Cell Bio 200 - UBCO PDF

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Biology 200 May 10, 2016 Find the syllabus and other data for this class on Natureboy.com under this class listing. If any articles require a username and password use ‘article’. Find the link for the quizzes on the syllabus. Read all the applicable Chapters. Testable material comes from the text and what was covered in class. Cell$Theory$-$Chapter$1!

Macromolecules!

DNA$Replication,$repair,$and$ recombination$-$Chapter$6!

Central!Dogma!

Bioenergetics!

Three!Basic!tenets!

Steady-state!metabolism!

DNA!Structure!

Cells!can!be!cultured!

Coupling!reactions!

History!

Basic!Properties!of!Cells!

Activation!Energy!

Chromosome!Structure!

Prokaryotic!

Biological!Catalysts!

Chromatin!

Eukaryotic!

(ES)!Enzyme!substrate!complex!

DNA!Replication!

Activation!Energy!

Replication!

Enzyme!Kinetics!

Enzyme!Recap!

Scale! Plant!Cell!vs!Animal!Cell! Features! Cytoplasm!

Chapter$4$–$Proteins! Complexity!of!Proteins!

Organelles! Primary!Structure! Cellular!Respiration! Tertiary!Structure! Flagella! Quaternary!Structure! Prokaryotic!Diversity! How!proteins!work! Eukaryotic!Diversity! Induced!Strain!

DNA!Polymerase! Proofreading! Eukaryotic!Replication! Eukaryotic!Replication!Fork! Chromatin!Structure! DNA!Repair! DNA!Repair!

Model!organisms!pg.!27! Enzyme!inhibition!

Central$Dogma-$RNA$-$Chapter$7!

Genome! Regulation!of!Enzymes!

Central!dogma!

Protein!phosphorylation!

Amplification!

Viruses! Essential!Concepts:! Basic$Chemistry$-$Chapter$2!

Nucleus:$DNA$and$Chromosomes$-$ Chapter$5!

Chemistry!of!Life!

DNA!

Bonding!

Nucleotides!

Water!

Structure!of!Chromosomes!

pH!

Nuclear!Envelope!

Acidic/Basic!

Nuclear!Matrix!

Hydrocarbons!

Nucleolus!

Fatty!Acids!

Transcription!(in!bacteria)! Eukaryotic!transcription! Differences!between!Prokaryote! and!Eukaryote!transcription! Table!7-1!Types!of!RNA!produced! in!cells! Eukaryotic!Genomes! Exporting!mRNA! Transfer!RNA!

Assembly!

Proteolytic!venoms!

Photophosphorylation!

Translation!

Interaction!with!cells!

Light!Independent!reactions!

Digesting!Proteins!

Cell-ECM!junctions!

Carbon!fixation!

Cell-cell!junctions!

Calvin!cycle!

Plant!Cell!Walls!

Carbohydrate!synthesis!

Cell!wall!matrix!

Photorespiration!

Membranes$Chapter$11$-12! Membrane!functions! Basic!structure!of!the!Plasma! membrane! Membrane!composition! Cholesterol! Fluidity! Dynamic!Properties! Chemical!composition! Membrane!Proteins-!attached! asymmetrically! Protein!Movement! Barriers!to!Movement! Distribution!of!proteins! Transport!and!Permeability! Osmosis! Diffusion!of!Ions! Potassium!Channels!(Kv)! Glucose! Active!Transport! Coupling!Transport! Membrane!Potential! Chapter$20! Tissues! Extracellular!space! Basement!Membrane!(Epithelial! tissue)! ECM!fibers! Collagen!Problems! ECM!Fibers! Proteoglycan!complexes! Fibronectin! Laminins!

Respiration$Chapters$13-14! Metabolic!pathways! Redox!reactions!

C4!Plants! CAM!Plants! Chapter$15!

Mitochondria!

Internal!membranes!

Cellular!respiration!

Origins!

Oxidizing!agents!

Transport!of!Proteins!

Cellular!Respiration!

Pathways!

Glycolysis!

Endoplasmic!Reticulum!

Sources!of!Acetyl!CoA!

Biosynthesis!in!RER!

Fatty!Acid!Spiral!

Endoplasmic!reticulum!

Citric!acid!cycle!

Golgi!Bodies!

Electron!Transport!

Glycosylation!

Proton!motive!force!

Vesicle!shuttles!

Binding!change!mechanism!

Exocytic!pathway!

Energy!Accounting!

Non-lysosomal!proteins!

Anaerobic!

Release!of!materials!

Anaerobic!Eukaryotes!

Lysosome!enzyme!sorting!

Related!Organelles!

Lysosomes!

Autotrophic!organisms!

Lysosomal!disorders!

Photoautotrophs!

Uptake!of!materials!

Plant!Structure!

RME-!Receptor-mediated! endocytosis!

Chloroplasts! Photosynthesis! Harvesting!Light! Structure!of!Photosystem!2! Harvesting!Light! Photosystems! Splitting!Water!

Clathrin!Structure! Endocytic!Pathway! Metabolizing!cholesterol! Engulfing!particulate! Plant!Cell!vacuoles! Chapter$17$–$Cytoskeletal$hydrolases!

Production!of!NADPH!

Major!Functions!

Mitochondria vs Chloroplasts

Microtubules

How!Microtubules!Form!

History Invention of the microscope • • • •

Galileo Galilei – 1609 Robert Hooke – 1665 – Micrographia Anton Van Leewenhoek – 1676 o Was able to visualize cells from teeth Schleiden & Schwann (1800’s) o Developed cell theory and that all organisms are made up of cells.

We don’t know who invented the microscope

Cell$Theory$-$Chapter$1$$ Central Dogma – p.3 – The flow of information from DNA to RNA to protein – is so fundamental to life Proteins are built from Amino acids; all organisms use the same set of 20 amino acids to make their proteins. (they are simply linked into different structures (conformations) for the different proteins) Cells are the fundamental unit of living matter, nothing less than a cell can be called living

Three Basic tenets • • •

All organisms are composed of cells (Schleiden & Schwann) Cell is the structural unit of life (Schleiden & Schwann) Cells only arise from division of cells

Cells can be cultured • •

HeLa cells (Henrietta Lax – who had a tumor and these are still being used and into the future) You can grow cells outside of the organism (culture a cell) – this duplication process is not perfect so over time the cell creation starts to break down

Basic Properties of cells •

Complex but organized o Cells from different species share characteristics o Each type of cell exhibits structural consistency o Cells are structurally conserved o Possess genetic information o Can produce proteins • Can copy themselves • Acquire and utilize energy

Basic Properties of Cells •

Carry out chemical reactions

•

• • •

o Metabolism Have mechanical activity o “motor” proteins (can be used to move things along the cytoskeleton, grabs onto 2 things, uses energy and changes shape which causes movement and then changes back to original shape) Can respond to stimuli Robustness – cells can regulate themselves and change - maintain an interior homeostatic condition Cells evolve o All cells evolved from LCA (last common ancestor)

Two main types of Cells

Prokaryotic • •

•

• • • •

Archaea and Bacteria No nucleus o DNA packaged up in unbound nucleoid region o Single circular DNA No true membrane-bound organelles o Reproduction by binary fission (replicating DNA, moving it to either end and dividing in half) Most diverse and numerous cells Flagellum usually is very simple in prokaryotes and just spins Some have an extra membrane Shapes: Rod, spherical and corkscrew (spiral)

Eukaryotic •

•

• • • • • •

Eukarya (true nucleus) o Fungi, Animalia, Plantae, Protists o These 4 all share a common ancestor o Membrane bound organelle o Usually have a nucleus o Typically, quite a bit bigger than prokaryotes Nucleus o Separated by complex nuclear membrane o Complex chromosomes Complex organelles Complex cytoskeletal system (acts as a scaffolding for the cell) Possess ability to (ingest) phagocytize particles, or other particles by creating a vesicle Cellulose - cell wall in plants Divide through mitosis/cytokinesis 3 different RNA polymerase

*Cell types can’t be used to tell relatedness of organisms

Endoplasmic Reticulum (ER)- an irregular maze of interconnected spaces enclosed by a membrane. Where most cell- membrane components, and exported materials are made. Can be enormous in cells that are specialized for secretion of proteins. Golgi Apparatus – modifies and packages molecules made in the ER that are destined for secretion or transported to another cell compartment. Lysosomes – small, irregular shaped organelles that intracellular digestion occurs, releasing nutrients from food or breaking down unwanted molecules recycling or secretion from the cell. Peroxisomes – small, membrane enclosed vesicles that provide a safe environment for reactions that hydrogen peroxide is used to inactivate toxic molecules. Transport Vesicles – ferry materials between one membrane enclosed organelle to another. Endocytosis – at the surface of the cell, portions of the plasma membrane tuck inward and pinch off to form vesicles that carry material captured from the external medium into the cell. Membrane enclosed vesicles – the vesicles produced in endocytosis Exocytosis – the reverse of endocytosis, the vesicles inside fuse to the plasma membrane and are released into the external medium. (most hormones and signal molecules are secreted this way) Cytosol – the part of the cytoplasm that isn’t contained in the intracellular membranes, it’s usually the largest single compartment, most proteins are made by ribosomes in the cytosol. The early steps in the breakdown of nutrient molecules takes place here. Cytoskeleton – the system of protein filaments (see below for the 3 types) that criss-cross in the cytosol. Gives the cell its mechanical strength, shape control, and drives and guides movement. • • •

Actin filaments – thinnest, present in all eukaryote cells but in muscle cells they are especially abundant Intermediate filaments – strengthen the cell. Microtubules – thickest, have tube form, reorganize in dividing cells to pull duplicated chromosomes to opposite sides and distribute them to the 2 daughter cells.

Motor Proteins – use the energy stored in molecules of ATP to move along the ‘tracks and cables’ (the filaments) of the cytoplasm.

Scale • • •

Microns (micrometers, 10-6 m, µm) Nanometers (nm, 10-9 m) Size constraints o Surface area to volume ratio Volume

Surface Area

Cube with 1 cm sides

1 cm3

6 cm2

Cube with 5 cm sides

125 cm3 (5x5x5)

150 cm2 (5x5x6)

*Volume increases faster than surface area so organisms adapt to have more surface area

Plant Cell vs Animal Cell

Features Prokaryota Don’t have: •

Eukaryota Have:

Mitocondria, cytoskeleton, other organelles

• •

Mitocondria, cytoskeleton, other organelles Whole collection of other features

Cytoplasm Prokaryota • • •

Relatively simple Mainly use diffusion More constraint by surface area to volume ratio

Eukaryota • • • •

Cytosol Cytoskeleton Ribosomes (workbenchs for the production of protiens) Think of it as a bag of sticks and rocks with a gelatanous goo

Organelles Prokaryota •

none

Eukaryota •

membrane bound organelles o nucleus o ER o Golgi apparatus

o Mitochondria (specialized envir where cellular respiration happen, dbl membrane) o Cholorplasts (only arise from other plastids) o Vacules (longer term storage organelles)

Cellular Respiration Prokaryota Don’t neseccarily need to reproduce

Eukaryota • •

Involves mitosis/meiosis Spindle fibers

Flagella Prokaryota •

Simple protien filaments that rotate quickly

Eukaryota •

complex

Protozoans – single celled (unicellular) eukaryote, that is a free-living, actively motile micro-organism.eg. Didinium

Prokaryotic Diversity •

•

•

•

Archaea o Often extremophiles (a microorganism, especially an Archaean, that lives in conditions of extreme temperature, acidity, alkalinity, or chemical concentration.) Bacteria o Includes mycoplasma (any of a group of small typically parasitic bacteria that lack cell walls and sometimes cause diseases.) o Includes cyanobacteria (Blue green algae) General Diversity o Identified by specific DNA sequences (to some degree) o Species concepts perhaps not appropriate Identification o Culture – only 0.1% identifiable by traditional means o DNA sequencing § Metagenomes

Eukaryotic Origins •

Endosymbiont Theory – symbiogenesis - Andreas Schkimper

o Mitochondria – eubacteria o Chloroplasts – cyanobacteria

Eukaryotic Diversity • • •

•

•

Eukarya o Fungi, Protista, Animalia, plantae Uni-cellularity o Protist groups, algae Multicellularity o Evolved multiple times o Specialization of cells § Differentiation § Doesn’t take much to go from a colonial organism to a barely multicellular organism (sponge) 5 Clades: o Archaeplastida (plants and some algae) o Excavata (lots of flagellates) o Amoebozoa (Amoeba) o Opisthokonta (fungi etc.) Sponges

• • •

Pinacocytes - mainly cover the body - contractile have pores Archaeocytes - serving immune function, engulfing things that are foreign Choanocytes - creating water flow and picking things out of the water - can act like stem cells and become other cells

Model organisms pg. 27 •

reductionism! o E. coli (bacterium)- easy to culture, easy to come by o Saccharomyces Cerevisiae (brewers yeast) - can be haploid or diploid, small genome, carry out the same basic tasks that all eukaryotes do, contain mitochondria but not chloroplasts. o Arabidopsis (mustard plant) - small genome, flowering plant, short generation time, large seed production o Caenorhabditis Elegans (aka. C. Elegans - nematode) - easy to culture, short generation time, you can dry them and keep them, then add water and use them, possess a character called eutely (have a set number of cells for each species) o Drosophila melanogaster (fruit fly) – small but complex creatures, short generation time, life cycle complete in a week. o Mouse- small, short generation time,

May 11, 2016

Genome o A cell’s genome (the entire sequence of an organism’s DNA) – provides a genetic program that instructs the cell how to behave. o The simplest bacterium contains only about 500 genes. o The human genome is not the largest genome (some plants and some species of amoeba are bigger)

Viruses •

Considered to be non-living o Because they can’t live without a host o They don’t have characteristics of living things, o Not made of cells o Can’t reproduce without a cell (which they don’t have)

• •

•

• •

o They don’t have a metabolism o They are inanimate objects o Usually have a specific host range (some are generalized like rabies, but most don’t spread from 1 species to another) Virions Structure o DNA or RNA o Surrounded by capsid o Some surrounded by lipid envelop (which they steal from the host) Classified as: o Lytic o Lysogenic – assert DNA into host and stays there, then host has integrated DNA until something happens that can cause cancer and various other issues and ailments. Viroids o Potato spindle-tuber disease Prions – a mis-folded protein that can cause other similar proteins to also have this misshapen form o They are communicable, antibodies can’t deal with these o Not living o BSE – mad cow disease o They can spontaneously arise o We can’t really protect ourselves from these

Essential Concepts: • • • • • •

Cells are the fundamental units of life. All cells are enclosed by a plasma membrane, which separates the inside of the cell from tis environment. All cells contain DNA as a store for genetic information and use it to guide the synthesis of RNA molecules and proteins. Cells in a multicellular organism, though all contain the same DAN, can be very different. Animal and plant cells are typically 5-20 µm in diameter and can be seen with a light microscope, which reveals some internal components, incl. larger organelles. See pg. 36 for more

Basic$Chemistry$-$Chapter$2$ Chemistry • Structure and function o Cells o Molecules

Chemistry of Life 1. Based on carbon compounds 2. Depends almost exclusively on chemical reactions that take place in aqueous solutions in narrow range of temperatures 3. It’s very complex 4. It’s dominated and coordinated by collections of huge polymeric molecules (chains of chemical subunits linked end to end, whose unique properties cells and organisms to grow and reproduce and do things that are characteristic to life. 5. It’s highly regulated, there are a variety of mechanisms that make sure chemical reactions happen at the right place and time. Isotopes – an element which can exist in several physically distinguishable but chemically identical forms. Each having a different number of neutrons but the same number of protons

Bonding •

•

•

Covalent bonds – very strong and stable, when water is present o Shared pairs of electrons o Can vary in strength and whether they are single, double or triple bonds o Usually only broken in chemical reactions controlled by enzymes Polarity o Polar molecules – asymmetrical charge, the positive charge is concentrated toward one end of the molecule, and negative at the other - dipole o Non-polar molecules (relatively even distribution of charge over the molecule) § Affects the ability to dissolve § Like dissolves like o Some molecules have polar and non-polar regions § Polar functional groups are hydrophilic o Generally, if a molecule has an oxygen it will be polar because oxygen is very electronegative Non-covalent bonds o Ionic bonds – the complete transfer of valence electron(s) between atoms o 10-100 times weaker (in water) than covalent bonds § Ions held together solely by ionic bonds are generally called salts • NaCl § Many salts are highly soluble in water, and the ions dissociate § Positive ions are cations, negative ions are anions o Proteins associated with DNA often form ionic bonds o Hydrogen bonds – bonds that exist due to polarity (weaker than covalent bonds) § Water cohesion – when a positively charged region of H2O comes close to a negatively charged region of a 2nd H2O molecule, that electrically attraction is a hydrogen bond (but many weak bonds make a strong one)

§ § §

•

•

Easily broken by random thermal motions This bond typically happens between hydrogen and oxygen or nitrogen DNA base pairs are very strong because of the numerous hydrogen and the folding into a helix that make it strong Van der Waals interactions - are driven by induced electrical interactions between two or more atoms or molecules that are very close to each other. Van der Waals interaction is the weakest of all intermolecular attractions between molecules o Due to fluctuations in charge o Aided by complimentary surfaces o Very weak interaction but can be strong with lots of van der Waals interactions and complimentary surfaces o Geckos feet have van der Waals interactions, tarantulas on there toes on the hairs, lots of interactions working together, and lifting foot releasing a few at a time rather that lifting perpendicular to the surface. Hydrophobic interactions – don’t ...