Midterm 2

Viral replicative cycles

1. The virus enters the cell and is uncoated, releasing viral DNA and capsid proteins. The mechanism of genome entry depends on the virus and the host cell. Some use their tail to inject DNA into the bacterium, some are taken up by endocytosis, or some fuse with the cell's plasma membrane if they have a viral envelope. 2. Host enzymes replicate the viral genome. The proteins that the virus encodes takes over the host cell and reprograms the cell to copy its genome and manufacture viral proteins. DNA viruses often use DNA polymerase from the host cell to synthesize new genomes along with their own genome. 3. Meanwhile, host enzymes transcribe the viral genome into viral mRNA, which host ribosomes use to make more capsid proteins. The host provides everything it needs to make these proteins. 4. Viral genomes and capsid proteins self-assemble into new virus particles, which exit the cell. The proteins and capsomeres spontaneously assemble into new viruses. Then the viruses can exit the cell, damaging or destroying it. This damage is what makes the body respond to the destruction, which causes symptoms. The viruses then go onto infecting other cells, spreading the infection.

Evolutionary development biology

A change in gene regulation during development can lead to a change in the body. This idea gave rise to "evo-devo" biology. Gene regulation controls the transformation of a fertilized egg into a multicellular organism. It is balanced by turning on/off genes at the right time and place. When an organism is fully developed, gene expression is regulated in a fine-tuned manner.

The lytic cycle

A phage replication cycle that results in the death of the host cell. During the last stage of infection, the bacterium lyses (breaks down) and releases phages that were produced in the cell. The viruses then go on to infect other cells, which can result in an entire bacterial population dying. T4 lytic cycle: 1. Attachment: the phage uses its tail fibers to bind to specific surface proteins on an E. coli cell that act as receptors. 2. Entry of phage DNA and degradation of host DNA: the sheath of the tail contracts, injecting the phage DNA into the cell and leaving an empty capsid outside. The cell's DNA is hydrolyzed. 3. Synthesis of viral genomes and proteins: the phage DNA directs production of phage proteins and copies the phage genome by host and viral enzymes, using components within the cell. 4. Self assembly: three separate sets of proteins self form phage heads, tails and tail fibers. The phage genome is packages inside the capsid as the head forms. 5. Release: the phage directs production of an enzyme that damages the bacterial cell wall, allowing fluid to enter. The cell bursts, releasing 100 to 200 phage particles. Virulent phage: a phage that replicates only by a lytic cycle. Bacterial defense: natural selection favors bacteria mutants with surface proteins that are no longer recognized by a certain phage. DNA call also be cut up by restriction enzymes if the cell can identify the DNA as foreign, restricting the phages ability to replicate. However, natural selection also can allow viruses to mutate.

Insertions and deletions

Additions/ losses of nucleotide pairs in a gene. Have a very bad effect more often than substitutions. Frameshift mutation: alters the reading frame of a genetic message. Occurs when nucleotides are inserted/deleted without being in a multiple of three. All downstream nucleotides will be screwed up bc they will be grouped into different codons. Lots of missense/probs premature termination (nonsense). Unless it is near the end of the gene, the protein will probably not be functional.

Protein processing and degradation

After translation: final opportunities for controlling gene expression. E polypeptides have to be processed to form functional proteins/chemical modifications. Regulatory proteins can reversibly add phosphate groups/ some proteins need sugars added to them. Cell surface proteins have to be transported to their final destinations to function. Length of time that each protein functions is regulated by selective degradation. Proteins are marked for when they should be destroyed by small proteins called ubiquitin that attach to the protein. Huge protein complexes called proteasomes recognize proteins tagged with ubiquitin and degrade them.

The lysogenic cycle

Allows replication of the phage genome without killing the host. Prophages are capable of generating active phages that lyse the host cell when it is triggered to do so. Then, the virus switches over from the lysogenic to the lytic mode. Expression of the prophage genes is seen in preventing transcription, and also by altering the hosts phenotype (can be very harmful to humans). Temperate phages: phages capable of using both modes of replication within a bacteria. Lambda bacteria: a temperate phage like a T4, but it only has one short tail fiber. The lambda DNA forms a circle, and it chooses whether it wants to replicate by the lytic cycle or the lysogenic cycle. During the lysogenic cycle, the lambda DNA is incorporated into a chromosome by viral proteins that break the circular DNA and the chromosome and join them together. This DNA is now known as a prophage, which codes for a protein that prevents transcription of most other prophage genes, so that the phage is mostly silent and doesn't do anything. E. coli will replicate the phage DNA every time it divides, so every daughter cell is a prophage.

Elongation of the polypeptide chain

Amino acids are added to the previous amino acid at the C terminus. Involves protein structures called elongation factors. Goes through a 3 step cycle, and each codon recognition needs one hydrolysis of GTP. Another GTP is needed for the translocation step (moving the chain along the ribosome). Moves only in the 5' to 3' direction. The ribosome and the mRNA move relative to each other in the same direction. 1) Codon recognition: the anticodon of an incoming aminoacyl tRNA base pairs w a complementary mRNA codon at the A site. GTP hydrolysis= increased accuracy/efficiency in this step. Many tRNAs are present, but only one will bind to the anticodon. 2) Peptide bond formation: rRNA molecule of the large subunit catalyzes the bond between the amino group of the new amino acid in the A site and the carboxyl end of the new polypeptide in the P site. This removes the polypeptide from the tRNA in the P sire and attaches it to the amino acid on the A site. 3) Translocation: the ribosome translocates the tRNA in the A site to the P site (moves it one over). At the same time, the tRNA in the P site is moved to the R site and it is released there. The mRNA moves along with the tRNAs that are bound, bringing the next codon into the A site.

What is a virus?

An infectious particle consisting of genes packaged in a protein coat. They are much smaller and simpler that E or P cells, and they lack structures and metabolic machinery found in a cell. They cannot reproduce or carry out metabolism outside of a host cell, so most biologists wouldn't consider them as being alive. Viruses can be used as agents for gene transfer in gene therapy.

Halobacterium

Archaea that have red membrane pigments to capture light energy for photosynthesis. They thrive in salinities that would kill/dehydrate other cells by pumping K+ into the cell until the concentration outside matches the concentration inside. Bacteria and other prokaryotes can survive in extreme conditions, such as extreme salinity, pH and temperature. Prokaryotes have an ability to adapt to a broad range of habitats, which is why they are the most abundant organisms on Earth.

Chromosomes

Bacteria has one double stranded circular DNA molecule associated with a small amount of protein. his is called a chromosome, but it is different from a E chromosome. Certain proteins cause the chromosome to coil/supercoil densely so that it fills part of the cell. This region is called to the nucleoid, and it is not membrane bound like a nucleus. Eukaryotic chromosomes have one linear DNA molecule and a large amount of protein. This complex is called chromatin, and it fits in the nucleus by a packing system. In interphase, chromatin looks like a diffused mass, but it is looped and attached to the nuclear lamina/fibers in the matrix. In interphase, centromeres and telomeres of chromosomes as well as other regions are in a highly condensed state, similar to metaphase chromosomes (called heterochromatin), opposed to the less compact euchromatin. Euchromatin can be transcribed because it is looser and more accessible. As the cell prepares for mitosis, chromatin coils up and folds, eventually creating metaphase chromosomes. Chromatin packing in an Eukaryotic chromosome: 1) DNA double helix 2) Histones: proteins responsible for the first level of DNA packing into chromatin. Helps to organize the DNA within cells. 3) Nucleosomes/beads of fiber on a string/ 10nm fiber: a basic unit of DNA packing, DNA is wound twice around a protein core of 8 histones. The N-terminus end of each histone extends outwards from the nucleosome. They are involved in the regulation of gene expression. 4) 30nm fiber: interactions between the histone tails of one nucleosome and the linker DNA and nucleosomes on the other side. These interactions cause the 10nm fiber to coil, forming chromatin fiber 30nm thick. Prevalent in interphase. 5) Looped domains/300nm fiber: the 30nm fiber forms loops called looped domains. 6) Metaphase chromosomes: In a mitotic chromosome, looped domains coil further, compacting all of the chromatin, 700nm thick (one chromatid). Genes always end up in the same places of the metaphase chromosomes.

Evolutionary origins of bacterial flagella

Bacterial flagellum contains the motor, the hook and the filament, each composed of 42 different proteins. They probably evolved from simper structures, and a lot of its protein components aren't necessary for it to function. The proteins are related from an ancestral protein that formed a pilus-like tube, which suggests that bacterial flagellum evolved as proteins were added to its secretory system (example of exaptation: existing structures take on new functions through descent with modification).

Evidence that viral DNA can program cells

Bacteriophages: means bacteria-eaters, known as phages. They are viruses that infect bacteria. Additional evidence of DNA cam from these phages. Viruses are basically just DNA enclosed in a protective coat made of protein. Viruses infect cells and take over its metabolic machinery. Scientists didn't know if the DNA or the protein of the phages was reprogramming the host cell to produce more viruses. Hershey and chase: proved that it was DNA entering bacteria cells during infection by using radioactive sulfur tags on protein in one T2 virus, and another on DNA. E. coli cells were infected with both batches of labeled viruses, and they found that the phage DNA had entered the host cell but the protein had not. E. coli continued to produce phages with radioactive DNA. Therefore, they concluded that DNA was the hereditary material (at least in these viruses).

Nutritional mutants in Neurospora

Beadle and Edward Tatum: used radiation to make mold mutants and looked t the survivors that differed in their nutritional needs from the wild type. It can grow in a minimal nutrient environment/medium. They found mutants that couldn't survive on minimal medium because they were unable to synthesize certain molecules from the medium. Then they allowed them to grow on complete growth medium, and the mutants could grow on this. They put the mutant into vials that contained the minimal growth medium and only one more nutrient to see if they could grow. This allowed them to conclude which metabolic defect the mutant had. They found that the mutant couldn't synthesize arginine. Won the Nobel Prize for their discovery that genes act by regulating definite chemical events. Adrian Srb and Norman Horowitz: colleagues, tested the mutants to distinguish between three arginine requiring mutants. Each class was blocked at a different step in the pathway because the mutants lacked enzymes that catalyzed the blocked step. This showed the one gene-one enzyme hypothesis.

Structural and functional adaptions that contribute to prokaryotic success

Because prokaryotes were the first to inhabit earth, they have been subjected to natural selection is lots of different environments, which results in their genetic diversity. They are usually 0.5-1nm and come in a variety of shapes. They are unicellular and small but well organized, and they achieve all functions of life in a single cell.

Pattern formation

Body plan: the 3D arrangement. Must be established and superimposed on the differentiation process. Cytoplasmic determinant and inductive signals contribute to the spacial organization of tissues/organs (pattern formation). This begins when the organism is an embryo when the axes of an anima are established. Positional information: the molecular cues that control pattern formation that are provided by the cytoplasmic determinants and inductive signals. These cues tell the cell where it is in reference to the body axis and neighboring cells/how the cell and new cells will respond to more molecular signals.

Evolutionary significance of small ncRNAs

Can regulate gene expression at multiple steps in many ways, allowing for more complexity.

Types of genes associated with cancer

Cancer: a disease in which cells escape from the control mechanisms that normally limit their growth. Gene regulation systems that cause cancer are the same ones that play important roles in embryonic development, the immune response and many other important processes. Mutations: in somatic cells in genes responsible for cell growth, division, growth factors, receptors, intracellular signaling pathways etc. can lead to cancer. Oncogenes: cancer causing genes.Arise from a genetic change that leads to an increase in the amount of a protein or in the activity of a protein in a proto-oncogene. Genetic changes have to do with movement of DNA within the genome (gene is moved to a new locus under new controls), amplification of a proto-oncogene (makes multiple copies of a gene/the growth stimulating protein in excess), and point mutations in control elements or in the proto-oncogene itself. Proto-oncogens: normal versions of cellular genes that code for proteins that stimulate normal cell growth and division. Cancer cells: often found with broken chromosomes/chromosomes rejoined incorrectly/translocation fragments from one chromosome are in another. If a translocated proto-oncogene is near an active promoter or control element, transcription may increase, making it an oncogene. Amplification increased the number of copies of the proto-oncogene through lots of gene duplication. Mutations in the promoter or enhancer can cause an increase in the proto-oncogene expression or a protein is more resistant to degradation. These cause cancer cells because they lead to abnormal stimulation of the cell cycle. Tumor-suppressor genes: proteins they encode help prevent uncontrolled cell growth/ contain genes that inhibit cell division. A mutation that decreases the activity of one of these genes/proteins can contribute to the onset of cancer because it lets cell growth go uncontrolled. These genes can repair damaged DNA to prevent the cell from accumulating mutations that cause cancer, control the adhesion of cells to each other (adhesion is often absent in cancer) and are components of cell-signaling pathways that inhibit the cell cycle.

Cell surface structures

Cell wall: maintains cell shape, protects the cell and prevents it from bursting in a hypotonic environment (although in a hypertonic environment they will shrivel). P cell walls are different from E cell walls, as most bacterial cell walls contain peptidoglycan, a polymer composed of modified sugars, cross linked with short polypeptides (E cell walls are made of cellulose/chitin). This encloses the bacterium and anchors other molecules that extend from its surface. Archaea have cell walls made of polysaccharides and proteins, but they don't have peptidoglycan. Gram stain: can categorize bacteria based on differences in their cell wall composition. Samples are stained with violet dye/iodine, rinsed with alcohol and stained with red dye. The structure of the cell wall shows differences in staining. Gram positive bacteria: simple cell walls with large amounts of peptidoglycan. Gram negative bacteria: less peptidoglycan and structurally more complex (outer membrane contains carbs bonded to lipids a.k.a lipopolysaccharides). Gram staining can be used to determine if a patient is infected with gram positive or gram negative bacteria. Gram negative bacteria are toxic due to the lipopolysaccharides, and they can defend against the body's defenses/are more resistant to antibiotics. Antibiotics: effectiveness sometimes derives from their inhibition of peptidoglycan cross-linking, which can destroy the cell wall of some bacteria (especially gram-positive). Capsule: a sticky layer of polysaccharide or protein that surrounds the cell wall of many prokaryotes. Called a slime layer if it is not dense/organized/well defined. These enable prokaryotes to adhere to their substrate or other members of their colony. It can also protect them from dehydration or their host's immune system. Endospores: A resistant cell developed by the bacteria when it lacks an essential nutrient/ a way to withstand harsh conditions. The bacteria produces a copy of its chromosome and surrounds it with a tough structure, forming an endospore. Water is removed from the endospore and metabolism is halted. The original cell lyses, releasing the endospore, which can survive in harsh conditions. Fimbriae: hairlike appendages that allow some prokaryotes to stick to their substrate or one another.

Other evidence that DNA is the genetic material

Chargaff: he analyzed the nucleic acid sequence of DNA in different organisms and found that the composition of DNA varies in different species. He showed that there was molecular diversity amongst DNA molecules of different species, whereas previously people thought that there was not. He also found a regularity in the ratios of nucleotide bases (A=T, G=C). There were known as Chargaff's rules: 1) the base composition variation of DNA arises between species and 2) for each species, the percentages of A and T bases are roughly equal and the percentages of G and C bases are roughly equal. However, these rules weren't super clear until the double helix was discovered.

Histone modifications and DNA methylation

Chemical modifications to histones (what wraps around DNA in nucleosomes) regulate gene transcription. Histone acetylation: promotes transcription by opening the chromatin structure. Histone tails protrude outward from the nucleosome and the acetylation of histone tails promotes a loose chromatin structure that permits transcription. DNA methylation: inhibits transcription by condensing chromatin more. Inactive DNA are more methylated than actively transcribed regions of DNA. Individual genes are also more methylated when they are not expressed. At sites where a gene is methylated, enzymes methylate the daughter cell also. These patterns are passed on, which allows tissues to have the same genes expressed in each cell (unified). Also accounts for genomic imprinting in mammals, where methylation permanently regulates gene expression of an allele at the start of inheritance.

Regulation of chromatin structure

Chromatin: Packages of DNA in a complex that is complex so that it fits inside of the nucleus. Also helps regulate genes. Regulation: location of the promoter relative to nucleosomes and the sites that DNA is attached to the chromosome scaffold affects transcription. Genes inside heterochromatin aren't expressed because they are so condensed. Modifications of histone proteins and to DNA of chromatin can influence chromatin and gene expression.

Nuclear architecture and gene expression

Chromosomes aren't completely isolated from one another in interphase. Some regions of different chromosomes are associated with one another by loops of chromatin. Relocation of particular genes from their chromosomal territories to transcription factories (sites rich in RNA pol and transcription proteins) may be part of the process for making genes ready for transcription.

Conjugation and plasmids

Conjugation: DNA is transferred between two prokaryotic cells (usually same species) that are temporarily joined. One cell donates the DNA and the other receives it (only goes one way). Conjugation mechanism of E. coli: The pilus of the donor cell attaches to the receiving cell. The pilus retracts, pulling the two cells together. Then the cells form a mating bridge (a structure between the two cells through which the donor can transfer DNA to the receiver). F factor: a piece of DNA that gives the cell the ability to form pili and donate DNA during conjugation. The F stands for fertility. It can exist as a plasmid or a segment of DNA within the chromosome. F plasmid: the F factor of a plasmid. Cells containing the F plasmid are known as F+ cells, and cells without it are known as F- cells. The F+ ell can transfer DNA to the F- cell, and if the entire F plasmid is transferred, the F- cell becomes and F+ cell. F factor in the chromosome: Chromosomal genes can be transferred during conjugation if the F factor of the is built into the chromosome (this is called a high frequency recombination or Hfr). Hfr cells function as donors, and when the Hfr DNA enters a F- cell, homologous chromosomes can align so that their DNA sequences are exchanged. This results in a recombinant cell. R plasmids/antibiotic resistance: A mutation in a chromosomal gene can sometimes make a pathogen resistant to antibiotics. The bacteria can either have a mutation that makes the antibiotic unable to bind/inhibit, or it may have resistance genes, like enzymes that destroy the antibiotic. R plasmids: Resistance genes carried by plasmids, which code for enzymes that are able to destroy or hinder the effectiveness of certain antibiotics. Because of this, when a bacterial population is exposed to antibiotics, all of them will die unless they have an R plasmid. These bacteria can use up all of the resources and increase in number. This is why some bacterial infections are very difficult to treat.

Axis establishment

Cytoplasmic determinants: substances in egg that initially establish the axes (in this case of Drosphila). Ecoded by genes from the mother (maternal genes). Maternal effect gene: a gene that, when mutant in the mother, results in a mutant phenotype of the offspring, regardless of the offspring's genotype. When the mother has a defect, she makes a defective gene product and her eggs are defective. When the eggs are fertilized they fail to develop properly. Mutations in the maternal effect genes are usually lethal. Egg-polarity genes: They control the orientation (polarity) of the egg hence the fly. Maternal effect genes. Maternal mRNA: crucial during development. Gradients of specific proteins encoded by maternal mRNA establish crucial things. Morphogens: establish an embryo's axes and other features of its form.

Synthesizing a new DNA strand

DNA polymerase: catalyzes DNA synthesis by adding nucleotides onto the preexisting chain. They require a primer, a DNA template strand, and complementary DNA nucleotides lined up. Rate of elongation= 500 nucleotides/sec in bacteria and 50/sec in humans. E. coli: DNA Polymerase III adds DNA nucleotide to the RNA primer and then continues adding DNA nucleotides. Nucleotides: sugar attached to a base and three phosphate groups (kinda like ATP). Nucleotides used for DNA synthesis are chemically reactive bc of their triphosphate tailed (cluster of negative charge). As each nucleotide is added, two phosphate groups are lost (pyrophosphate). This pyrophosphate is hydrolyzed to form two molecules of inorganic phosphate, which is an exergonic reaction that drives polymerization.

Evolutionary significance of altered DNA nucleotides

DNA replication and damage repair of DNA are super important for passing accurate info onto the next generation. Even though the rate of error is very low, errors do still occur. Once an error is replicated, the sequence change is permanent. Mutations can change the phenotype of an organism. Although mutations are harmful in some cases, many times they do not have any affect or are beneficial, leading to natural selection and evolution.

DNA replication

DNA replication is incredibly fast and accurate, producing very few errors. More than a dozen enzymes are involved in DNA replication, and this process is very similar in prokaryotes and eukaryotes. Origin of replication: short stretches of DNA having a specific sequence of nucleotides at which the replication of a chromosome begins. Circular bacterial chromosomes have only one origin of replication, whereas linear chromosomes have many. Prokaryotes (circular DNA): Proteins recognize a sequence (origin of replication) and attach to the DNA, separating the two strands and opening a replication bubble. Replication proceeds in both directions until the entire molecule is copied. Eukaryotes (linear DNA): Multiple replication bubbles form and eventually fuse, which speeds up the replication process (much longer DNA molecules). Replication proceeds in both directions from each origin. Replication fork: At each end of a replication bubble there is a replication fork, which is a T-shaped region where parental strands of DNA are unwound. Helicase: an enzyme that untwists the double helix at the replication fork, separating the two parental strands and making them available as template strands. Single-strand binding proteins: bind to the unpaired DNA strands, keeping them from repairing. Topoisomerase: relieves the strain from the untwisting of the double helix (causes tighter twisting and strain ahead of the replication fork), and it helps this strain by breaking, swiveling and rejoining DNA strands. Primase: an enzyme that synthesizes a a short stretch of RNA called a primer. Enzymes that synthesize DNA are unable to initiate the synthesis of a strand, and they can only add nucleotides to an existing chain. The initial chain is a stretch of RNA. Primase starts a complementary RNA chain from a single RNA nucleotide, adding more RNA nucleotides one at a time using the parental DNA strand as a template. This 5-10 nucleotide primer is base paired to the template strand, and the new DNA strand will start at the 3' end of the RNA primer.

Antiparallel Elongation

DNA strands have directionality, and are antiparallel in the double helix (oriented in opposite directions to each other). They therefore must be replicated in an antiparallel fashion. DNA polymerases can only add nucleotides to the 3' end of a primer and never the 5' end, so it elongates in a 3'->5' direction. Leading/lagging strand: DNA polymerase III remains in the replication fork on the template strand and adds nucleotides to the new complementary strand as the fork progresses. The DNA strand made in this way is called the leading strand. Only one primer is needed by DNA polymerase III to replicate the whole leading strand. To elongate the other new strand of DNA, DNA pol III must work along the template strand in the direction away from the replication fork. This is called the lagging strand, which is synthesized discontinuously in a series of segments (Okazaki fragments). Each Okazaki fragment has to be primed separately on the lagging strand, whereas the leading strand only needs one primer. Leading strand: 1) After the RNA primer is made, DNA pol III starts to synthesize the leading strand. 2) The leading strand is elongated continuously in the 5'->3' direction as the fork progresses. Lagging strand: 1) Primase joins RNA nucleotides into a primer. 2) DNA pol III adds DNA nucleotides to the primer, forming Okazaki fragment 1. 3) After reaching the next RNA primer to the right, DNA pol III detaches. 4) Fragment 2 is primed and DNA pol III adds DNA nucleotides, detaching when it reaches the fragment I primer. 5) DNA pol I replaces the RNA with DNA, adding nucleotides to the 3' end of fragment 2. 6) DNA ligase forms a bond between the newest DNA and the DNA of fragment 1. 7) The lagging strand is complete.

Sequential regulation of gene expression during cellular differentiation

Determination: the point at which an embryonic cells is irreversibly committed to becoming a particular type of cell. Once this happens, it has a certain fate even when in a different location. The outcome is expression of genes for tissue-specific proteins that are only found in a specific cell type. Transcription is the main regulatory point where this happens. Differentiated cells: specialize in making tissue-specific proteins. All genes activated by the specific cell have enhancer control elements that are recognized by the cell and are coordinately controlled. Secondary transcription factors activate the genes for proteins that confer to the properties of the cell. Master regulatory gene: capable of changing fully differentiated cells in some kinds of cells, not all. They have to be cells that respond to only that gene and not a combination of genes. Happens in muscle cells by MyoD, which can change some kinds of differentiated nonmuscle cells (like fat and liver cells) into muscle cells. MyoD: 1) Determination: signals from other cells lead to activation of the master regulatory protein myoD, and the cell makes MyoD protein, a specific transcription factor that acts as an activator. 2) MyoD protein stimulates the myoD gene further and activates genes encoding other muscle-specific transcription factors, which activate genes for muscle proteins. Turns on genes that block the cell cycle, stopping cell divisions.

The life cycle of Drosophilia

Drosphila structure: head, thorax (mid body) and the abdomen. Cytoplasmic determinants: localized in the unfertilized egg, provide positional info for the placement of the axises before fertilization even happens. Embryonic development: The egg develops in the female's ovary and are surrounded by support cells with nutrients, mRNA and other substances to make the egg shell. After fertilization, embryonic development results in larvae that go through three stages (like a butterfly).

Making multiple polypeptides in bacteria and eukaryotes

E and B cells: Cells often need many copies of the protein, not just one. Multiple ribosomes can translate an mRNA at the same time, so that multiple polypeptides can be made at the same time. Ribosome has to be far enough from the start codon for a new ribosome to attach to the same mRNA (called polyribosomes/polysomes). They can also transcribe multiple mRNAs from the same gene to make more protein. Difference between E and B cells: bacterial cells don't have compartmental organization, so it can transcribe and translate the same gene at the same time. E cells segregate transcription and translation/process RNA, so there is many more steps.

Organization of eukaryotic genes

E gene: has a cluster of proteins called a transcription initiation complex that assembles on the promoter upstream. RNA pol II transcribes the gene/ the primary RNA transcript. Then RNA processing adds on a 5' cap and a poly A tail, and also splices out introns to produce a mature mRNA. Control elements: segments of noncoding DNA that serve as binding sites for transcription factor proteins that regulate transcription.

Operons

Each reaction of a chemical pathway is catalyzed by a specific enzyme. Genes of related function can be grouped so that one mRNA molecule can code for multiple polypeptides that encode for enzymes in a chemical pathway. This means that a single on/off switch can control the whole cluster of structurally related genes (coordinately controlled). All enzymes can therefore be synthesized at one time for a metabolic pathway. An operon is an example of how gene expression can respond to changes in the cell's environment. Operator: the on/off switch for a segment of DNA. It is positioned within the promoter or in between the promoter and the enzyme coding genes. It controls the access of RNA polymerase to the genes. Operon: he operator, the promoter and the genes that they control/entire stretch of DNA for enzyme production. RNA polymerase can bind to the promoter and transcribe genes of the operon. Repressor: The operon can be switched off by a repressor, which binds to the operator and attaches RNA polymerase to the promoter, preventing transcription of genes. When the repressor binds to the operon, production of the molecule is switched off. The binding of repressors is reversible, and the operator alternates between repressor bound and no repressor bound. The time with the repressor bound increases when more repressor molecules are present. It also has an active state and an inactive state (allosteric), so only when the molecule thats being encoded accumulates and binds to the repressor does the repressor become active. More molecules=more active repressors. Corepressor: a small molecule that cooperates with the repressor protein to switch an operon off. Regulatory Gene: The repressor is a product of a regulatory gene, located on its own promoter. Regulatory genes are expressed continuously at a low rate.

Genetic analysis of early development

Edward Lewis (1940s): showed how valuable genetics are in studying embryonic development. Located mutations in mutated flies on the genetic map and connected this to developmental abnormalities in specific genes. Showed that genes direct the developmental process. He discovered homeotic genes (control pattern formation in the late embryo, larva and adult). Volhard and Wieschaus: wanted to identify all genes in Drosphila. Embryonic lethals: mutations with phenotypes causing death at the embryonic level or larval stage, so they cannot be bred to study. Tons of genes. Cytoplasmic determinants in the egg played a role in axis formation (known), so they had to study the mother's genes and the embryo. Found segmentation genes by exposing flies to mutagens and scanned for abnormal segmentation. Identified 1200 genes that had a role in pattern formation during embryonic development, and 120 were essential for normal segmentation. This gave a more coherent picture of Drosphila development.

Termination of translation

Elongation keeps going until a stop codon in the mRNA reaches the A site (UAG, UAA or UGA). A release factor shaped like aminoacyl tRNA binds to the stop codon in the A site, and causes the addition of a water molecule instead of an amino acid. This breaks/hydrolyses the bond between the polypeptide and the tRNA in the P site, and the polypeptide is released through the exit tunnel in the large subunit. Two GTP are required for the two subunits/the other components to dissociate.

Emerging viruses

Emerging viruses: viruses that suddenly become apparent. HIV is an example, and it appeared incredibly quickly. Another example is Ebola, which causes hemorrhagic fever (fatal, characterized with fever, vomiting, bleeding and circulatory system collapse). Viruses emerge from mutation of existing viruses, and RNA viruses have a high rate of mutation because viral RNA polymerases don't proofread and correct errors in their genome like DNA does. Some of these mutations will cause new strains, and these strains can infect those who are immune to the previous strain (why you have to get a flu shot every year). Another way that viruses can emerge is by spreading from a secluded population to large populations. This is why some viruses emerged quickly when travel/drugs/sex/technology etc. became popular and global. Finally, viruses can also spread from an animal to a human (3/4 of viruses come to infect humans this way). The animal that originally had the virus may be unaffected by it, but when it spreads to humans it is dangerous (like the swine flu). Epidemic: A widespread outbreak. An example of this is the 2009 H1N1 flu (Swine flu), which started in Mexico and the US. Pandemic: a global epidemic (2009 H1N1 flu eventually spread across the world, turing from an epidemic into a pandemic). Influenza: shows how viruses can move between species. There are three types (A, B and C). Types B and C only infect humans and never cause epidemics, but type A infects a wide range of animals, making it more infectious and dangerous. Strains of influenza are given standardized names that have to do with the viral surface proteins present: H (hemagglutinin) and N (neuraminidase: an enzyme that releases new virus particles from infected cells). There are 16 types of H and 9 types of N. Mutations and recombination allow viruses to gain the ability to move from one animal to another.

Viral envelopes

Envelope: animal viruses have an envelope/outer membrane that is used to enter a host cell. The surface of the envelope have glycoproteins that bind to specific receptor molecules on the surface of the host cell. Ribosomes bound to the ER make protein parts of the envelope glycoproteins and enzymes in the ER and Golgi add the sugars to them. Viral proteins are therefore embedded in the membrane of the host/transported to the cell's surface. By exocytosis, the viral capsids are wrapped in the membrane and they bud from the cell. Therefore, the envelope is derived from the host's plasma membrane, an the viruses now go onto infect other cells. This process does not usually kill the cell. Herpesvirus: Viruses don't always get their envelope from the plasma membrane though (Herpesviruses use membrane from the Golgi). They leave behind their DNA in some nerve cells, and distress of the body triggers a new round of virus production.

Proofreading and repairing DNA

Errors in a complete DNA molecule happen every 10 billion base pairs, whereas errors in the template strand occur every 10^5 nucleotides. This is because DNA polymerases proofread each nucleotide against the template strand once it is covalently bonded to the growing strand. If it finds an incorrect nucleotide, it removes it and resumes synthesis. Mismatch repair: other enzymes remove and replace incorrectly paired nucleotides as a result of replication errors/nucleotides that evaded proofreading by DNA polymerase. Errors can also occur after replication by harmful chemicals, X-rays, etc, or by spontaneous chemical changes under normal cellular conditions. Permanent changes that are not corrected are called mutations, are are replicated. If DNA has an error, nuclease can cut out the strand containing the damage, resulting in a gap that is then filled with nucleotides (undamaged strand is the template, done by DNA polymerase and ligase). Nucleotide excision repair of DNA damage: 1) Teams of enzymes detect and repair damaged DNA that has distorted the DNA molecule. 2) A nuclease enzyme cuts the damaged DNA strand at two points, and the damaged section is removed. 3) Repair synthesis by a DNA polymerase fills in the missing nucleotides. 4) DNA ligase seals the free end of the new DNA to the old DNA, making a complete strand.

Rapid reproduction and mutation

Eukaryotes: Mutations very rarely will generate a new allele in a sexually reproducing species. Genetic variation usually happens by existing alleles arranging in new combinations during meiosis and fertilization. Prokaryotes: They do not reproduce sexually, but they still have lots of genetic variation, which is a combination of rapid reproduction and mutation. Because bacteria have short generation times and large populations, new mutations actually happen quite frequently, even though they are rare when you look at the individual cell. This can lead to lots of diversity and rapid evolution, because individuals that have a mutation that gives them an advantage will survive and reproduce at higher rates than those who do not have that mutation. Therefore, prokaryotes can adapt rapidly to new conditions.

RNA processing

Gene expression doesn't just have to due with transcription, and a lot of the synthesis of RNA contributes to the protein activity in the cell. This allows for fine tuning of gene expression in response to environmental changes without altering transcription patterns. Alternative RNA splicing: different mRNA molecules are produced from the same primary transcript depending on what is treated as an exon and what is treated as an intron in the gene. Regulatory proteins control the intron-exon choices by binding to regulatory sequences within the primary transcript. Makes the E genome way bigger, and it shows why there are relatively few human genes (similar to worms and plants lol). Multiplies the number of human proteins, showing why so much complexity exists.

Evidence from the study of metabolic defects

Gene expression: the process by which DNA directs the synthesis of proteins/sometimes RNA. Expression codes by transcription and translation. Archibald Gerrod (1902): first to suggest that genes dictate phenotypes through enzymes that catalyze specific chemical reactions. Thought that symptoms of an inherited disease reflect a person's inability to make a particular enzyme. May have been the first to recognize that Mendel's principles of hereditary apply to humans and not just peas. Later called "one gene-one enzyme" hypothesis. George Bealdle and Ephrussi (1930s): Drosphila have mutations that affect eye color (prevent enzymes that catalyze that step).

Basic principles of transcription and translation

Genes do not make proteins directly, they are transcribed into RNA first and then into proteins. RNA is like DNA except that it has ribose instead of deoxyribose, and U instead of T. Monomers of DNA/RNA= nucleotides. Monomers of protein= amino acids. Transcription: the synthesis of RNA using information in DNA, the DNA serves as a template. The resulting protein coding RNA (mRNA) contains the instructions for building a protein. Translation: the synthesis of a polypeptide using mRNA. During this stage, the cell translates the nucleotide sequence in mRNA into the amino acid sequence of a polypeptide (there is a change in language). Ribosomes: the sites of translation. Molecular complexes that facilitate the orderly linking of amino acids into polypeptide chains. Difference between bacteria and eukaryotes: bacteria don't have nuclei, so their DNA is not separated by a nuclear envelope from ribosomes. This allows for translation of mRNA while transcription is in progress. In a Eukaryotic cell, these processes happen one at a time. Transcription in a E cell happens in the nucleus, and then the mRNA is transported into the cytoplasm where translation occurs. The mRNA is modified to produce the final mRNA that will be encoded into a protein. The initial mRNA (pre-mRNA) has to be spliced/modified (also called primary transcript). Central Dogma of Molecular Biology (Francis Crick, 1956): DNA to RNA to protein.

Genetic recombination

Genetic recombination: the combining of DNA from two sources. This is another reason why prokaryotes are diverse. In meiosis of Eukaryotes, two cells with different DNA are combined to create one zygote. In prokaryotes, DNA is brought from different individuals through transformation, transduction and conjugation. This is called a horizontal gene transfer.

Positive gene regulation

Glucose/Lactose for energy: When glucose and lactose are present, cells would rather use glucose. When lactose is present and there isn't much glucose, the cell will use lactose as an energy source. Only then will it make enzymes to break down lactose. More glucose=cAMP concentration is less, and CAP detaches from the operon so that there is less transcription for the enzyme b/c CAP increases transcription. Cyclic AMP (cAMP): allosteric regulatory protein interacts with the cAMP, which is a small organic molecule that accumulates when there isn't much glucose. Catabolite activator protein (CAP): an activator protein that binds to DNA and stimulates transcription of a gene. When cAMP binds to the regulatory protein, CAP is in its active shape and can attach to a promoter and increase its affinity to RNA polymerase (increases the rate of transcription). This is positive regulation. Controls the rate of transcription if the operon is repressor-free.

Evidence that DNA can transform bacteria

Griffith: He was trying to find a vaccine for pneumonia, and he had two strains of bacterium, one that was pathogenic/disease causing, and one that was nonpathogenic/harmless. When he killed pathogenic bacteria with heat and then mixed the dead cells with living nonpathogenic bacteria, the nonpathogenic bacteria became pathogenic. This new trait was then passed down to all descendants of the newly pathogenic bacteria. He called this transformation: a change in genotype and phenotype due to the assimilation of external DNA by a cell. Before this, people thought that proteins were the source of hereditary information.

Bacterial DNA replication proteins and their functions

Helicase: unwinds parental double helix at replication forks. Single strand binding protein: Binds to and stabilizes single stranded DNA until it is used as a template. Topoisomerse: Relieves overwinding strain ahead of replication forks by breaking, swiveling, and rejoining DNA strands. Primase: Synthesizes an RNA primer at 5' end of leading strand and 5' end of each Okazaki fragment of lagging strand. DNA pol III: Using parental DNA as a template, synthesizes new DNA strand by adding nucleotides to an RNA primer or a pre-existing DNA strand. DNA pol I: Removes RNA nucleotides of primer from 5' end and replaces them with DNA nucleotides. DNA ligase: Joins Okazaki fragments of lagging strand. On leading strand, joins 3' end of DNA that replaces the primer to the rest of the leading DNA strand.

Cytoplasmic determinants and inductive signals

How a cell tells what genes to express at a given time in embryonic development: 1) egg's cytoplasm contains RNA and proteins from the mother's DNA. Messenger RNA, proteins and other substances/organelles are distributed unevenly in the unfertilized egg, which has a big effect on the development of the future embryo. Cytoplasmic determinants: maternal substances in the egg that influence the course of early development. After fertilization, mitotic divisions separate the cytoplasm into different cells and the nuclei of these cells are exposed to different cytoplasmic determinants depending on what they received from the cytoplasm. Cytoplasmic determinants help with the developmental fate by regulating expression of genes during differentiation. 2) Interactions between embryonic cells induce differentiation into specialized cells. Environment around the embryonic cells also have an impact. Most influential are the signals from other embryonic cells in the same area, which have cell surface proteins/binding of growth factors secreted by other cells (induction). These signal molecules can make a cell change its gene expression/production of certain proteins that creates observable cellular changes.

New mutations and mutagens

How mutations arise: incorrect nucleotide on the chain during replication that isn't found during proofreading= incorrect base pair (called a spontaneous mutation). Mutagens: physical/chemical agents that interact with DNA to cause mutations. Muller found that X rays cause mutations in Drosophila/radiation in general is a mutagen. Are used to screen/ identify chemicals that cause cancer. Most carcinogens are mutagenic. Types of mutagens: Can be something that is very similar to a nucleotide so that the DNA pairs incorrectly with it during replication, distorting the double helix. Can be something that causes chemical changes in bases that change their pairing properties. Can insert themselves into the DNA to interfere with DNA replication/distort the helix.

Viral diseases in animals

How viral infections produce symptoms: can damage/kill cells by the release of hydrolytic enzymes from lysosomes, can cause cells to produce toxins, or they can have molecular components like envelope proteins that are toxic to the cell. The amount of damage often depends on the ability of the tissue to regenerate (for example, colds go away quickly because the tissue in your throat can regenerate quickly, but if a virus infects a nerve cell it usually can't replace itself). Symptoms like fever and body aches are the body's efforts to defend itself and fight against the infection so that the cells do not die. Vaccine: a harmless variant of the pathogen that stimulates the immune system to create defenses against the pathogen. Antiviral drugs: Although you can use vaccines to prevent many viruses, it is very hard to cure a viral infection once it occurs (antibiotics don't do anything). Antiviral drugs resemble nucleosides and interfere with viral nucleic acid synthesis. These drugs can inhibit viral polymerase that synthesizes viral DNA but not cellular DNA, or by interfering with reverse transcriptase (ATZ, HIV drug), etc. For HIV, cocktails are the most helpful, and they combine two nucleoside mimics and a protease inhibitor, which interferes with an enzyme that is necessary for viral assembly.

Epigenetic inheritance

Inheritance of traits transmitted by mechanisms not involving the nucleotide sequence. Mutations in the DNA are permanent, but modifications of chromatin can be reversed (like methylation).

Replicating the ends of DNA molecules

Linear E DNA replication machinery cannot complete the 5' end of daughter DNA strands, because DNA polymerase can only add to the 3' end. As a result, repeated rounds of replication produce shorter DNA molecules with staggered ends. Shortening does not occur in circular chromosomes of prokaryotes. Eukaryotic cells are protected by telomeres (a nucleotide sequence at the end of DNA molecules that do not contain genes, but are made up of repeated nucleotide sequences. In humans, this is TTAGGG repeated hundreds to thousands of times. Telomeres become shorter in every round of replication, so DNA is shorter in diving somatic cells of older individuals (could have something to do with aging). Telomerase catalyzes the lengthening of telomeres in E germ cells, storing their original length and compensating for the shortening during replication. It is not active in most human cells, but in germ cells it allows the zygote to have maximum DNA length. Telomere functions: 1) Specific proteins associated with telomeric DNA prevent the telomeric DNA from activating the cell's system for monitoring cell damage. 2) It acts as a buffer zone, providing protection against the organism's gene shortening. 3) It may protect the organism from cancer by limiting the number of divisions that a cell can undergo. Tumor cells often have short telomeres because they undergo so many cell divisions/ telomerase is high in cancer cells, meaning the telomere is stabilized so that the cell can continue to divide.

Replicative cycles of animal viruses

Many animal viruses with RNA genomes have an envelope, as well as some DNA genomes. Bacteriophages on the other hand usually do not have an envelope or an RNA genome. 1. Glycoproteins on the viral envelope bind to receptor molecules, promoting uptake by the cell. 2. The capsid of the viral protein enters the cell, and digestion of the capsid by enzymes releases the genome. 3. The viral genome functions as a template for the synthesis of complementary RNA by a viral RNA polymerase. 4. New copies of the viral genome are made using complementary RNA strands as templates. 5. Complementary RNA strands function as mRNA, which is translated into capsid proteins in the cytosol and glycoproteins in the ER/Golgi. 6. Vesicles transport envelope glycoproteins to the plasma membrane. 7. Capsid assembles around each viral genome molecule. 8. Each new virus buds from the cell.

The structural model of DNA

Most biologists were convinced that DNA was the genetic material, but they didn't know how the structure of DNA could account for inheritance. In the 1950s, scientists already knew that there were covalent bonds in between polymers and they tried to focus on the 3D structure of DNA. Pauling, Wilkins, Rosalind Franklin, Watson and Crick: they were all working on the 3D structure of DNA. Watson and Crick were the first to come up with the correct 3D structure. Watson used the lab of Wilkins, and he saw the X-ray diffraction image that Franklin had made. This showed the spots were the X-ray had deflected as they passed through purified DNA. Watson worked with Wilkins and determined that the DNA was helical in shape. He also used Franklin's data to suggest the width of the helix and how the nitrogenous bases were spaced. Pauling had previously thought that DNA was in a helix, but he thought that there were 3 strands. With all of this evidence together, the double helix was discovered. Watson and Crick began building models, using Chargaff's rule and Franklin's work on sugar-phosphate backbones on the outside of the DNA molecule. The backbone on the outside made sense because nitrogenous bases are relatively hydrophobic, so they would want to be facing away from the aqueous solution surrounding DNA. They created a model in which two sugar-phosphate backbones are antiparallel (their subunits run in opposite directions) twisting in a ladder to form a helix. They used Franklin's data to determine that each full turn was 3.4nm in length and bases were stacked 0.34nm apart. By trial and error, they found that A and T/ G and C were paired. This didn't make sense at first, because DNA was shown to have a uniformed diameter in Franklin's X-ray diffraction, as two purines are twice as wide as two pyrimidines. However, they found that the pyrimidines(A and T) can form two H bonds, and the purines(G and C) can form three (bond is shorter). This was the Watson Crick model. This model suggested the mechanism of DNA replication.

Inherited predisposition of environmental factors contributing to cancer

Multiple genetic changes required to induce cancer: cancers run in families if you inherit an oncogene or mutant allele. BRCA1 and BRCA 2: tumor suppressor genes. Their WT alleles protect against breast cancer, and their mutant alleles are recessive. Mutants damage the DNA repair pathway, and DNA breakage can contribute to cancer. Important to minimize exposure to DNA-damaging agents (UV light, chemicals).

Mutations of one or a few nucleotides can affect protein structure and function

Mutations: changes responsible for diversity among organisms and the source of new genes. Chromosomal rearrangements are large scale mutations. Point mutations: a change in a single nucleotide pair. If it occurs in a gamete/ a cell that gives rise to gametes, it can be transmitted to offspring and future generations. If it causes a problem it is called a genetic disorder/ a hereditary disease.

Bacteria often respond to environmental change by regulating transcription

Natural selection: favors bacteria that can conserve energy and resources (express only genes whose products are needed by the cell). Metabolic control: cell adjusts to the activity of enzymes present (relies on sensitivity/chemical cues to increase/decrease catalytic activity). Activity of first enzyme is inhibited by the activity of the end product (feedback inhibition). Cell can also adjust to the production level of certain enzymes to regulate the expression of genes encoding the enzymes. This control happens at the level of transcription. Many genes can also be switched on or off by changes in the metabolic status of the cell (operon model).

Cracking the code

Nirenberg (1960s): deciphered the first codon. He synthesized an artificial mRNA by linking identical RNA nucleotides containing uracil as their base. No matter where the message started/stopped, it only contained uracil (lots of repeating uracils). He added the poly U to a test tube with amino acids, ribosomes and other ingredients for protein synthesis, and the system translated the poly U into a polypeptide containing many units of the amino acid phenylalanine strung together. He determined that the mRNA codon UUU encodes for Phe. After that, AAA, GGG and CCC were determined. All 64 codons were deciphered during the 1960s, showing that 61 out of 64 of them coded for amino acids, and the other 3 coded for stop signals. Also, AUG encoded methionine (Met), which functioned as the start signal/initiation. There is redundancy in the genetic code, but no ambiguity, meaning that we know which codons code for which amino acid, but there are repetitions. This redundancy is not random, and usually an amino acid differs in the 3rd nucleotide. Reading frame: The grouping of codons that allows us to read the correct code. The cell reads the message with no spaces in between codons in a series of non-overlapping three-letter words.

Substitutions

Nucleotide-pair substitution: the replacement of one nucleotide pair with another. Silent mutation: no effect on phenotype/ no affect on the protein because of redundancy of the genetic code. Missense mutation: one amino acid into another. May have little effect on the protein if the new amino acid has similar properties or it is in a region that doesn't effect the protein's function. Some cause a big effect though (either good or bad, bad is more common). Sickle cell anemia= Glu in hemoglobin changed to Val from a single change in the nucleic acid sequence. Nonsense mutation: changes a codon for an amino acid into a stop codon. Causes the translation to be terminated prematurely and the polypeptide will be shorter than the normal gene, leading to a nonfunctional protein.

Coordinately controlled genes in eukaryotes

Operons don't work in E cells the way that they work in bacterial cells. Co-expressed genes (genes that code for multiple things of a similar function) are scattered over different chromosomes usually. Therefore, expressing these genes depend on a combo of control elements for all the genes of a dispersed group. Activator proteins in the nucleus recognize control elements and bind, promoting simultaneous transcription of the group of genes that go together, even though they are spread out. This coordination happens in response to chemical signals outside of the cell like steroids. Many signaling molecules only have to bind to the outside of the cell to control gene regulation indirectly, and genes with the same set of control elements are activated by the same chemical signals.

Differential gene expression

P and E cells regulate which genes are expressed, and must be always turning on/off genes in response to signals in the environment. Regulation of genes is important in multicellular organisms for specialization of cells in order for particular cells to have different rolls. Highly differential cells: muscle/nerve cells etc that express a small fraction of their genes, very specialized. Differential gene expression: subsets of genes expressed in different cell types are unique, which allow these cells to carry out specific functions. The different cell types don't have to do with different genes being present, but to different ways that they are expressed. Transcription factors have to locate the right genes, and when something goes wrong disease can be caused. It is commonly controlled at transcription by signals coming from outside of the cell like hormones/other signaling molecules. The more complex the organism, the more opportunities for regulation of the gene at different stages.

Internal organization and DNA

Prokaryotes don't have membrane bound organelles, but they can perform metabolic functions in the infoldings of the plasma membrane. They have less DNA/usually circular chromosomes/fewer proteins compared to E cells, which have more DNA/linear chromosomes/more proteins. Prokaryotic ribosomes are smaller than Eukaryotic ribosomes, and they differ in their protein and RNA content. This allows certain antibiotics to bind/inhibit prokaryotic ribosomes to block protein synthesis without disrupting eukaryotic ribosomal protein synthesis. This allows antibiotics to kill the bacteria without killing the organism. Nucleoid: where the chromosomes of a prokaryote are located. A region of the cytoplasm that is not enclosed by a membrane. Plasmids: smaller rings of independently replicating DNA molecules, carrying only a few rings.

Reproduction

Prokaryotic features of cell division: they are small, reproduce by binary fission and have short generation times. Binary fission: a single prokaryotic cell divides into 2 cells, and the cells keep dividing. Divide every 1-3 hours, or as little time as 20 minutes. However, even though they can divide quickly, once their nutrients are gone they poison themselves with metabolic waste, are in competition with other organisms, or are consumed by other organisms. Therefore, bacteria cannot keep reproducing indefinitely.

Noncoding RNA roles in controlling gene expression

Protein coding DNA only accounts for a very small amount of the genome, and an even smaller amount codes for RNA or transfer RNA. Noncoding DNA is still important though, and most of DNA is transcribed into RNA, most of which is noncoding RNA (ncRNA). Probably plays a roll in gene expression.

Protein folding and post-translational modifications

Protein modifications: The polypeptide chain coils/folds spontaneously during synthesis because of the primary structure of the amino acid sequence, forming a 3D molecule with tertiary structure. Therefore, a gene determines the structure. A chaperone protein helps the polypeptide fold in the right way. Post-translational modifications: sometimes need before the protein can do its job, Amino acids can be modified by attaching sugars/lipids/phosphate groups/etc. Enzymes can remove amino acids from the leading end or the chain can be cleaved into one or more pieces. Polypeptides can also be put together even if they were synthesized separately.

Elongation of the RNA strand

RNA pol moves along DNA, untwisting the double helix and exposing 10-20 nucleotides at a time for pairing with RNA nucleotides. It adds nucleotides to the 3' end of the RNA molecule, and the new RNA peels away from the DNA template/the DNA double helix reforms. 40 nucleotides/sec in eukaryotes. One gene can be transcribed by multiple RNA pol molecules following each other. Multiple molecules allows for making proteins in large amounts.

Roles of transcription factors

RNA pol needs transcription factors to initiate transcription. General transcription factors: essential for transcription of all protein coding genes. Some bind to the TATA box within the promoter, and most bind to proteins (other transcription factors and RNA pol II). Protein-protein factors are essential for initiating transcription in E, because the initiation complex has to be assembled before the polymerase can move along DNA. Specific transcription factors: High levels of transcription in particular genes at a certain time and place from interaction of control elements with another set of proteins. General transcription factors have a lot rate of transcription in some genes, but in some cells these are high because of specific TFs. Activators (STF) bind to the enhancer DNA sequences and go to a group of mediator proteins which bind to general transcription factors and ultimately RNA pol II to assemble the transcription initiation complex. Enhancers: distal control elements, farther away from the promoter (upstream, downstream or in an intron). Genes can have multiple enhancers that are active at different times or in different cells. Each enhancer is only associated with one gene. In E cells, gene expression is increased/decreased by the binding of transcription factors (activators or repressors) which control enhancers. Bending of DNA be a protein enables enhancers to influence a promoter hundreds/thousands of nucleotides away. Mediator proteins: protein mediated bending of DNA that brings the bound activators in contact with these mediator proteins that interact with proteins at the promoter. These interactions help assemble/position the initiation complex on the promoter. Combinatorial control of gene activation: E cells, transcription depends on binding of activators to DNA control elements. Enhancers can only bind to one or two transcription factors. The combination of control elements in an enhancer associated with a gene (rather than a single control element) is important to regulating transcription.

Alteration of mRNA ends

RNA processing: both ends of the primary transcript are altered, and certain interior sections of the RNA molecule are cut out/ the remaining parts are spliced together. This makes the mRNA ready for translation. 5' cap: a modified form of G nucleotide is added onto the 5' end after transcription of the first 20-40 nucleotides. Poly-A tail: the 3' end of the pre-mRNA is modified before mRNA exits the nucleus. 20-250 A nucleotides. UTRs: untranslated regions on both the 5' and 3' end that help with ribosome binding. Functions of end modifications: they facilitate the export of mature mRNA from the nucleus, protect the mRNA from degradation by hydrolytic enzymes, and help ribosomes attach to the 5' end of mRNA once mRNA reaches the cytoplasm.

Split genes and RNA splicing

RNA splicing: Only in Eukaryotic cells, large portions of the RNA molecule are removes that were originally synthesized. These regions are not translated. They are interspersed between coding segments of the gene/ the pre-mRNA. Therefore, the sequence of DNA is not continuous/is split into segments. Introns: the noncoding segments of nucleic acids that lie in between coding regions. Exons: the regions that are eventually expressed/translated into amino acid sequences. Exceptions are the UTRs of the exons at the ends of RNA, which aren't made into proteins. The exons are joined together forming a continuous mRNA molecule. RNA pol II: transcribes both introns and exons from the DNA, but the mRNA molecule that enters the cytoplasm is a shorter version of just the exons. Spliceosome: Removes introns, a large complex of proteins and small RNAs. It binds to short nucleotide sequences along an intron, including sequences at each end. The intron is released and raplidly degraded, and the spliceosome joins together the exons that were separated by the intron. The small RNAs of the spliceosome assemble/splice site recognition/catalyze the splicing reaction.

Interference with normal cell-signaling pathways

Ras gene: a G protein that relays signal from a growth factor receptor to synthesize a protein that stimulates the cell cycle. Certain mutations can make it hyperactive, causing increased cell division. p53 gene: A tumor-suppressor gene that promotes the synthesis of cell cycle inhibiting proteins. Can turn on genes for DNA repair, and when the DNA cannot be repaired it can activate suicide genes that lead to cell death.

Effects on mRNAs by microRNAs and small interfering RNAs

Regulation by small/large ncRNA occurs at several points in gene expression (mRNA translation, chromatin modification etc). MicroRNAs (miRNAs): small, single stranded RNA molecules that can bind to complementary sequences in mRNA. Longer RNA is processed into an miRNA by enzymes. The muRNA can bind to any mRNA with 7 or 8 nucleotides that have a complementary sequence. The miRNA can either degrade the mRNA that it targets or block translation. At least a half of genes are regulated this way. Small interfering RNAs (siRNAs): similar to size and function of miRNAs. Blocking gene expression by siRNAs is called RNA interference (RNAi).

Repressible and inducible operons (negative gene regulation)

Repressible operon: transcription is usually on, but it can be stopped with a small molecule that binds allosterically to a regulatory protein. Inducible operon: usually off, but it can be stimulated when a molecule interacts with a regulatory protein. Ex: lactose absent=repressor active=operon off. Lactose is only in the colon if the host drinks milk, so the operon is usually off. However, if it is added, B-galactoside, which helps digest lactose, can increase a ton from hardly any molecules super quickly when needed. Inducer: a specific small molecule that inactivates the repressor. Inducible enzymes: synthesis is induced by a chemical signal. Function in catabolic pathways, break down nutrients into simpler ones. Repressible enzymes: function a anabolic pathways. Synthesize essential end products from raw material by suspending production of an end product when there is a lot of it so that it can save energy.

Retroviruses

Retroviruses: have the most complicated replicative cycle. They have an enzyme called reverse transcriptase which transcribes RNA into DNA, which is the opposite of the normal flow of genetic information. An example of this kind of virus is HIV, which causes AIDS. Retroviruses have an envelope and contain two identical molecule of single stranded RNA and two molecules of reverse transcriptase. The retrovirus enters the host cell, reverse transcriptase molecules are released into the cytoplasm and they catalyze the synthesis of viral DNA. The new DNA enters the nucleus and integrates into the DNA of a chromosome. This integrated DNA is called a provirus, and it never leaves the genome (permanent to the host cell, whereas other viruses like prophages leave at the start of the lytic cycle). The RNA polymerase (from the host cell) transcribes the proviral DNA and makes proteins/RNA out of them, which can function as genomes and new viruses that will be released from the cell. Step by step process of HIV infection: 1) The envelope glycoproteins enable the virus to bind to specific receptors on certain white blood cells. 2) The virus fuses with the cell's plasma membrane, and the capsid proteins are removed which releases viral proteins and RNA. 3) Reverse transcriptase catalyzes the synthesis of a DNA strand complimentary to the viral RNA. 4)Reverse transcriptase catalyzes the synthesis of a second DNA strand complementary to the first. 5) The double stranded DNA is incorporated as a provirus into the cell's DNA. 6) Proviral genes are transcribed into RNA molecules, serving as genomes for new viruses and as mRNA that can be translated into proteins. 7)Viral proteins (which include capsids and reverse transcriptase) are made in the cytosol and envelope glycoproteins are made in the ER. 8) Vesicles transport glycoproteins into the cell's plasma membrane. 9) capsids are assembled around viral genomes and reverse transcriptase. 10) New viruses with envelope glycoproteins bud from the host cell.

Revisions of the "one gene- one enzyme" hypothesis

Revisions of the one gene-one enzyme hypothesis: not all proteins are enzymes, many proteins are constructed by multiple polypeptides, and each gene encodes for only one polypeptide. This hypothesis turned into the "one gene-one polypeptide hypothesis." Not completely accurate bc a E cell can encode for similar polypeptides by alternate splicing. Also, many genes encode for RNA molecules that are never translated into proteins.

Targeting polypeptides to specific locations

Ribosomes are either in the cytosol (free) or the ER (bound). Ribosomes can alternate between being bound/free because they are all identical. All protein synthesis starts off in a free ribosome in the cytoplasm, and then the ribosome will stay there unless the polypeptide signals it to go to the ER. Signal peptide: a mark that targets a protein to the ER. Around 20 amino acids near the leading end, recognized by the signal-recognition particle on the ribosome (escort that brings to ribosome to a receptor protein in the ER membrane, part of the MTC). Synthesis continues in the ER, going across the ER lumen by a protein pore. The signal peptide is removed by an enzyme, and the polypeptide is released into the ER lumen/acts as a membrane protein/travels in a transport vesicle. Other signal peptides can also make the polypeptide go to other locations, but translation is completed in the cytosol if it isn't an ER signal peptide.

The discovery of viruses

Scientists could detect viruses before they were able to see them during the end of the 19th century. It was found that you could transmit disease between tobacco plants by rubbing sap on them, but no bacteria were visible under a microscope. It was discovered that the pathogen could replicate within the host in infected, but the disease couldn't be cultivated on nutrient media or on petri dishes. This is where the concept of a virus was found by Beijernick, and it was confirmed in 1935.

Functional and evolutionary importance of introns

Some introns contain sequences that regulate gene expression, and many affect gene products. Introns allow for a single gene to encode more than one polypeptide, depending on which segments are treated as exons during RNA processing (alternative RNA splicing). Domains are discrete structural/functional regions in proteins. Different exons code for different domains of a protein (one domain could be an active site of an enzyme, whereas another domain could bind the enzyme to the membrane, etc. Different functions). Introns/evolution: facilitate the evolution of new proteins by exon shuffling (increase the probability of crossing over between exons of alleles of a gene by providing more terrain for crossovers without interrupting coding sequences). Results in new combinations of exons and proteins with altered structure and function. Mixing/matching of exons between different genes. Could lead to new proteins with new combinations/functions. Most of this shuffling is probably not beneficial, but sometimes it could be.

RNA as a viral genetic material

Some phages/most plant viruses have RNA as their genetic material. But the most broad RNA genomes are those than infect animals. All viruses that use an RNA genome as a template for mRNA transcription require more RNA synthesis. The viruses therefore need a viral enzyme to help them carry out this process. The enzyme is packaged during viral self-assembly with the genome inside of the viral capsid. Types of single stranded RNA genomes found in animal viruses: class IV (can be used as mRNA and translated into viral protein immediately after infection), class V (RNA genome serves as a template for mRNA synthesis, and the genome is transcribed into complementary RNA strands that function as mRNA and templates for synthesis of more copies of the genome) and class VI (retroviruses).

Ribosomes

Structure: Consists of a large subunit and a small subunit made up of proteins/ one or more rRNAs. In Eukaryotes, the subunits are made in the nucleus, and the rRNA genes are transcribed/processed/assembled by proteins from the cytoplasm. Complete subunits are exported through nuclear pores into the cytoplasm. E and bacteria have a large and small subunit joined to form a ribosome that is only functional when it is attached to an mRNA molecule. There are 3rRNAs that make up the ribosome in bacteria and 4 in E cells. E ribosomes are slightly larger and differ in composition (certain antibiotics can inactivate only bacterial ribosomes). Has a binding site for mRNA and three for tRNA. The P site holds the tRNA that carries the polypeptide, and the A cite holds the tRNA carrying the next amino acid that is going to be added to the chain. The E cite is the exit site where the tRNAs leave the ribosome. (Order left to right= EPA). The tRNAs and mRNAs are in close proximity so that the new amino acid can be added to the carboxyl end of the polypeptide. The polypeptide passes through the exit tunnel in the large subunit/ is released through the exit tunnel. Function: facilitates the specific coupling of tRNA anticodons with mRNA codons during protein synthesis. rRNA (not protein) is responsible for the structure/function of the ribosome, and the proteins support the shape of the rRNA.

The structure and function of transfer RNA

Structure: Each tRNA molecule translates a given mRNA into a certain amino acid, because each one has a specific amino acid on one end. It has a single RNA strand that is 80 nucleotides long, and one side base pairs with the complementary codon on mRNA. The strand folds onto itself to form a 3D shape(it hydrogen bonds to itself), kind of L-shaped. One side of the L has the anticodon (nucleotide triplet that base pairs to a specific mRNA codon), and the other ends has an attachment site for an amino acid. Function: transfers amino acids from the cytoplasmic pool to a growing polypeptide. The cell keeps a stock on all 20 amino acids in the cytoplasm (synthesizes them or takes them from surrounding solution). The ribosome adds each amino acid that is brought by the tRNA. mRNA moves through the ribosome. Codon by codon, genetic message in translated. tRNAs deposit amino acids in the order on the mRNA, and the ribosome joins the amino acids, forming a chain. tRNA kind of acts as a translator, interpreting the protein. It is made in the nucleus, and travels to the cytoplasm. Each tRNA is used over and over. It picks up its designated amino acid in the cytosol and deposits it onto the polypeptide chain on the ribosome. aminoacyl-tRNA synthetases: makes sure the correct tRNA is matched up. The active site of each enzyme fits only to one amino acid and tRNA. There are 20 different ones, one for each amino acid, and it binds to all of the tRNAs that code for that particular amino acid. It is driven by the hydrolysis of ATP. The tRNA with the amino acid on is released from the enzyme and heads over to deliver its amino acid to the polypeptide chain. Some tRNA can bind to more than one codon, because there are only 45 of them instead of 61. This is because the third position of the base of a codon is more versatile/relaxed compared to the other two. This is called the wobble position, and it explains why multiple codons can pair to the same amino acid.

Motility

Taxis: a directed movement directed towards or away from stimulus (1/2 of bacteria are capable of this). Can move towards nutrients/oxygen (positive chemotaxis) or away from toxic substances (negative chemotaxis), at up to 50nm/sec. Flagella: Allow prokaryotes to move. Can be scattered or concentrated on one or both ends of the prokaryote. Much smaller than E flagella and aren't covered by a plasma membrane. They are also composed of much different proteins from E cells, which probably means that they evolved separately from each other (analogous but not homologous structures).

Termination of transcription

Termination is different in bacteria/eukaryotes. Bacteria: transcription happens through a terminator sequence in the DNA, which functions as the termination signal causing the pol to detach and release the transcript. There is not further modification to the molecule. Eukaryotes: RNA pol II transcribes a sequence onto the DNA called the polyadenylation signal sequence, which signifies a signal in pre-mRNA. This signal of 6 nucleotides is immediately bound by proteins in the nucleotides, and then 10-35 nucleotides down releases the pre-mRNA. Then it undergoes processing. Even though the cleavage is the end of the mRNA, RNA pol II continues to transcribe, but enzymes degrade the RNA from the 5' end because it isn't protected by a cap.

Ribozymes

The catalytic role of the RNAs in the spliceosome. Shows that RNA can function as an enzyme. In some organisms, the intron RNA can function as the ribosyme/catalyze its own excision. The pre-rRNA can remove its own introns (a component of ribosomes). RNA as enzymes: specific structure/3D shape, certain bases contain functional groups that can participate in catalysis, and RNA can hydrogen bond with other nucleic acids, which adds specificity.

Evolution of the Genetic Code

The genetic code is pretty much universal across all organisms. Because of this, one species can be programmed to produce protein characteristics of another species by introducing DNA from the first species into the next. Bacteria can be inserted with human genes to produce things like insulin.

RNA polymerase binding and initiation of transcription

The promoter includes the start point (the nucleotide where RNA synthesis begins), and extends more nucleotides upstream from the start point. RNA pol binds to a location/orientation on the promoter. In bacteria, the RNA pol recognizes and binds to the promoter, but in E cells, a collection of proteins called transcription factors mediate the binding of RNA pol and initiate transcription. Transcription factors: Only after they are attached to the promoter can the RNA pol II bind to it. The whole complex is called the transcription initiation complex. This interaction shows the importance of protein-protein interactions in controlling E transcription. Once the transcription factors are attached and the polymerase in bound in the correct position, the enzyme unwinds the two DNA strands and begins transcribing the template strand at the start point.

The structure of viruses

The smallest viruses are 20nm in diameter, which is smaller than a ribosome. They can be crystalized, whereas cells cannot. They are an infectious particle consisting of nucleic acid enclosed in a protein coat and some of them are surrounded by a membranous envelope. Viral genomes: consists of either double stranded DNA, single stranded DNA, double stranded RNA or single stranded RNA depending on the virus. Viruses are called DNA or RNA viruses depending on what kind of genetic material they have. The genome is usually a single linear nucleic acid or a circular molecule of nucleic acid. Some viruses have multiple molecules, though. Capsid: The protein shell enclosing the genome. Depending on the virus, it can be rod-shaped, polyhedral or more complex. They are built from lots of protein subunits called capsomeres, which are usually a small amount of different kinds of proteins, but a lot of them. Rod shaped viruses are called helical viruses, and adenoviruses which affect respiratory tracts of animals are called icosahedral viruses. Viral envelopes: Accessory structures that help the virus infect their host. They are derived from the membranes of the host cell, contain host phospholipids and membrane proteins, as well as the proteins and glycoproteins of the virus. Bacteriophages (phages): viruses that infect bacteria. They have some of the most complicated capsids. E. coli has seven different phages that can infect it (T1, T2,...,T6), and they are all very similar in structure. The head of the protein has a tail with fibers that allow the phage to attach to the bacterial cell.

Codons

There are 20 amino acids, so there has to be enough powers of 4 nucleotides to make enough amino acids. Two letter code would only be 16, which isn't enough. Triplets are the smallest length possible that could code for all amino acids, but there are 64 possible combinations. Experiments have verified that the flow of information from gene to protein is based on a triplet code (non-overlapping, three nucleotide words). During transcription the gene determines the sequence of bases for the RNA molecule that is being synthesized. The template strand is the strand of DNA that is transcribed, and only this strand provides the pattern for the RNA. Each gene only uses one DNA strand as the template for transcription into mRNA. The mRNA molecule is complementary, not identical to the DNA template. RNA is synthesized in an antiparallel direction, 5'-3'. The mRNA nucleotide is called a codon (codon is also used to describe the triplet of nucleotides on the non template strand, which matches up identically with the mRNA). During translation, the codon is translated into a sequence of polypeptides, and they are read in the 5'-3' direction. It takes 3x the number of nucleotides to make x amount of amino acids.

Transformation and transduction

Transformation: the genotype and sometimes the phenotype of a P cell are altered by the uptake of foreign DNA from their surroundings. It occurs when a cell takes a piece of DNA carrying an allele, and it replaces its own allele with the foreign allele (exchanges homologous DNA segments). Many bacteria have cell-surface proteins that recognize DNA from closely related species, and they can transport this into the cell to be incorporated into its genome. Recombinant: a cell's chromosomes contain DNA derived from two different cells. Transduction: Phages (viruses) carry prokaryotic genes from one host cell to another. This usually happens when an accident occurs in the phage replicative cycle. The phage can attach to another prokaryotic cell and inject the prokaryotic DNA from the first cell, creating a recombinant cell.

Initiation of translation and mRNA degradation

Translation also can regulate gene expression, especially at initiation. Some mRNAs are blocked from initiation by regulatory proteins that bind to sequences/structures within the untranslated region (UTR), preventing the attachment of a ribosome. All mRNAs in a cell can be regulated at the same time by activating or inactivating protein factors required to initiate translation. mRNAs: life span is short within a cell, but longer in E cells than bacterial cells. Sequences that affect how long the mRNA stays intact are found in the UTR at the 3' end.

Ribosome association and initiation of translation

Translation: 1)first brings together mRNA and the tRNA that has the first amino acid of the polypeptide/ the two subunits come together. The small subunit binds to the mRNA and the first tRNA (Met). In bacteria this can happen in any order, but in E the small subunit with Met tRNA is already bound, and it binds to the 5' cap of the mRNA and then it scans the mRNA until it reaches the start codon. Then, the Met tRNA hydrogen bonds to the codon and starts translation. 2) Then the large ribosome subunit is attached, completing the translation initiation complex. Initiation factor proteins are required to bring all components together, and the cell also has to spend GTP as energy to form the initiation complex. 3) After the completion of the initiation complex, the tRNA is in the P site, and the A site is vacant. The polypeptide is always synthesized in one direction, from the Met at the amino acid (N terminus) to the final amino acid at the carboxyl end (C terminus).

The role of viruses in cancer

Tumor viruses: can cause cancer in some animals/ are linked to cancer. Viruses can interfere with gene regulation if they integrate their DNA into the cell. Possibility for them to incorporate an oncogene/disrupt a tumor-suppressor gene/convert a proto-oncogene to an oncogene. Some viruses product proteins that inactivate the p53 gene and other tumor suppressors.

Multistep model of cancer development

Usually more than one somatic mutation to lead to cancer/ an accumulation of mutations throughout life (older we are, risk of cancer gets worse).

DNA replication complex

Various proteins participating in DNA replication form a single large complex, and protein-protein interactions facility the efficiency of the complex. The DNA moves through the complex during replication, not the proteins. In Eukaryotes, multiple copies of the complex can be present, which are anchored in the matrix of fibers extending into the nucleus. Two DNA polymerase molecules (one for each strand) reel in the parental DNA to make daughter DNA molecules (trombone model). DNA replication: 1) Helicase unwinds the parental double helix. 2) Molecules of single strand binding protein stabilize the unwound template strands. 3) The leading strand is synthesized continuously in the 5' to 3' direction by DNA pol III. 4) Primase begins synthesis of the RNA primer for the fifth Okazaki fragment. 5) DNA pol III completes synthesis of fragment 4. When it reaches the RNA primer on fragment 3, it detatches and begins adding DNA nucleotides to the 3' ends of the fragment 5 primer in the replication work. 6) DNA pol I removes the primer from the 5' end of fragment 2, replacing it with DNA nucleotides by adding one by one to the 3' end of fragment 3. After the last addition, the backbone is left with a free 3' end. 7) DNA ligase joins the 3' end of fragment 2 to the 5' end of fragment 1.

Viral diseases in plants

Viral diseases in plants can destroy crops and stunt growth. Plant viruses have the same structure and replication process as animal viruses, and most also have an RNA genome. They spread either by horizontal transmission or vertical transmission. Once the virus enters the cell, viral genomes and proteins can spread throughout the plant by plasmodesmata. Viral molecules can pass from cell to cell, facilitated by virally encoded proteins that cause enlargement of the plasmodesmata. Horizontal transmission: A plant is infected from an external source. The plant is more susceptible to infection if the outer layer of cells is damaged. Herbivores can damage the outer layer and transmit the disease from plant to plant, which makes them especially dangerous. Farmers can accidentally do this as well with using the same tool on lots of plants. Vertical transmission: a plant inherits the infection from the parent plant. This can either occur in asexual propagation or in sexual reproduction.

Viroids and prions

Viroids: Circular RNA molecules that are only a few hundred nucleotides long that infect pants. They don't encode proteins, but they can replicate in the host cell by using the host's enzymes. They cause errors in the plant's regulatory system, causing irregular growth patterns/abnormalities. Shows that a single molecule can spread disease, in this case a molecule made up of nucleic acids. Prions: infectious proteins that can cause degenerative brain diseases in some animal species. Since they are proteins, they can be transmitted though food. They can have an incubation period of up to 10 years before symptoms develop, which allows them to go unidentified until tons of organisms are infected. They are also indestructible, and heating them when cooking will not harm them. There is no cure for prions, and they are scary AF (mad cow disease)! They are misfolded forms of proteins that are normally present in brain cells. When it gets into a normal form of protein, it converts normal proteins to misfolded prion proteins. This creates a chain of them, and they disturb normal cellular functions and cause disease.

Evolution of viruses

Viruses can't replicate/carry out metabolic processes on their own, but they do still evolve and have a genetic code. Viruses probably evolved after the first cells appeared, since they cannot do anything without a host cell. They may have evolved from random pieces of nucleic acids that moved from one cell to another. The original viruses were probably plasmids (small, circular DNA molecules found in bacteria and unicellular E cells/yeast. They can replicate/exist independently of a bacterial chromosome and can be transferred in between cells) or transposons (DNA segments that move from one location to another in a cell's genome). Both plasmids and transposons are candidates because they are mobile genetic elements. This also makes sense because most viruses are incredibly similar to aspects of the cells they inhabit; much more similar than they are to other viruses. There is also another kind of virus called a mimivirus that encodes for genes that are usually just found in the cell's genome, as they are important to cell function. Therefore, we don't know if this virus came before the first cells or after.

Viruses replicate only in host cells

Viruses lack metabolic enzymes and equipment for making protein, so that have to replicate within a host cell. They can't do anything by themselves. Host range: the limited number of host species that a virus can infect. Host specificity results in evolution of recognition systems by the virus, and they identify the cell they want to infect by the "lock and key" fit between the surface of the proteins and the receptor molecules on the outside of cells. The receptor molecules on cells originally carry out functions that benefit the cell, but the viruses use the receptors as ways to enter the cell. Some viruses can only inhibit one species, whereas others can infect many. In multicellular Eukaryotes, the virus can usually only infect certain cells (colds infect the respiratory tract).

Base pairing to a template strand

Watson and Crick hypothesis for how DNA replicates: Thought that the hydrogen bonds are broken, the two chains unwind and separate. Each chain acts as a template for the formation of itself on a new chain, so instead of having one chain now there are two. The sequence of base pairs are duplicated exactly. Semiconservative model: predicted from Watson and Crick's model, showing that each daughter molecule will have one parental molecule and one new strand. There were also two other models, the conservative model (two parent strands come back together after acting as templates) and the dispersive model (Each strand of both daughter molecules contains old and new DNA). However, these were ruled out. DNA replication: the two strands of DNA are complementary and each one stores the information needed to reconstruct the other, each strand serving as a template. Nucleotides line up along the template and new strands are made.

Genetic program for embryonic development

Zygote: a fertilized egg that gives rise to many different types of cells, each with a structure that goes with its function. Produces cells that form higher level structures arranged in a 3D shape. Forms from cell division, cell differentiation and morphogenesis. The zygote produces lots of cells through mitotic divisions. These three processes depend on gene expression and regulation. Differentiated cells have a particular mix of activators that turn on parts of genes whose products are required in that cell. Cell differentiation: the process by which cells specialize in structure and function during embryonic development. The cells are organized into tissues/organs in a 3D shape. Morphogenesis: the physical process that gives an organism its shape/forms the organism and its structures. Can be traced back to shape, motility and other characteristics of cells that make up regions of the embryo.

Molecular components of transciption

mRNA carries information from DNA to protein synthesizing machinery, transcribed from the template strand. The direction of transcription is downstream, and the other direction is upstream. RNA polymerase: pries the two strands of DNA apart and joins together RNA nucleotides complementary to the DNA template strand, elongating the RNA polynucleotide. It can only assemble in the 5' to 3' direction. Unlike DNA polymerase, it can start a chain from scratch and doesn't need a primer. Bacteria have a single type of RNA polymerase to make mRNA and for protein synthesis/ ribosomal RNA. Eukaryotes have at least 3 types in the nuclei. Pre-mRNA synthesis= RNA pol II, and the others transcribe RNA molecules that are not translated into proteins. RNA pol II binds onto the promoter creating the transcription initiation complex, and then it unwinds the DNA double helix and RNA synthesis begins at the start point of the template strand. Promoter: The sequence where RNA polymerase attaches and initiates transcription. It is upstream from the terminator. Eukaryotic promoters usually include a nucleotide sequence including TATA 25 nucleotides upstream from the start point (nucleotide sequences are given as they are on the non-template strand). The TATA box has to bind to DNA before RNA pol II can bind to the correct position. Terminator: The sequence that signals the end of transcription in bacteria. Transcription unit: The stretch of DNA downstream from the promoter that is transcribed into an RNA molecule.

Chromatin remodeling by ncRNAs

ncRNAs can also remodel chromatin structure in addition to regulating mRNAs.