BIS 002A: Midterm #2

Video: telomeres

Telomeres are structures made from DNA sequences and proteins found at the ends of chromosomes. Cap the ends of chromosomes. Required for cell division. With each cell replication, telomeres get shorter. They become so short that cells can no longer divide (leading to aging). Telomeres can be rebuilt by telomerase. If a cell keeps diving uncontrollably, a tumor can form. Balance between limiting cellular lifespan and keeping cancer growth at bay. DNA polymerases can only elongate from a 3' hydroxyl group. RNA primers provide 3' hydroxyl groups along the lagging strand. Leading strand elongates from 5' to 3'. The lagging strand would not be complete. There would be no 3' hydroxyl group to prime DNA synthesis. The primers would eventually be removed, leaving a gap. Chromosomes would progressively shorten. Telomeres are repeat sequences. Telomerase elongates the strand from the 5' to 3' direction. It adds additional repeats. DNA is damaged all the time. Damage can cause cancer. Nucleotides can get matched up incorrectly. Nicks can interfere with DNA replication. Common error: base mismatches. Polymerase is supposed to bring the right partner to each base. If it makes a mistake, it often catches itself. Removes a section of the DNA. A second set of proteins checks its work (mismatch repair). Environmental exposure can influence mutations. Specific enzymes are assigned to reverse DNA damage. Base excision repair: one enzyme snips out the base and other enzymes trim around the site and replace the nucleotides. UV light can cause two nucleotides to stick together (destroying DNA's shape). Nucleotide excision repair: a team of proteins removes a long strand of ~24 nucleotides and replaces them with fresh ones. Gamma rays or x-rays can sever one or both strands of DNA. Double strand breaks: homologous recombination and non-homologous end-joining. Homologous recombination: uses an undamaged section of similar DNA as a template. Enzymes are used. Damaged and undamaged strands exchange nucleotides. Non-homologous end-joining: a series of proteins trim off a few nucleotides and fuses the broken ends back together. Process isn't as accurate and doesn't involve a template strand. Not all mutations are bad. Cancer and premature aging can result from mutations in DNA.

Random notes

Template strand = antisense strand. A leading strand is the strand which is synthesized in the 5'-3'direction while a lagging strand is the strand which is synthesized in the 3'-5' direction

DNA structure and properties

Template strand = blue. High energy bonds = phosphoanhydride bonds. A phosphodiester bond is made. Pyrophosphate is released. Hydrolysis occurs to break the phosphate bonds. A condensation reaction also occurs somewhere else. A nucleotide is added to the 3' end of the growing strand. Added to the hydroxyl group of 3'. Phosphoanhydride = in between phosphate groups.

Termination

Termination methods are conserved among species. RNA and RNA polymerase are released. Proteins facilitate this.

Eukaryotic transcription

The 5' end: a modified GTP is added. This becomes the 5' cap. It protects RNA from becoming degraded, increasing stability. This is found in mature mRNA. The 3' end: an enzyme cuts the end and replaces the missing sequence with a poly A tail.

Fluorescent chromatograms

The Sanger sequencing process emits radioactivity. Chain terminators with fluorescent tags were hence developed. Synthesizes a series of DNA strands that are specifically fluorescent at the termination sequence. The strands are passed through a capillary electrophoresis system. As the fragments of DNA pass a laser and detector, a chromatogram is generated. Fluorescent chromatograms are used to score the nucleotide chain termination. The amplitude of each peak corresponds to the strength or certainty of the nucleotide call.

Addition of nucleotide during transcription

The addition of nucleotides during the process of transcription is very similar to nucleotide addition in DNA replication. The RNA is polymerized from 5' to 3', and with each addition of a nucleotide, a phosphoanhidride bond is hydrolyzed by the enzyme, resulting in a longer polymer and the release of two inorganic phosphates

Bacteriochlorophyll

The bacteriochlorophyll gets excited from exposure to photons. An electron gets removed from the magnesium and it becomes oxidized. It needs to be reduced immediately for stability concerns.

Cytoskeleton

The cytoskeleton is composed of rigid filaments called monomers (actin that forms microfilaments or tubulin that forms microtubules). Intermediate filaments. Example: myosin. Filaments provide structure and stability. We originally thought actin and tubulin originated in eukaryotes, but they originated in the microbial world.

Leading strand replication

The daughter strands are what are produced by DNA Polymerase III.

Translation

The decoding of an mRNA message into a polypeptide product. The language of nucleotides is translated into the chemical language of amino acids. Amino acids are connected by peptide bonds (a covalent bond). Ribosomes are ribonucleoprotein complexes that link amino acids. Translation requires, at minimum, an mRNA template, amino acids, ribosomes, tRNAs, an energy source, and various additional accessory enzymes and small molecules. Protein synthesis has three steps: initiation, elongation, and termination.

Evolution, natural slection

The development/change of something over time. Natural selection is a process by which nature filters organisms in a population. The factors that influence the ability of an organism to reproduce are known as selective pressures. Evolution stipulates that change in biology happens over time and that the variation in a population is constantly subjected to selection based on how differences in traits influence reproduction. A differential likelihood of generating offspring is required. Organisms in a population that have phenotypes, which enable them to pass the selective filter more efficiently than others, are said to have a selective advantage and/or greater fitness. If neither variation nor populations in which that variation can reside exist, there is no opportunity or need for selection. Nature does not identify features that would make an organism more successful and then start creating diverse solutions that meet this need. The generation of variation is not guided.

Eukaryotic initiation

The eukaryotic complex recognizes the 7-methylguanosine cap at the 5' end of the mRNA. A cap-binding protein (CBP) assists the movement of the ribosome to the 5' cap. Once at the cap, the initiation complex tracks along the mRNA in the 5' to 3' direction, searching for the AUG start codon. Not all eukaryotic mRNAs are translated from the first AUG. According to Kozak's rules, the nucleotides around the AUG indicate whether it is the correct start codon. A consensus sequence must appear around the AUG: 5'-gccRccAUGG-3'. The R (for purine) indicates that this site can be A or G, but cannot be C or U. The closer the sequence is to this consensus, the higher the efficiency of translation.

mRNA processing

The first RNA that is made is called pre-mRNA. Termination site and start codon on ends. Introns are removed. The removed nucleotides can be recycled

Summary/review

The genetic code is degenerate because 64 triplet codons in mRNA specify only 20 amino acids and three stop codons.

Transcription factors

The genomes of most eukaryotes encode for three different RNA polymerase, each made of ten protein subunits or more. Each eukaryotic polymerase requires a distinct set of proteins known as transcription factors to recruit it to a promoter. RNA polymerases attach to promoters. Enhancers and silencers, both of which are proteins, help regulate the synthesis of RNA from each promoter. These proteins affect the efficiency of transcription, but are not necessary for the initiation of transcription or its procession. Basa; transcription factors are crucial in the formation of a preinitiation complex on the DNA template that subsequently recruits RNA polymerase for transcription initiation.

Interactions between cargo and microtubules

The light chains interact with receptors on the various cargo vesicles and the globular motor domains specifically interact with the microtubules.

Kinesin

The motor proteins have two peptides and two feet that bind to the microtubule. Feet move from the - to + direction. These proteins bind to ATP, hydrolyze it, and releases the back foot. The back foot then binds to the tubule again. The cargo is attached at the very end.

Endosymbiosis continued

The nucleus might have come after the engulfment. It is easy to transfer DNA from the prokaryote to the rest of the genome if there is no nuclear membrane.

NADP+ vs. NADPH

The only difference between NADP+ and NADPH is the presence of an additional hydrogen atom in the nitrogenous base of NADPH. NADP is the reduce form.

Prokaryotic elongation

The preinitiation complex is formed. The polymerase is released from the other transcription factors, and elongation occurs as it does in prokaryotes (RNA polymerase synthesizes pre-mRNA in the 5' to 3' direction). RNA polymerase II transcribes the major share of eukaryotic genes.

Translation elongation

The ribosome moves along the mRNA. Two antiparallel strands of complementary nucleotides are used to ensure the correct tRNA molecules are used. The large ribosomal subunit comprises three compartments: the A site binds incoming charged tRNAs (those with their attached amino acids), the P site binds charged tRNAs carrying amino acids that have formed bonds with the growing polypeptide chain but have not yet dissociated from their corresponding tRNA, and the E site which releases dissociated tRNAs so they can be recharged with another free amino acid. tRNAs shift: A --> P --> E. Ribosomal steps are induced by conformational changes that advance the ribosome by three bases in the 3' direction. An elongation factor hydrolyzes GTP to provide energy for each ribosomal step. Peptide bonds form between the amino group of the amino acid attached to the A-site tRNA and the carboxyl group of the amino acid attached to the P-site tRNA. Formation of peptides bonds are catalyzed by peptidyl transferase, an RNA-based enzyme that is integrated into the 50s ribosomal subunit. The energy for each peptide bond formation is derived from GTP hydrolysis, which is catalyzed by a separate elongation factor. The former P-site tRNA enters the E site. It detaches from the amino acid, and is expelled. A charged tRNA enters the complex with each step. An uncharged tRNA simultaneously departs.

Genomics

The study of entire genomes, including the complete set of genes, their nucleotide sequence and organization, and their interactions both within a species and with other species.

Transcription initiation

The template strand is blue. The complementary sequence is the RNA DNA hybrid. RNA polymerase is a complex protein. It unwinds DNA. Mediates transcription itself. Transcription bubble is created.

Anoxygenic photosynthesis continued

There is a choice at FeS. Depends on electrons flow. Noncyclic = electrons are removed from the pathway. Electron can be used to reduce NADP or make ATP. There are two choices. Bacterial and anoxygenic photosynthesis don't require oxygen. evolved after anaerobic respiration. The proteins are all the same.

Glucose

There is no good reason why glucose is the best carbon source. Monosaccharides are rearranged to form glucose. Enzymes facilitate this. Disaccharides can be cleaved and broken down into monosaccharides. Central metabolism starts with glucose, then pyruvate, acetyl CoA, then CO2.

Bacteria and archaea morphology

Three most common shapes: Cocci (spherical). Bacilli (rod-shaped). Spirilli (spiral-shaped).

Summary/review

Transcription generates messenger RNA (mRNA), which contains U instead of T. 20 amino acids. Each amino acid is associated with a codon on the mRNA strand and an anticodon on a given tRNA molecule. The relationship between a nucleotide codon and its corresponding amino acid is called the genetic code. 64 possible codons. Amino acids are encoded for by more than one codon. 3 codons terminate protein synthesis (stop codons). AUG specifies the amino acid, methionine, and serves as the start codon. Exists at the 5' end of the mRNA strand.

Eukaryote translation

Transcription processing occurs in the nucleus. Removing the introns, adding a 5' and 3' cap.

Termination in bacteria

Two main types of termination signals: RNA-based and protein-based. Rho-dependent termination is controlled by the rho protein, which tracks along with the polymerase on the growing mRNA chain. Near the end of the gene, the polymerase encounters a run of G nucleotides on the DNA template, and it stalls. The rho protein then collides with the polymerase. This collision releases the mRNA from the transcription bubble. Rho-independent termination is controlled by specific sequences in the DNA template strand. The polymerase nears the end of the gene being transcribed and encounters a region rich in CG nucleotides. The mRNA folds back on itself, and the complementary CG nucleotides bind together. The result is a stable hairpin that causes the polymerase to stall as soon as it begins to transcribe a region rich in AT nucleotides. The complementary UA region of the mRNA transcript forms only a weak interaction with the template DNA. This, coupled with the stalled polymerase, induces enough instability for the core enzyme to break away and liberate the new mRNA transcript

Double-Strand Breaks (DSBs)

Two mechanisms: Direct joining: Direct joining of the broken ends. This requires proteins that recognize and bind to the exposed ends and bring them together for ligating. They would prefer to see some complementary nucleotides but can proceed without them so this type of joining is also called Nonhomologous End-Joining (NHEJ). Errors in direct joining may be a cause of the various translocations that are associated with cancers. Homologous Recombination: Also known as Homology Directed Repair (HDR). Here the broken ends are repaired using the information on the intact sister chromatid (available in G after chromosome duplication), or on the homologous chromosome (in G; that is, before each chromosome has been duplicated). This requires searching around in the nucleus for the homolog — a task sufficiently uncertain that G cells usually prefer to mend their DSBs by NHEJ. or on the same chromosome if there are duplicate copies of the gene on the chromosome oriented in opposite directions (head-to-head or back-to-back).

Review: lysosomes

Uses chemicals to break down food and worn out cell parts. Lysosomes degrade polymers into monomers.

Video: Genomics

Video Notes: A genome is the set of instructions needed to create an organism. DNA: deoxyribonucleic acid. 2% of genes code for proteins in humans. Genomics: the study of the genome and its environment. Human Genome Project. The goal is to read the entire human genome. Billions of dollars have been spent. Copy Number Variation. Large segments of DNA can be duplicated or deleted. CNVs can be studied. Mountain pine beetle is being studied to save pine trees and manage forests. Genomes can be compared. Open access to sequenced genomes is available online. Genomics enables research and discovery.

Professor Dave: Transcription and Translation

Video Summary: Chromosomes consist of millions of base pairs. Genes are on average 10-50,000 base pairs long. Transcription: process by which enzymes use one of the strands of DNA as a template to produce mRNA. RNA Polymerase binds to the promoter. Template strand is the antisense strand (used to generate the mRNA). Sense strand is the nontemplate strand. Elongation: reading the antisense strand from 3' to 5' and generating the mRNA from 5' to 3'. RNA contains a ribose instead of deoxyribose. It contains uracil instead of thymine. RNA Polymerase keeps only 10-20 bases exposed at a time. Termination occurs. Enzyme detaches from the gene. RNA processing occurs. mRNA leaves the nucleus and finds a ribosome. During translation, the mRNA's codons code for a specific anticodon. Each tRNA is linked to a particular amino acid. 64 possible codons. There is some redundancy. There is no ambiguity, however. AUG is the start codon and codes for methionine. 3 stop codons. Large and small ribosomal subunits, tRNA, mRNA, and more join together. The mRNA shifts over and a polypeptide is created. A stop codon is eventually reached. The completed polypeptide leaves and likely enters an organelle. Translation is responsible for creating proteins.

Video: Sanger Sequencing

Video Summary: Sanger sequencing by capillary electrophoresis. Sanger sequencing is named after Dr. Frederick Sanger. A primer binds to the region of interest. Polymerase extends the primer by adding the complementary nucleotide from the template strand. Sanger removed the oxygen atom from the ribonucleotide, creating a dideoxynucleotide. The polymerase enzyme can no longer extend the chain. Four fluorescent dyes are used. A dideoxynucleotide is added to the ends of genes. The molecules are sent through capillary electrophoresis. Negatively charged DNA fragments are attracted to the positive end. Fragments move based on their weight. A laser excites the DNA fragments as they pass through the capillary. Software can interpret the results. DNA fragments are measured and separated base by base. A text file is created for analysis, as is a graph.

CrashCourse: Transcription

Video Summary: Transcription: DNA is copied into mRNA. Enzymes break down and combine. Transcription unit: length of DNA that will be transcribed on to an RNA molecule. The promoter is upstream and contains a sequence of two of the four nitrogenous bases. Often involves the TATA box. DNA strands run in one of two directions (depends on the orientation of the nucleotides). Upstream: towards 3'. Downstream: towards 5' RNA polymerase copies DNA downstream of the TATA box. Towards the 5' end. RNA polymerase binds to the DNA at the TATA box. Helicase unzips the double helix. RNA doesn't have thymine. Instead, it has uracil. Polymerase rewinds the DNA behind it. Termination signal tells it to pull off. 5' gap: a special type of guanine is added to the 5' end. Poly-A tail: 250 adenines are added to the 3' end. Caps protect it from degradation and makes it easier to connect to organelles later on. RNA splicing. Spliceosome edits the mRNA. Exons stay and introns get cut out. Introns get recycled in the nucleus. The mRNA can now move out of the nucleus. Translation: mRNA is fed into ribosomes. Ribosomes contain rRNA, which has binding sites for mRNA. tRNA translates the language of nucleotides to amino acids and proteins. Each of our 20 amino acids has a unique nucleotide sequence. The anticodon of the tRNA binds to triplet codon. The 5' end is fed through the ribosomes. AUG is the first codon (creating the amino acid methionine). A polypeptide chain is created. Different triplets encode for the same amino acid. Protein structure: Primary structure: amino acids are connected by covalent bonds. Alpha helix and pleated sheets: formed from hydrogen bonds. This is the secondary structure. Hydrophobic groups, hydrogen bonds, and more create the tertiary structure. Quaternary structure: multiple polypeptides joined together. Example: hemoglobin.

Coordinated division

When the cell divides, the endosymbiont also has to divide. They need coordinated division.

Termination of replication

When the daughter cells are synthesized, the RNA primers still need to be removed. There is no way to add molecules to the 5' end of the lagging strand of the daughter strand, so an overhang occurs. If this gap wasn't fixed, then genetic information would be lost.

Deamination reactions

Will an organism grow faster with glucose or valine? With valine, it can enter the TCA cycle immediately. However, the ATP generated from previous oxidation of pyruvate and from glycolysis wouldn't be made. Glycolysis produces two ATP. We would have to run the process reductively. If growing on valine, you would have to expend more energy to make necessary compounds. Organisms that grow on amino acids as carbon sources grow a lot slower than those that rely on glucose. Cells grow at rates that reflect their energy needs.

Random notes

tRNA synthetase charges tRNAs by attaching an amino acid. Requires an ATP. Recognizes the structure of tRNA and adds the correct amino acid. The main recognition site is not the anticodon. It recognizes other parts. tRNA is made by RNA polymerase. Average half life of mRNA in bacteria is two minutes. A gene can take 5-10 minutes to transcribe. It is also being translated and degraded at the same time, Eukaryotic mRNA tends to have a longer lifespan, especially due to the 5' and 3' caps. The rRNAs listed are stable. tRNA, ribosomal RNA, microRNA, spliceosome RNA, etc. These are all stables because they are all attached to proteins. Lots of proteins have an RNA active site and this site is protected by the protein. Transcription = producing mRNA. The promoter sequence orients RNA polymerase what strand to read and where to start. Initiation starts at the promoter. Translation = producing proteins. Requires a AUG start codon in eukaryotes. Eukaryotes first recognize the 5' cap then find the AUG. Bacteria require a Shiner Dalgarno sequence. Not all translation has to start with AUG. In bacteria, translation can start with GUG. There can be a mixture of everything. Translation termination involves three stop codons: UAA, UAG, and UGA. Ribosomes don't care about transcriptional signals. Only reads what's in the RNA. RNA polymerase does not care about translation factors.

Controlling carbon flow

1. ATP can be hydrolyzed to kick start or force a reaction to occur. 2. Keep products low so that EQ will flow to the products and more products will form. 3. Metabolite interactions are near the Km. You can change reaction rates very quickly. Cell can respond rapidly. 4. If the products build up, they can inhibit reactions. If there are too many reactants, they can quicken the reaction.

Characteristics of eukaryotes

1. Cells with nuclei that is surrounded by a nuclear envelope and pores. 2. Mitochondria, which can be reduced or normal in size. 3. A cytoskeleton containing actin filaments and microtubules. 4. Flagella and cilia that can be used for locomotion. Any organisms that don't have them currently are descendants of those that did. 5. Chromosomes, each consisting of a linear DNA molecule coiled around basic (alkaline) proteins called histones. The few eukaryotes with chromosomes lacking histones clearly evolved from ancestors that had them. 6. Mitosis, a process of nuclear division wherein replicated chromosomes are divided and separated using elements of the cytoskeleton. Mitosis is universally present in eukaryotes. 7. Sex, a process of genetic recombination unique to eukaryotes in which diploid nuclei at one stage of the life cycle undergo meiosis to yield haploid nuclei and subsequent karyogamy, a stage where two haploid nuclei fuse together to create a diploid zygote nucleus. 8. It might be reasonable to conclude that the last common ancestor could make cell walls during some stage of its life cycle. This ability must have been lost in many groups. 9. All extant eukaryotes descended from an ancestor with mitochondria.

Functions of the cytoskeleton

1. Maintaining/controlling cell shape. 2. Controlling the internal organization of the cell. 3. Force generation - transport of cellular payloads, movement of cell, cytokinesis.

Defense mechanisms against mutations

1. Redundancy and proofreading. 2. Repairing the damaged strand using the other strand as a template (can involve multiple DNA repair pathways). 3. Repair one mutant duplex using the sister duplex as a model (homologous recombination repair). 4. Natural selection. Removes unfixed deleterious mutation from the population.

Nitrogenous bases and hydrogen bonds

3 bonds: G + C. 2 bonds: A + T.

Hydrogen bonds in DNA

3 hydrogen bonds between G and C. 2 hydrogen bonds between A and T.

Calvin cycle continued

6CO2 = 1 Glucosee

Nucleotide excision repair (NER)

A DNA repair system in which several nucleotides in the damaged strand are removed from the DNA and the undamaged strand is used as a template to resynthesize a normal strand. Removes bulky lesions, such as pyrimidine dimers and chemically altered nucleotides. 20-30 bases, which is larger than BER. Takes place over a larger area. Repair with a thymine dimer. Thymine dimer = cut DNA and polymerase and ribose fixes the DNA. Excision = cuts DNA backbone.

Hydrothermal vents

A breakage or fissure in the Earth's surface that releases geothermally heated water.

Extremophiles

A cell wall is a protective structure that allows an organism to survive in both hyper and hypo-osmotic conditions. Soil can form endospores that allow them to resist heat and drought.

Genome arrangements

A class of large-scale changes that can occur. These changes can be facilitated by enzyme catalysts (i.e. transposases). Include the following: Deletions: segments of the chromosome are lost. Duplication: regions of the chromosome are inadvertently duplicated. Insertions: the insertion of genetic material. Can be acquired from viruses or the environment. Deletion/insertion pairs may occur across chromosomes. Inversions: regions of the genome are flipped within the same chromosome. Translocations: segments of the chromosome are translocated (moved elsewhere in the chromosome).

Ribosomes

A complex macromolecule composed of structural and catalytic rRNAs and many distinct polypeptides. Exist in the cytoplasm of bacteria and archaea and on the rough endoplasmic reticulum in eukaryotes. Mitochondria and chloroplasts have their own ribosomes in the matrix and stroma, which look similar to bacterial ribosomes. Dissociate into large and small subunits when they are not synthesizing proteins and reassociate during the initiation of translation. Mammalian ribosomes have a small 40S subunit and a large 60s subunit. The small subunit binds the mRNA template, whereas the large subunit sequentially binds tRNAs. Many ribosomes can simultaneously synthesize a protein from the same mRNA molecule. Read mRNA from 5' to 3'. Synthesize the polypeptide from the N terminus to the C terminus. Polysome: the complete mRNA/poly-ribosome structure.

Comparative genetics

A core assumption in the field of comparative genetics is that the more recently two species have diverged, the more similar their genetic information will be.

Glycosidic bonds

A covalent bond that connects the nitrogenous base to the sugar. Two atoms are involved: a carbon from the sugar and a nitrogen from the nitrogenous base. Are polar bonds.

Microtubules

A dimer of two proteins. Polymerization and depolymerization (can also occur at the negative end) can occur at the + end. Actin binds to ATP. Tubulin binds to GTP.

Proofreading by DNA polymerase

A is added instead of G. A mismatch results. The number of hydrogen bonds doesn't match. They cannot match in a stable way. Proofreading takes place to correct this. Incorrect base is removed by 3' to 5' exonuclease. The 3' OH is recovered. Exonuclease: only from 3' to 5'. DNA polymerase has exonuclease activity. Endonuclease: single strand or double strand mistakes are removed.

Gram stain

A method for the differential staining of bacteria that involves fixing the bacterial cells to a slide and staining with crystal violet and iodine, then washing with alcohol, and counterstaining with safranin. Iodine: creates crystal structures. Results in gram-positive bacteria retaining the purple dye and gram-negative organisms having it decolorized so that the pink counterstain shows up. Doctors can use this information to determine what antibiotics to prescribe.

Microbial mats

A microbial mat is a multi-layered sheet of microbes composed mostly of bacteria but that may also include archaea. First occurred 3.5 bya. Microbial mats are a few centimeters thick, and they typically grow at the interface between two materials, mostly on moist surfaces. Organisms are held together by a sticky extracellular matrix. The first microbial mats likely harvested energy through redox reactions from chemicals found near hydrothermal vents

Cytoskeleton

A network of fibers that holds the cell together, helps the cell to keep its shape, and aids in movement. Three fibers: microfilaments, intermediate filaments, microtubules. Molecular motors: dyneines and kinesins. Functions: Maintains and changes the shape of the cell. Secures organelles in specific positions. Enables movement of the cytoplasm and vesicles within the cell. Enables the cell to move in response to stimuli.

Listeria monocytogenes

A pathogen that enters the cell. It attracts actin monomers and polymerizes the actin into filaments. It pushes the membrane to a neighboring cell. This pathogen coevolved with eukaryotes. It uses actin to form actin filaments, and pushes the infected cell to another cell. Polymerization = making macromolecules (polymerizing DNA would involve joining monomers to form DNA). Joining monomers together.

Oligonucleotides

A polynucleotide that contains a relatively small number of nucleotides. Applies to both RNA and DNA. Consist of ~20 nucleotides.

Whole genome sequencing

A process that determines the DNA sequence of an entire genome. Can be used to cure mysterious genetic diseases. First human genome sequence was published in 2003.

Telomerase

A reverse transcripttase, which is a class of enzymes that creates single-stranded DNA using single stranded RNA as a template. RNA has a complementary strand in DNA. The reverse in reverse transcriptase means that DNA is made from RNA. Transcription is typically from DNA to RNA. Telomerase contains an RNA primer. Mediates telomere activity. Telomerase has a complementary sequence to the 3' overhang. Telomerase creates more repeats. Primase makes RNA primer. DNA polymerase makes DNA. Uses free-floating nucleotides to synthesize DNA. Telomerase has a RNA primer, meaning that it will have uracil instead of thymine.

Stromatolites

A sedimentary structure formed when minerals precipitate out of water due to the metabolic activity of organisms in a microbial mat. Stromatolites form layered rocks made of carbonate or silicate.

Base Excision Repair (BER)

A single base is first removed from the DNA, followed by removal of a region of the DNA surrounding the missing base. The gap is then repaired. Cytosines in DNA sometimes undergo deamination (removal of the amino group) to form the base uracil. Because cytosines pair with guanines and uracils pair with adenine, the conversion of cytosine to uracil in the DNA would lead to the insertion of an A in the newly replicated strand instead of the G that should have gone in across from a C. Since the bases cytosine, adenine, and guanine have amino groups on them that can be deaminated, deamination can cause mutation in DNA. The hydrolysis reaction (deamination) of cytosine into uracil is spontaneous. Uracils are removed.

Translation sites

A site: tRNA has amino acid. T site: amino acid is joined to the polypeptide. E site: tRNA exits.

Model organisms

A species that is studied as a model to understand the biological processes in other species that can be represented by the model organism. Research is often done on model organisms (i.e. the fruit fly, nematode, and mouse).

Centrosome

A structure in animal cells containing centrioles from which the spindle fibers develop. Functions as the microtubule organizing center.

Operon

A unit of genetic function common in bacteria and phages, consisting of coordinately regulated clusters of genes with related functions. Monocistronic mRNA can make monocistronic RNA. Prokaryotes have operons. Eukaryotes do not. Three genes are connected together downstream of the promoter. Prokaryotes can make a poly-cistronic mRNA (multiple genes are making RNA at the same time). These genes can be translated separately. Multiple proteins can be made. A cluster of genes collectively controlled by a promoter.

Video notes

A white blood cell is found in your bloodstream. It has receptors to proteins inside the blood vessels. It moves by pseudopods. Proteins are held in rafts. Rafts are dense and rigid. Severing proteins can cleave actin filaments. Microtubules spontaneously form. Kinesins walk across the microtubule and hydrolyze ATP. Mitochondria can also move across the microtubules. RNA is transported out through nuclear pores. Ribosomes bind to mRNA. Membranes attach to the Golgi. Proteins are segregated and are sorted based on signals on proteins. White blood cells move across the walls of blood cells and squeeze in between the cells of red blood cells. Actin is severed so that everything below it is broken off. This can control the direction of movement.

Practice question: FCCP

A. False. B. False. C. False. D. True. E. False.

Microfilaments

Actin is the monomer found in microfilaments. Added at the + end and removed at the - end. Found in the periphery of cells. It is an ATPase and hydrolyzes ATP. It is sensitive to the ATP/ADP ratio.

E. coli

After replication, adenine in the parental DNA gains a methyl group. The parental strand will have such groups, while the newly synthesized strand will lack them. Mismatch repair enzymes can scan the DNA and remove the wrongly incorporated bases from the newly synthesized, non-methylated strand by using the methylated strand as the "correct" template from which to incorporate a new nucleotide. In eukaryotes, the process is unclear. Unsealed nicks in the new strand may have a role in recognition.

Post-translational protein modification

After translation, individual amino acids may be chemically modified. Common modifications: adding phosphate groups, methyl, acetate, and amide groups. Proteins that are sent to membranes are lipidated (a lipid is added). Other proteins are glycosylated (a sugar is added). Cleavage may occur. This involves the linking of parts of the protein to itself. Examples: signal-peptides may be cleaved, parts may be excised from the middle of the protein, or new covalent linkages may be made between cysteine or other amino acid side chains.

Examples of mutations

Altered information: the nucleotides are correctly paired, but it is still a mutation. Leads to no instability in structure.

Microfilaments

Amoeba send a pseudopod. Filaments form rigid rods, stretching the membrane towards a given direction. The myosin cross-link the actin and squeeze the bundles to push the cytoplasm into the pseudopod. If you stop breathing while exercising, your muscles will run out of ATP and will no longer be able to undergo cellular respiration. Fermentation will occur and lactic acid will be made.

Endosymbiosis

An ancestral organism. A nucleus is created. This new cell then engulfs prokaryotes to form mitochondria and chloroplasts. An archaeal host engulfs an alpha proteobacterium.

Autotrophs vs. heterotrophs

An autotroph or primary producer is an organism that produces complex organic compounds using carbon from simple substances such as carbon dioxide, generally using energy from light or inorganic chemical reactions. A heterotroph is an organism that cannot produce its own food, instead taking nutrition from other sources of organic carbon, mainly plant or animal matter. In the food chain, heterotrophs are primary, secondary and tertiary consumers, but not producers.

Mismatch repair (MMR)

An enzymatic system for repairing base mismatches (non-Watson Crick pairs) in DNA. Corrects mispaired bases, typically immediately following replication. Mismatch repair: mechanism after DNA replication. Structurally, the DNA strand is not stable. Mismatch proteins excise mismatched bases. DNA polymerase fills the gap by adding nucleotides. DNA ligase connects the added nucleotides by creating a covalent bond. Nick = one small gap that needs to be joined by a covalent bond. Gap = several covalent bonds are required to join nucleotides in a large stretch of DNA. Methyl groups can be used by prokaryotes to determine that one nucleotide should be removed instead of its opposite nucleotide. It is hard to determine when there is a mistake, especially when the mismatch doesn't lead to a significant change in structure.

Telomerase

An enzyme composed of protein and RNA. Attaches to the end of the chromosome by complementary base pairing between the RNA component of telomerase and the DNA template. Uses the RNA as a complementary strand for the short elongation of its complement. Telomerase elongates the lagging strand such that primase can create a primer. DNA polymerase can then add nucleotides complementary to the ends of the chromosomes. Not active in adult somatic cells. These cells continue to have their telomeres shortened. Telomerase reactivation has the potential for treating age-related diseases in humans.

Genome

An organism's complete collection of heritable information stored in DNA. Genomes can be distributed into chromosomes and plasmids. Human genome is 3.2 billion base pairs. Polyploid: when genomes contain multiple similar, but not identical, homologous copies of each chromosome. Diploid organisms have two homologous copies of each chromosome. Humans contain two homologous copies of 23 chromosomes. Tetraploid: four homologous copies of each chromosome. Haploid: single copy. Diagram: Much of the human genome doesn't contain exons. In other words, it is noncoding.

Origins of the cytoskeleton

Ancient relatives of both actin and tubulin in bacteria. May have also originated in archaea. Early ancestors to actin in bacteria: MreB = maintains cell shape. ParM = plasmid partitioning. FtsZ = a GTPase involved in cytokinesis. Ancient form of tubulin.

Purple sulfur bacteria

Anoxygenic photosynthesis. Purple bacteria generate NADPH by using an external electron donor (H2, H2S, S, SO32-, or organic molecules, such as succinate and lactate) to feed electrons into a reverse electron transport chain.

Practice question: central metabolism

Answer: phenylalanine is an amino acid that is used to build proteins. If you don't have it, protein synthesis stops. By interconnecting pathways, cells can adjust to the absence of compounds.

Structure of chlorophyll

Antennae collect photons. The chlorophyll reaction center is where the chemistry occurs. Purple bacteria have carotenoids that gather energy. Tail anchors it in the membrane.

Parts of the cytoskeleton

Antibodies can highlight features of the cytoskeleton. Actin is in red and is found in the periphery of the cell. Microtubules are in green. Start in the center and move out. The nuclei are in blue.

Polymerization

Any process in which relatively small molecules, called monomers, combine chemically to produce a very large chainlike or network molecule, called a polymer.o

Cyanobacteria

Appeared 3.5 bya. Relatively complex and large.

Mitochondria

Arise from the division of existing mitochondria. Can be moved using the cytoskeleton. Most mitochondria are shaped like alpha-proteobacteria and are surrounded by two membranes, which would result when one membrane-bound organism is engulfed into a vacuole by another membrane-bound organism. Contain foldings called cristae and a number of enzymes involved in respiration.

Early photosynthesis

Around 3.5 billion years ago, some bacteria and archaea began using energy from sunlight to power anabolic processes that reduce carbon dioxide to form organic compounds. Used the hydrogen found in water to reduce carbon dioxide during the Calvin cycle. O2 was released as the byproduct during this process. Gram negative bacteria were the first ones to perform this process.

Signal peptides

As the protein is being made in the cytosol, a small protein recognizes a specific site on a peptide that is being made. It stops translation and moves it to the rough ER. Interacts with a docking protein. Translation resumes in the lumen of the ER. If it is soluble, it goes to the lumen. Membrane proteins are made at the outside. Membrane proteins often go to the Golgi.

Reading frames

At least three reading frames per mRNA. In phage or viruses, you can overlapping genes. One gene can be read in frame one and another gene can be read in frame three. For the most part, this doesn't happen in the three domains of life. The first starting codon tells us what frame for translation to occur. Moving the register can fundamentally change the sequence of amino acids. If the mRNA is not correct, that won't affect the next generation of mRNA. Bad proteins are created and energy is wasted, but it won't kill you. If it is dominant and lethal. A mutation caused by DNA polymerase is only lethal, not by RNA polymerase.

Phototrophs

Autotrophic organisms that convert solar energy into chemical energy.

Diction concerns: prokaryotes

Bacteria and archaea are distinct and very different. They independently evolved. Don't use the term "prokaryote" for shared ancestry. Use the term for common physical characteristics.

Gram positive bacteria

Bacteria that have a thick peptidoglycan cell wall, and no outer membrane. A gram stain leaves them with a dark purple stain. In your skin, you have far more gram positive cells than gram negative cells. They are more resistant to UV light. Easier to kill with antibiotics.

Gram negative bacteria

Bacteria that have a thin peptidoglycan cell wall covered by an outer plasma membrane. A gram stain leaves them with a light pink stain. Gram negative bacteria are typically more resistant to antibiotics than Gram positive bacteria. Penicillin works very well on gram positive organisms.

Transcription: initiation

Begins with the binding of RNA polymerase to the promoter. The double helix partially unwinds, enabling one strand to be used as a template for RNA synthesis. The unwinding region is called a transcription bubble. Transcription proceeds from the template strand (one of two strands in DNA). The other strand in DNA is called the coding strand. The RNA product is complementary to the template strand and is almost identical to the nontemplate (coding) strand. The only difference is that RNA contains a uracil (U) in place of thymine.

Bacterial vs. eukaryotic elongation

Begins with the release of the sigma subunit from the polymerase. This release allows the polymerase to proceed along the DNA template, synthesizing mRNA in the 5' to 3' direction. DNA is continuously unwound and rewound. The base pairing between DNA and RNA is not stable enough to maintain the stability of the mRNA synthesis components. Instead, the RNA polymerase acts as a stable linker between the DNA template and the RNA strands to ensure that elongation is not interrupted prematurely.

Advantages/disadvantages based on size

Being small: Can rely on diffusion, which is a passive process that doesn't require energy . Less maintenance and less energy requirements. Reproduce faster, but have a shorter lifespan. Often have undeveloped transport systems. Often lack compartmentalization. Being large: Diversity in electron source. Larger organisms tend to have to use oxygen.

Compartmentalization

Benefits: Offers solution to diffusion problem for biochemistry that needs multiple steps. Sequesters "bad" reactions from rest of cell (e.g. can make local low pH environment, or put digestive enzymes in a single confined space etc.). Offers greater regulatory control - separation of processes - minimized unwanted "cross-talk." Additional notes: There is a diffusion problem in the cell. The cytoplasm is very viscous. All substrates are concentrated within a membrane.

Diction concerns: prokaryote

Biologists don't like the term prokaryotes because it lumps bacteria and archaea together, even though they have significant differences.

DNA transcription vs. DNA replication

Both DNA replication and Transcription involve the generation of a new copy of the DNA in a cell. DNA transcription is involved in replicating the DNA into RNA, while the DNA replication makes another copy of DNA. Both the process is involved in the production of new nucleic acids- DNA or RNA. RNA polymerase: transcription. DNA polymerase: replication.

BER vs. NER

Both repair chemically modified bases. BER repairs a small area. NER repairs a large area.

RNA vs. DNA

Both require a 3' hydroxyl to continue DNA synthesis. The 3' OH increases the possibility of interactions with substrates. RNA can make hydrogen bonds.

Single-Strand Breaks (SSBs)

Breaks in a single strand of the DNA molecule are repaired using the same enzyme systems that are used in Base-Excision Repair (BER).

Helicase

Breaks the hydrogen bonds between nucleotides, which allows the double-helix to separate. When helicase unwinds DNA, the DNA can become over-twisted in front of the helicase (supercoiling) and under-twisted behind it.

Calvin cycle

CO2 is oxidized and stable. We add electrons to it and generate reduced carbon. The end product is G3P. 3 CO2 and 3 five carbon molecules (RuBP) make 6 three carbon compounds. Rubisco is the most abundant protein and enzyme in the planet. We form 5 three carbon units (3 PGA). We use 6 ATP, 6 ADP, and 6 NADPH to make six G3P. One G3P is taken out. The rest return to the cycle. Similar to the pentose pathway: take three six carbon units and decarboxylate to generate 3 CO2s and 3 five carbon units. Starch is used for storage, and is made of sucrose. Plants use sucrose as their main carbon compound; we use glucose. Costs 9 ATPs total. Advantage because CO2 is abundant.

Motor proteins

Cargo is often stored in vesicles, which move across cytoskeleton filaments. Two families of motor proteins: dyneines and kinesins.

Practice test notes

Cells that have cell walls can't engulf other cells. Transcription always moves from 5' to 3' on the template strand. The promoter tells RNA polymerase where to begin transcription, how often to begin transcription, and which strand to transcribe. There are three ways of reading a given strand of DNA (three reading frames). The reading frame determines how the mRNA is divided up into codons.

Redox tower

Chemoorganotrophs use NADH as an electron donor. It has a low reduction potential. We use chemical energy.

Comparing the structure of chlorophyll a and b

Chlorophyll a is used in photosystem II. Chlorophyll b is used in photosystem I.

Inhibition/activation of enzymes

Citrate is an intermediate in the TCA cycle. It inhibits the reaction. If there is too much citrate, glycolysis slows down (inhibition). This controls the amount of carbon in the system. ADP or AMP build up stimulates the reaction. ATP build up inhibits glycolysis. ATP to ADP ratio is important. Substrates are often activators. Products (i.e. citrate or ATP) are often inhibitors.

tRNA

Cloverleaf structure on the left.

RNA structure

Complex 3D structure. formed by hydrogen bonding. Can form a secondary structure.

Ligase

Connects the 5' PO4 and 3' OH groups together in the backbone between the two Okazaki fragments. Requires ATP to create a phosphodiester bond.

Consensus sequences

Consensus sequences = regions similar across many promoters and across various species. The consensus sequence contains the most common sequence elements. In bacterial cells, the -10 consensus sequence (-10 region) is AT rich, often TATAAT. The -35 sequence, TTTGACA, is recognized and bound by the protein sigma. Once this protein-DNA interaction is made, the subunits of the core RNA polymerase bind to the site. Because of the relatively lower stability of AT associations, the AT-rich -10 region facilitates unwinding of the DNA template, and several phosphodiester bonds are made.

Models for DNA replication (hypotheses)

Conservative: Each whole double-stranded molecule could act as a template for the synthesis of a new double-stranded molecule. If one were to put a chemical tag on the template DNA molecule after replication, none of that tag would be found on the new copy. Semi-conservative: This hypothesis stipulated that each individual strand of a DNA molecule could serve as a template for a new strand to which it would now associate with. In this case, if a chemical label were placed on a double-stranded DNA molecule, one strand on each of the copies would keep the label. Regarded as true. Each strand is used as a template for the creation of the new strand. Dispersive: A copied double helix would be a piecewise combination of continuous segments of "old" and "new" strands. If a chemical label were placed on a DNA molecule that were copied using a dispersive mechanism, one would find discrete segments of the resulting copy that were labeled on both strands separated by completely unlabeled parts.

Amino acid structure

Consist of a backbone composed of an amino group, a central carbon (alpha carbon), and a carboxyl group. An alpha hydrogen and an R group are attached to the alpha carbon. The R group determines the chemical properties and reactivity of the amino acid. There are 20 amino acids.

Practice question: photosynthesis and cellular respiration

Correct answer: B. A. False. Photosynthesis: final electron acceptor is NADP+, which is reduced to NADPH. B. True. We see an ETC with both photosynthesis and cellular respiration. C. False. NADPH only concerns photosynthesis. D. False. E. False.

Mismatch repairs

Corrects mistakes after replication is complete. Specific enzymes recognize errors and replace base pairs with the correct versions.

Prokaryotes vs. eukaryotes

Coupled vs. uncoupled. In prokaryotes, there are no introns. Everything is coding. Introns are unique to eukaryotes. Modification of mRNA does not occur in prokaryotes. Proteins can be made immediately after transcription. mRNA are processed in prokaryotes, but not to the same extent as eukaryotes.

Chlorophyll a

Cyanobacteria evolved chlorophyll a. It sits right under oxygen. When it is oxidized, it can take electrons from water. This can create oxygen. Created the Great Oxidation Event and led to the first mass extinction. Organisms can either run away from it, detoxify it, or can learn to use it. Oxygen levels tend to be between 20-24%. Infinite supply of electrons with water.

Importance of surface area

Cyanobacteria evolved into chloroplasts, and are responsible for the Great Oxidation Event. Ribosomes sit on the rough ER. The mores surface area it has, the more ribosomes can attach to it. The Golgi apparatus has surface area so that vesicles can fuse to the surface. Packages proteins. The internal membrane of mitochondria is used to make ATP through the ETC. The ETC is found in the inner membrane of mitochondria in eukaryotes, as opposed to the cell membrane of prokaryotes. Chloroplasts have an antennae complex in order to absorb light. Increased surface area means increased exposure to photons.

DNA overview

DNA polymerase adds nucleotides in one direction: 5' to 3'. The leading strand allows for continuous synthesis. Lagging strand: there is no place for the primase to land and synthesize an RNA primer so that the synthesis of the missing lagging strand DNA fragment at the end of the chromosome can be initiated by the DNA polymerase. Nucleases break off pieces of the chromosomal ends.

Elongation

DNA polymerase can not start strand synthesis on its own. Rather, it requires a short stretch of double-stranded structure followed by a single-stranded template. The enzyme, primase, creates a short oligonucleotide polymer of RNA (not DNA) called a primer. Primers are used to nucleate and grow a new strand. DNA polymerase polymerizes a new covalently linked strand of DNA nucleotides. It reads the strand of DNA from 3' to 5' and synthesizes a new strand from 5' to 3'. The primer provides a hydroxyl on which to begin synthesis. The next deoxyribonucleotide triphosphate enters the binding site of the DNA polymerase and is oriented in the polymerase such that a hydrolysis of the 5' triphosphate can occur. This reaction releases pyrophosphate and couples the exergonic hydrolysis of the phosphoanhydride to the synthesis of a phosphodiester bond between the 5' phosphate of the incoming nucleotide and the 3' hydroxyl group of the 3' primer. In summary, DNA polymerase adds the phosphate group (5') from the incoming nucleotide to the existing hydroxyl group (3') of the previously added nucleotide. Correct base pairing: based on structural constraints and the formation of energetically favorable bonds. Process is driven by the hydrolysis of the incoming 5' triphosphate and the energetically favorable interactions formed by the inter-nucleotide interactions in the double helix. Strands can grow from 3' to 5', but the energy needed to do so would have to come from a nucleotide already incorporated into the growing strand rather than the new incoming nucleotide. A different DNA polymerase comes in to remove the RNA primer and to synthesize the remaining portion of missing DNA.

DNA polymerase

DNA polymerase has nuclease activity. We can't call it a nuclease, however.

Proofreading

DNA polymerase reads each newly added base and detects any abnormalities. If a mistake is made, the misshaped double helix will cause DNA polymerase to stall and it will eject the newly made strand from the polymerizing site. The DNA strand enters an exonuclease site. From there, DNA polymerase can cleave off the last several nucleotides that were added to the polymer. Once done, the DNA strand can return to the polymerizing site. Trade-off: speed of replication and energy vs. more accurate polymerase. Mutations are errors that aren't corrected.

Base excision repair (BER)

DNA repair that first excises modified bases and then replaces the entire nucleotide. Fixes non-deforming lesions of the DNA helix by removing the base leaving an apurinic/apyrimidinic site (AP). AP endonuclease removes the damaged sequence which can be filled in w/ the correct bases by DNA polymerase (strand is sealed by DNA ligase). Used to correct cytosine deamination. Loss of amino group from cytosine resulting in the conversion of cytosine to uracil. Bases can be modified by deanimation. AP site = damaged base.

Origins of DNA replication

DNA replication begins at the origin of replication (ORI). In prokaryotes, replication is bidirectional and there is only one ORI. Helicase binds to the origin of replication.

Why do eukaryotes have more than one origin of replication?

DNA replication is faster this way, as eukaryotes have considerably more base pairs than their prokaryotic counterparts.

Organic Chemistry Tutor Video

DNA replication proceeds bidirectionally. Replication fork is Y shaped. Helicase separates the two strands. Breaks hydrogen bonds. Topoisomerase reduces supercoiling and torsional strain. Single stranded binding proteins (SSBs). Protect the strands and prevent them from joining together. RNA primer is a sequence of RNA nucleotides. DNA polymerase III attaches to the RNA primer. Template strand: runs in the 3' to 5' direction. DNA polymerase III adds nucleotides in the 5' to 3' direction. Primase makes the RNA primers. DNA polymerase III only adds nucleotides in the 3' to 5' direction. Lagging strand: 5' to 3'. DNA polymerase synthesizes the daughter strand from 5' to 3'. Leading strand moves in the same direction as the replication fork. Lagging strand is opposite. On the lagging strand, DNA synthesis is discontinuous. DNA replication is semicontinuous. DNA Polymerase I removes the RNA primer and replaces it with DNA. DNA ligase fuses the nicks between okazaki fragments. Exonuclease activity shows proofreading. DNA polymerase III has proofreading ability. DNA polymerase I has 5' to 3' exonuclease activity. DNA replication is semiconservative. Each copy of DNA has one old strand and new strand. Lagging strand is produced in the opposite direction as the replication fork. SSB proteins protect the strands from cleavage. DNA polymerase I has both 3' to 5' and 5' to 3' exonuclease activity. DNA polymerase I can remove the primer and repair it. Lagging strand is 5' to 3'. DNA polymerase III also reads it from 5' to 3'. It is read away from helicase, away from the replication fork. DNA is said to be semiconervsative because it is made of one old (conserved) strand and one new one. RNA primers attach one by one. They don't attach at the same time. RNA primase attaches a primer to the lagging strand. DNA polymerase III synthesizes an Okazaki fragment. RNA primase then attaches a new primer.

Differences between Bacteria and Archaea

DNA replication, transcription, translation, DNA repair in the archaea appears to be more closely related to that of the eukaryotes than to the bacteria.

Central Dogma

DNA serves as a repository of genetic information. Genetic information is expressed by DNA that first serves as a template for the synthesis of messenger RNA (transcription). mRNA then serves as a template, which is read by ribosomes and translated into protein. The protein end products can be enzymes or structural proteins. Genes can encode functional RNA, tRNAs, and rRNAs (needed for translation), etc. Functional RNA is functional immediately when they are transcribed (or with minor alterations via processing), such as tRNAs and rRNAs. The model asserts that DNA has a static role. It does not provide an active cellular function, but rather it encodes macromolecules that are functional. RNA can be converted to DNA (some viral RNA genomes are converted into DNA proviruses integrated into the genome). Reverse transcriptase can make a DNA copy of RNA.

History of DNA

DNA structure proposed by Watson and Crick. A few years later, they proposed the existence of a less stable nucleic acid, RNA. mRNA is messenger RNA that provides a transient copy of genetic material that can be translated into a protein product.

DNA damage vs. mutations

Damage: An abnormality in DNA structure (i.e. missing bases, incorrectly paired bases, etc). Anything that violates Watson-Crick base pairing. Repair enzymes recognize wrong DNA structures. Mutations: Cannot be recognized. Mutation DNA is structurally normal. Cannot easily repair a finished mutation.

Decay

Decay: when an electron returns to its ground state. As it decays, the excess energy can be given off as heat or fluorescence (light energy). The energy can be transferred to another atom. You can also couple the energy with a redox reaction to remove an electron and donate it to something else. Chlorophyll accepts energy from photons and excites electrons in the magnesium ions in the center of chlorophyll. The high energy state is used to move electrons through an ETC to generate ATP, and eventually can be used to make NADPH.

Promoters

Def. A DNA sequence onto which various proteins, collectively known as the transcription machinery, bind and start transcription. Often exist upstream to the genes they regulate (5' to the coding region). Gene sequence determines the regularity of transcription. Eukaryotic promoters are much larger and complex. They tend to have an AT-rich region called a TATA box.

Endosymbiosis

Def. One cell engulfing another such that the engulfed cell survives and both cells benefit. Players: an alpha proteobacterium took residence in an archaeon. Eukaryotes may have been a product of one cell engulfing another (one living within another) and evolving until the separate cells were no longer recognizable as such. Developed by Lynn Margulis in 1967. Nuclear genes and the cellular machinery responsible for the replication and expression are found in archaea. However, the metabolic organelles and genes responsible for many of the energy harvesting processes have their origins in bacteria. It is not known whether the endosymbiotic event that led to mitochondria occurred before or after the host cell had a nucleus.

Deoxyribose vs. ribose

Deoxyribose: 2' carbon is attached to two hydrogen atoms. Ribose: 2' carbon is attached to a hydroxyl group and one hydrogen atom.

RNA vs. DNA

Difference is the hydroxyl group in RNA. DNA has a H atom at the 2' position and RNA has a OH molecule at the 2' position. Uracil replaces thymine. RNA is singe stranded. DNA is double-stranded. RNA is less stable. DNA is less chemically active than RNA.

Repairing damaged/inappropriate bases

Direct chemical reversal of the damage. Excision Repair: The damaged base or bases are removed and then replaced with the correct ones in a localized burst of DNA synthesis. There are three modes of excision repair, each of which employs specialized sets of enzymes. 1. Base Excision Repair (BER). 2. Nucleotide Excision Repair (NER). 3. Mismatch Repair (MMR).

DNA replication in bacteria

E. Coli has 4.6 million base pairs. Occurs from a single origin of replication and proceeds around the chromosome in both directions.

Redundancy of DNA

Each strand carries equivalent information to its complementary strand. Redundancy allows DNA to act as genetic material.

Termination in eukaryotes

Elongation by polymerase II takes place 1000-2000 nucleotides beyond the end of the gene being transcribed. This pre-mRNA tail is subsequently removed by cleavage during mRNA processing. RNA polymerases I and III require termination signals. Genes transcribed by RNA polymerase I contain a specific 18-nucleotide sequence that is recognized by a termination protein. The termination process in RNA polymerase II is similar to rho-independent termination in prokaryotes in that it involves a mRNA hairpin.

Diagram: translation

Elongation factors hydrolyze GTP. To make a peptide bond, it requires 3 ATP. Very expensive. 2 GTPs and an ATP

Endocytosis

Endocytosis: a membrane-mediated process that takes something from the outside to the inside. Can be a solid particle (phagocytosis). White blood cells engulf a bacterium by endocytosis. Viruses can get into cells this way, too. Pinocytosis: Bringing extracellular fluid into the cell to maintain turgor pressure. Receptor-mediated endocytosis: A virus binds to a receptor, which signals the cell to bring the virus in. Coated pits are sites at which a conformation change occurs in the proteins in that region.

Endonuclease vs. exonuclease

Endonuclease cleaves phosphodiester bonds within the polymer. Exonuclease cleaves phosphodiester bonds at the ends of the polymer

mRNA processing

Eukaryotic cells modify mRNAs at the 3' end by the addition of a poly-A tail. This adenine residue is added by an enzyme that does not use genomic DNA as a template. The 5' end contains a 5'-cap. The 5'-cap and poly-A tail increases the lifespan of the mRNA (prevent its premature degradation in the cytoplasm) and help mRNA start translation. In eukaryotes, the 5′ cap (cap-0), found on the 5′ end of an mRNA molecule, consists of a guanine nucleotide connected to mRNA via an unusual 5′ to 5′ triphosphate linkage. Introns are noncoding, and are hence removed. Exons stay.

Oxygenic photosynthesis

Evolved in cyanobacteria. Plants came later. Photosystem II is first. Takes light energy and passes the electrons to PSI. Chlorophyll is then oxidized, so it takes electrons from water and becomes reduced again, creating oxygen. PSII creates ATP. PSI creates NADPH. Enough NADPH means that you can create a cycle and donate electrons to PSII again.

Endocytosis vs. exocytosis

Exocytosis enables the secretion of proteins. Vesicles fuse with the outer membrane and the contents are released outside. Vesicles are made of a double membrane.

Codon table

First letter is the first row. 2nd letter is row. Third letter is right column. This table reads the mRNA, not the anticodon. The message looks like the coding strand (nontemplate strand). Template strand is used as a template to make the coding strand (3' to 5'). The code is degenerate. Multiple combinations can encode for the same amino acid. A mutation may occur, but it might not change anything. In the microbial world, this property is especially important. In a bacteria that is high in GC, it will likely use GUC or GUG for valine. This gives organisms flexibility. Most eukaryotes don't have a preference for a codon combination. Last codon is a wobble codon. The third codon is not as important as the first two. Provides fleixbility. You don't want to mess with the first and second nucleotides.

Flagella and cilia

Flagella are long, hair-like projections that are used for movement. Cells contain just one or a few flagella. Cilia are short, hair-like structures that are used to move entire cells or substances along the outer surface. Can trap matter. Can extend across the entire surface of a membrane. A single flagellum or cilium is made of a ring of nine microtubule doublets, surrounding a single microtubule doublet in the center.

Translation initiation

Formation of initiation complex. The small ribosomal subunit binds to the mRNA at the ribosomal binding site. The methionine tRNA binds to the AUG start codon through complementary binding with its anticodon. The large ribosomal subunit attaches. The initiation complex then recruits the second tRNA and translation begins.

Negative and positive feedback w/ enzymes

G is the end of the pathway. When G builds up, it can activate the D to E branch. Increase in G inhibits the C to F reaction. Decrease in G means that C to F is activated and D to F is inhibited. Binding of G allosterically inhibits the reaction. Removing G increases the activity. ADP or NAD+, along with ATP or NADH, controls the reactions.

Goal of DNA replication

Goal of DNA replication: produce two identical copies of the double-stranded DNA template.

Introduction to DNA

Human cells require 24 hours to divide. E. coli can divide in 20 minutes. Composed of two strands of covalently linked nucleotides. Nucleotides are joined via phosphodiester bonds that link sugars through the 5' and 3' hydroxyl groups. Backbone = sugars and phosphates. 5' end = phosphate is linked to the 5' carbon. 3' end = hydroxyl group is linked to 3' carbon. 5' to 3' is convention. Strands are antiparallel. Hydrogen bonds between purine/pyrimidine pairs. Complementary strands. Twisting causes major and minor grooves. Function as binding sites for DNA binding proteins. The nucleotides start off as nucleotide triphosphates. Nucleotides are composed of a nitrogenous base, deoxyribose (five-carbon sugar), and a phosphate group. Purines: adenine (A) and guanine (G). Purines have a double ring structure with a six-membered ring fused to a five-membered ring. Pyrimidines: cytosine (C) and thymine (T). Pyrimidines are smaller in size; they have a single six-membered ring structure. The phosphate residue is attached to the hydroxyl group of the 5' carbon of one sugar, and the hydroxyl group of the 3' carbon of the sugar of the next nucleotide.

Exergonic and endergonic reactions

Hydrolysis of the phosphoanhydride bond between the alpha and beta phosphate groups of a nucleoside trisphosphate releases energy (exergonic). This energy can be coupled with the endergonic reaction of forming a phosphodiester bond between two nucleotides. The endergonic reaction joins the 3' -OH group on the existing nucleotide chain and the -P on the α phosphate attached to the 5' carbon to generate the phosphodiester bond. This reaction is considered a condensation reaction. However, it does not produce water. It generates a pyrophosphate [P2O7]4-, which splits into two organic phosphates. You always need a free 3' OH group in order to attach new nucleotides. DNA is built 5' to 3'.

Practice question: mutations

If RNA polymerase makes a mistake, this won't affect the next generation. All that happens is that an incorrect protein is made and energy is wasted. If mistakes are made in translation, this won't affect offspring. If mistakes are made in DNA, this is a problem. DNA needs to have high fidelity. RNA polymerase doesn't have a proofreading function, nor do ribosomes.

Practice questions: mutations

If something can be classified as a mutation, then it has been undetected by DNA repair mechanisms and can't be repaired at that point.

Eukaryotic cells

If you're larger, you can eat your neighbor. Protection from predation. Eukaryotic cells have compartmentalization.

Bacterial vs. eukaryotic initiation

In E. coli mRNA, a sequence upstream of the first AUG codon called the Shine-Dalgarno sequence (AGGAGG) interacts with an rRNA molecule. This interaction anchors the small ribosomal subunit (30S) at the correct location on the mRNA template.

Practice question: mutations

In both cases, arginine is created. The same protein will be made. Mutations can collect that don't affect the engendered proteins. The numbers of complementary pairs can vary. High GC organisms may have more G's and C's. Why this happens is unclear. Allows organisms to speciate and become more diverse. Organisms can also be high AT. Most organisms are 50/50.

mRNA structure

In eukaryotes, both a 3' and 5' UTR region are present. The 5' end by a protective cap (modified guanine). The poly-A tail covers the 3' end.

Energy production

In eukaryotes, our mass and energy comes from the same thing, which is from glucose. In archaea, carbon and electrons can come from different things. Diffusion requires a membrane, as does the ETC. If there is no membrane, then a gradient isn't created. A gradient represents potential energy. The more membranes you have, the more ETC systems you can have, and the more energy you can create. Surface area is desired.

Diagram: percent of protein-coding genes

In humans, protein-coding genes only make up 48 million of the 3.2 billion bases of the haploid genome.

Sanger sequencing

In the 1970s, Fred Sanger's group discovered a new way of reading the linear DNA sequence using special bases called chain terminators or dideoxynucleotides. The absence of a hydroxyl group at the 3' position blocks polymerization, resulting in termination of replication. Sanger dideoxynucleotide chain-termination method. This method originally used a radioactively labeled primer to initiate the sequencing reaction. Four reactions take place and each reaction is intentionally "poisoned" with a dideoxy chain terminator. For example, one reaction involves 4 dNTPs (deoxynucleotide triphosphates) and a small amount of ddATP (dideoxyadenosine triphosphate). This reaction results in a series of premature terminations of the polymerization specifically at different locations where an Adenine would be incorporated. Diagram: dATP has the hydroxyl group at the 3' end. ddATP lacks the hydroxyl group. The product of these four reactions is run on a large polyacrylamide sequencing gel. The smallest fragments run through the gel and create a ladder-like pattern. The results can be viewed using an x-ray film. Each line of the gel corresponds to one of the four chain-terminating reactions. The bases are read from the bottom up and reveal the sequence of the DNA.

Primase

Informs DNA Polymerase III of where to begin daughter strand synthesis. Considered an RNA polymerase. RNA primers are removed by DNA polymerase I and are replaced by the appropriate DNA nucleotides.

Alternative splicing

Introns are removed from the mRNA sequence and exons are ligated together. Allows cells to mix and match which exons are incorporated into the final mRNA product. This can lead to multiple proteins being encoded by a single gene.

Repairing Strand Breaks

Ionizing radiation and certain chemicals can produce both single strand breaks (SSBs) and double-strand breaks (DSBs) in the DNA backbone.

Anoxygenic photosynthesis

It gets excited, then passes the electron to a series of proteins. The last electron acceptor donates the electron back to the once excited electron donor. The only thing that evolved is P870. Everything else was already present. ATP and NADPH are required for photosynthesis. NADH = catabolic. NADPH = anabolic. ETC's can be run backwards. We can push electrons from Q to NADH to form NADPH. Cyclic = electrons are reused over and over again. If you make NADPH, you remove electrons from the cycle. You have to find an external electron source now. H2X is used as a donor. These are purple sulfur bacteria because they use sulfur as an external electron source. The reaction proceeds in the normal direction, stops at Q, then goes backwards to NADH. Reverse electron flow. First type of photosynthesis evolved. Not efficient.

AP site

Known as: apurinic/apyrimidinic site or an abasic site. A position in DNA where there is no base attached to the sugar of the backbone. No nitrogenous base exists in the region. Energy is required to cut the backbone of DNA. A location in DNA (also in RNA but much less likely) that has neither a purine nor a pyrimidine base.

Diagram: translation

Large subunit attaches. tRNA attaches to the A site. Everything moves over.

Microtubules

Largest component. Found throughout the cytoplasm. Made of globular protein subunits called alpha-tubulin and beta-tubulin. Found in some bacteria. Nucleation event: the tubulin subunits bind to GTP, causing the formation of the microtubule to begin. GTP becomes hydrolyzed by beta-tubulin to form GDP. Tubulin bound to GDP is less structurally strong. Polarity (start and end) exists. Beta-tubulin of one subunit contacts the alpha-tubulin on another. Can elongate at the + and - ends, but the elongation at the + end is more rapid. Help cell resist compression, provide a track along wihich vesicles move through the cell, pull replicated chromosomes to opposite ends of a dividing cell, and are the structural elements of flagella, cilia, and centrioles (which are perpendicular bodies that form the centrosome).

Leading and lagging strand

Leading strand: Strand can be synthesized continuously. 5' to 3'. Lagging strand: Is synthesized through a series of RNA priming and DNA synthesis events into short segments called Okazaki fragments. 5' to 3'. Polymerization occurs in the opposite direction that helicase, or the front of the replication fork, is traveling. The initiation of synthesis of each Okazaki fragment requires a primase to synthesize an RNA primer, and each of these RNA primers must be removed and replaced with DNA nucleotides by a different DNA polymerase. Covalent bonds between each Okazaki fragment must be formed from DNA ligase.

Telomerase

Lengthens the pre-existing parent strand (with "junk" DNA). Primase will place an RNA primer and DNA polymerase III will add the complementary bases on the daughter strand. It contains an RNA template for a repeated sequence (5'-TTAGGG-3' in humans) and catalyzes polymerization of an "extension" to the single-stranded "overhang" on the lagging strand.

Termination in archaea

Less understood, though similarities exist with the other two domains.

Calvin Cycle

Light-independent. Occurs in the stroma. Products: ATP, NADPH, G3P. Three phases: 1. Carbon fixation. Carbon fixation is the process of taking carbons from inorganic molecules, such as carbon dioxide, and using them to generate organic molecules such as glucose (a sugar). 2. Reduction. 3. Regeneration of ribulose.

Early history of earth

Low concentration of molecular oxygen. Subject to strong radiation. First organisms lived in areas where they were protected from radiation (ocean depths or beneath the Earth's surface). High temperatures, volcanic activity. Mutagenic radiation from the sun. Anoxic atmosphere during the first two billion years. Therefore, only anaerobic organisms existed. Phototrophs appeared within one billion years of the Earth's formation. Cyanobacteria evolved one billion years later. Developed more efficient oxygen utilized catabolic pathways. Increased colonization of land. O2 was converted to ozone, which protected organisms from the mutagenic sun rays. Bacteria diverged from common ancestral species between 2.5 and 3.2 billion years ago, whereas archaea diverged earlier: between 3.1 and 4.1 billion years ago. Early bacteria had to resist drying out and had to evolve means to grow in an anoxic environment.

Intermediate filaments

Made of several strands of fibrous proteins that are wound together. Size is in between the microfilaments and larger microtubules. Most diverse group of cytoskeletal elements. Contain keratin. No role in cell movement. Role is only structural. They bear tension, maintain the shape of the cell, and anchor the nucleus and other organelles in place.

What do single cells need to be able to do?

Make proteins. Grow and divide (reproduce). Metabolize. Move. Flagella, cilia, amoeboid. Amoeba are single celled predators that use the actin filaments of their cytoskeletons to move. Communicate with the environment.

RNA molecules

Many different kinds of functional RNA molecules can be made, not only coding genes. microRNA, ribosomal RNA, and transfer RNA can all be made. RNA has flexibility in its structure. It can hence be specialized. Transcription does not always make a protein.

Direct chemical reversal

Methyl residue can be removed. No excision of the DNA backbone and no energy is needed.

Microfilaments and actin

Microfilaments are composed of actin. They are the narrowest fibers, and form into two intertwined strands. Actin is very abundant. Actin amino acid sequence is conserved and has barely changed. Actin can be either a free monomer called G-actin or part of a polymer microfilament called F-actin; f = filamentous). Actin must be bound to ATP to assemble into its filamentous form. Actin filament must have polarity (two distinct ends: + and - end). + end = actin subunits are added onto the elongating filament. - end = actin subunits disassemble and fall off the filament. Assembly and disassembly is controlled by the ATP to ADP ratio. Actin participates in muscle contraction, cell motility, cytokinesis during cell division, vesicle and organelle movement, and the maintenance of cell shape. Actin filaments serve as as a track for motor proteins called myosins. Elongation of actin filaments can't occur.

Dynein and kinesin

Microtubules can be thought of as railroad tracks that extend from the nucleus to the cell membrane. They connect to organelles, the cytoplasmic membrane, and more. Proteins are asymmetrical and have a polarity. Microtubules have polarity (which has nothing to do with charge). The polarity involves the + and - end. Polarity is dependent on hydrogen bonds. There are two classes of motor proteins: kinesin and dynein. Kinesin goes from - to +. Dynein goes from + to - (towards the nucleus). The motor proteins read the polarity of the microtubules. Bacteria don't have these systems; they use diffusion.

Coordinated division

Mitochondria and chloroplasts have their own genomes. This isn't enough for an organism to live on its own. The nuclear genome began to take over the functions of the endosymbiont so that it become reliant on the host cell.

Kinesins

Motor-protein complexes that walk along the microtubules and are involved in vesicle transport. Polarity: moves from the - end to the + end, which is different from dyneins. Movement requires the hydrolysis of ATP. Moves away from the nucleus. Movement is often from the center of the cell towards the plasma membrane. Anterograde/orthograde transport. Involved in vesicle movement and chromosome movement during cell division. Structure is similar to dyneins. Motor subunits form a protein dimer that binds to light chains.

Redundancy

Multiple codons code for the same amino acid. The code is not ambiguous. If you are given a codon, you always know which amino acid it codes for.

Kinesin continued

Neck linker is flexible and connects the two. Red portion. ADP is bound to move the blue parts. The feet bind to the microtubule. ATP then binds, and swings the back leg. Two ATPs are involved a full swing of both feet. One foot moving costs one ATP.

Requirements of an intracellular network

Network needs to be extensive. Needs to be flexible. Needs to adapt to a growing cell, a dividing cell, and a cell that physically moves. Strong and able to withstand pressure. Composed of different fibers that have specific functions. Fibers need to have directionality (a clear start and end). Fibers need to work with proteins that can convert chemical energy into kinetic energy to transport compounds along the fibers.

Basic DNA notes

Nitrogenous bases store genetic information. Uracil replaces thymine. Uracil is a pyrimidine. Purines have two rings. Pyrimidines have one. 5' end is analogous to the N-terminus. the 3' end is analogous to the C terminus. DNA is antiparallel. Phosphate groups in DNA are negatively charged, giving DNA and RNA an overall negative charge. Which bases can form hydrogen bonds with each other? Adenine and thymine (DNA). Adenine and uracil (RNA). Guanine and cytosine (DNA & RNA).

Telomerase continued

Not active in most somatic cells. As telomeres shorten, the cell is signaled to stop dividing in order to preserve the ends of the DNA. Most somatic cells don't divide (quiescence). Quiescence is the reversible state of a cell in which it does not divide but retains the ability to re-enter cell proliferation. Cells still have the capacity to divide, but prefer not to. Senescence is a process by which a cell ages and permanently stops dividing but does not die.

Non-cyclic photophosporylation

Note: only cytochrome b6f and PSII translocate protons across the thylakoid membrane. PSI cannot. When P680 absorbs a photon, an electron is excited from the ground state into an excited state. This is denoted by P680*, which is a good reducing agent. P680* will transfer the electron to oxidized pheophytin. This is the reaction: P680* + pheophytin (oxidized) → P680⁺ + pheophytin (reduced). P680* has lost an electron and is now P680⁺, a very strong oxidizing agent. P680⁺ will oxidize water, which replenishes the electron on P680⁺. Therefore, P680⁺ has become reduced. This is necessary so that P680 can absorb another photon and exit an electron to transfer to pheophytin again.

Nucleosides vs. nucleotides

Nucleosides have a hydroxyl group connected to the 5' carbon, instead of a phosphate group.

Nucleotide Excision Repair (NER)

Nucleotide excision repair enzymes replace incorrect bases by making a cut on both the 3' and 5' ends of the incorrect base. The entire segment of DNA is removed and replaced with correctly paired nucleotides by the action of a DNA polymerase. Once the bases are filled in, it seals the remaining gaps with a phosphodiester linkage catalyzed by the enzyme DNA ligase. This repair mechanism is often employed when UV exposure causes the formation of pyrimidine dimers.

Mutations

Occur during DNA replication or through environmental exposure to chemical mutagens or radiation. Changes occur at the level of single nucleotides.

Phosphodiester bond

Occurs between the oxygen atom of the 3' ribose sugar and the phosphorous atom of the phosphate group. Polar bond.

Coupled transcription and translation

Occurs in bacteria and archaea. RNA polymerase transcribes RNA directly into the cytoplasm. Ribosomes can bind to the mRNA even when transcription is still occurring. The synthesis of the mRNA transcript happens in the 5' to 3' direction and translation happens in the 5' to 3' direction. Coupling can occur because transcription and translation occur in the same compartment and because they occur in the same direction (5' to 3').

Transcription in bacteria and archaea

Occurs in the cytoplasm. Translation often starts before transcription has finished. mRNA is used as the template for a protein before it produces the entire mRNA.

Transcription overview

Occurs in the nucleus in eukaryotes and in the cytoplasm in archaea and bacteria. Three phases: initiation, elongation, and termination. Def. The process of creating a RNA copy of a segment of DNA.

Transcription in eukaryotes

Occurs in the nucleus. mRNA is completed before translation. There is time to adjust or edit the mRNA before translation starts. This can extend the lifespan of the mRNA or alter the protein product that will be produced from the mRNA.

Initiation of replication

Origins of replication exist. To break base stacking interactions and hydrogen bonds, energy is required (endergonic). Proteins called initiators can bind DNA at or very near origins of replication. The interaction between this protein and DNA destabilizes the double helix and recruits other proteins. DNA helicase is a multi-subunit protein that couples the exergonic hydrolysis of ATP to the unwinding of the DNA double helix (endergonic). Primase and DNA polymerase are also used during initiation. Replication forks are Y-shaped structures in the DNA. For any replication event, two replication forks can form at each origin of replication, extending in both directions. Multiple origins of replication exist in eukaryotic chromosomes. E. coli only has one, however.

Practice question: coupled vs. uncoupled transcription and translation

Other differences between eukaryotes and prokaryotes: RNA must be transported to the cytoplasm from the nucleus in eukaryotes. Prokaryotes don't have a nucleus.

Origins of oxygen

Oxygen-rich environments were localized. Organisms that were anaerobic had to remain in oxygen-free environments.

Diagram: replication

Parent strands are antiparallel.

Oxygenic photosynthesis equation

Photosynthesis requires energy to occur. It is hence endergonic and unfavorable.

Cyclic photophosphorylation

Photosystem II is not involved. It is pictured here, but is not used.

Polymerization

Polymerization of nucleic acids occurs in the 5' to 3' direction. Polymerization depends on two functional groups (the 3' OH on the hexose sugar and the 5' phosphate group) in order for a dehydration synthesis reaction to occur. Polymerization extends the phosphate backbone.

Aminoacyl tRNA Synthetases

Pre-tRNA synthesis by RNA polymerase III creates the RNA portion of the adaptor molecule. The amino acid is added later, once the tRNA is processed and exported into the cytoplasm. tRNA charging involves the linkage of an amino acid and its correct tRNA molecule. This is done by a group of enzymes called aminoacyl tRNA synthetases. At least one of these enzymes exists for each of the 20 amino acids. These enzymes first bind and hydrolyze ATP to catalyze a high-energy bond between an amino acid and adenosine monophosphate (AMP). This process expels a pyrophosphate molecule. The activated amino acid is then transferred to the tRNA and AMP is released.

Telomeres

Protect the ends of chromosomes. In humans, telomeres consist of repeats of TTAGGG, which can be repeated ~1000 times. Repeats tend to consist of six base pairs.

Dyneins

Protein complex that functions as a molecular motor. Converts the chemical energy of ATP hydrolysis into the mechanical energy of movement to walk along the microtubule while carrying a vesicle. Walk from the + end to the - end. Towards the nucleus. They are "minus end directed motors." Retrograde transport: vesicular transport. Moves along the microtubule and hydrolyzes ATP with each step. Move organelles, move chromosomes during cell division, and transport cargo such as the movement of vesicles made by the ER, endosomes, and lysosomes. Axonemal dyneins are motor proteins used in the sliding of microtubules in the axonemes of cilia and flagella in eukaryotic cells.

Posttranslational modifications

Proteins can be cleaved into small fragments or modified. Enzymes within the Golgi can read these signals.

Origins of the cytoskeleton

Proteins in bacteria are homologous to actin. Tubulin is related to FtsZ in bacteria. This protein is involved in cytokinesis in bacteria and involves the pinching of the plasma membrane. MreB have a weak homology with actin, but it is still present.

RNA

RNA is composed of nucleotide triphosphates that are composed of a ribose sugar, a nitrogenous base, and three phosphate groups. Contain uridine (nucleotide's name), which contains a uracil nitrogenous base (instead of thymine). Thymidine is the nucleotide that contains thymine. Uracil and thymine are structurally similar. Uracil lacks a methyl (CH3) functional group, while thymine has this methyl group.

Transcription: elongation

RNA polymerase proceeds along the DNA template. Adds nucleotides by base pairing with the DNA template in a manner similar to DNA replication. However, the RNA strand that is synthesized does not remain bound to the DNA template. DNA is unwound ahead of RNA polymerase and rewound behind it. Direction of synthesis: 5' to 3'. mRNA is synthesized in this step.

Transcription

RNA polymerase recognizes a promoter to initiate transcription. RNA polymerase generates a new strand. RNA polymerase recognizes a combination sequence. The RNA molecule and RNA polymerase are released.

Review: 3' overhang

RNA primer at the end of the lagging strand is removed, creating a 3' overhang. There is no 3' OH for DNA polymerase to fill in the gap. Telomerase can extend this 3' overhang.

Topoisomerase

Reduces supercoiling by cutting the backbone and allow the DNA to move more freely, entering a relaxed state.

Telomeres

Repetitive sequences that nearly all eukaryotes have. Non-coding fragments that act as replication buffers and are shortened with each round of DNA replication instead of critical genes.

DNA Polymerase III

Responsible for synthesizing daughter strands. Moves along the template strand from the 3' to 5' direction. Synthesizes the daughter strand in the 5' to 3' direction.

Central dogma

Reverse transcription makes DNA based on a RNA sequence.

Practice question: mutations

Ribosome binding site needs to be between the promoter and the initiation site. Translation signals come after the transcription signals. Come after promoter and transcription initiation site. Ribosomes only care about the binding site. If a mutation is made at a promoter, RNA polymerase won't bind to it, no mRNA is made and no protein is made. The gene could be overexpressed (can be harmful if you are wasting energy to make more than you need). Thirdly, nothing could happen at all. Three possibilities (increase, decrease, or nothing). Much more likely to prevent activity than to enhance activity.

Exceptions to the universal genetic code

Selenocystine is another amino acid that is often found in bacteria.

Bacteria and archaea

Similarities: Both bacteria and archaea lack a membrane bound nucleus and membrane-bound organelles, which are hallmarks of eukaryotes. They face similar problems, such as the transport of nutrients into the cell, the removal of waste material from the cell, and the need to respond to rapid local environmental changes. Most common shapes: cocci (spherical), bacilli (rodshaped), and spirilli (spiral-shaped). Smaller than eukaryotes. Both are unicellular. Contain a phospholipid membrane. Lack nucleus (nucleoid instead). Genome: a single covalently closed circular double stranded DNA molecule. However, some bacteria have linear chromosomes, and some bacteria and archaea have more than one chromosome or small non-essential circular replicating elements of DNA called plasmids. Contain a cytoplasm and a cytosol. Most contain cell walls. They are ubiquitous (found everywhere). Bacterial cells outnumber human body cells by about ten to one. Drive the evolution of new ecosystems. Essential for creating new biomolecules.

Direct chemical reversal

Simplest form of DNA repair and the most energy efficient. Does not require a reference template. Does not involve the breaking of the phosphodiester backbone of DNA. Perhaps the most frequent cause of point mutations in humans is the spontaneous addition of a methyl group (CH3-) (an example of alkylation) to Cs followed by deamination to a T. Most of these changes are repaired by enzymes, called DNA glycosylases, that remove the mismatched T restoring the correct C. This is done without the need to break the DNA backbone.

Alternative splicing

Some exons are included and some are removed. Different proteins can be made. This is common in eukaryotes. One gene can hence encode several proteins. Provides flexibility. Different forms may be required by different cell types. Evolutionarily, these modifications may provide a selective advantage.

Spliceosome

Splicing is mediated by spliceosomes, which is an ribonucleoprotein complex that contains RNA. Based on base complementarity, the spliceosome can find a specific site to splice out. Once things are cut out, it becomes a snRNP (small nuclear ribonucleoprotein). A loop is created.

Where is telomerase active?

Stem cells/germ cells in embryos and adult testes. Note that germ cells don't proliferate in adult ovaries. Cancer cells can proliferate forever. No control over division. Telomerase is not maintained.

Diagram: translation

Stop codons don't have a tRNA. Instead, they have a release factor. It hydrolyze the bond between the tRNA and the protein. Very few free ribosomes in the cell. Most are being used. Free floating ribosomes is a signal that there are too many ribosomes, which inhibits the production of ribosomes.

Translation termination

Stop codons: UAA, UAG, and UGA. When a stop codon is encountered, tRNA molecules stop entering the A site. Instead, a release factor binds to the complex. This destabilizes the translational machinery and prompts the release of the polypeptide and the dissociation of the ribosome subunits from the mRNA. After many ribosomes have used the same mRNA for translation, the mRNA is eventually degraded and the nucleotides are recycled for use in transcription.

tRNAs

Structural RNA molecules that were transcribed from genes. 40-60 types of tRNAs exist in the cytoplasm. Serving as adaptors, specific tRNAs bind to the sequences on the mRNA template and add the corresponding amino acid to the polypeptide chain. 64 possible mRNA codons (contain uracil instead of thymine). 3 specify termination and 61 specify the addition of amino acids to the polypeptide chain. Of the 61 amino acid tRNAs, the AUG codon encodes the initiation of translation. Each tRNA anticodon can base pair with one of the mRNA codons and add an amino acid or terminate translation. The anticodons also contain U instead of T.

Double helix

Structure was identified by Rosalind Franklin in the 1950s using x-ray crystallography. Watson and Crick were also involved. Reported the structure in Nature. Took twenty years to confirm this structure. Rosalind Franklin passed away from ovarian cancer.

CrashCourse: DNA replication

Summary: DNA is the instructions for life. 46 chromosomes that are held together by proteins. Nucleic acids are one of the four macromolecules. DNA is made of nucleotides, composed of a sugar molecule, phosphate group, and nitrogenous base. DNA is found as a double helix. Sugars and phosphates bond in the backbone of DNA. 5' = phosphate is connected to 5' of the sugar molecule. 3' = phosphate is connected to the 3' of the sugar molecule. Nitrogenous bases are linked together by hydrogen bonds. Base pairs are complementary (A and T, and G and C). Chromosome 1 is the largest of our chromosomes. Roughly six billion base pairs in every cell. RNA has a sugar phosphate backbone with bases attached to it. Difference between DNA and RNA: the sugar is a ribose. RNA is a signal stranded molecule. Does not contain thymine (contains uracil instead). DNA was discovered in 1869. Rosalind Franklin used x-ray diffraction. Watson and Crick were also involved and only hinted at her contribution. Franklin was exposed to significant radiation. Helicase unwinds the double helix. Breaks hydrogen bonds. Replication fork is where the splitting starts. The top strand is the leading strand. The other strand is the lagging strand. The two strands are opposite in direction. DNA polymerase adds matching nucleotides to the leading strand. DNA polymerase requires a primer to hook onto. Only requires it once at the very beginning. DNA polymerase can only copy strands from the 5' to 3' direction. The lagging strand has to be copied in a series of segments. RNA primase gives DNA polymerase a starting point for DNA polymerase to bind to. These starting points are established at a number of segments. Okazaki fragments are each of the fragments that are synthesized in short bursts. The final enzyme is DNA ligase. 1 mistake for every 10 billion nucleotides. DNA polymerase can edit DNA and proofread.

DNA replication video

Summary: Both strands act as templates for the formation of new DNA molecules. Copying occurs at the replication fork (Y shaped structure where new DNA strands are synthesized). First step is the separation of the two strands by an enzyme called helicase. DNA is spun to unravel it. Strands are called 3' and 5'. 3' (leading strand) is used as a continuous template for the synthesis of the first daughter DNA helix. Lagging strand has the opposite orientation. Organized into Okazaki fragments, which are presented to a second enzyme. Synthesized backwards. Exposed strands of DNA are covered by protective binding proteins.

Promoter

TATA is the transcription start site. 10 base pairs. Recognized by sigma factor (protein). Part of the RNA polymerase. This is what recognizes specific sequences of the DNA. TATA box is conserved among eukaryotes and prokaryotes.

Protein sorting

Tags are used to designate where a protein is supposed to go. Usually takes the form of a short string of amino acids (signal peptide). A system is required to read and sort proteins. Proteins can identify the tag (signal peptide), bind to this tag, and direct the synthesis of the protein to the plasma membrane. This specifically occurs in prokaryotes. In eukaryotes, the reading and sorting steps start in the endoplasmic reticulum and proceed in the Golgi apparatus, where proteins are modified and packaged into vesicles bound for various parts of the cell.

Telomerase length, aging, and disease

Telomerase positive = activity is present. Telomerase negative = activity is deactivated. Egg and sperm cells are called germ cells, in contrast to the other cells of the body, which are called somatic cells.