Cell Bio Study Guide - Lecture notes All PDF

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All notes for cellular and molecular biology with Dr. Tenjo...

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Cell Biology Study Guide Exam #1 Chapter 1: Fundamental Units of Life DNA>>RNA>>Protein= Central Dogma Cell Biology: the study of cells and their structure, function, and behavior Unity and Diversity of Cells:  Cells Vary in appearance and function  Cells differ in size, shape and chemical requirements  Cells differ in their function o Specialization o Too much specialization can spoil cells ability to leave decedents Living Cells all have Similar Chemistry:  Similar molecules  Genes, DNA  Flow of information is the same  Proteins are important for shape, function and support All Present day cells have evolved from same ancestral cell: mutations, good bad, neutral. Genes Provide instructions for all cell form, function and complex behavior:  Blue print for structures and helps to package into chromosomes in nucleus o Genes direct cell activities o Genes contain program for making more cells o Changes in genes=evolution Cells Under the Microscope:  Light microscope led to the discovery of cells o Uses staining to see live samples  Samples must be larger than .2 micrometer, (200nm)  Fluorescence Microscopy: single ribosome o Confocal: lazer beam label cell components with fine detail, specific depth o Robert Hooke (1665), cork, Leeuwenhooke- “animalcules” o The Cell theory: (1838), Schlieden- plants are made of cells and embryos from single cell o 1839: Schwann Cells from plants, and animals are similar o all organisms are composed of cells o Cells are the structural unit of life o 1855-virchow- cells divide from other cells o Pasteur-spontaneous generation  Light Microscopy: fixed, light probes, confocal, lower resolution  Electron Microscopy: fine structure, cells are dead, higher resolution

o Samples must be very thin o Can see single molecules  Transmission Electron Microscope: uses beam of transmitted elections to see sections of thin tissue  Scanning Electron Microscopy: looks at surface, scatters electrons off surface Why are Cells Small?  Most eukaryotic cells have a single nucleus with 2 copies of most genes  Have a limited # of mRNA  Need a large SA for exchange with environment  Takes less energy to function  Need to get in and out wastes and nutrients  Easier to replace if small Are Virus’s Bigger than Bacteria? In most cases no they are 100 times smaller, but the Pandora virus is actually larger Can Bacteria be Multicellular? No some bacteria function as if they were multicellular when they are in colonial form Do Bacteria have Floating DNA? Yes The Prokaryotic cell is the most diverse and numerous on earth  Food source is organic carbon sources, nitrogen fixing photosynthetic  Spherical, rodlike, corkscrew There are more bacteria cells on us than there are human cells, 1:1 ratio of bacteria to human cells Archaea:  Extremeophiles Bacteria:  Every niche on earth  Mycoplasma-smallest cell, smallest genome o Cyanobacteria are more complex o Photosynthetic nitrogen fixers Bacteria and Archaea differ from one another as much as they do from eukaryotes Yeasts are simple free-living eukaryotes Basic Properties of Cells:    

ER: Materials designed for export Golgi: stacks of flattened disks, modifies and packages ER products Lysosomes: intracellular digestion Peroxisomes: hydrogen peroxide inactivates toxic molecules

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Cytoskeleton: o Actin filaments-thinnest, muscle cells o Microtubules-thickest, help move chromosomes, hollow o Intermediate filaments- strengthen cell, separates initial components into daughter cells in cell division Prokaryotic diversity o Classified on DNA sequences o Very diverse Eukaryotic cells: o Nucleus o Mitochondria o Chloroplasts o Internal and external membranes o Cytosol o Cytoskeleton o Cytoplasm Mitochondria o Generate energy, internal and external membranes o Evolved from the aerobic bacteria that lived inside the anaerobic ancestors of todays eukaryotic cells o Oxidize sugars to form ATP=cellular respiration o Contain own DNA Chloroplasts: o Turn light into energy, internal and external membranes o Contain own DNA Cell Specialization: o Unicellular eukaryotes, complex single celled organisms o Multicellular eukaryotes, different cell types for different functions  Differentiation  Happens during embryonic development in other organisms Number and arrangement of organelles relate to the function of the cell Protist: most complex eukaryote o Uni>multicellular Endosymbiotic Theory: o It is the belief that a host eukaryotic cell engulfed bacterium to help each other to survive, giving rise to these present-day organelles: mitochondria and chloroplasts. These two organelles are unique and resemble bacterium in that they contain their own DNA, reproduce by dividing in two, and have a double membrane.

Model Organisms:  6o Escherichia Coli (E. Coli)

 How cells replicate DNA  How decode genetic code for proteins o Yeast  Cell division cycle  Reproduces rapidly  1st genome sequenced o Arabidopsis (mustard plant)  Model plant  Similar to crop plants o Nematode  Exact # of cells  Apoptosis o Drosophilia (fruit fly)  Genes are carried on chromosomes  Genetic instructions encoded in DNA direct the development of a fertilized egg cell into adults  Mutated flies help identify what genes are needed to properly form body parts o Zebra Fish:  Transparent for first 2 weeks of life o Mouse:  Almost every gene has a human counterpart  Good because of short life cycles  Easy to control Ribosomal evidence shows that archaea and anaerobic eukaryotes split later than we thought Bacteria have Protein Bound organelles while eukaryotes have membrane bound organelles. Chapter 2: Chemical Components of Cells  Cells are made of a few types of atoms: C, N, O, H  Atoms are neutral  Mass= P+N  Atomic #= P  Outer shell determines reactivity Proteins can interact with ionic bonds Hydrogen Bonding: Water, Proteins, DNA Hydrophobic: insoluble, no charges, hydrocarbons Hydrophyllic: polar, soluble, carboxyl groups, reactive pH can affect cellular reactions

Buffers resist changes in pH Why is Si worse than C?  Its large, si-si bonds are weak, not as stable, polarity, can have more than 4 bonds, need carbon compounds for life! 4 Bio Molecules:  Carbohydrates: simple sugars, storage o Linear or ring o Very diverse because of (D, L) forms o Glycosidic bonds link by OH groups in condensation reaction o Glycoproteins:  Used to display info to others outside the cell  Covalently bond to carbohydrates o Glycogen and starch: energy/sugar storage, differ in glycosidic bonds o Oligosaccharides: 2-10  Bound to cell surface proteins and lipids  May be used for cell recognition o Polysaccharides: 1000’s o Can have H bonds  Cellulose  Chitin  GAGS o Peptide bonds in peptidoglycan- bacterial cell walls o Because each monosaccharide in a polysaccharide has many free hydroxyl groups, it can be harder to determine the arrangement of complex polysaccharides than it is to sequence a DNA molecule or amino acid sequence of a protein o Sugars help with production and storage of energy AND structural support and protection  Lipids: nonpolar, fats, fatty acids o Fats: Glycerol with 3 ester bonds to fatty acids o Diverse o Fatty Acids: unbranched hydrocarbons with 1 carboxyl group  Amphipathic  Saturated: contain no CC double bonds, solid at room temp, hard to break down  Unsaturated: have 1 or more CC double bond, liquid at room temp o Steroids: 4 ringed lipids implicated in ?????  Proteins: Polymers of amino acids, most diverse o Carboxylic acid and amino group attached to A-carbon o Contain L amino acids o R group determines name and function

o Know polar and non polar amino acids o Each protein has an N-terminus and a C-Terminus: growing end  Nucleic Acids: polymers of nucleotides, DNA, RNA o A,G,T,C o Pyrimidine’s and purines o Energy from ATP o Signal molecules o Sugar, phosphate, base o Ribose=2OH, 3’ and 2’ o Deoxyribose= 1 OH 3’ o Phosphodiester bonds between phosphate and 3’ carbon of sugar  Stereoisomers: asymmetric, 4 groups can form mirror image configurations o Enantiomers- (D,L) Condensation: expels H2O>>>forms glycosidic bond (hold sugars together, disaccharides) >>hydrolysis (water is consumed to break bond) Non covalent bonds specify precise shape of macromolecules:  Numerous Conformations formed from covalent bonds  Non covalent bond help choose the most preferential conformation Conditions that disrupt non-covalent bonds:  Stable folded conformation  Unstructured polymer chains  DNA- 3 conformations  Proteins  Enzymes  RNA-clover leaf structure Non covalent bonds are very important for macromolecule connections Hydrophobic interactions are key in the folding of proteins into a compact globular form Why can covalent bonds not be used in place of non covalent bonds in most macromolecule interactions? Because you need the ability to disassociate in order to form other stable conformations, help to bind more specifically and flexibly. Chapter 4: Protein Structure and Function  Proteins account for most of a cells dry mass  Proteins are found in all living systems  Made up of amino acids  1000’s of genes make many different proteins o enzymes (intra cellular chemical reactions) , structural, transport, motor, storage, signal, receptor, gene regulation, special purpose o Shape of proteins is determined by the amino acid sequence

Folding and Bonding: occurs in cytosol and ER  Proteins can fold and bond 3 ways: o Backbone-backbone o Backbone-side chain o Side chain-side chain o Formation of peptide bond is a condensation reaction o R group is not involved in peptide bonding o Non covalent bonds that assist in protein folding:  Hydrogen bonding  Electrostatic  Vander waals  Hydrophobic o Proteins fold into a conformation of lowest energy o Folding releases heat and increases disorder! o Ability of a protein to refold after being denatured is proof that all the information needed for its folding is contained in its amino acid sequence  4 Ways to Depict Protein Folding: o Backbone: overall organization of polypeptide chain  helps to compare structure of related proteins o Ribbon Model: Polypeptide backbone that emphasizes various folds o Wire Model: position of all amino acid side chains o Space filling: contour map of protein surface  Primary: Amino acids linked by peptide bonds  Secondary: Hydrogen Bonding, Alpha Helix and Beta sheet: easy to form because amino acid side chains are not involved. This mean many proteins can adopt these repetitive folding patterns o Alpha Helix:  Most common structural protein shape  Helical shape with H bonds to neighbor AA  Proline cannot participate as a donor in H bonding b/c helix breaking  H bonding vertically  Handedness: right, 3.6 AA per coil  “coiled-Coil”- 2 or 3 coil together when have hydrophobic side chains on one side  can cross the lipid bilayer because of exposed hydrophobic amino acid side chains o Beta Sheets: rigid structure at core of many proteins  Accordion shape  Antiparallel or parallel  H bonding horizontally  Very stable  Involved in permitting formation of amyloid fibers  bacteria use this stability to colonize host tissues

Tertiary: Disulfide Bonding, electrostatic, weak non covalent, hydrophobic, hydrogen bonding  Quaternary: Disulfide Bonding, non covalent b/w two or more polypeptides Proteins can form: Filaments, sheets or spheres  Globular: o Spherical  Fibrous: o Long rod like o Triple helical o Coiled coils o Antiparallel beta pleated sheets o Structural component of cells  Ability of macromolecules to be broken into components and spontaneously reform is proof of their ability to house all the necessary information to form complex structures. 

Extracellular proteins are often stabilized by covalent cross-linkages 

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Protein Domains: o Occur when proteins are composed of two or more distinct functional regions o Subunits can have more than one domain o Any segment of a polypeptide chain that can fold independently into a compact stable structure. o 40-350 amino acids folded into a helices and beta sheets Dimer: 2 identical folded polypeptide chains Tetramer: 2 non-identical binding sides on each monomer Conformational Changes: o Non random triggered by binding of specific molecules Proteins can be classified into families o Each member has an amino acid sequence and 3d conformation that is similar to the other family members Unstructured Regions: o Short loops that don’t exhibit defined secondary structure o Can bind with more specificity and less affinity o Intrinsically disordered sequences o Often link domains o Provide flexibility while increasing frequency of encounters MEMORIZE POLAR AND NON POLAR AMINO ACIDS Amino acids are amphoteric: different charge based on pH 22 Amino Acids Can you find amino acids in nature?? Why are only L conformations found in nature?

o Only contain L because amino acids can only form proteins when 1 stereoisomer is used. Combining L and D forms would give multiple conformations and the forms wont be able to make a specific protein  D amino acids are found in some micro organisms but don’t use ribosomes  D amino acids are made from L amino acids by a post transcriptional process  D amino acids lead to more potent venom Residues: series of peptide bond linked amino acids Constraints on polypeptides:  Must have stable 3d formation  Functional proteins cant engage in unwanted associations to form insoluble protein aggregates 2 amino groups = basic 2 carboxyl groups=acidic  insulin was the first protein synthesized  hemoglobin too  conformation is determined by energy, -G is minimized  All information for a protein is contained in the AA sequence Prion=misfolded protein o Prion only Hypothesis of infection: lack of immune response characteristic of infectious disease  Long incubation time  Resistance of the infectious agent to radiation that destroys living microorganisms o Infectious agent is called PrP sc, unusual ability to replicate within the body o Same AA sequence as Prp c but different folded 3D structure. o PrP sc is resistant to enzymatic attack, has insoluble fibrils o Prions aggregate to form amyloid fibrils o Prions can bind with normal proteins and change them to abnormal formations “seeding” o Primary cause of Transmissible Spongiform Encephalopathy’s (TSE’s)  Progressive neurodegeneration  Dementia  Loss of muscle control  NO CURE o Human Forms:  Kuru  Creutzfeldt-Jakob (CJD)  Fatal Familial Insomnia o Animal Forms:  Scrapie  Bovine Spongiform encephalopathy  Chronic wasting disease o Human Sporadic TSE

PrP misfolds spontaneously and generates prions by “autoinfection”-CJD o Human Inherited TSE:  Mutated PrP gene with tendency to spontaneously fold to PrP sc  Fatal Familial o Human Infectious TSE:  Eating infected meat/brains  Kuru Pathway from Infection to disease:  Penetration>>translocation>>multiplication>>pathogenesis 

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Chaperones: o Assist in protein folding o Bind to partly folded proteins o Form isolation chambers o Make folding more reliable and efficient o No instructions, just helpers to find most favorable pathway energetically

Polar AA:  Serine  Threonine  Cysteine  Tyrosine  Asparagine  Glutamine Non-Polar AA:  Glycine  Alanine  Valine  Leucine  Isoleucine  Methionine  Phenylalanine  Tryptophan  Proline Acidic: (-)  Aspartate  Glutamate Basic: (+)  Lysine  Arginine  Histidine How Proteins Work:  All Proteins Bind to other molecules

o Ligand binds to an active site of protein by non covalent bonds  Ligand is any substance bonded to a protein  Proteins can bind with high specificity and low affinity to a ligand due to non covalent interactions  Billions of different Antibodies with different binding sites o Antibodies are proteins that bind very tightly to targets (antigens) o Produced in vertebrates as defense against infection o Each antibody is made of two identical light chains and 2 identical heavy chains o Thus, both antigen binding sites are identical o Y shaped  Antibody Specificity: o Individual humans can make billions of different antibodies each with a distinct antigen binding site, each antibody recognizes its antigen with great specificity!!  Enzymes are powerful and highly specific catalysts o Hydrolase: catalyze hydrolytic cleavage reaction o Nuclease: breakdown nucleic acids by hydrolyzing bonds b/w nucleotides o Protease: break down proteins by hydrolyzing peptide bonds b/w AA o Ligase: joins 2 molecules o Isomerase: catalyzes rearrangement of bonds within a single molecule o Polymerase: catalyzes polymerization reactions like the synthesis of DNA and RNA o Kinase: catalyzes addition of phosphate groups to molecules o Phosphatase: cleaves phosphate groups  Enzymes can encourage a reaction in several ways: o Holding reacting substrates together in a precise alignment o Rearranging the distribution of charge in the reaction intermediate o Altering bond angles in the substrate to increase the rate of a particular reaction. Lysozyme Illustrates how Enzyme Works:  Enzymes are biological catalysts o Lower activation energy-speed up reactions o Substrate forms a tight complex with an enzyme by binding to active site o Most act through induced fit mechanism o Bind to substrates, and convert them into chemically modified products  EX: o Lysozyme catalyzes breakdown of polysaccharides from E. Coli peptidoglycan o Active site is long deep cleft that can bind 6-NAG and NAM o Lysozyme brings the reacting species together in a geometry that favors a reaction

o The 4th NAG-NAM unit to fit in the active site must be distorted to a less stable conformation o ASP 52 and GLU 35 residues of lysozyme interact with the 4th and 5th NAG-NAM units breaking the C-O bond  Transition state is very important in determining if a reaction will proceed How Proteins are controlled: 

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Catalytic activities of enzymes are often regulated by other molecules o Feedback Inhibition: negative regulation  Product inhibits production of more product  Prevents enzyme from acting o Gene expression o Rate of protein degredation o Containing sets of enzymes o Positive regulation is when a product stimulates enzymes in another pathway o Allosteric enzymes: 2 or more binding sites that influence one another can be + or – o Phosphorylation can control protein activity by causing a conformational change o Enzymes are solely regulated by the binding of small molecules o Phosphorylation and dephosphorylation are both post transcriptional modifications Covalent modifications also control the location and interaction of proteins o P53 cancer, has many known phosphate modifications GTP binding proteins are regulated by the cyclic gain an loss of a phosphate group o GTP=on GDP=off o Process is reversible ATP Hydrolysis allows motor proteins to produce directional movement in cells o ATP binds and cleaves a phosphate to excite movement o Unidirectional movement is possible with the coupling of a conformational change with the hydrolysis of ATP Proteins form large complexes that function as protein machines Proteins and enzymes do not work continuously or at full speed o Instead regulate activities in a coordinated fashion Proteins regulate activity + and – by feedback inhibition, phosphorylation and gene expression Protein phosphorylation involves the enzyme catalyzed transfer of the terminal phosphate on ATP>>hydroxyl group on serine, threonine and tyrosine Phosphorylation cycles are good b/c they allow the protein to change in response to the environment o Uses energy! Covalent Modifications also control location and interaction of proteins

o Phosphorylation can create docking sites for other proteins o Many docking positions allow cells to respond rapidly to the environment o Allow for optimal use of proteins How Proteins are studied:  Proteins can be purified from cells or tissues  Determining structure begins with determining the AA sequence  Geneti...