BMS 300 Exam 1 Study Guide
BMS 300 Exam 1 Study Guide BMS 300
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This 12 page Study Guide was uploaded by Bailey Sniffin on Sunday October 9, 2016. The Study Guide belongs to BMS 300 at Colorado State University taught by John P Walrond in Fall 2016. Since its upload, it has received 2 views.
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Date Created: 10/09/16
BMS 300 EXAM 1 NOTES 8/22 Water: essential to most environments o How is water organized? Components: H2O Molecular weight of 18 Covalent bonds: electrons being shared between oxygen and hydrogen Has a much higher boiling point (100 C) than nitrogen and oxygen Why? Because of water’s peculiar structure Because water has a dipole moment Has polarity – negative end and positive end o Give rise to idea of hydrogen bonds Water can form crystals because of the peculiar structure of water and hydrogen bonds Ion solubility: o Because water is polar, ions can easily interact with water o All these actions take place in a salt solution There has to be ions in the solution o Cations: positive o Anions: negative Both are hydrophilic: water loving o Cations and anions are surrounded by shell of hydration o The orientation of charges of water (dipole moments) permit the shell of hydration o Diffusion: by entropy, they move down a concentration gradient 8/24 Ion solubility and diffusion: o Charged ions distribute themselves randomly in the water column Initially there are higher concentrations of ions in the immediate vicinity of the sodium chloride crystal Over time, these ions distribute randomly in the water column How can ions move across a barrier? o Take a beaker and separate it into two compartments One side has water The other has sodium chloride Put holes in the barrier – some selective for sodium and some selective for chloride Over time, the random walk of the ions will redistribute the ions from region of higher concentration to lower Diffusion across a barrier Generate a concentration gradient (more so in biology) Water can also diffuse o By aquaporins – water channels o If there is a difference in concentration on one side of the barrier, which way will water diffuse? Water moves from a region of higher concentration to lower concentration Cations and anions can interact with dipole moments o Considered to be hydrophilic o Want to go into solution cause they’re charged Hydrophobic: lack of charge/polarity determines ideas of hydrophobic o Triglycerides: extremes of hydrophobia Like vegetable oil Have a backbone based on a 3carbon alcohol (glycerol) Each hydroxyl on the glycerol can now be chemically utilized to link with the fatty acid side chain Fatty acid: carboxylic acid end o COOH o Gives the fatty acid its acid nature Hydroxyl on carboxylic acid + hydroxyl on the 3carbon alcohol can be used to general reaction called dehydration synthesis Generates water from this reaction o Forms an ester bond between the carbon on the glycerol and the carbon on the carboxylic acid on the fatty acid Going to covalently link Equal sharing of electrons so the molecule doesn’t have an obvious charge or polarity o Hydrophobic Lipids are important for our diet so our bodies compensate to include them Phospholipids: modified triglyceride o Retain 2 fatty acid side chains but the 3 carbon on the glycerol will have a charged phosphate head group instead of a third fatty acid Gives us a whole new molecule One end is charged, one is uncharged Allows a phospholipid bilayer to form Fundamental structure of all membranes and cells 8/25 Triglycerides: 3carbon alcohol linked by 3 ester bonds to 3 fatty acids o Hydrophobic molecule – not easily soluble because of equal sharing of electrons Can be altered to generate the phospholipid bilayer o Must modify the structure of the triglyceride Leave 2 fatty acids unchanged Add a phosphate, then link it through an oxygen to a head group Head group is charged This new molecule can interact with aqueous world or a world with no water Association of phosphate head group with H2O: o If we could somehow sprinkle phospholipids onto the surface of water, they would turn their tails upward and face the water o But we know that most biological systems are aqueous, so how do we get the phosphate head groups under water? Using a micelle Rare but can be formed – unstable because of hydrophobic tails o Will blow up if water touches the tails o Liposomes: by organizing the phospholipids so that tails face each other and heads face toward water, we can make a bilayer Backbone of all biological membranes Difference between bilayer is size and scale o Proteins are needed to make a functional membrane Transmembrane proteins Extend across the lipid bilayer Forms a kind of pathway from the inside of the cell to the outside world of the cell Proteins o Primary structure: amino acid sequence o All proteins are polymers of amino acids 20 amino acids Used to construct all proteins Can be laid out from one to the next in one chain Peptide bonds between amino acids form the chain o Amino acids: Amine group Carboxylic acid Rgroup o Particular orientation of amino acid chains: amino acid terminus and carboxy terminus 8/26 Secondary structure of proteins: o Because of the backbone and charged Rgroups, additional structures of proteins begin to form o Hydrogen bonding between the carbonyl oxygen to a hydrogen on an amine some distance away This hydrogen bonding can form either alpha helix or beta sheets Beta sheets: back and forth arrangement between adjacent strings of amino acids Alpha helices: easier to recognize because they’re a spiral staircase o Instead of steps, its amino acids Tertiary structure of proteins: o Comes from a combination of alpha helices and beta sheets o Arises from the Rgroups Rgroups can be divided into categories: Charged/unipolar: hydrophilic Uncharged: hydrophobic o 3D shape gives rise to binding pockets, sites where neurotransmitters bind, to where antibodies bind to antigens It’s all about the 3D shape Orientation of hydrophobic and hydrophilic parts with water Must have some way to string amino acid across a bilayer o Channels Fold amino acids across a membrane, first with its secondary structure, across the lipid bilayer o All the transmembrane proteins span the lipid bilayer as an alpha helix o So, spiral staircase spans the bilayer Its Rgroups are primarily hydrophobic because the amino acid’s Rgroups face the hydrophobic region of the lipid bilayer so the lowest energy state will be the hydrophobic amino acids It’s fine to spin one alpha helix across the membrane, but to make a pathway from the outside of the cell to the inside, we have to go with some other ideas o To do this, spin several alpha helices across the bilayer o Thread in and out of the layer about 4 times so that tails and heads of the phospholipids face different directions 8/29 Transmembrane proteins o When a protein is in an aqueous environment, it has a specific purpose o We can thread an amino acid sequence across a lipid bilayer Amino acids: o What kinds of Rgroups are going to be found on those amino acids? Hydrophobic Rgroups face phospholipid bilayer o Thread alpha helical regions across the membrane several times o Generate a transmembrane protein that has 4 alphahelical regions Some will point outward (hydrophobic) and other point inward toward the channel (hydrophilic) Prokaryotes versus Eukaryotes; o Central dogma: idea that information is stored in deoxyribonucleic acid (DNA) then transcribed to ribonucleic acid (RNA) and then translated into protein True for prokaryotes and eukaryotes o Distinction comes when we look at morphology of the cells o Prokaryotes: lack membranebound compartments o Eukaryotes: have many membranebound compartments o For the first billion years of earth, we started to generate prokaryotes, then years later were eukaryotes o Eukaryotes have an advantage due to membranebound compartments Eukaryote: “true kernel” o Nucleus where DNA is sequestered o Organized into chromosomes o Single molecules of DNA chromosomes wrap around histones (DNA binding protein) o 23 chromosomes from mother and 23 chromosomes from father o 46 chromosomes stuffed into one nucleus Histones help organize Have very similar amino acids, doesn’t matter what type of cell it is Wraps and folds the DNA in a particular fashion o Parts of the DNA must be unwrapped and accessible for transcription Histones play a role in finding the site to open the gene o RNA synthesis (transcription) is in the nucleus o All protein synthesis (translation) is in the cytoplasm Prokaryotes: o DNA is circular o Not highly organized, not sequestered, no chromosomes There has to be traffic in and out of the nucleus o Nuclear pores 8/31 Ribonucleic acid is exported from the nucleus RNA is destined to leave the nucleus o Through nuclear pores Endoplasmic reticulum is a membranebound bag in the cell o Appears to be one continuous membranebound bag throughout the cell o Smooth and rough o Openings between cytoplasm and the nucleus through the nuclear pores are not covered by ER But covering the remainder of all the membrane of the nucleus is the ER Ribosomes are made of RNA (mostly) o Been transcribed from the DNA in the nucleus and shipped to the cytoplasm o Free ribosomes: in cytoplasm o Bound ribosomes: bound to the rough ER (RER) o Different proteins are made by these different ribosomes Rough ER: produce 3 proteins: Secreted: destined to leave the cell by exocytosis Transmembrane: destined to become incorporated into bilayer Lysosomal These 3 types are glycosylated (sugars are added) The final folding of glycosylation and decision of the protein’s function happens in the Golgi apparatus o Golgi apparatus: A finishing factor for the initially generated proteins from the RER Final folding of the protein in their 3D shape How do we get proteins from one place to another? o Vesicles Small spheres Cargocarrying containers Final destination of proteins o Some destined to go to plasma membrane: secreted o Alpha helical across bilayers – transmembrane sets o Destined to go to lysosomes Lysosomal proteins are enzymes Break down lipids Destructive o Important to take these destructive lysosomal proteins and deliver them to a membrane boundcompartment where they can be sequestered away the lysosome o Endocytosis: bring proteins/pathogens in from the outside of the cell into a macrophage Bringing things into the cell o Exocytosis: Taking things out of the cell 9/1 Exocytosis: vesicle fuses with plasma membrane to release contents to outside world o Or use transmembrane protein to take things out of the cell Endocytosis: into the cell o Macrophage: particular kind of endocytic cell o Bacterium binds to macrophage and enters cell o Guide the vesicle containing the bacterial cells to the membranebound lysosome where they are digested or destroyed Mitochondria: o Membranebound structures where ATP is generated Oxidative phosphorylation Taking ADP and phosphorylating to ATP o Mitochondria are in our cells because of an ancient capture event Reducing atmosphere years ago – no oxygen Cyanobacteria developed a trick to capture photons of light, then would split water into hydrogen and oxygen and generated carbohydrate The oxygen was built up into the air Started as toxic to many organisms but some found it useful Cytoskeleton o Highly ordered structure inside the cell is because of this o Protein polymer makeup Gigantic proteins that are further polymerized from proteins themselves o Tubulin o Filamentous actin o Intermediate filaments Intermediate filament proteins o Keratin and keratinocytes o Polymers of microtubules and actin Generated as gigantic molecules from plugging together smaller subunits One end of the monomer can be added onto and the other end is taken away Gives the molecules a kind of endedness o Plus end (assembly) o Minus end (disassembly) o Motors: Kinesin: + end directed motor Dynein: end directed motor Move vesicles over microtubules in long distances Microtubules: long distance Actin: short distance (local to membrane) 9/2 Microtubules in a neuron o There are 2 kinds of transport o Dynein: microtubule binding protein Moves vesicles in the opposite direction of kinesin Actin filaments o Movement located around the edges of the cell Long distant: happens in the middle of the cell Motors function as ATPase o Convert chemical energy to mechanical energy (movement) Central Dogma: o DNA stores info in base sequences (genes) o Nucleic acid of DNA isn’t enough, we need an intermediate This will be a ribonucleic acid, which is very similar o Expressing genes through RNA to make protein DNA structure: o Life has to be able to replicate itself and change over time DNA can do both of those characteristics o Composed of a 5carbon sugar called Deoxyribose Each of these are attached to a nitrogenous base 4 forms: adenine, guanine, thymine, and cytosine A and G: purines T and C: pyrimidines Link the sugars to the bases with a triphosphate Form phosphodiester linkages Makes a polymer of DNA o But the 2 strands of DNA will organize one with the other, and the covalent bonds hold together the adjacent sugars through phosphodiester bonds whereas the strands are held together by hydrogen bonds in the middle o Antiparallel o 5’ – 3’ (synthesizing) o 3’ – 5’ (reading) 9/7 Antiparallel organization of DNA o Using the structure to look at how DNA replicates o DNA is the fundamental molecule of life – must make copies of itself DNA replication: o Semiconservative: which means that we use one strand (the old strand) to generate a new complementary strand Each newly synthesized molecule of DNA is made up of one old strand and one new strand This requires a “complicated dance” DNA strands are a spiral staircase, or helix This must be unwound by a helicase o An enzyme that takes energy to break hydrogen bonds between the 2 strands o Remember, the two strands themselves are bound covalently by phosphodiester bonds, but the bases BETWEEN the strands are hydrogen bonds o Helicase unwinds molecules and separates bonds o Strands are oriented in opposite directions 3’ – 5’ 5’ – 3’ o DNA polymerase: Polymerizes a new molecule of DNA Action: to polymerize the Deoxyribose sugars by linking them through phosphodiester bonds Chooses which bases pair Reads from 3’ – 5’ Because the strands are laid out in antiparallel orientation, leading strand can be read continuously 3’ – 5’ But, the complementary strand in the opposite direction can’t be continuously read Ribonucleic Acid (RNA) o Very similar to DNA but has some structural and functional differences o Ribose instead of deoxyribose o In ribose there’s a hydroxyl group A big, bulky group which seems to play a role in determining whether the molecule can begin for form the spiral helix Seems to be more difficult o Bases: Purines: Adenine Guanine Pyrimidines: Cytosine Uracil o Single stranded 5’ – 3’ o Because of the base pairing, there can be base pairing within the RNA molecule itself Internal base pairing Gives RNA the rudimentary 3D shape o Important because if you can take a macromolecule and generate a 3D structure, you can generate an enzymatic activity o There is enzymatic activity in rRNA Ribosomal RNA o Plays a role in forming peptide bonds in amino acids Transcription: o Trans: across o Scription: to write o Take info in the DNA molecule and impart it to an RNA molecule o Synthesize an RNA molecule based on DNA sequences o Eukaryotes: a chromosome is one continuous molecule of DNA but that chromosome may contain 100s of genes So how in that linear pattern do we decide where to begin to read the DNA molecule to make a complementary strand of RNA? How do we make that RNA strand? Answer: has to do with organization of bases in the DNA strand o TATA box: promoter Promoter: sequence of bases in the DNA molecule Provides a binding site for a DNA binding protein called a transcription factor o When the transcription factor binds to the promoter, RNA polymerase is recruited to start reading the DNA and bases, then find a complementary base for RNA to make a continuous strand with phosphodiester linkages between adjacent ribose molecules 9/8 Transcription: o Part of the Central Dogma o DNA RNA Chromosome is a continuous DNA molecule Use a promoter (TATA box) as a start site o Sequence that says “lets use this site to recruit a protein” Recruits transcription factor Provides a site to which we can bind a protein called RNA polymerase o Finds its way to the site and then begins to read the DNA from 3’ – 5’ Make a new molecule with bases of newly synthesized RNA has DNA complements now Make the appropriate base sequence o That RNA transcript has a certain fate In eukaryotes: there’s an ability to take the RNA transcript (pre RNA) and edit it Nuclear enzymes read sequences of bases in the pre RNA and can cut sections o Cut out whole regions of pre RNA and splice them together You are able to cut out regions and splice them to other regions to edit RNA transcript These regions are exons (expressed) and cut out introns Because of this, eukaryotes can use a fairly small number of genes to make slightly different RNA transcripts o Gives rise to slightly different amino acid sequences in proteins So eukaryotes can use a single gene to make multiple proteins Making a protein: o Translation Information in a ribonucleic acid to info in a protein Use sequence information in mRNA Requires the process to happen in the cytoplasm Shipped out through nuclear pores tRNA: fundamental role of recognizing 3 base sets of mRNA and delivering amino acid to appropriate site in ribosome rRNA: factory, machine, which we make new proteins mRNA: contains info about amino acid sequence o Bases come in sets of 3 because it creates 64 possibilities We have 64 ways to make 20 amino acids o Use a codon to code for a single amino acid o mRNA transcript is recognized by the small ribosomal subunit This subunit glides along the mRNA until it finds the 3 bases AUG Start codon Once the subunit stops at AUG, it recruits the large ribosomal subunit to attach to make a “sandwich” with the mRNA in the middle Use the units to march along the mRNA and each codon has a particular amino acid inserted o Which one is inserted depends on the complimentary anticodon Keep reading the strand until a stop codon is reached o UGA, UAG, UAA o All start with uracil, then the two purines follow 9/9 Generation of a protein on a ribosome o Deposited in the cytoplasm – cytoplasmic proteins Generated on free ribosomes RER made a certain kind of protein – ones destined for the lysosomal system, secretion, and transmembrane proteins Outline the rules for which we generate one protein versus the other kinds o Cytoplasmic (free) proteins How do we guide those ribosomes that are generating the special subset of proteins to their sites on the ER? Signal peptide: series of 1720 amino acids o Predominantly hydrophobic o The amino terminus of the molecule that will tell that set of amino acids to bind to a structure in the cytoplasm called a signal recognition particle Has the function of recognizing the hydrophobic amino acids in the signal peptide Once the signal particle recognizes the hydrophobic amino acids, There are another series of events that guide the entire machine (small and large ribosomal sub unit, mRNA, protein being generated) to the ER Generates the RER o This is how we take a ribosome and transfer it Ribosome receptor: stabilizes machinery SRP receptor (signal recognition particle) binds to signal peptide and will find a site to settle in on the ER o GTP tells the SRP to let go of the signal peptide Transfers the binding of the signal peptide from the signal recognition particle to a transmembrane protein called a translocon Translocon: Protein complex spans lipid bilayer of ER o Bind to hydrophobic amino acids on the signal peptide o Begins moving the rest of the protein across the bilayer of the ER o That’s how we get proteins, as they’re being synthesized, into the ER Hydrophobic amino acids Tissues: o A group of similar cells performing a similar function o 4 types: Epithelia Connective Muscle Nerve o Epithelia: boundary layer, skin, interface between dermis and underlying world of our bodies Continuous layer of cells 9/12 EXAM 1 Triglyceride: made up of 3 carbon alcohol + 3 fatty acid o Dehydration synthesis forms ester bond o
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