1. Chapter 5
1.1. The Structure of DNA
1.1.1. DNA is comprised of two strands that are bound together by hydrogen bonds. The strands are made up of nucleotides.
1.1.2. Nucleotides are made of a 5-carbon sugar, a base that contains nitrogen, and an attached phosphate group.
1.1.3. The bases are adenine, cytosine, guanine, and thymine.(A, C, G, T ).
1.1.4. Phosphodiester bonds hold the nucleotides in DNA pairing the 5' end of a sugar in one nucleotide to the 3' end of another sugar in the next nucleotide. This forms a sort of "Backbone".
1.1.5. The two strands in DNA are complementary to one another.
1.2. The Structure of Eukaryotic Chromosomes
1.2.1. DNA is packaged into chromosomes by proteins that bind to the DNA and fold it.
1.2.2. DNA is packaged into one circular DNA molecule in prokaryotes unlike eukaryotes in whihc DNA is packaged into multiple chromosomes in the nucleus.
1.2.3. DNA is packaged into 23 chromosome pairs for a total of 46 chromosomes. A cell posses either 23 or 24 types of chromosomes(male-24 female-23).
1.2.4. Chromatin is the name for the singular long strand of DNA and proteins that are binding/packaging it in the chromosome.
1.2.5. Homologous (maternal/paternal version of chromosome) and nonhomologous(sex chromosomes in humans) chromosomes form a full set of chromosomes which is the human genome.
1.2.6. Genes are parts of the DNA in chromosomes that encode for proteins or RNA molecules. All of the genetic info in the complete set of chromosomes of an organism is called the genome.
1.2.7. Cell cycle is how cells divide and chromosomes are duplicated in interphase and distributed to the daughter cells in mitosis.
1.2.8. The DNA has many replication origins where the DNA replication begins. There are also telomeres that are the ends of the DNA and they help ensure the DNA is fully replicated as well as serving as a protective cap.
1.2.9. Nucleolus forms during interphase and its a large structure formed when chromosomes carrying genes that encode for ribosomal RNAs come together.
1.2.10. Histone and nonhistone proteins are responsible for packaging the DNA in chromosomes. Histones-2 of each-H2A, H2B, H3 and H4 are what the DNA wraps around and H1 keeps the DNA from unwrapping.
1.2.11. Nucleosomes are basically repeated DNA (packed by histones) and protein groups.
1.3. The regulation of Chromosome Structure
1.3.1. Histone tails can be modified so that a cell can regulate the structure of its chromatin.
1.3.2. Genes can be expressed when chromatin is loosened.
1.3.3. There is heterochromatin and euchromatin. Heterochromatin is highly condensed while euchromatin is not highly condensed and is therefore expressed.
2. Chapter 6
2.1. DNA Replication
2.1.1. DNA has two complementary strands. Each strand acts as a template to synthesize another strand from them creating two new strands by the end of replication.
2.1.2. Origin of replication is were DNA replication begins. There are any origins on eukaryotes but only one origin on prokaryotes.
2.1.3. DNA is split by an enzyme called DNA helicase. DNA gyrase stops the DNA from spiraling and single strand binding proteins keep the two strands from reconnecting. DNA polymerase 3 binds to a primer set by DNA primase and begins adding new nucleotides to each strand and the new strand is made in the 5'-3' direction.
2.1.4. The lagging strand is used in to make the daughter strand in a discontinuous synthesis in which okazaki fragments are added by DNA ligase and DNA polymerase 1 combines the okazaki fragments and ensures no gaps are in between the nucleotides on either daughter strand as well as removing the primer.
2.2. DNA Repair
2.2.1. Telomerase helps repair the telomeres on chromosomes were there are no okazaki fragments on the lagging strand forming incomplete synthesis. The telomerase will add nucleotides in order to repair the incompletion.
3. Chapter 7
3.1. From DNA to RNA
3.1.1. Transcription is when DNA is used to make RNA.
3.1.2. Many types of RNA are made such as rRNA(ribosomal RNA which helps the ribosome function), mRNA(messenger RNA which leaves the nucleus and goes to the ribosome and acts as a template for assembling amino acids) , tRNA(Transfer RNA helps amino acids bind to mRNA and helps attach amino acids to the ribosome.), miRNA(micro RNA is used for control of gene expression and is found only in eukaryotes).
3.1.3. RNA polymerase in prokaryotes transcribes for rRNA, mRNA, and tRNA.
3.1.3.1. In prokaryotes RNA polymerase 1 is fro rRNA, 2 is for mRNA, and 3 is for tRNA.
3.1.4. RNA polymerase requires transcription factors in eukaryotes in order to bind to the promotor (TATA box) while in prokaryotes sigma factors help it do so. Also, there are less promotors in prokaryote than eukaryotes making transcription initiation much simpler in prokaryotes.
3.1.5. TFIIH is what phosphorylates the RNA polymerase in order to start transcription. Transcription ends with dephosphorylating in eukaryotes.
3.1.6. When a terminator is transcribed, it causes RNA polymerase to stop transcription in prokaryotes.
3.1.7. mRNA is processed in the nucleus of eukaryotes in order to remove introns. Not required in prokaryotes since they don't have introns.
3.1.8. Introns are removed by snRNPS which are snRNAs and proteins that remove the introns form mRNA. The result is mRNA with no introns and only exons. A poly-A tail and 5' cap are added to prevent degradation and the mRNA is now mature and can exit the nucleus.
3.1.9. Once mRNAs have been used up, they are recycled along with the introns in the nucleus.
3.1.10. Alternative splicing means that yo can create various combinations of exons from the same gene resulting in multiple proteins being created from the same gene.
3.2. From RNA to Protein
3.2.1. Translation is whe RNA is used to make proteins.
3.2.2. In eukaryotes translation and transcription are decoupled. In prokaryotes, translation and transcription are coupled.
3.2.3. Codons speicfy amino acids. They are found on the mRNA and the anticodon, binds to the codon in mRNA, on the tRNA binds to the mRNA codon.
3.2.4. To bind to the mRNA correctly, tRNA must to the correct amino acid through enzymes called aminoacyl-tRNA synthetases.
3.2.5. The ribosome synthesizes proteins with the help of rRNAs. The small and large subunits bath play important roles. The large subunit is where the reaction for tRNA takes place binding the amino acid to it while the small subunit is were the mRNA codons are paired with tRNA anticodons.
3.2.6. In the ribosome there is a P, A, and E site. The P site is where the first tRNA enters carrying the amino acid methionine. The A site loads a new tRNA growing the polypeptide chain and the E site is where the tRNA with no amino aid attached exits.
3.2.7. The initiator tRNA binds to 5' cap in eukaryotes. In prokaryotes there is no 5' cap and has a six nucleotide long ribosome binding sequence that signals translation start.
3.2.8. Eukaryotic mRNA has information for a single amino acid while prokaryotic mRNA information that can code for multiple amino acids.
3.2.9. Polysomes are found in eukaryotes and prokaryotes but prokaryotes benefit from them more. They help speed up protein synthesis with multiple ribosomes working on one mRNA molecule.
3.2.10. Antibiotics are inhibitors of prokaryotic protein synthesis making them effective at stopping bacteria.
3.2.11. Proteases are enzymes that break down proteins.
3.2.12. Proteasomes are proteases only found in eukaryotes. They are large and contain many proteases.
4. Chapter 8
4.1. An Overview of Gene Expression
4.1.1. Gene expression is basically when genes are expressed when proteins are made from RNA encoded in the genes.
4.1.2. DNA is the same in all the cells of an organism but different parts of the DNA are used in different types of cells.
4.2. How Transcription is Regulated
4.2.1. Regulatory DNA sequences are found in the majority of genes and control if the gene is expressed or not.
4.2.2. Transcription regulators are proteins that bind to regulatory DNA sequences in order to express or not express a gene ultimately controlling its transcription.
4.2.3. In bacteria the trp and lac operon exist.
4.2.4. Trp operon is the tryptophan operon and is transcribed whenever tryptophan concentration is low. The mRNA produced can be translated to make proteins that synthesize tryptophan. When tryptophan is available, however, the repressor is activated and the trp operon is repressed so excess tryptophan is not made. (look at Figure 8-6 pg273 )
4.2.5. The lac operon is expressed whenever lactose is present and glucose is absent. The bacteria produces cAMP which binds to CAP whenever glucose is absent (also the presence of lactose stops the repressor from repressing the lac operon). This then causes the RNA polymerase to transcribe the lac operon and proteins can be made to transport nd break down lactose to form glucose. If lactose is absent, the repressor represses the lac operon. (Look at figure 8-9 pg 275)
4.2.6. A transcription initiation complex forms in eukaryotes. It is made up of enhancers and promotors and DNA that brings the activator protein close to the two and a mediator protein and other proteins help close the loop formed.
4.3. Generating Specialized Cell Types
4.3.1. A combinational control is when multiple transcription regulators determine how a gene is expressed. An example of this is the lac operon in bacteria.
4.3.2. Combinational control allows different cell types to exist.
4.3.3. Embryonic stem cells are pluripotent meaning they can become any type of cell in the body.
4.3.4. Master transcription regulators control the expression of multiple genes. They produce multiple regulators that result in a groups of specialized cells forming that eventually will form tissue and an organ.
4.3.5. Induced pluripotent stem cells are artificially created. They can be formed by using transcription regulators to revert differentiated cells back to cells that behave lie embryonic stem cells.
4.3.6. Cell memory is responsible for maintaining a cell's identity through future generations. It is done by creating a positive feedback loop. this loop is created when a master transcription regulator creates its own self by activating its own gen's transcription.
4.3.7. DNA methylation involves modifying the cytosine bases attracting proteins that block gene transcription. This would effectively stop a gene from being expressed.
4.4. Post-Transcriptional Controls
4.4.1. The RISC is a RNA induced splicing complex. A miRNA binds to the RISC and is an antisense strand. It guides the RISC to the mRNA with a matching sequence and the mRNA is targeted for destruction by proteases.
4.4.2. SiRNAs are formed when RNA interference occurs. Foreign RNA is cut by dicers into smaller fragments that form double-stranded RNAs. They are used by the RISC to find RNA molecules that are complimentary to one of the strands on the siRNA.
5. Chapter 9
5.1. Generating Genetic Variation
5.1.1. Mutations that occur in germ cells can only be passed down to the next generation. This is why scientists look at the germ line when studying evolutionary changes.
5.1.2. Point mutations alter a single nucleotide. There are three types- missense, nonsense, and silent mutations. A missense mutation changes the amino acid to a different one, a nonsense mutation results in the codon becoming a stop codon, and a silent mutation is one that results in no change occurring to the amino acid so it basically doe not do anything.
5.1.3. Gene duplication can occur and this can allow the two duplicate genes to mutate freely leading to one of the genes eventually creating multiple specialized genes called gene families.
5.1.4. Exon shuffling occurs when one gene's exons are added to another gene.
5.1.5. Mobile genetic elements are basically sequences of DNA that can relocate themselves in the chromosome. They can have profound effects on the entire genome.
5.1.6. Horizontal gene transfer is the transferring of genes from one organism to another. This is more common in prokaryotes.
5.2. Reconstructing Life's Family Tree
5.2.1. The phylogenetic tree allows us to compare evolutionary changes in a group of organisms. It provides an overview of the evolutionary relationships between that group of organisms.(Alberts, 2019, pg 310)
5.2.2. There is conserved synteny in organisms. Conserved synteny is when two species have genes that are grouped together in an identical fashion. This most likely occurred due to purified selection which would eliminate any organisms with mutations that negatively impact the organism in a huge way.
5.3. Mobile Genetic Elements and Viruses
5.3.1. Transposons are genes that can move around in our genome. These can result in genome alterations. They move with the help of transposase which mediate the movement of the transposons.
5.3.2. Viruses move around and find host cells to survive. They inject the DNA they carry into the host cell and that genetic material must combine with the host's genetic material in order to take over the host cell. This will reprogram it to make more of the virus until it makes too may to hold and busts open releasing more viruses that will do the same. Retroviruses work the same except they carry RNA that must be reverse transcribed to DNA before they can take over the host cell.
6. Chapter 10
6.1. Isolating and Cloning DNA Molecules
6.1.1. Restriction enzymes are used for DNA cloning. They "restrict the transfer of DNA between trains of bacteria."(Alberts, 2019, pg 335)
6.1.2. Gel electrophoresis is a technique that separates DNA by size. The DNA are loaded into one end of the gel and a positive electrode is on the other end. A negative charge is run through the gel attracting the DNA to the positive electrode. Smaller DNA will move quicker towards the positive electrode and larger DNA will move much slower. The DNA can be seen when dyed with a dye that reacts to uv light so you can see the DNA molecules in the gel.
6.1.3. DNA cloning uses the fragments of DNA after being separated. These fragments are combined with another piece of DNA (vector) that can be copied in cells. The vectors are plasmids and each plasmid has its own replication origin so you can mass produce the DNA fragment contained in it. The resulting DNA is called recombinant DNA.
6.1.4. A genomic library is basically the entire organism's genome. They are a collection of multiple DNA clones form an organism's genome.
6.1.5. A more specific genomic library is a cDNA library. This is made using DNA clones from mRNA using reverse transcriptase. This can be used to make a protein in mass amounts since the DNA in it is made from mRNA only.
6.1.6. Hybridization is when you denature a DNA molecule and then allow it to slowly come back together. You can use it to place probes in DNA/RNA and detecting a specific nucleotide sequence.
6.2. DNA cloning by PCR
6.2.1. PCR uses a primer that is hybridized into a DNA strand. This primer is found and bound by DNA polymerase and the DNA molecules can then be cloned multiple times. You can use PCR to create a cDNA or genomic library.
6.2.2. PCR can be used in a wide range of applications such as forensic medicine and testing food products for microbes.
6.3. Sequencing DNA
6.3.1. Dideoxy sequencing uses DNA polymerase and deoxyribonucleoside triphosphates. They make partial copies of DNA and we can use it to figure ut the nucleotide sequence of purified DNA fragments.
6.3.2. There is also illumina sequencing which is the same as automated deoxy sequencing except with removable florescent tags/chemical group that blocks elongation. (ALberts, 2019, pg347)
6.4. Exploring Gene Function
6.4.1. RNA-Seq uses the complementary DNA so that the transcriptome can be analyzed quantitively.
6.4.2. In situ hybridization uses probes to detect a target sequence within a chromosome or in tissue such as with the VR1 receptor.
6.4.3. A reporter gene can be used to track a specific protein. A reporter gene will be like the gene being studied and will produce protein that can easily be tracked.
6.4.4. CRISPR uses cas9 which binds to a guide RNA.. The cas9 will then find the target sequence in the genome and bind t it and cut it. Since the cut gets repaired, scientists can provide their own template for repair which alters that pat of the genome.