Exam 1 study guide
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This 13 page Study Guide was uploaded by Lyric Jamerson on Monday September 19, 2016. The Study Guide belongs to ECON 204 at Colorado State University taught by Steven J Shulman in Fall 2016. Since its upload, it has received 4 views.
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Date Created: 09/19/16
EXAM 1 Study Guide Monday, September 19, 2016 11:20 PM This is all the overviews with some notes from what the professor said during the class included into them. Some have question marks with parts I couldn’t read on the board and some of the spellings are wrong. Good Luck to Everyone! (the purple I added) Week 2 1. Day 1 1. We need water in our lives 2. In a range where water is liquid 3. Simple molecule a. One atom of oxygen and two atoms of hydrogen b. Molecular weight is 18 c. Covalent bonds d. Compare and contrast nitrogen and oxygen e. Electrons equally shared f. In water hydrogen is slightly positively charged g. In water oxygen in slightly negatively charged i. Unequal sharing ii. Gives water a dipole charge iii. Gives water unusual characteristics iv. Role of dipole moment 1. Allows for solubility v. Ions that are hydrophilic 1. Water loving 4. Components of water a. 1 atom of Oxygen b. 2 atoms of hydrogen c. = one atome of H20-MW of 18 d. (MW= molecular weight) 2. Day 2 1. Change in ions a. Equilibrium where all ions are equally distributed through the water i. Sodium chloride ions b. Diffusion into water column i. Reaching equilibrium through water? c. Diffusion across a barrier i. Ions bounce across barrier 1. Ion goes across barrier 2. Ion selective channels 3. Reaching equilibrium d. Water diffusion through aquaporin i. Osmosis ii. Reaching equilibrium e. Hydrophilic and hydrophobic i. Lipids hydrophobic molecules 1. Lacking charge 2. Cant easily move through dipole moments 3. Equally shared electrons b. Triglyceride structure i. Glycerol 1. Three carbon alcohol? ii. Fatty acid c. Phospholipid i. Fatty acid retains ii. Hydrophobic iii. Equally charged iv. Hydrophilic v. Can live in both worlds vi. Can live in water worlds vii. Converting triglyceride into a phospholipid viii. The basic structure of the phospholipid bilayer. 3. Day 3 1. Triglyceride structure a. Three ester bonds to three fatty acids 2. Phospholipids structure a. Two fatty acids (hydrophobic) b. One phosphate head group (hydrophilic) i. Feeling molecule ii. Interact with both water and no water 3. Association of phosphate head groups with H2O a. Surface i. Turn tails upward and heads face the water b. Micelle i. Very rare in biology ii. Can form them iii. Are unstable because of hydrophobic tails c. Liposome i. Stable structure ii. Bilayer of phospholipids d. Plana A bilayer 2. Day 4 1. Protein structure a. Primary structure i. amino acid sequence b. Secondary hydrogen bonding i. Carbonyl oxygen to ii. alpha helix or iii. Beta sheets 1. All based on hydrogen bonding 2. Use negative and positive charge to generate secondary structure c. Tertiary i. r-group interactions with water 1. Either toward or away from water a. Determines three demensional shape 2. Role of R-groups a. Charged or polar i. Hydrophilic b. Uncharged i. Hydrophobic 3. Generating 3-d structure a. Alpha helix and beta sheets b. Arrangement of R- groups 4. Enzymes/ binding Pockets and 3-d shape 5. Threading alphahelasses 6. a. Lipid bilayer i. ? ii. Role of hydrophobic region R-groups iii. Forming a channel 1. ? Week 2 1. Day 5 1. Transmembrane proteins a. Threading an AA sequence across a lipid bilayer b. Role of r Groups c. Generating a channel i. Role of hydrophobic r groups ii. Multiple loops 2. Prokaryote VS Eukaryote a. What is common i. DNA - RNA - Protein 1. Transcribed from DNA to RNA 2. Translation RNA to Protein 3. Central dogma b. What is different i. Nucleus means true cornel where things happen ii. Compartments iii. DNA orientation iv. RNA editing` 2. Compartmentation a. The ? i. Membrane bound compartment for sequencing DNA ii. Organization of DNA 1. Chromosomes a. Separate strands of DNA 2. Histones a. DNA binding proteins b. Organization revolves around them c. Organizes folding and wrapping of DNA d. RNA can only be made in the nucleus iii. site of RNA synthesis- Transcription 1. Creation of protein happens in the cytoplasm iv. Ribosomes 1. Mostly RNA 2. Photosynthesis functions 3. Function in cytoplasm v. Nucleus pores-access in and out of nucleus 1. Has complex make up 3. Endoplasmic reticulum 2. Day 6 1. Nuclear pore-gateways to the nucleus a. Endoplasmic reticulum i. Intracellular membrane- bound bag ii. Location relative to nuclear pores iii. Rough vs. smooth ER 1. RER- ER with ribosomes attached 2. Free ribosomes - in cytoplasm free of ER. a. Ribosomes - mostly RNA 1. Nuclear origin via transcription iv. Protein synthesis on RER 1. Secreted proteins, transmembrane proteins, lysosomal proteins 2. Glycosylation v. From ER to Golgi apparatus 1. Vesicles as cargo-carrying-containers b. From Golgi to tarset i. Plasma membrane 1. Secreted proteins, trans membrane proteins 2. Exocytosis ii. Lysosomes 1. Membrane bound bags of hydrolytic enzymes 2. Endocytosis and target to lysosomes iii. Endocytosis in macrophages 1. Target to lysosomes c. Mitochondria 3. Day 7 1. Endocytosis in macrophages a. Into the cell b. From plasma membrane to the lysosomes i. Pulling them into the cell and packing them into vesicles and sending them to the lysosome ii. Will be destroyed or digested b. Mitochondria i. Important to all eukaryotic cells ii. Structure and function 1. Origins of mitochondria 2. Adenosine Diphosphate and adenosine triphosphate. 3. Role in ATP generation 4. Genetics a. Important organelle for generating ATP b. Came in and became a part of Eukaryotic cells c. The cytoskeleton i. Protein polymers 1. Gigantic proteins that are made from several proteins 2. Microtubules a. Tubulin polymer 2. Actin a. Action polymer 3. Intermediate filaments a. Nero filaments b. keratin d. Directionality i. And assembly end and a disassembly end ii. Positive (+) end and negative (-) dependent on assembly end and disassembly end. iii. How we move things b. Motors i. Kinesin 1. Microtubules a. ( + ) end 2. Move one way or another 3. Great long distances ii. Dynein 1. Microtubules a. (-) end 2. Move one way or another 3. Great long distances ii. Myosin 1. Actin polymer a. (+ ) end e. Functional traces i. MT 1. Long distance ii. Actin 1. Short distance (local to membrane) 2. Day 8 1. Microtubule and Actin- Based Transport a. Microtubles i. Kinesin (+) end ii. Dynein (-) end b. Actin i. Myosin (+) end ii. Originally isolated 1. From muscle 2. The Central Dogma a. DNA stores information in base sequence called genes b. RNA is an intermediate nucleic acid between DNA and Protein i. Similar but different from DNA c. Information stored in DNA is expressed as Amino Acid sequence in protein 2. DNA structure a. Components i. 5-carbon sugar, Deoxyribose ii. Nitrogenous bases 1. Adenine 2. Guanine 3. Thymine- 4. Cytosine iii. Triphosphate 1. Made form one 5 carbon sugar to the next over and over 2. To form phosphodiester bonds 3. Use it to form the link between adjacent sugars 2. Organization of two stands of DNA a. 5' to 3' b. 3' to 5' Week 3 a. Day 9 1. DNA structure and replication 1. Replication is semi conservative i. Each old strand acts as a template for the new strand 1. Old strand generates complimentary strand 2. Unwinding the strands i. Helicase 1. Breaks h bonds 3. Strand orientation i. 3' to 5' ii. 5' to 3' 4. Role of DNA polymerase i. Polymerize a new molecule of DNA ii. Base pairing iii. Phosphodiester bond formation 5. DNA polymerase reads 3' to 5' 6. Concept of leading and lagging strand i. Lagging strand has to wait for the DNA to break up before it can go down the DNA that is 5' to 3' 2. RNA structure 1. Very similar molecule to DNA 2. Also very different 3. Components of RNA i. Ribose 1. Number 2 carbon has no oxygen but has hydrogen ii. Bases 1. Adenine 2. Guanine 3. Cytosine 4. Uracil a. Thymine is similar but it is five methyl uracil 4. Single strand i. Internal base pairing 1. Can have base pairing within the molecule itself ii. Rudimentary 3-d shape 1. Create a certain level of enzymatic activity 3. Transcription 1. Role of promoter in DNA i. Base sequence TATA 2. Role of transcription function i. DNA binding protein 3. RNA polymerase i. Synthesize RNA b. Day 10 1. Transcription 1. DNA to RNA 2. Finding the start site i. Promoter -- base sequence 1. TATA Box 3. Role of Transcription factors i. DNA Binding protein complex 4. Assembly of RNA polymerase i. Read DNA 3' to 5' ii. Generation of the RNA transcript 2. Fate of RNA transcription (Pre RNA) 1. Complementary to DNA 2. Pre-RNA -- edited by nuclear enzymes i. Edited RNA 1. Exons -- expressed 2. Introns -- intervening 3. Translation RNA to protein 1. Players i. tRNA, rRNA, mRNA 1. Exported from nucleus through nuclear pores 4. Concept of the codon 1. 4, 16, 64 2. Set of 3 -- bases encode for an Amino Acid 3. Concept of start codon AUG i. s.Ribosomal subunit 1. Small ribosomal subunit ii. "Begin Here" site iii. Sets the open reading frame iv. Stop codon 1. UGA UGA UAA 2. UGG can also be included c. Day 11 1. Protein synthesis at cytoplasmic proteins on free ribosomes 2. Protein synthesis on Rough ER 1. The signal peptide i. Series of 17-20 amino acids ii. Mostly hydrophobic iii. Tell the set of amino acids to bind to the structure signal recognition particle 2. The signal recognition particle i. Role of hydrophobic binding ii. Another series of events that guide the machine 3. Arrival at the ER i. Ribosome receptor ii. S.R.P. receptor iii. Translocon -- protein translocation 1. Bind to the peptide and take to the endoplasmic reticulum a. Being shoved across b. Needs to then go to the lumen of the ER 2. Hydrophobic binding 4. Depositions the protein in the ER i. Secreted and lysosomal proteins 5. Depositing -- transmembrane segments of T.M.P. 3. Tissues 1. Definition i. Group of similar cells reformations ii. A similar function 2. Types i. Epithelia 1. Will return to 2. Essential for life 3. A boundary land 4. A point of interface a. Skin, tongue, lips, inside of cheek b. All throughout the body ii. Connective iii. Muscle iv. Nerve Week 4 a. Day 12 1. Tissues a. Definition b. Types Epithelia i. ii. Muscle iii. nerve 2. Structure of Epithelium a. Form surfaces and boundaries Epithelia in stomach skin and kidney are some examples i. b. Composed of cells organized in a continuous sheet c. Cells attached to a basal lamina i. Will have boundary of plasma membrane ii. Provide attachment site Anchoring point and orientation iii. iv. Role of extracellular proteins d. Cells are oriented with respect to basal lamina i. Basal AM Apical ii. 1. Inside of mouth 2. From cheek to anus iii. Endothelium 1. Forms around blood vessels iii. Mesothelium 1. Organs and body cavity e. Cells replicate Self-replacement i. 1. Fix problems 2. Capable of replicating 3. Carcinoma a. Can become a cancer cell because they can lose ability to control how they divide 3. Cell Junctions a. Anchoring junctions i. How cells associate with one another and basal lamina ii. Hemi desmosomes 1. Integrin a. Lash the cell to the basal lamina and effect the cystocele to the cytoplasam iii. Desmosomes 1. Symmetrical junction 2. Cadherin b. Occluding Junctions i. Tight junctions c. Communicating junctions i. GAP junctions ii. Intercellular communication 1. MW < 1000 4. Exocrine cells as epithelial b. Day 13 1. Gap Junction structure and control 2. Epithelium and structure of the exocrine gland a. Have to go in some way to the outside world. Below is some of the glands that do b. Surface epithelium c. Duct epithelium d. Secretory epithelium 3. Types of exocrine glands 4. Connective tissue types and the cells that produce them a. Embryologic originates as mesenchymal cells i. The below are from the mesenchymal cells that change from the proteins that they recognize ii. CTP 1. Fibrocytes iii. Cartilage 1. Chondrocytes iv. Bone 1. Osteocytes v. Blood 1. Hematopoietic stem cells 5. Chondrocytes as typical connective tissue cells a. Elastic b. Fibro c. Hyaline i. See them in our ribs and in joints when broken away from each other 6. Skin as an organ a. Organ i. Two or more tissues working together is what the professor described as an organ ii. Epithelium of keratinocytes iii. Dermis of connective tissue proper 7. Organization of cells in skin a. Keratinocytes i. Epithelial cells. b. Fibrocytes i. Generated in the dermis c. Melanocytes i. Sits on the basal lamina and gives the skin color c. Day 14 1. Skin as an organ a. Skin structure i. Epithelium - layers ii. Connective tissue proper 1. Dermis iii. Melanocytes 1. Pigment generates cells a. Evolutionary history 2. Role of keratinocytes a. Vitamin a production 2. Bone a. As an organ Osteocytes - connective tissue i. 1. Muscle in blood vessels 2. Nerve 3. Long bone structure a. Epiphysis b. Diaphysis c. Spongy / trabecular bone and compact bone i. Made of individual struts ii. Highly organized iii. Malleable and can be changed b. Compact bone and the osteon i. Circular rings of osteocytes 1. Calcium phosphate 2. Collagen for shear strength 3. Hydroxyapatite for compression strength a. Crystal b. Can break if from the side 4. Similar to building a building 2. Bone growth a. Role of chondrocytes in growth plate i. As they divide, push the epiphysis away from the diaphysis 4. Bone remodeling a. Osteocytes- bone makers i. Also called osteoblasts ii. phosphate b. Osteoclasts - bone breakers i. Secrete low PH fluid c. Osteoporosis i. Bone with holes ii. Osteoclasts moving faster than osteocytes d. Day 15 1. The endocrine System secretion without ducts 2. Function: intercellular chemical communication a. Autocrine b. Paracrine c. Endocrine i. Has to be delivered by the blood to a target 3. The chemical signal a. Hormones i. Peptide/ protein 1. Hormones 2. Four percent is dedicated to this kind of communication in the genome 3. Large = charged a. Hydrophilic i. Doesn’t pass easily through lipid bilayer ii. Has to go through transmembrane protein receptor Modified amino acids ii. 1. Tyrosine a. Thyroid hormone b. Catecholamine i. Dopamine ii. Epinephrine iii. Hydrophilic 1. Need new receptors 1. Hydrophobic or nuclear receptors 2. Needs transmembrane proteins 2. Tryptophan a. Serotonin 4. Modified cholesterol a. Steroid hormones All start out as cholesterol i. ii. Hydrophobic derivative of cholesterol 1. Slither through lipid bilayer 2. Act as transcription factors 5. Modified fatty acids a. Prostaglandins i. Series of these Intracellular ii. iii. Act in cytoplasm 6. Receptors for the signal a. Hormone receptor b. Law of mass actin [H] + [R] --> <-- [HR] i. Forms hormone receptor complex ii. Charged interaction 1. Some hydrophilic, some hydrophobic 2. Some charged some uncharged iii. Concept of equilibrium 1. The probability of forming is equal to coming undone c. Concept of affinity - stickiness i. Need hormone to stick to receptor d. Concept of specificity i. Needs to be a specific interaction ii. Dissociation constant k d 1. Concentration at which half the hormones are occupied e. Agonist and antagonist i. Agonist fits in and gives response ii. Antagonist fits in and blocks from giving hormonal response Monday (week 5) a. Day 16 1. Hormone Actions and the hypothalamic pituitary Axis a. Large hydrophilic hormones i. G-protein coupled receptors 1. G 25 GLi aq 2. What happens after it is bound a. Downstream see changes in exocytosis and endocytosis b. See changes in gene transcription and gene translation c. Do a lot of things inside the cell d. G 25act through cyclic AMP b. Steroid hormones i. Hydrophobic hormone derived from cholesterol 1. Water insoluble 2. These molecules can go zipping through the lipid bilayer and into the cytoplasm and sometimes nucleoplasm ii. Cytoplasmic/nuclear receptors 1. Function as transcription factors a. Turn on genes 2. Structure of steroid hormone receptors a. Tells us what they do and how they do it b. How they start transcription 2. The hypothalamic pituitary Axis a. Posterior pituitary i. Extension of hypothalamus b. Neurons secreting hormones into blood i. Oxytocin - smooth muscle contraction ii. Vasopressin - water balance in kidney 1. Regulate kidney function 3. Anterior pituitary a. Arises as epithelial cells from Rathke's pouch b. Rathke's pouch i. Epithelial cells c. Troph cells in anterior pituitary i. Release into the blood from the hypothalamus to anterior pituitary and bind to troph cells 1. Now will go to the target organ and target gland to release those hormones d. Blood supply to hypothalamus an anti-pit i. Hypothalamic porta system e. Negative feedback
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