explains the process of linking amino acids during the formation of proteins, turning them into chains of amino acids.
The ribosome links amino acids by taking the amino group from one amino acid and joining it to the carboxyl group from the other amino acid. This covalent bond is called the peptide bond which creates a protein, a chain of amino acids that has an amino group at one end and a carboxyl group on the other end.
The secondary and tertiary structures of a protein are determined by the backbone structure of amino acids but not all proteins have a quaternary structure.
The genetic code relies on codons, which are triplet codes from the DNA that are copied into RNA. There are 64 possible triplet codes of DNA, three of which code for stop codons and not for amino acids. 61 of the 64 possible codons code for amino acids. More than one codon probably codes for the same amino acid.
The start codon, also known as the initiation codon, is AUG. This is the codon that codes for the amino acid methionine. The termination codon, or stop codon, only directs the translation process to stop; there is no amino acid that it codes for. Any one of these three codons will direct translation to stop if it's in frame right on during the process of translation.
There are 64 different codons and only 20 different amino acids. This is why the genetic code is degenerate; there is a lot of redundancy, so you can have more than one codon code for the same amino acid. The wobble position is the least strict binding between the tRNA and the wobble positions on the mRNA.
Chapter12 - Control of Gene Expression
We will be discussing chapter 12 from our Genetics Essentials Concepts and Genetics Fourth Edition textbook, which covers the concept of controlling gene expression.
Gene expression is a vital process for all living organisms. For instance, in humans, the pancreas must inform one of its cells to express the insulin gene. Similarly, a skin cell can shut off unnecessary genes and only express the ones it needs to function as a skin cell. Even single-cell organisms like E. coli have mechanisms, such as the lac operon, to activate genes that are necessary for the breakdown and metabolism of lactose only when needed.
Regulating gene expression is a critical process both for prokaryotes and eukaryotes. There are two types of genes; the structural gene that codes for useful proteins, and the regulatory gene that codes for products affecting transcription. Regulatory elements are segments or sequences of DNA that do not transcribe but play a role in gene expression.
There are different levels of regulation that can occur in gene expression:
Changing the DNA structure to give access to the promoter
Sequestering DNA to inhibit gene expression
A constitutive gene is always on and continually expressed. Some proteins are inactive when produced and need to be post-translationally modified to become active.
Gene expression is often regulated early in the protein production process to increase cellular efficiency.
There is one promoter in front of three genes, all involved in lactose breakdown and metabolism. A regulatory gene is a DNA sequence that encodes products
Chapter 13 Gene Mutation and DNA Repair
We will be discussing chapter 13 from the Genetics Essentials Concepts and Connections fourth edition book. This chapter focuses on gene mutations, transposable elements, and DNA repair. In this video, we will be focusing on gene mutations and gene mutation repair.
What are mutations, and why are they essential to genetics? Dr. D is here to explain. In order for an individual to pass on a mutation to their offspring, that mutation should be germline, meaning the sperm or the egg should have that mutation in them. There are two ways for that to happen; one is if you were born with that mutation, and the other way is through another spontaneous mutation or an induced mutation by exposure to chemicals or something but that specifically happens in your germline cells.
There are three basic types of gene mutations, which are:
Substitutions: where you have transitions or transversions. In transversions, you
switch from a purine with two rings to a pyrimidine with one ring.
Insertions: where nucleotide bases are added to the DNA sequence.
Deletions: where nucleotide bases are removed from the DNA sequence.
You can also have expanding nucleotide repeats.
The genetic code should read GTA GAT and now it reads GTT AGA instead of GTA.
Frame shift mutations cause gibberish for the rest of the gene. These are highly deleterious mutations. Frame shift mutations are highly degenerative mutations.
Mutations can occur where there are repeats. Some mutations can result in those repeats being copied even more, and that can cause large segments of repeats to form fragile X syndrome. Fragile X syndrome is associated with a characteristic
constriction called the fragile site on the long arm of the X chromosome and is caused by expanding nucleotide repeats.
Silent mutations are an actual change in the DNA, but it doesn't change the amino acid sequence of the protein. Missense mutations are a change in DNA that does change the amino acid sequences of the protein. Nonsense mutations are a mutation that results in a premature stop codon. A neutral mutation is kind of like the in-between between silent and missense.
