bio 204 Chapter 1-5

What is the difference between a molecule and an element?
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What is the difference between a molecule and an element?
An element consists of only one type of atom and a molecule consists of multiple different atoms.
Know the usual number of bonds made by the following atoms a. Sulfur (S) b. Phosphorus (P) c. Oxygen (O) d. Nitrogen (N) e. Carbon (C) f. Hydrogen (H)
2,5,2,3,4,1
Combine each of the following elements with your choice of S, P, O, N, C, or H, using the proper number of covalent bonds. Draw the stick model of your molecule. Do this once to make a polar molecule, and once to make a nonpolar molecule.
IN FOLDER
Know how to recognize an unlikely molecule. For example (other examples are open season on quiz), which of these is unlikely in nature (and for each one, why?):O=O H-O-H H-C=C=O H=O
The third one doesn't molecule is unlikely because one of the carbons is only making 3 bonds and the fourth one doesn't work because H can't have two bonds.
Know the difference between covalent and hydrogen bonds.
Covalent bonds are strong intramolecular forces that strongly hold molecules together and share electrons. Hydrogen bonds on the other hand are weak intermolecular attractions.
How are covalent and hydrogen bonds formed?
Covalent bonds are formed when atoms of two or more come together and share their electrons. These atoms come together to seek stability by either gaining or losing an electron. Hydrogen bonds are formed when a partially positive hydrogen gets attracted to a partially negative charged atom.
What is covalent and hydrogen bonds relative strength?
Covalent bonds are stronger than hydrogen bonds
Give an example of a covalent and hydrogen bond.
An example of a covalent bonds would be CO2.An example of a hydrogen bond would be when a water molecule is bonded with another water molecule.
Which kind of bond gives water its many unique qualities?
Hydrogen bonding
Be able to draw (with the correct number of covalent bonds) a polar molecule as well as a non-polar molecule, and describe what makes each polar or non-polar.
IN FOLDER
Name and describe three of the five unique characteristics of water.Heat capacity: hydrogen bonds store energy of heating/cooling Ice formation: H bonds separate atoms of water more in solid (ice) than in liquid state. → ice floats Heat of vaporization: H bonds retard evaporation. Evaporation cools surrounding atmosphere Cohesion: water molecules stay together in face of (gravity, wind, making drops, waves) Polarity: water molecules attracted to other polar compounds and ionsChemistry of water. Draw three water molecules as they would tend to exist near each other in nature.IN FOLDERName 4 of the 5 most common molecules (these are small molecules, not biomolecules) on prebiotic earth, the raw materials for the primordial soup (the starting solution of the Miller-Urey experiments).Hydrogen gas (H2), ammonia (NH3), water (H2O), methane (CH4), and perhaps carbon dioxide (CO2)What kind of molecules were predicted by Oparin to form in the high-energy reducing atmosphere of pre-biotic earth?monosaccharides, fatty acids/glycerol, amino acids, and nucleic acidsName the four main types of biomoleculescarbohydrates, fats, proteins, and nucleic acidsGiven elements in the first three rows of the periodic table: Be able to draw the electron distributions in shells and from these electron distributions, be able to predict the bonds that would form between elementsFOLDERWhat were the important characteristics of the Miller-Urey experiment regarding pre-biotic earth? How would the addition of an oxygenated environment change the outcome of the experiment?Intense electrical and high heat energy that was similar to what was found on early earth and a lack of oxygen. The addition of an oxygenated environment would change the outcome by reducing the amount of polymerization that could have occurred in the experiment.Polymerization (dehydration; condensation) and depolymerization (hydrolysis) and all four biomolecules occurred chaotically in the primordial soup. What process is the only way a chemical form can persist in this chaos?In order for a chemical form to persist in this chaos is through the process of replication. The molecule can repeatedly make a replica of itself, so it will be preserved.Name (one-letter abbreviation) the four "charged" nucleosides that were the building blocks of the first RNA molecules.A, U, G, C (adenine, uracil, guanine, cytosine)In one or two sentences, describe the steps of a dehydration condensation reaction, and include the initial reactants and final products. Ditto for hydrolysis.Dehydration condensation is when water molecules are removed and a new bond is formed. Since water molecules are being removed, this requires energy input. The initial reactants for condensation are monomers and the final product is the polymer, which are monomers linked up. Hydrolysis is when water molecules are added in order to break a bond. This process produces an energy output. The initial reactant is a polymer and the products are smaller polymers or monomers.What is the general formula for a carbohydrate monomer? A lipid? A protein?The general formula for a carbohydrate monomer is CnH2nOn. A lipid is mainly consumed of H and C and rarely any O's. Protein general formula is C-C-N.Be able to either name or recognize a carbohydrate, protein, or nucleic acid monomer, dimer, and polymer.Monomer = one monosaccharide Dimer = two monosaccharides Polymer = three or more monosaccharidesWhat are the defining characteristics of a lipid?Lipids mostly contain carbon and hydrogens and not as many oxygens, which is why they are usually hydrophobic and insoluble in water. Lipids have no particular ratio or shape. Some examples include fats, oils, and wax.Be able to recognize the structure of triglyceride and a phospholipid when you see them.Triglyceride does not have many oxygens and phospholipids have a polar head and a two non-polar tails.What structural feature of an amino acid is responsible for the huge diversity in protein shapes?The R-group. They help amino acids stay in solution where they can interact with other solutes, and they affect the amino acid's chemical reactivityHave a general understanding of what is meant by primary, secondary, tertiary, and quaternary structure of a protein. Which bonds are relatively strong? Relatively weak?Primary structure contains peptide bonds which are strong and secondary, tertiary, and quaternary structure contains H bonds, which are relatively weak.Given one of the types of molecules shown in lecture, be able to predict whether it will be hydrophobic or hydrophilic (or a little of each J). Be able to explain your reasoning.Hydrophobic does not contain a lot of oxygen and hydrophilic does contain a lot of oxygen.Name (one-letter abbreviation) the four "charged" nucleosides that were the building blocks of the first RNA moleculesA, U, G, CKnow how to draw the internal ribose and how to number its carbon molecules.FOLDERKnow how to position the three phosphates (circled "P" is fine) on the appropriate carbon of the ribose.On the 5th carbon of the riboseKnow which carbon of the ribose the base attaches to.On the 1st carbon of the riboseWhich part of these charged nucleosides provides the energy to drive polymerization?The breaking off of the two phosphates is what provides the energy necessary to drive polymerizationWhich part of a growing RNA polymer does a "charged" nucleotide (the triphosphate version) attack?It attacks the 3' OH group by attaching their first phosphate thereWhat's the term for a protein monomer?Amino acidKnow what type of bonds (hydrogen or covalent) hold the string of amino acids together in a protein (primary structure). Know whether these bonds strong or weak. And know the name for this type of bond occurring specifically between amino acids.Amino acids are strung together by peptide bonds which is a covalent bond and strong.In template-directed polymerization, which (can be more than 1) of the following involve hydrogen bonding, and which involve covalent bonding? a. Breaking of two phosphates off of the 5' C of an incoming nucleotide. b. Attraction of A to U, and G to C. c. Addition of new monomer to the 3' C of the end of a growing polymer of RNA d. The process that determines the complementary base pairsCovalent bonding Hydrogen bonding Covalent bonding Hydrogen bondingWhat ingredients did Spiegelman include in the test tube at the very start of his experiment.A single "species" of RNA that was about 3000 nucleotides long, a protein enzyme that catalyzes the replication of RNA, and all four of the RNA monomers.Describe in words what a catalyst does.A catalyst speeds up a particular chemical reaction.What is so important about three-dimensional shape of RNA of protein?It allows it to catalyze certain chemical reactions and it makes the breaking of hydrogen bonds easier and more efficient.What gives any single-stranded RNA molecule its three-dimensional shape?The pattern of its internal base pairings.What is a "ribozyme"?A ribozyme is a RNA enzyme that is capable of catalyzing reactions.The persistence delivered by replication is not sufficient for evolution of chemical form. What else is needed? Why?Mutations are needed in order to find out what new strands of RNA replicate the fastest.Know and be able to distinguish the 4 different kinds of mutation discussed in lecture.Substitutions, additions, deletions, and duplications.Starting with a 5 nucleotide polymer of RNA as a template, describe template directed polymerization of RNA. Use sketches representing three successive time points as RNA is polymerized along the template strand: What is the relative role of hydrogen versus covalent bonds? Use the words, 3' carbon, 5' carbon, polymerization, triphosphate versus monophosphate nucleotide, monomer, hydrogen bonds, covalent bonds A-U, G-C.Polymerization occurs one nucleotide at a time. It grows in the 3' carbon direction and the 5' carbon is distinguished by the phosphates. A single monomer is attracted to a polymer because of the weak hydrogen bonds formed between complementary base pairs (A-U, G-C) these hydrogen bonds really set the molecule up for polymerization by making sure that each base goes to its complement. Two phosphates in the triphosphate molecule break off along with a water. This gives the energy necessary for a covalent bond to form between the phosphate of one ribose and another ribose. This process continues one nucleotide at a time until a complement is made of the original RNA strand. However, this complement isn't a replica of the original strand, rather it is the complete opposite. Therefore a complement is made of the complement strand which is a replica of the original strand. This whole process is catalyzed by the RNA molecule acting as a self-catalyst.Sol Spiegelman performed experiments in the 1970's on RNA. He started with a test tube with salt water. What additional ingredients did he add?Single species of RNA that was about 3000 nucleotides long.After several minutes, Spiegelman put a sample from the first test tube into a second one. List the ingredients present in the second test tube before he transferred the contents of the first test tube.Replicase and nucleotidesWhat three hypotheses were supported by Spiegelman's experiment?RNA replication was imperfect, RNA will replicate outside the cell, and smaller RNA will be replicated faster.What part of this experimental set-up was least like what we think happened in the primordial soup leading to RNA replication?Addition of replicaseHow did the contents of the final test tube differ from the contents of the first?The contents of the last test tube differed from the first because the last test tubes relative population was steadily increasing, while the first rapidly increased then dramatically decreased There were much shorter strands of RNA in the last tube than in the first tubeBe able to make a graph that describes the role of a catalyst in any chemical reaction. You should be able to graphically depict an exergonic or endergonic reaction. This graph should show free energy on the vertical axis and progress of reaction on the horizontal axis. Draw one curve without a catalyst and superimpose another with a catalyst. Your graph should identify the following: substrates (reactants), products, change in free energy (deltaG), energy of activation (EA).How does an enzyme work: Include active site, induced fit, reactants, products, what hydrogen and covalent bonds are made and broken.The substrates or reactants enters into the enzyme's active site which then changes conformation to bind the enzyme with a hydrogen bond which is called induced fit. Once the catalyzed chemical reaction has occurred a product is released breaking the hydrogen bonds but keeping the covalently bonded product together from the active site and it goes back to its original conformation.Based on a graph, be able to tell whether a reaction is exergonic or endergonic.Endergonic energy starts low and ends high. Exergonic energy starts high and ends low.Be able to draw a graph containing the progress of a reaction that illustrates how an enzyme works, both for exergonic and endergonic reactionsPICTUREBe able to design an RNA molecule that can take a particular shape. Draw that molecule in its linear, and 3-dimensional form.PICTUREName and describe the function of the type of ribozyme that is thought to have accelerated replication of RNA polymers in the primordial soup. Explain how this ribozyme was able to speed up RNA replication.RNA replicase is thought to be capable of speeding up replication by catalyzing polymerization. It slides up to another RNA polymer and steadies incoming RNA monomers that are hydrogen bonding to the temple chain. The replicase decreases energy of activation making polymerization faster.Explain what we mean when we say that the newly forming RNA strand in template-directed RNA synthesis is "antiparallel".Antiparallel is a term used to describe opposite orientations of the 2 strands of a RNA or DNA helix; the 5' end aligns with the 3' endConnecting with the previous chapter, you should be able to describe/draw the processes of both non-template directed AND template directed RNA polymerization.Non-template directed RNA polymerization is free from nucleotides bonding to to one another (like the primordial soup). Template directed RNA polymerization is a chain of nucleotides that are bonded with the appropriate RNA monomers in an anti-parallel fashion. Two phosphates group to provide energy for a covalent bond to occur between a ribose and phosphate (5'-3'). Template directed RNA polymerization involves replication.Explain how RNA replicates itself. Use the terms: nucleotide, hydrogen bond, A-U, G-C, complement, complement of the complement, replica.In order for RNA to survive in a competitive atmosphere, they must create many replicas. To start, a complement is made using nucleotides. Nucleotides only form hydrogen bonds with their complements, such as A-U and G-C. The starter RNA has a complement of a complement is made. The two-step process replicates the original RNA strand, with an identical nucleotide sequence.Be able to identify the partial charges (positive or negative) on a stick diagram of each of the 4 nucleotides that contribute to the Watson-Crick base pairing. Be able to use those partial charges to predict to which nucleotide any given (unnamed) nucleotide would be bound by hydrogen bonds.ON = partial negative SPCH = partial negativeWhich type of bond is intramolecular and which type is intermolecular?Intramolecular= covalent Intermolecular= hydrogenBe able to draw (with the correct number of covalent bonds) a polar molecule as well as a non-polar molecule and describe what makes each polar or non-polar.O2 is a nonpolar molecule because each oxygen has the same electron affinity and therefore there is equal sharing of the electrons in the covalent bonds and the molecule has no partial charges. Water is a polar molecule because oxygen has a much stronger electron affinity than hydrogen, therefore the electrons are closer to the oxygen than the hydrogens in the covalent bonds. This creates a partial negative charge on the oxygen and a partial positive charge on each hydrogen.List the characteristics of an amphipathic molecule. Name one amphipathic molecule.An amphipathic molecule is a molecule that has a polar region that is hydrophilic and a nonpolar region that is hydrophobic. Triglyceride is an example of an amphipathic molecule. The three fatty acids make up the nonpolar, hydrophilic end and a glycerol molecule makes up the polar, hydrophobic end. Phosopholipids are another example of amphipathic molecules. The phosphate head makes up the polar, hydrophilic region and the two fatty acids make up the nonpolar, hydrophobic tails.Define liposome and describe how liposomes are made.A liposome is an amphipathic molecule in the shape of a sphere with water trapped inside it. When an amphipathic molecule is added to turbulent water, it will spontaneously form itself into a liposome.Name and describe the problem that the evolution of a membrane solved.The evolution of a membrane solved the diffusion crisis. Membranes are selectively permeable, so they can replicate outside the cell.Describe the circumstances (use the appropriate words from this list: solute, inside, outside, hyperosmotic, hypoosmotic, flow of water) that would a. lyse a red blood cell b. shrink a red blood cell c. make a red blood cell happy (neither shrink nor swell/lyse).a. When the fluid outside the red blood cell is hypoosmotic, there are more solutes inside the cell, water will flow towards the solutes in the cell, causing the cell to swell and eventually burst (lyse). b. When the fluid outside the red blood cell is hyperosmotic, there are more solutes outside the cell than inside the cell, causing water to leave the cell towards the solutes outside the cell and shrink. c. When the fluid outside the red blood cell is isosmotic to the fluid inside the cell, there is the same concentration of solutes inside and outside of the cell, there is no net flow of water, so cell remains the same size.Describe what is meant by the "osmosis crisis." What, exactly, caused it?Osmosis crisis refers to the problem that water will flow into a cell due to osmosis, causing it to swell and eventually lyse. This is because of the large RNA molecules trapped inside the fatty acid liposomes, meaning that they could not diffuse toward lower concentrations outside at all. Since there are a ton of replicating RNA molecules and other solutes in the cell this increases the concentration, which means that water will tend to flow into a cell and newly replicated polymers remain trapped inside.Name the cellular structure evolved to solve the osmosis crisis. Describe how this structure solved this crisis, and name important energy molecule that was also required for this solution.The evolution of the proton pump solved the osmotic crisis of a cell. The proton pump evolved from a specific RNA molecule whose catalytic function was to pump protons. The energy for pumping protons out of the cell is supplied by ATP.Describe how natural selection works using the following words: replication, mutation, variation, competition, extinction.Mutations are caused during replication in the RNA creating polymorphisms amongst the RNA species. These mutations help diversify the population of RNA and create competition between the different species based on which one can replicate faster. Eventually, because of the competition, the species that are slower go extinct.Explain how a constraining micro-environment improves replication. Use the words, RNA nucleotides, RNA polymers, ribozyme replicase, diffusion.A catalyst, which is an RNA replicase, can catalyze the replication of more strands of RNA because the RNA strands are closer together higher density, which prevents diffusion. The higher concentration of RNA and catalyst improves replication and limits diffusion.Draw a fatty-acid membrane surrounding a liposome with the following labels: water, polar heads, non-polar tails.Define osmosis using the following words in your answer: solute, solvent, diffusion, semi-permeable membrane.Osmosis is the diffusion of water, which are solvent molecules, through a semi- permeable membrane to an area of high concentration to an area of low concentration in a direction that should equalize the solutes.Define diffusion (across a lipid bilayer)Diffusion is when a molecule finds itself in a higher concentration at one site it will move towards the less concentrated site. Specifically for the lipid bilayer, a molecule dissolves in the lipid bilayer, diffuses across it, and dissolves in the solution that's on the other side of the membrane.Know what types of molecules can diffuse across a phospholipid bilayer. Name some examples of each.Only small nonpolar molecules can diffuse freely through the phospholipid bilayer. Some examples include O2 and CO2Know what types of molecules can't diffuse across a phospholipid bilayer. Name some examples.Polar molecules are unable to diffuse through the lipid bilayer even if they are small enough. Some examples include H20 and H+Be able to answer diffusion and osmosis questions like the homework problems.Describe how active transport, facilitated transport and diffusion differ from one another. Name one protein associated with each of these mechanisms.Active transport: occurs against a concentration gradient by using energy from ATP and uses transmembrane proteins Facilitated transport: occurs through a concentration gradient and uses transmembrane proteins but does not require cellular energy Diffusion: substance passes between phospholipids and doesn't require a proteinKnow how to distinguish RNA from DNA, how to number the carbons on the sugar, and where (which Carbon) each part of the nucleotide is connected to.RNA contains ribose but DNA contains deoxyribose (where an OH is replaced by an H). Numbering the carbon is the same for RNA and DNA (right of O is C 1')Explain why DNA is a better template than RNA and why proteins are better catalysts than RNAs.DNA is a better template than RNA since the OH group on the 2' carbon is replaced with an H making the DNA more stable, and DNA prefers double-stranded form which also minimizes chemical damage. Proteins are better catalysts than RNAs since it has greater versatility and more range in structural differences. It's faster growing which means that it was more naturally selected.Know the name of the scientist from who an essential photograph for the discovery to the structure of DNA was stolen from.Rosalind FranklinKnow how to explain why DNA replication is semiconservative.DNA replication is a semi-conservative process, because when a new double-stranded DNA molecule is formed: One strand will be from the original template molecule. One strand will be newly synthesised.Know in which direction replication (of RNA or DNA) occurs.DNA and RNA replication only occurs in the 5' to 3' directionDescribe in simple words what each of the 5 enzymes that are involved in DNA synthesis do.Helicase: unwinds double helix Primase: polymerizes RNA "primers" on DNA template DNA Polymerase III: polymerizes new DNA and old DNA template DNA Polymerase I: removes RNA primer, and replaces with DNA DNA ligand: joins the ends of DNA polymersA figure in chapter 5 of the Primer depicts the "Central Dogma". Use the words protein, translation, transcription, information, RNA and DNA to explain the central dogma in words.The Central Dogma is a one-way transfer of information from DNA to protein. It utilizes a short piece of the long DNA molecule to direct polymerization of an RNA middle-man, called messenger RNA. Messenger RNA (mRNA) carries the code for the second step, which is to translate the mRNA into protein. This second step is called translation because it changes the chemical form from that of a string of mononucleotides (nucleic acid) to that of a string of amino acids (protein). Thus, the overall function of transcription and translation is to produce a protein from the DNA blueprintDuring the process of replication, compare and contrast the process by which the leading strand and the lagging strand are formed. What is the difference between how the leading strand and the lagging strand are polymerized? How does the direction of polymerization of a new strand relative to the direction of travel of the helicase clue you into which strand is leading and which is lagging?Leading strand- When the new strand's 3' OH is facing the helices unwinding the DNA this is a problem. After the primer starts, the DNA's polymerase III can carry on for millions of bases until it comes to the end of the DNA strand. Everything in the leading strand happens in 1 go. Goes with the helices Lagging strand- The growing strand has to face its 3' OH away from the helixes since the parent strand has its 3' OH facing toward the helices. Everything in the lagging strand happens multiple times (slower). the direction of the 3' end directs you to what strand is leading and what strand is lagging, also helicase runs WITH leading and AWAY from lagging.Be able to make a sketch and narrate in detail how replication proceeds on the leading strand using the following words (more or less in order of appearance): helicase, primase, 3' vs 5' carbon, RNA, DNA polymerase III, DNA polymerase I, DNA ligase.From the 5' phosphate to the 3' OH; helicase unwinds the double helix by breaking hydrogen bonds between the bases, primase synthesizes RNA primers which are needed so DNA polymerase has a 3' OH to attack; DNA polymerase III synthesizes and elongates the DNA, making nucleotides; DNA polymerase I erases the RNA primers and fills in gaps and makes h-bonds between the nucleotides; DNA ligase joins the ends of the DNA segments completing the covalent bonds in the sugar-phosphate backboneBe able to make a sketch and narrate in detail how replication proceeds on the leading strand at the level of the individual nucleotide using the following words (more or less in order of appearance): primase, 3' vs 5' carbon, RNA nucleotide, DNA polymerase III DNA nucleotide, DNA polymerase I, DNA ligase. Be sure to explicitly state how hydrogen and covalent bonds are made and broken for each step. This is like what you did on the replication worksheet in class.Polymerization of the lagging strand occurs anti-parallel of the of the leading strand. The lagging strand goes from 5' to 3'so replication occurs from 3' to 5'which is the opposite way and creates a "rocky" build. After helicase unwinds the double helix of DNA, Replication occurs in Okazaki fragments from 3' to 5.' For each fragment, primase lays down RNA primer first, thenDNA polymerase III carries on after the primer, DNA polymerase I replaces the RNA nucleotides with DNA, and finally DNA ligase binds all the DNA strands, including the adjacent fragments, togetherBe able to clearly sketch where and how Okazaki fragments are made. Use the words, polymerization, 3' vs 5' carbon, primase, primer, DNA polymerase 3, ligase, anti-parallel, Okazaki fragment, leading strand, lagging strand.When polymerization hasto run away from the helicase to unwind the DNA, Okazaki gragments come into play for DNA replication happens in short segments starting at the 3' facing the helicase and moving away from it. Primase lays down a RNA primer, DNA polymerase III carries on after the primer, DNA polymerase I replaces the RNA nucleotides with DNA. Finally, ligase binds all DNA strands, including the adjacent and antiparallel fragments together.In simple terms that your family and friends would understand, explain the important difference in function between transcription and replication? Even though they serve entirely different purposes, what is similar about transcription and replication?transcription: the process by which DNA is copied to mRNA which carries the information needed for protein synthesis replication: the process by which a double stranded DNA molecule copies and forms 2 separate but identical DNA molecules they are similar because they both involve copying DNA to produce another molecule of DNA, but they are different in the aspect that transcription requires information needed for protein synthesis and replication only involves the process of replication.Be able to make a sketch and narrate how transcription proceeds, using the following words (more or less in order of appearance): Promoter region, RNA polymerase, template strand, RNA triphosphate nucleotide, non-template strand, GC hairpin. Be sure to explicitly state how hydrogen and covalent bonds are made and broken for each step.The promoter region is in the template strand which is the starting point for where RNA polymerase starts. As helicase opens up RNA triphosphate nucleotides are laid down as the coding strand forms for amino acid. When the DNA strand comes closer to the active site then the GC hairpin forms causing RNA polymerase to stop running. When transcription stops, H-bonds are broken.Please narrate and make a sketch to describe how amino-acyl tRNA synthetase ("charger enzyme") places the correct amino acid onto tRNA. a. What are the three different kinds of reactants that the enzyme works with? b. What happens to those reactants (what are the products of the reaction)? Be sure to mention all hydrogen and covalent bonds made and broken.amino acid and ATP brought into active sites of CE. They are brought together by a hydrogen bond. ATP loses 2 phosphates (breaking covalent bonds) to provide energy to bind tRNA to AA. This bond is covalent. Charged tRNA is released by tRNA The charger enzyme covalently bonds each tRNA to its correct amino acid. The process uses ATP to preform hydrolysis to attach the a.a. to the top of the tRNA. A) tRNA, amino acids, ATP B) The amino acid, tRNA, and ATP are hydrogen bonded into the synthetase. The ATP is then converted into ADP plus phosphate which gives the energy necessary for a covalent bond to be formed between the amino acid and tRNA. The hydrogen bonds between the amino acid and tRNA are then broken off leaving us with the empty synthetase, the amino acid and tRNA covalently bonded together and ADP plus phosphateIf you were provided with the genetic code (in a table, like the in chapter 5 of the Primer), you should know how to translate any codon into an amino acid. Conversely, if you are given an amino acid, you should be able to write down a possible sequence of codon(s) for that amino acid. You should also be able to list all tRNAs that specify a particular amino acid.Please narrate and make a sketch to describe how translation proceeds, using the following words (more or less in order of appearance): ribosome, mRNA, codon, anti-codon, tRNA, AUG, Methionine, P-site, A-site, peptide bond, translocate, E-site, stop codon, release factor. Be sure to explicitly state how hydrogen and covalent bonds are made and broken for each step. Hint, use http://www.youtube.com/watch?v=D5vH4Q_tAkY to help you till you narrate the whole story without assistance.In translation a ribosome attaches to an mRNA strand. It begins when the codons are read. The P-site of the ribosome codon is AUG. The matching anti-codon (on tRNA molecule) and tRNA molecule enter the P-site and attach to the codon and mRNA strand. The next codon is UCA. It's anti-codon tRNA comes into the ribosome A-site. AUG's amino acid (methionine) breaks its covalent bond with its tRNA molecule and forms a new peptide bond with serene. After this, the ribosome translocates (moves over 3 nucleotides) to the new codon A-site CCG. The tRNA molecule in the E-site is ejected from the ribosome. This repeats until a stop codon appears.Describe 3 different ways that RNA has maintained its role as "middle-man" in the overall process of protein synthesis.mRNA- the middleman between DNA and protein tRNA- the middleman between the charger enzyme and the protein rRNA- the middleman between mRNA and the polypeptide chainKnow how to mutate mRNA in order to create the following types of mutations: silent, nonsense, missenseSilent: mutates by adding in a different base (ex: A instead of G) but it doesn't do anything to the amino acid Nonsense: leads to a premature stop Missense: change in codon leads to a change in amino acidKnow why the genetic code is considered to be both specific and redundant.Specific: a single codon never codes for more than one amino acid Redundant: multiple codons code for the same amino acidIn principle, how many different tRNA molecules are there?61 tRNAHow many different synthetases are used to prepare for translation?20 different charger enzymesTo how many different amino acids can a particular synthetase bind?Each charger enzyme can bind to only one amino acidTo how many different tRNA molecules can a particular synthetase bind?Each can bind to 1 of 6 tRNA's it recognizesName the evolutionary crisis that glycolysis solved and explain what caused that crisis.The energy crisis which was caused by the lack of ATP needed to power replication and the proton pumpName the new evolutionary crisis that glycolysis createdThe food crisis (glycolysis used all of the food which was glucose)Consider glycolysis as a whole, starting from when glucose is inside the cell. How many ATPs are made total?4Consider glycolysis as a whole, starting from when glucose is inside the cell. How many ATPs are invested2Consider glycolysis as a whole, starting from when glucose is inside the cell. How many ATP's does glycolysis of one glucose molecule net for the cell?2Consider glycolysis as a whole, starting from when glucose is inside the cell. Describe the reaction that replenishes NAD+. Name the reactants that get reduced and oxidized. What are the products and where do they go next?NAD+ gets replenished by the fermentation of pyruvate. The fermentation oxidizes the NADH becomes NAD+. Byproducts are lactate and ethanol. They are secreted from cell.Describe the sodium/potassium pump. What is pumped out, what is pumped in? Where does the energy come from? How can this pump help solve the osmosis problem if it is pumping solute both out and in?It pumps Na+ out and K+ in. 3 Na+ ions leave for every 2 K+ ions pumped in for a net flow of 1 ion. the energy comes from the primordial soup. This pump helped solve the osmosis crisis as it helped compensate for the high concentration of solutes, and change the concentration gradient outside the cell, as there was a net of more 3 Na+ outside of the cell.Explain how the sodium gradient achieved by the pump facilitates food acquisition?The co-transport canal allows for the capture of sugar from outside to inside is used as energy. It is able to do this because the concentration outside is higher.Know which side (in or out) of every living prokaryotic cell has more hydrogen, sodium,potassium, and calcium.The outside of the cell has more hydrogen, sodium, and calcium. The inside of the cell has more potassium.Explain the mechanism by which a cell establishes ionic gradients across its membrane and describe at least 1 way a cell can use ionic gradients.Remind yourself how the proton pump solved the osmosis crisis.The proton pump solved the osmosis crisis because RNA was replicating more quickly inside of the liposome due to the increased catalytic efficiency inside the cell. This caused a higher concentration of ions inside the cell than outside the cell, which would eventually cause the cell to lyse. When the proton pump evolved, it pumped out one hydrogen ion for every RNA strand, thus equalizing the ion concentration inside and outside the cell.What crisis does the proton pump cause?the proton pump caused the energy crisis because in order to pump the hydrogen ion out, it used ATP converted to ADP plus phosphate and the ATP was running outWhat solves the crisis caused by the proton pump?GlycolysisAn atom or molecule with reducing power tends to (choose one) gain / donate electrons?DonateAn atom or molecule that gains an electron is oxidized / reduced?ReducedAn atom or molecule that loses an electron is oxidized / reduced?OxidizedKnow the four ways we learned in lecture to identify which player in a redox reaction is being reduced, and which is being oxidized. And be able to apply them to equations like those on the in-class worksheet.X reduces Y: if Y... 1. Gains an electron 2. Gains H 3. Loses O 4. Charge is more negativeKnow how to assign oxidation numbers to C, H and O within a molecule.O= -2 H=1Use oxidation numbers to recognize which molecules (for example out of a set of single carbon molecules) are most reduced or oxidizedMore negative= more reduced More positive= more oxidizedUse sketches to help you describe the first phase of glycolysis (Mickey Mouse version of glycolysis). Start with glucose (not the detailed structure, just depict glucose as a circle as we did in lecture). What happens to the glucose molecule? Use the words, glucose, investment (what is invested?), phosphorylation, ATP, ADP, splitting, glyceraldehyde-3-phosphate.In the investment phase, the energy of ATP being converted into ADP was used to add phosphates to glucose, splitting into two phosphorylated 3-carbon molecules (G3P). More specifically, glucose is phosphorylated on both sides, and split into two 3-carbon molecules at the expense of ATP turning into ADP. Lastly, of the investment phase, the 3-carbon molecules are converted to G3P*Use sketches to describe the second phase of glycolysis (Mickey Mouse version of glycolysis). How does glyceraldehyde-3-phosphate get phosphorylated without ATP? Where exactly does the phosphate come from? Use the words, glyceraldehyde-3- phosphate, NAD+, NADH, reduction, oxidation, ATP, ADP, harvesting, pyruvate.1. When glucose becomes two molecules of glyceraldehyde-3-phosphate (G3P), the chemical transformation is creates a very high reducing power 2. With the high reducing power, G3P reduces NAD+ to NADH and NAD+ oxidizes G3P 3. From the reducing power, the G3P also phosphorylates without the use of ATP, therefore G3P has two phosphates instead of one. 4. These four phosphates are now harvested onto the two 3-carbon compounds onto 4 ADPs therefore creating 2 pyruvates In the second phase, G3P gives up an electron, causing NAD+ to be reduced to NADH. Thus, G3P was oxidized; the large difference in reducing power between the two molecules generates enough energy to add a phosphate to G3P without having to use ATP. This phosphorylation is the pivotal movement in the breakdown of glucose. It converts an oxidation reduction step into a phosphorylation that is immediately used in the harvesting phase. The rest of glycolysis involves harvesting the 4 phosphates from the two 3-carbon molecules onto 4 ADPs, thereby phosphorylating all of them to 4 ATPs, creating pyruvate.Draw an overall (net only) input output diagram of glycolysis. This is the bubble version of glycolysis. Include in your diagram pyruvate, NADH, NAD+, ADP, Pi, ATP, Glucose. Also include in your diagram where all the inputs come from and where all the outputs go.Net inputs; ADP + P (from proton pump) NAD+ (from fermentation), glucose (from primordial soup) Net outputs; ATP (to proton pump), pyruvate (to fermentation), NADH (to fermentation)Name the most important output of the investment phase. This is the input to the payoff phase. What characteristic of this molecule gives the payoff phase the capacity to create ATP's?The most important output of the investment phase is G3P. Its most important characteristic is its ability to pull phosphates out of the water without using ATP. This is because it has a lot of reducing power.Know how to find two RNA molecules in NAD+.look for sugar, base, phosphates (hexagon)Know how to draw the bubble version of glycolysis and know how to add fermentation to that drawing, to help bring NAD+ back. (this is from Chapter 6)In specific steps of all our metabolic pathways, as well as other oxidation-reduction reactions, you should be able to identify what molecule is being reduced/oxidized and how you know that.Define Le Chatelier's principle.When the equilibrium of a system is altered (by changing concentration, pressure, etc.), the system shifts to counteract this change, and restore the equilibrium.Be able to use Le Chatelier's principle to explain how the evolution of photosynthesis alters the functioning of the H+ pump and glycolysis.Since photosynthesis made protons go out of the cell, to create equilibrium, it had to change the proton pump and glycolysis by reversing some of their features.Why doesn't making energy by photosynthesis completely solve the problem caused by glucose depletion?When the sun goes down, photosynthesis stops working.Explain how H2S-splitting photosynthesis simultaneously solves the energy and osmosis crises, at least while the sun shines.Osmosis crisis: electron carrier ejects protons from inside the cell to outside of the cell which relieves osmotic stress caused by all the other large molecules Energy crisis: when concentration of protons get too high due to the electron carrier pumping H+ out of the cell, the reverse proton pump will come into play by pumping protons back into the cell, converting ADP back to ATP to solve the energy crisisName the pathway that takes reducing power (NADH, FADH2), ATP and CO2 as its inputs. Name the main product of this pathway. Tell where this product goes.The cell can makes its own food by the reversed Krebs cycle, which uses reducing power, ATP, and CO2 as inputs. Excess pyruvate from the reversed Krebs cycle, in addition to ATP and NADH from photosynthesis, ultimately synthesizes the food, i.e. glucose.Draw a sketch of a membrane oriented vertically with "Reducing Power" increasing in the vertical axis (label this) to describe in detail how H2S-splitting photosynthesis solves the osmosis problem. Use the words, chlorophyll, light, photon, electron, H2S, S, H+, electron carrier, reducing power, NADH, inside cell, outside cell, H+ gradient. Explicitly explain how photosynthesis relieves the osmosis problem.when two particles of light, called the photon strike the chlorophyll, two electrons in the covalent bonds of H2S are excited to such a level that they abandon H2S eliminating those covalent bonds and turing that compound into S+ 2 e- and a free protons H+. it then hands off the two electrons to NAD+ which immediately uses both electrons to create a single covalent bond with the nearest proton. The newly formed NADH has a high reducing power which makes it very useful. A relevant effect of the electron hand off is that the electron carrier also ejects a proton from inside the cell to outside the cell.Draw a sketch of an entire cell that shows how photosynthesis solves the energy problem. Use the words, electron carrier, NAD+, NADH, H-gradient, original H+ pump, ADP, ATP, Krebs cycle in reverse, carbon fixation.photosynthesis helps solve the energy problem by driving the proton pump in reverse the more protons that pile up outside the cell the more ATP that can be made from ADP within the cell. the strong proton gradient outside the cell can drive other processes. photosynthesis also assist the cell being able to make its own glucose, the reducing power imparted to NAD+ by the photosynthetically excited electron as it passes over the electron comes into play. This converts NAD+ into NADH (plenty of reducing power) The photosynthetically generated reducing power combined with aTP from the proton pump can transform cO2 into carbohydrate and ultimately glucose (carbon fixation).Describe how the cell makes food as a dividend of photosynthesis. Sketch the pathways and use the words, proton pump, ATP, electron carrier, reducing power, NADH, carbon fixation, carbohydrate, "reverse Krebs cycle", glycolysis, and pyruvate in your narrative. Be sure to distinguish the different roles of reducing power and ATP as sources of energy during photosynthesis. Also be sure to make clear whether processes are going in forward or reverse mode (and do not forget arrow heads).CO2, ATP, and reducing power (NADH and FADH2) are inputs. The reducing power fixes CO2 into pyruvate by adding electrons. ATP provides the energy for the covalent bonds between the added carbons to the CO2 molecule.What would happen if a cell biologist darkens the cell, injects into it superabundant pyruvate and ATP, and finally arranges a reducing mechanism that selectively reduces all NAD+ that the cell makes to NADH. What would happen and why? What chemical(s) would accumulate?Since these are all products of the process of glycolysis, it would be conducted in backward direction to produce the products such as glucose, ADP, Pi and NAD+. According to Le Chatelier, when extra resources are provided to the system, which alters its balance, the system re-establishes the balance by running the process in reverse direction.What would happen if a cell biologist darkens the cell, chemically (and continuously) oxidizes all NADH to NAD+ and injects superabundant glucose into the cell. What would happen and why? What chemical(s) would accumulate?The process of glycolysis would take place and the product pyruvate will be accumulated.Describe the original function of the proton pump (when it first showed up in our story) (sketch)inputs: ATP outputs: ADP + Pi, eject H+Describe the proton pumps new function in the sunlight with photosynthesis.inputs: ADP + Pi, bring in a H+ outputs: ATPPlease make a sketch for each A-E below. Each sketch should show the process in a circle, placed appropriately within the cell. It should include all the inputs into that process and where they come from, as well as all outputs from that process and where they go. Some of these are similar to #7 and 8, but note that the inputs and outputs are not listed here! You will need to know them! Thus, you should start practicing right away. A. Proton pump solves the osmosis crisis (causes energy crisis). B. Glycolysis (and fermentation) of glucose from primordial soup solves energy crisis (causes food crisis). C. Chlorophyll, electron-carrier protein, and reversed proton pump (Le Chatelier) solves both osmosis and energy crises in the daylight. D. Products of photosynthesis work through reverse Krebs cycle and reverse glycolysis to make glucose for use in the night. E. Night-time is STILL anaerobic glycolysis and fermentation. Almost identical to B. What's different (ask where the reactants come from)?What other classes of molecule are synthesized from precursors produced by the Krebs cycle?The building blocks of fats (fatty acids and glycerol, nucleic acids (ribose and bases) and proteins (amino acids) and carbohydrates (glucose) produced by the Krebs cycle.Be able to draw a cell that can do aerobic respiration. The processes that should be included are: proton pump, Krebs cycle, glycolysis, ETC and running the cell. Know the inputs and outputs for each of those processes and how they connect with one another.Describe the advantage of the Calvin cycle over the reverse Krebs cycle (Why is it more efficient).More efficient because fewer enzymes need to go back and forth, three tenths of the enzymes normally used in glycolysis do not need to go both ways with CO2 Calvin cycle.Explain the great advantage that the evolution of oxygenic photosynthesis gave to cells.Able to use an electron donor (h2o) that is virtually everywhereList the two disadvantages of H2O-splitting photosynthesis, one inconvenient, the other deadly.-Inconvenient: the oxygen from the water molecule is so electron hungry that the energy level of the electron taken from it is much lower than an electron taken from H2S. The electron is not energetic enough to reduce NAD+.Therefore, the reducing power needed to reduce CO2 into a carbohydrate is not met. -Deadly: oxygen is a byproduct which was not yet on earth. Oxygen atoms are electron hungry and O2 gas tends to form a pair of exceedingly reactive ions ("free radicals") that steals electrons from covalent bonds from unprotected cells, thereby altering covalent chemical structures.What type of photosynthesis is linked to Calvin cycle? What is the carbon cycle associated with H2S photosynthesis?-Oxygenic photosynthesis -Krebs CycleSimilar to what you did for sulfurogenic photosynthesis in chapter 7, be able to draw a sketch of the entire cell that shows how oxygenic photosynthesis operates and what pathways are activated and involved in producing glucose when this type of photosynthesis is being used. Be sure to distinguish the different roles of reducing power and ATP as sources of energy during photosynthesis. Also be sure to make clear whether processes are going in forward or reverse mode (and do not forget arrow heads). Before the evolution of the ETC, what can a cell containing these pathways do once lights are off? How do these pathways used during the day in oxygenic photosynthesis differ from the ones used by sulfurogenic photosynthesis?Describe the inconvenient disadvantage (not the toxic one) of oxygenic photosynthesis. Please include a sketch showing the membrane with reducing power in the vertical axis. Include and explain the role of the following in the sketch: chlorophyll, electron carrier, NADP+, NADPH, H+The inconvenient disadvantage is that photosynthesis requires an unwieldy two step electron excitation. Since the electron is not energetic enough to reduce NADP+ to NADPH, the ell had to evolve an additional molecule of chlorophyll to take an additional photon from the sun thereby ejecting more energy into the low energy electron through the electron carrier. It is at the electron carrier where H+ ions are pumped out giving reducing power.What was the cell able to do after O2 accumulated in the atmosphere?Oxygen was very electron hungry so cells used oxygen to pass electrons down a chain of proteins therefore ejecting a lot of protons creating a concentration gradient and producing a lot of ATP.Know how to draw the electron transport chain on the zoomed in version of the membrane, the same way we did on the worksheet.Draw a sketch of a cell that can do aerobic respiration but that does not do photosynthesis (as usual, include all inputs and where they come from, and all outputs and where they go) to help you explain how the electron transport chain (ETC) really brought cellular life into the fast lane. a. What is the one direct function of the ETC? b. Where does the ETC get its electrons?a. Produce ATP by H+ gradient b. NADH/FADH2How many total ATPs can be generated from the oxidative breakdown of one molecule of glucose? How does this compare to the anaerobic breakdown of the same glucose?-32-36 ATPs -36 ATPs oxidative vs 2 net ATPs anaerobic (18:1)Name the most important output of the modern Krebs cycle in the aerobic world. Explain why this output is so important.Reducing power (NADH and FADH2) which is the electron donor for the ETCDescribe the big picture of Krebs cycle in the modern aerobic world. What are its reactants and where do they come from? What are its products and where do they go?-Reactants: Pyruvate from forward glycolysis -Products: CO2 exits the cell and produced NADH/FADH2 to be reduced by proteins in the ETC to make ATPWhy is it that what we can do at night only changes once we evolve the ETC?Since the ETC can eject protons even in the absence of light, we can keep the proton pump working in reverse and producing ATP. (We can make a lot more ATP this way than with glycolysis only.)Use a sketch to describe each stage in the evolutionary history of glycolysis, Krebs cycle, and the proton pump, including for each stage inputs and where they come from, outputs and where they go, and most important function. Start with the primordial soup and end with aerobic breakdown of glucose. Don't forget to describe processes in the light as well as the dark.Know which processes are anabolic or catabolic out of: glycolysis, reverse glycolysis, Krebs, reverse Krebs, Calvin.Glycolysis: catabolic Reverse glycolysis: anabolic Krebs: catabolic Reverse Krebs: anabolic Calvin Cycle: anabolic Catabolic (breaking) Anabolic (building)Know the processes that are on in cyanobacteria during the day and the processes that are on during the night. Be able to draw these.Know each new evolutionary alteration to the processes discussed (glycolysis, Krebs cycle, Calvin cycle, photosynthesis, ETC and proton pump), including inputs and where they come from, outputs and where they go to, and most important function. Be able to identify a correct version of this processes and how they would function under different scenarios.- Cyanobacteria performs oxygenic photosynthesis--> fixed carbon with calvin cycel and broke down glucose aerobically with the ETC -the purple bacteria eliminated photosynthesis and focused on capturing food and converting it aerobically to energy -archeabacteria--> never evolved metabolic improvement, instead species in this group still poke along in anaerobic (without oxygen) environmnets --> capturing their food through glycolysis and fermentationBe able to draw the cladogram of the three domains, Bacteria, Archaea, Eukarya, including the two "cross-over" events that initiated the Eukarya. Be able to identify a correct version of this cladogram.The Eubacteria and archaebacteria are separate but when formed with cyanobacteria or purple bacteria they form eukaryote.Which specific lineage evolved into mitochondria? What benefit does it obtain from the symbiosis? What benefits does it provide to its host?The purple bacteria evolved into mitochondria. It gets pyruvate and protection from symbiosis and it gives glucose to the host.Which specific lineage evolved into chloroplasts? What benefit does it obtain from the symbiosis? What benefits does it provide to its host?The cyanobacteria evolved from chloroplasts, it enters archaebacteria and provides food by photosynthesis. In return, cyanobacteria gains protection against phagocytosis. Eubacteria specifically Cyanobacterial evolved into chloroplasts. While it is still unsure what the Cyanobacterial got from its host cell they believe it may simply be protection from predatorial endocytosis by other archaebacteria. The cyanobacterial provides the host cell the ability to perform photosynthesis.What are the negative consequences of the lack of cell wall.More prone to lysing due to osmosis. The cell can get more damaged and is susceptible to mechanical and osmotic stressName two very different positive consequences of the lack of cell wall.1: multiple points of origin increase replication because DNA is not attached to the cell wall, which increases the rate of replication. 2. Phagocytosis: captors large food particles through phagocytosisHow did the loss of the cell wall lead to a symbiotic relationship with Bacteria?With the loss of the cell wall, archaebacteria could eat eubacteria- allowing endosymbiosisMake a sketch to help you describe aerobic metabolism in the dark in Eukaryotes. Starting with glucose outside the cell, use arrows between labeled processes put circles around each process) and indicate all inputs and outputs (indicate which outputs are the most important). Start by drawing a cell with its cytosol (Archaebacterial host), and a large mitochondrion (symbiont) as we did in the lecture exercise last week. Pay close attention to the membranes separating these two regions. Don't forget to resolve the host's NAD+ problem without fermentation. Map onto your sketch in its proper place: phagocytosis, outer membrane, inner membrane, intermembrane space, glucose, glycolysis, pyruvate, Krebs cycle, NADH/FADH2, NAD+, FAD+, electron transport chain, protons, proton pump, ATP, ADP + Pi.Know where in eukaryotic cells photosynthesis and Calvin cycle take place. Know where in eukaryotic cells the ETC and the Krebs cycle take place.Photosynthesis occurs in the chloroplast, Calvin Cycle takes place in the stroma of the chloroplast, the ETC takes place on the inner membrane of the mitochondria, Krebs Cycle takes place in the mitochondrial matrix.Know the different lines of evidence for the endosymbiosis theory.The endosymbiosis theory is where bacteria were engulfed and a mutually beneficial relationship evolved Evidence: -Mitochondria and chloroplasts contain their own DNA -Synthesize their own small ribosomes -Grow and divide independently of cell division -Internal membrane more similar to prokaryotic membraneDescribe three different ways that Bacteria/Prokaryotes and Eukaryotes differ in their mechanisms of protein synthesis (includes both transcription and translation).Bacteria/Prokaryotes: -transcribed mRNA often codes for several separate proteins -transcription and translation occur right next to each other -leaves the transcribed mRNA alone after transcription Eukaryotes: -each mRNA is ultimately translated into a single protein -transcription and translation occur in entirely different parts of the cell (transcription=nucleus; translation=cytoplasm) -changes mRNA after transcription before shipping it out to be translated (mRNA processing)Know how many proteins (one or more than one) an mRNA can code for in prokaryotes.Prokaryotes: several separate proteinsKnow how many proteins (one or more than one) a primary (immature) mRNA can code for in eukaryotes).primary immature eukaryote = more than 1 proteinKnow how many proteins (one or more than one) a mature mRNA can code for in eukaryotes.mature mRNA eukaryotes = 1 --> this is when all introns are removed and only extrons remainContrast where exactly in the cell transcription and translation occur in prokaryotes and in eukaryotes. The answer is NOT simply "ribosomes".-in prokaryotes: transcription and translation occur right next to each other. The mRNA can barely come off the DNA before it attaches to a ribosome for translation. electron microscope images even show that translation occurs before the entire mRNA has come off the DNA -in eukaryotes: the evolution of the nucleus means that transcription and translation occur in completely different parts of the cell. Transcription occurs in the nucleus --> where the DNA is, then the transcribed mRNA must exit the nucleus before it can land on a ribosome for translationDescribe what a lysosome is, how it functions, and explain why it doesn't consume itself. Be able to draw/identify an image of a lysosome fusing with a food vacuole and becoming activated (what needs to happen?)a lysosome is a vesicle full of digestive enzymes, their job is to break down structures of two different kinds. - they break down chunks contained within a membrane mound vesicle, which eventually fuses with a lysosome --> allowing digestive enzymes to have access to the food - they also break down old, disfunctional organelles. the lysosome fuses with the organelle and its contained enzymes break down the organelle, allowing the cell to recycle its building blocks.Know what steps are involved in RNA processing. Explain what exons and introns are and describe the fate of each. Know how to describe RNA processing, using the following words: nucleus, exon, intron, primary RNA transcript, mature RNA transcript, 5' cap, 3' poly-A tail, spliceosome, splicing.eukaryotes really change the mRNA after transcription, before shipping it out to be translated. 1. a cap made of a modified guanosine nucelotide is placed on the 5' end of the mRNA 2. a poly-A tai, composed of many adenosine nucleotides are added to the 3' end. - these two alterations of the two ends of the mRNA protect the mRNA from degradation AND assist the transport of the mature mRNA out of the nucleus and onto a ribosome (where translation occurs)Draw/identify several alternative mature mRNAs if given a drawing of a primary transcript. Know the name of the process that produces different mature transcripts from a starting immature RNA.mature mRNA is created by gene splicing. this is when a section of mRNA is removed called introns, and throws them away. the remaining segments left called exons, are spliced together producing the mature mRNA transcript. This is destined for export out of the nucleusDescribe with words and/or drawings the steps by which eukaryotes package their gene products, both for proteins that will remain in the cytoplasm, and those destined for other locations. Use the words, cytoplasm, ribosome, rough endoplasmic reticulum, transport vesicle, golgi apparatus, cis face, trans face.shortly after docking on a ribosome, the newly produced protein is moved into the endoplasmic reticulum (a complex of membranes that ultimately allows protein to be placed into secretory vesiclesBe able to describe these two main fates of protein products after they leave the Golgi apparatus (as described in the Primer). Use the words lysosome, exocytosis, phagocytosis, vesicle fusion, proton pump, acidic environment, digestive enzymes.1. the golgi can repackage protein into secretory vesicles that are bound for exocytosis (a reverse version of endocytosis) which rapidly removes large amounts of material from the inside of the cell. 2. proteins in the golgi may be repackaged into lysosomes.Name the main protein that microtubules are made of, and list one function of microtubules.microtubules are made of a protein called tubulin. function: Microtubules are conveyer belts inside the cells. They move vesicles, granules, organelles like mitochondria, and chromosomes via special attachment proteins. They also serve a cytoskeletal role. microtubules are very dynamic, with an average lifetime of less than an hourName the main protein microfilaments are made of, and list one function of microfilaments.microfilaments are made of the protein, actin (thin 7nm diameter) and generally resist tension. -actin filaments are quite dynamic, and contribute to such essential cellular activities as endocytosis and locomotion (ciliary motion)Name the main protein intermediate filaments are made of, and list one function of intermediate filaments.their size is intermideate to between microtubules and microfilaments. - the protein is vimentin, - intermediate filaments are much less dynamic than either of the two. they form a more permanent chassis for the cell.Rough ER fuctionmodification and packaging of newly synthesized proteinsSmooth ER functionsynthesis of lipidsCytoskeleton functionstrength and support, movement of cellular structures and materialsCytoplasm functionWhere the organelles resideribosomes functionsite of protein synthesisWhat is the purpose of mitosis? What is the purpose of meiosis?The purpose of mitosis (asexual) is to divide chromosomes in eukaryotes for cell regeneration and growth. The purpose of meiosis (sexual) is to produce gametes for sexual reproduction.What is the chromosomal difference between gametes and somatic cells?