Exam 2 Study Guide - Abreu (2019-2020 Fall) PDF

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Abreu (2019-2020 Fall)...

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I.

CENTRAL DOGMA A. DNA → RNA: Transcription 1. RNA polymerase produces RNA molecule with cbp to DNA 2. RNA polymerase begins transcription by binding to promoter sequences in DNA w the help of protiens↳ 3. EUkaryotic and bacterial promotor (sigma) vary 4. Eukaryotic basal transcription factors bind to promoter and being transcription. This causes RNA polymerase to bind to the site. 5. RNA elongates form 5’ → 3’ direction 6. Ends in bacteria when stem-loop forms in transcribed RNA; terminated in eukaryotes after RNA cleaved downstream of poly(A) signal B. RNA Processing 1. Initial transcript must be processed to make matrue RNA 2. Splicing primary transcripts removes introns and joins exons 3. MAcromolecular machines called spliceosomes splice the introns out of pre-mRNA 4. 5’ cap added ot end of pre-mRNA and poly(A) tail added to 3’ end a) Recognition signals for translation; protect message from degredation by ribonucleases 5. Occurs in nucleus C. RNA → Protein: Translation 1. Ribosomes translate mRNA into protein using tRNA 2. Bacteria does simultaneous transcription and translation 3. Eukaryotes do it seperately because trasncription in nuceus, and translation in cytoplasm 4. tRNA structure a) Carries amino acid corresponding to anticodon b) L shaped tertiary structure, one leg has anticodon c) Anticodon forms cbp w mRNA d) aminoacyl-tRNA synthetase links amino acid to tRNA e) Wobble pairing makes 40 antiocodons translate for 61 codons 5. Ribosomal structure + function a) Large macromolecular machines made of proteins and RNAs b) tRNA anticodon binds to mRNA codon to bring correct amino acid into ribosome c) Peptide bond catalyzed by ribosome d) Chaperone protein folds new proteins e) Usually post-translational modification to activate D. Vocab: Central Dogma, Transcription & Translation

II.

CELLS A. Bacterial and Arcahel Cells (prokaryotes) 1. Absence of nucleus 2. Has ribosome, cell wall, nucleoid, internal cytoskeleton, 3. Flagella and fimbria B. Eukaryotic Cells 1. Much larger size causes change in surface area-to-volume ratio 2. Organelles are required to make the rate of exchange of thing in and out of the cell more efficient 3. Nucleus in eukaryotes contains chromosome and stores information. Enclosed by double membrane nuclear enevelope and has nuclear lamina lining the inside surgace of membrane. Nucleolus is where RNA are dound in ribosomes and manufactured. 4. Ribosomes manufacturing proteins in cytoplasm 5. Endoplasmic reticulum has single membrane continuous w nuclear envelope. a) RER: Proteins are manufactured on ribosomes attached to the surgafe of the membrane and then they are processed in the lumen until they are later shipped

off. b) SER: lipids are synthesized by enzymes or enzymes break down molecules or lipids. Resevoir of calcium ions 6. Golgi Apparatus is like the mail room where protins pass before going to final

14. Cell wall in plasnts resisting pressure and providing structural support made up of polysacchari plasma membrane C. Studying the cell 1. Structures of cell varies tremendously based off of function a) Size and number of different types of organelles correlates with its function 2. Differential centrifugation allows researchers to isolate cellular components and break cells apa componenets in centrifuge. 3. Dynamic cells D. Vocab: Cells

III.

LIPIDS AND MEMBRANES A. Lipid Structure 1. Mostly hydrophobic because hydrocarbons 2. Fatty acid store chemical energy a) Fatty acid is hydrocarbon with carboxyl group b) Kinks caused by unsaturation (double bond) c) Steroids and phospholipids are key parts of membranes d) Length and degree of saturation has effect on properties 3. Fats, steroids and phospholipids; differ in structure and function a) Steroids (1) Four ring structure and then functional and side groups attached to the hydrophobic rings (2) Tail at bottom b) Fats store chemical energy (1) Three fatty acid → fats = triacylglycerols = triglycerides (2) Fatty acids joined by ester linkage c) Phospholipids in membranes (1) Hydrophilic head (2) Hydrophobic tail - fatty acids in eukaryotes and bacteria, isoprenoids in archaea d) Amphipathic lipids also have hydrophillic region containing polar or charged groups. Phospholipids have charged had that makes them amphipathic. Nonpolar tail is usaully fatty acid or isoprenoid B. Lipid Bilayers 1. Spontaneously assemble into bilayer that is barrier between external and internal environments a) Micelles and phospholipid bilayer (1) Micelles single hydrocarbon chains (2) Phospholipids have two hydrocarbon tails b) Heads face surrounding solution and tails face each other 2. Small nonpolar molecules can move across lipid bilayer readily a) Selective permeability- only some things can pass through membrane 3. Ions cross rarely 4. Permeability and fluidity related to many things a) Cholesterol → decreases permeability b) Temperature (1) As temperature increases so does permeability

c) Chemical strucutre of lipid - saturation and length (1) Unsaturated hydrocarbons have kinks which increase permeability C. Osmosis and Diffusion

D. Proteins and Membranes 1. Permeability of bilayers is altered by proteins (transmembrane proteins) a) Fluid-mosaic model 2. Channel proteins a) Provide pores in membranes that may be gated and can allow facilitaed diffusion of spe of the cell 3. Carrier proteins a) Undergo conformational changes that facilitate diffusion of molecules into and out of cell 4. Pumps a) Use energy to actively transport ions or molecules in a single direction b) Typically against gradient c) Often has secondary transport which uses the gradient caused by primary active transport to power the movement of different molecules against a particular gradient 5. Allows cell to have very different environment than exterior environment

E. Vocab: Lipids & Membranes

IV.

ENDOMEMBRANE System A. Nuclear Transport 1. Nuclear pore complex has openings in the nuclear envelope and 2. Proteins, and building blocks travel into the nucleus 3. Ribosomes and mRNA travel out of the nuclear pore complex 4. Small molecules passively diffuse through nuclear pore complex while larger molecules require a nuclear localization signal to

direct them through the pore with the help of nuclear transport proteins B. Endomembrane System

2. Pulse-Chase Experiment a) Tracked prtein movement by using a pulse - where you expose cells to modified amino for a period of time so that all the proteins synthesized during that intervel are radiolabe b) Then you put the normal version of the amino acid in the same molecule, this means th following proteins will not be radiolabeled c) Then you track protien movement thorughout the cell 3. Signal hypothesis a) At some point ribosomes attached to ER but what directs them to ER surface: proteins bound for ER have molecular zip code (1) Protein synthesis begins in ribosome in cytosol. Ribosome makes ER signal sequence using information from an mRNA (2) Signal sequence binds to signal recognition partical which causes the protein synthesis to stop (3) The ribosome + signal sequence + SRP then move to the ER where it attaches t (4) SRP then released and protein synthesis continues through translocon (5) Growin protein fed into ER lumen and ER signal sequence is removed b) Glycosylation creates sugar protein glycoprotein which serves as an idicator for shipme destination based of the number and arrangement of the sugars (indicating maturity) c) Membrane of transport vesicle fuses with destination’s plasma membrane and secretes 4. Lysosome consist of enzymes and endomembrane membranes a) Recycling products through autophagy, phagocytosis, and receeptor-mediated endocyto

b) Paths for moving intracellular structure c) Cellular locomotion through flagella, cilia, or cell crawling 2. Dynamic a) Actin polarity → + grows faster than b) Microtubule polarity → + grows faster than 3. Motor proteins move along actin filaments using energy from ATP a) Myosin binds and hydrolyzed ATP to ADP and then changed its shape b) This allows it to attach to actin and pull itself along the filament c) Used in cytokinesis to pinch the two membranes of daugther cells d) It is also involved in cytoplasmic streaming in plants 4. Motor proteins move along microtubules using energy from ATP a) Kinesin hydrolizes ATP to move vesicles along microtubules towards plus end b) Dynein 5. Axoneme of eukarytic cilia and flagella are bent by dynein motors move microtubules to let cells swim a) Flagella and cillia move the cell b) 9+2 structure called axoneme (1) 9 doublet pairs of microtubules (2) Surroiunding 2 central microtubules (3) Dynein arms connecting the doublets c) Dynein walks along doublets towards minus end causing doublets to bend D. Vocab: Nuclear Transport, Endomembrane & Cytoskeleton

V.

CELL CYCLE- Mitosis, Replication, Chromosome Theory, Meiosis A. Mitosis 1. Cell Replication a) Must copy chromosomes, separate copies and divide cytoplasm into two identical daughter cells b) Eukaryotic cells divide by cycling between interphase and M phase c) Interphase = G1 + S + G2 (1) S = replication (2) G1 = (3) G2 = d) M phase consists of mitosis or meisosi. (1) Chromosomes seprate (2) Cytokinesis - when cells divide into two daughter cells 2. M Phase a) Prophase (1) Chromosomes condense (2) Spindle apparatus beigns to form (3) Microtubules overlap b) Prometaphase (1) Nuclear envelope disintegrates (2) Microtubules attach to kinetochores (3) Kinetochores begin moving towards middle of spindle c) Metaphase (1) Chromsomes in middle of spindle (2) Spindle anchored to PM by microtubules d) Anaphase (1) Sister chromatids pulled apart

(2) Separated chromatids are new daughter chromosomes (3) Spindle poles moved further apart to fully separate replicated chromosomes

(2) b) Cyclin concentraions oscillate during cell cycle. Activity of Cdk is regualted y addition activating site and removing of one from its inhibitory site c) Progression trhough cycle is controlled by checkpoints in three phases (1) G1 → regulates progress based on nutrient availability, cell size, DNA damage (2) G2 → delays progress until replication is complete and damaged DNA is repair (3) M phase → (a) delay anaphase until chromosomes are correctly attached to spi and G1 until chromosomes properly positioned 4. Cancer a) No G1 checkpoint b) Rb protein and G1 cyclin-Cdk complexes (1) Rb prevents progression into S phase (2) G1 cyclin-Cdk complex trigger progression into S phase B. DNA Replication 1. DNA Synthesis Hypotheses a) DNA replication is semiconservative (proved by meselson-stahl experiment) b) Each strand of parental DNA molecule provides tempklate for synthesis of complementrary strand, resulting in two complete DNA double helices, each with one new and one old strand. 2. DNA Synthesis a) Occurs in 5→ 3’ direction only

b) Requires many proteins c) Requires template and RNA primer d) Takes place at replication fork where double helix is opened by helicase e) Leading strand is synthesized continuously (1) Primase synthesizes primer (type of RNA polymerase)

(2) (3) (4) (5)

DNA polymerase then forms ring sliding clamp surrounding DNA while ano Continuously synthesize adding deoxyribonucleotides to 3’ end of strand Enzyme moves into replication fork R li ti f k i d h d f it

3. Replicating ends of linear chromosomes a) Problem because after last okazaki fragment is synthesized the primer is removed from the laggin strnad and that part of the strand remains single stranded. There is a solution b) Enzyme telomerase adds short sequences of single stranded DNA that is made double stranded by enzumes for normal replication c) Telomerase is active in reproductive cells that undergo meiosis; this allows length of gamete chromosomes to remain maintained d) Chromosomes in cells without telomerase shorten with cell division untik they reach a critical length (1) Signal then sent out to not allow more division e) Telomerase replication...