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Cell Bio Week 1 Notes

by: Marin Young

Cell Bio Week 1 Notes BIOL 3510

Marin Young
GPA 4.0
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About this Document

Intro to Cells and Protein Structure, from lectures January 19 and January 21. Happy studying!
Cell Biology
Dr. Chapman
Class Notes
Cell Bio, Biology, Proteins, biochemistry




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This 3 page Class Notes was uploaded by Marin Young on Saturday January 30, 2016. The Class Notes belongs to BIOL 3510 at University of North Texas taught by Dr. Chapman in Spring 2016. Since its upload, it has received 256 views. For similar materials see Cell Biology in Biological Sciences at University of North Texas.

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Date Created: 01/30/16
Week 1: Chapters 1, 4 | BIOL 3510 Notes by Marin Young History of Cell Biology: • 1665:Robert Hooke saw dead cork cells (plant cell walls) under his early microscopeand coined "cells" to describe little roomslike monks lived in • 1838/1839:Schleiden says plants are made of cells, Schwann says animals are made of cells ○ Schwann cells, which wrap around and insulate long neurons, are named after this Schwann • Cell theory = idea that all living things come from division of existing cells, and cells are "basic unit of life" • Similarities among all cells support idea of commonancestry • Today, cell biology mainly focuses on eukaryotes ○ Prokaryotesare interesting in terms of the microbiome--communityof bacteria living in human or animal body (gut flora)  Prokaryoticcells evolved3.5-3.8 billion years ago (eukaryotesevolved 1.5 billion years ago) ○ Several model organisms are useful in studying cell bio  Yeast: Saccharomyces cerevisiae, the beer yeast; model unicellular eukaryote  Small flowering plant: Arabadopsis, nice simple plant to study  Fruit flies: Drosophila, useful in genetics experiments  Tiny worm: C. elegans, a little nematodeuseful for neuron studies □ Full genus name is Caenorhabditis (not mentioned in lecture but probably worth at least seeing)  Mouse: Mus musculus and others;good lab animal that bears enough similarity to humans for many preliminary experiments  Humans: Homo sapiens; not convenientlysimple like others but frequently studied in biology Techniques and Technology: • Microscopyis described in terms of resolution, or the smallest distance where two points are distinguishable Human eye 0.2 mm Resolution intuitively means how small a structure you can see: think of little 200 µm inconsistencies in a line written by a bad ballpoint pen, or features like tiny gaps or dots in a fingerprint. Resolution is limited by the wavelength of light, like you've probably seen in this physics demo: Light 0.2 µm •Visible-light microscopy:requires staining and fixing (usually with heat) to see well, or microscopy 200 nm differential interference contrast (phase-contrast)to see living cells with optics tricks (three types) •Epifluorescent: uses a fluorescent stain to label structures and a UV lamp to cause the dye to emit visible light; best for living cells •Confocal fluorescent: uses a laser beam instead of a UV lamp to illuminate sample, which improves image quality by helping focus on a 3-D sample •Remember,the resolution is still 200 nm, but focus depends on sample thickness; you've probably run into this problem in labs where you can't see an entire object in focus at the same time (I'm thinking of diatoms, for anyone who took micro) •Most eukaryoticcells are 10-50 µm across, so light microscopyis good for visualizing cells and many subcellular structures, including nucleus Scanning 20 nm Specimen coated with a thin layer of heavy metal like gold and blasted at an angle with a electron beam of electrons,which bounce off the metal and onto a detector. A connected microscopy computer uses the electron pattern to determinestructure based on angles of "reflection"where electrons bounced. Transmission 2 nm This is a lot more like light microscopywith electrons instead of light: a condenser electron focuses electrons on a thin sample, which can be stained with electron-densechemicals microscopy like uranium acetate or lead citrate. Some areas absorb more electrons than others. The microscopy like uranium acetate or lead citrate. Some areas absorb more electrons than others. The electrons go through electromagneticobjectiveand projectorlenses and hit a detector screen to make a digital image. • X-ray crystallography: Make a pure, solid crystal of a protein and shoot X-rays through it. The diffraction pattern can be mathematicallyanalyzed to find atomicstructures. This is how Rosalind Franklin (NOT Watson and Crick) figured out that DNA was a double helix. • Nuclear Magnetic Resonance spectroscopy:Applying a strong magnetic field to a protein sample causes measurable atomic vibrations in patterns depending on how close hydrogen atoms are to each other. This only works for fairly small proteins--it's the same NMR used in organic chem, and it gets really complicated really fast. Amino Acids: • Proteins are made of amino acids, which all include an amine (-NH )2functional group and a carboxylic acid (-COOH) functional group ○ The form on the right is more chemically accurate: a proton is naturally transferred from the carboxyl group to the amino group ○ Each amino acid has a different R group that gives it unique properties ○ Sometimescalled "alpha amino acids" because the amino group is on the "alpha carbon" (next to the carboxylic acid carbon) • There are 20 natural amino acids: know which property-based groups they all belong to and their three-letterabbreviations (almost always first 3 letters) ○ See chart in lecture slides or my Exam 1 study guide • Amino acids in proteins are joined by peptide bonds, which contain an amide functional group ○ You might hear "amino acid residues"--amino acids in proteins technically aren't "amino acids" anymore (because they don't have a carboxylic acid group and organic chemists are anal), so only individual, free amino acids can really be called amino acids Protein Structure: • Primarystructure: order of amino acids (Asp-Lys- Gly-Tyr…) ○ Determinedby covalentbonds in backbone • Secondary structure: alpha helices and beta pleated sheets ○ Determinedby hydrogen bonds in backbone ○ An alpha helix has R-groups facing out and 3.6 residues per turn--the carboxyl group on residue 1 accepts a hydrogen bond from the amino group on residue 5 (NCC-NCC-NCC- NCC-NCC) ○ Beta sheets are accordion-folded and can be parallel (NCC-NCC-NCC backbone runs the same direction) or antiparallel • Tertiarystructure: folding into actual shapes • Tertiarystructure: folding into actual shapes ○ Determinedby noncovalentinteractions (hydrogen bonds, hydrophobic interactions, ionic bonds) plus covalent disulfide bonds between R groups ○ Domains are sections of a protein that can fold independently (even without the other sections of the same protein)  Gene regions for domains can be spliced together to create new proteins, in the lab or in cells (translocationmutations) • Quaternary structure:interaction of multiple polypeptide subunits ○ Some proteins are a singoe polypeptide chain and don't really have 4 structure ○ Proteins can be called homo___mersor hetero___mers  The blank is the number (di, tri, tetra)  Homo = identical subunits, hetero = different subunits ○ Rubisco (a plant protein, most abundant protein on Earth) has 8 large subunits (encoded in nuclear genome)and 8 small subunits (encoded in chloroplast genome)


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