Chapter 3 & 4 Through January 27th
Chapter 3 & 4 Through January 27th Bio 1510
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This 0 page Class Notes was uploaded by Michelle Notetaker on Thursday January 28, 2016. The Class Notes belongs to Bio 1510 at Wayne State University taught by Dr. Nataliya Turchyn in Summer 2015. Since its upload, it has received 59 views. For similar materials see Basic Life Mechanisms in Biology at Wayne State University.
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Date Created: 01/28/16
Ch 3 The Chemical Building Blocks of Life 0 DNA vs RNA 0 Within each strand of DNA and RNA nucleotides are held together by phosphodiester bonds I Phosphodiester bonds are covalent bonds and are stronger than hydrogen bonds 0 In DNA 2 strands of deoxynucleotides are held together by hydrogen bonds Which form between their nitrogenous bases DNA is double stranded RNA is a single stranded A pairs With T with 2 hydrogen bonds DNA C pairs With G With 3 hydrogen bonds A pairs With U With 2 hydrogen bonds RNA The more hydrogen bonds the stronger the bond RNA Will only have hydrogen bonds during transcription by itself it does not have hydrogen bonds 0 Another Important Nucleotide 0 ATP adenosine triphosphate energy currency of the cell 0 ATP is comprised of an adenine ribose and 3 phosphates I Used to make RNA 0 Has 3 phosphate groups that are associated With energy 0 No organism can survive Without ATP 0000000 I What are Proteins made of 0 Proteins are enzymes that speed up chemical reactions 0 Consists of hydrogen R group N amino terminus carboxyl group c terminus all attached to a single C in the middle 0 20 different R groups and determines the chemical property of amino acid 0 Linking of Amino Acids 0 To make polypeptides dehydration synthesis must occur to link two amino acids together Which makes a dipeptide I A peptide bond is created and a peptide bond is polar covalent 0 Special Amino Acids O Proline causes a polypeptide to bend 0 Methionine is the 1st amino acid used to make a protein 0 Cysteine I its sulfur atom participates in the formation of a disulfide bond With S of another cysteine disulfide bond non polar covalent I Nonpolar Amino Acids O Nonpolar hydrophobic don t like water I Their R groups are nonpolar If R group consists of C or H atoms then they are nonpolar SC is nonpolar in Methionine Aromatic amino acids have benzene rings Nonaromatic amino acids do not have benzene rings OOOO Polar Amino Acids 0 Polar are hydrophilic which loves water 0 Their R groups are polar I Because there is oxygen which is far more electronegative O O H OCN I polar covalent O S H polar 0 Only tyrosine is aromatic Charged Ionizable Amino Acids 0 Can be positive or negative charged R groups 0 Negatively charged amino acids are acidic I Acidic carboxyl group Positively charged amino acids are basic 0 ALL ARE POLAR I Which means they are also all hydrophilic 0 Some Important Facts about Proteins 0 Amino acid sequence causes polypeptide to assume a particular shape 0 Shape of protein determines its specific function 0 Protein s shape depends on levels of structure I Primary structure I Secondary structure I Tertiary structure I Quaternary structure Folding of Polypeptides 0 Primary structure sequence of amino acids joined by peptide bonds 0 Primary structure is nonfunctional 0 Secondary structure is nonfunctional I Secondary structure can be a beta pleated sheet or an alpha helix 0 They form because of hydrogen bonds 0 Oxygen of one amino acid and hydrogen in another amino acid 0 They also have polypeptide bonds The Final Stages of Folding Tertiary structure the overall 3D shape of a polypeptide Forms because of interactions between R groups of various amino acids The polypeptide folds up assuming its 3D shape The tertiary structure makes other bonds with disulfide bridge 2 cysteines ionic bonds van der Waals attraction and hydrophobic exclusion O PEPTIDE BONDS ARE ALWAYS PRESENT Bonds That Make Polypeptides to Fold 0 Van der Waals attraction Forms between atoms at very close distance due to uctuating electrical charges 0 Ionic bonds form when there are positive R group and a negative R group O Hydrophobic exclusion Hydrophobic R groups of amino acids exclude O O O O themselves from water by staying together away from the water 0 Disulfide bridge is the strongest because it s a covalent bond it is followed With ionic bonds hydrogen bonds hydrophobic exclusion and then van der Waals 0 The Final Stages of Folding attraction O Quaternary structure arrangement of two or more polypeptide chains subunits in space 0 Importance of Chaperons 0 Proteins that help other proteins fold correctly I Many are HSP heat shock proteins 0 HSP they are expressed When cells are exposed to elevated 0 Denaturation vs Dissociation temperatures 0 Denaturation the process in Which protein becomes unfolded denatured When exposed to heat pH or chemicals nonfunctional Protein With 2 or more polypeptides it loses 4 3 and 2 structures Protein is made of 1 polypeptide loses its 3 or 2 structures In some cases denaturation can be reversed renaturation Dissociation is When polypeptides found in a protein come apart protein loses its 0 O O O O 4 structure ONLY 39 Salts cause dissociation 0 Lipids Don t Like Water Lipids I Fats triglycerides 0 Composed of 1 glycerol and 3 fatty acids 0 Saturated fatty acid no double bonds between C atoms 0 Usually solid at room temperature because their fatty acids lack double bonds causing them to pack closely together ex Coconut oil is saturated fat even though it s liquid at room temperature 0 Unsaturated fatty acid 1 or more double bonds 0 O O O Polyunsaturated fatty acid can have 2 or more double bonds Monounsaturated fatty acid has 1 double bond Double bonds cause tails to bend Usually liquid at room temperature because their fatty acids contain double bonds preventing them from packing close together 0 Cis fats have H atoms present on one side of the double bond 0 2 hydrogen bonds face up or down 0 Trans fats have H atoms present on opposite sides of the double bond 0 One hydrogen faces up and the other faces down 0 Fats and carbs store energy but FATS store MORE energy I Phospholipids 0 Form all biological membranes 0 It creates the cell membrane and internal membranes enclose organelles 0 Amphipathic lipids are lipids with hydrophobic and hydrophilic regions all steroids and phospholipids I Steroids 0 Found in animal cell membranes 0 Makes cell membrane less permeable to watersoluble molecules 0 Cholesterol 0 LDL lowdensity lipoprotein or bad cholesterol I has more cholesterol than proteins 0 HDL highdensity lipoprotein or good cholesterol I more proteins than cholesterol 0 A high level of cholesterol blood I atherosclerosis narrowing and hardening of blood arteries I May lead to heart attack or stroke 0 Cholesterol has a hydrophobic side and a hydrophilic side I Estrogen 0 Female sex hormone 0 Is needed for the development of female 2 sex characteristics 0 Testosterone 0 Male sex hormone 0 Is needed for the development of male 2 sex characteristics 0 Micelles and Lipid Bilayers O Micelles monolayered structures that form by adding detergents lipidlike molecules to water 0 Phospholipid bilayer more complicated structure where 2 layers form I Hydrophilic heads point outward I Hydrophobic tails point inward toward each other Chapter 4 Cell Structure 0 Cells 0 Prokaryotic lack nucleus before nucleus I Unicellular organisms I Bacteria I Archaeans O Eukaryotic true nucleus I Can be unicellular or multicellular 0 Yeast is a unicellular fungi I Some protists 0 2 or more cells I Animals I Fungi I Protists I Plants 0 Bacterial Cell 0 Pili I allows bacterium to attach to different surfaces 0 Cytoplasm I semi uid matrix that contains macromolecules and ribosomes O Ribosomes I non membranebound organelles that are involved in protein synthesis I The only organelles found in bacteria 0 Nucleoid I region where bacterial DNA is found I Prokaryotes have this 0 Cell wall I protects the cell maintains its shape and prevents excessive uptake or loss of water 0 Flagellum I help bacterium move around 0 Capsule I provides an extra layer of protection 0 Plasma membrane I encloses the cytoplasm 0 Bacteria O GramPositive I retain the gram stain purple color stain I Cell wall contains a thick peptidoglycan layer 0 Polysaccharides and peptides I Ex streptococcus O GramNegative I lose purple color stain and becomes light pink I Cell walls contains lipopolysaccharides other materials and a thin layer of peptidoglycan O Lipopolysaccharides are polysaccharides with lipids O Peptidoglycan is targeted by penicillin I Destroys cross links I Can use penicillin for grampositive bacteria I Cannot use penicillin with gramnegative I You need to destroy lipopolysaccharides but penicillin targets peptidoglycan which gramnegative bacteria don t have 0 Archaeans lack peptidoglycan in their cell walls so you can t use penicillin 0 How Do Bacteria Move Around 0 O O Bacteria move with one or more agella Bacterial agella are inserted in the cell membrane while other agella are on the cell membrane Flagella rotates but sperm adulates wave like motion 0 Animal Cell 0 Nuclear Envelope I surrounds nucleus 0000 O O Nucleus I membrane bound organelle where majority of DNA and RNA are found Rough Endoplasmic Reticulum RER I membrane bound organelle with ribosomes attached I Contains a hollow interior called lumen I Worm like structures in the lumen of RER are proteins Smooth Endoplasmic Reticulum SER I membrane bound organelle without ribosomes I Contains a hollow interior called lumen Cytoplasm Golgi I membrane bound organelle consisting of stacks of attened sacs Plasma Membrane Mitochondrion I membrane bound organelle where majority of ATP is produced I ATP is a modified nucleotide I Our muscles have the most mitochondrion because it needs ATP to contract Peroxisome I membrane bound organelle which contains enzymes that produce hydrogen peroxide and split it into water and oxygen Lysosome I membranebound vesicle that digests food and old organelles Centrioles I made of microtubules I Every animal cell has 2 centrioles which make up one centrosome microtubule organizing center it is a place in the cytoplasm where microtubules separates chromosomes during cellular division grow out from Ribosomes Eukaryotes have both plasma membranes and internal membranes surrounds organelles Animal cell lacks cell wall 0 Plant Cell 0 Nuclear envelope RER peroxisome mitochondrion plasm membrane cytoplasm Golgi apparatus SER Ribosomes and nucleus Plant cells have central vacuole chloroplast cell wall and an adjacent cell wall that are NOT found in plants Central vacuole I membranebound vesicle that stores water waste products and food I It needs to store water because they don t know when they ll receive water again Chloroplast I membranebound organelle where sugars are made I Chlorophyll makes the chloroplast look green because it s a green pigment 0 Capture light to make sugar In plants and some protists cell wall is made up of cellulose O In fungi cell wall is made up of chitin 0 Not all plants have lysosomes 0 Plants lack centrosomes with centrioles Nucleus 0 Nuclear pores I control passage of molecules in and out of nucleus 0 Nucleolus I region where rRNA are made I Where rRNA combine with proteins to make small and large ribosomal subunits Nuclear lamina I composed of intermediate filaments that provide support to the nucleus Chromatin made up of DNA and proteins I Makes up a chromosome 0 Nuclear envelope has an inner and outer membrane I 2 lipid bilayers Ribosomes O Cell s protein synthesis machinery O 0 Each ribosomal subunit is composed of rRNAs and proteins Ribosomes work together with mRNA Rough Endoplasmic Reticulum RER O O O O 0 Synthesis and modification of proteins Contains chaperons proteins that help other proteins fold properly Proteins short sugar chains glycoproteins The proteins in RER are at 3 destinations I Some proteins are released from the cell I Some are sent to lysosomes I Embedded into cell membrane and internal membranes White blood cells have a lot of RER I Antibodies are proteins Smooth Endoplasmic Reticulum SER O O O 0 Synthesis of lipids Store of Ca2 in the muscles cell Detoxification of drugs and poisons in the liver cells Ovaries and testes have lots of SER because it synthesizes lipids Golgi Apparatus 0 Functions in packaging distribution and an additional processing of molecules 0 Lipids short sugar chains glycolipids 0 In the lumen of Golgi apparatus lipids from SER become modified to glycolipids O Cis face receives 0 Trans face sends out Secretory Pathway O 0 Transport vesicle is not the organelle it is a membrane bound pocket which is derived from the membrane of the organelle Transport vesicle derive its membrane from the RER or SER O Secretory vesicle is derived its membrane from Golgi O Secretion is when proteins and lipids are released from the cell I Secretory proteins secretory lipids O Secretory pathway is a series of steps that the cell use to move proteins and lipids from endoplasmic reticulum to Golgi through transport vesicles then Golgi to cell membrane inside secretory vesicles and from cell membrane to outside of the cell 0 Lysosomes I membrane bound digestive vesicles 0 Lysosomes have digestive enzymes are proteins that are made in the RER and modified in the Golgi 0 Work best at acidic environments 0 Digests bacteria food damaged organelles 0 If lysosomes open then it will digest all macromolecules in cytoplasm 0 Central Vacuole 0 Membranebound vesicle in plant cells 0 Tonoplast is the membrane that encloses a central vacuole I Regulates materials that go in and out of the central vacuole 0 Some protists have contractile vacuoles and food vacuoles I Contractile vacuoles deal with water balance 0 Mitochondria 0 Found in almost all eukaryotic cells 0 Cristae folds of inner membrane I Increase the surface area of inner membrane Matrix semi uid Mitochondria can make some of their own proteins Some protists lack mitochondria 0 Contains ribosomes and circular double stranded DNA 0 Chloroplasts 0 Found in plants and some protists Makes sugar using solar energy in the process of photosynthesis Has an outer and inner membrane both are lipid bilayers and thylakoid membrane Thylakoid membrane contains chlorophylls and encloses thylakoids Granum is a stack of thylakoids Stroma is a semi uid I Circular double stranded DNA I Ribosomes I Hollow donut shaped disks called thylakoids O Cyanobacteria can photosynthesize because they have chlorophyll 0 The Endosymbiotic Theory 0 Endosymbiosis I living together in close association 0 Cyanobacterium or photosynthetic bacterium were engulfed 000 00000 0 Evidence in Support of Endosymbiotic Theory 0 Both mitochondria and chloroplasts surrounded by 2 membranes 0 DNA inside mitochondria and chloroplasts similar to bacterial DNA in size of shape 0 Ribosomes inside mitochondria and chloroplasts are similar to bacterial ribosomes O Chloroplasts and mitochondria replicate by binary fission not mitosis 0 Cytoskeleton Binary fission is asexual reproduction found in bacteria I division in half 0 Network of protein fibers found in all eukaryotic cells 0 Cyto Supports the shape of the cell Keeps organelles in fixed locations Involved in cell movement and movement of materials and organelles within cells 6 Cell 9 0 Skeleton supporting structure 0 Actin Filaments vs Microtubules 0 Actin Filaments contains 2 globular shaped proteins called actin They are twisted in a helix In our muscles actin filaments work together with proteins called myosin causing muscles to contract Maintains cell s shape Participate in cell movements such as crawling and contraction 0 Allows our white blood cells and protists such as amoebas to move by crawling 0 Microtubules are hollow tubes Globular shaped proteins called tubulins 0 Alpha and Beta Support and shape the cell Involved in movements of organelles and vesicles within cells Guide the movement of chromosomes during cell division Found in centrioles agella and cilia 0 Both are dynamic which means they can disassemble and reassemble easily 0 Intermediate Filaments 0 They don t break easily 0 Rope like assembly of fibrous proteins 0 Supports the nuclear envelope 0 Maintains cell s shape 0 Motor Proteins O Microtubule is like a highway 0 Motor proteins are like the trucks that move along microtubules 0 Dynein and kinesin motor proteins 0 Vesicle or organelle is cargo being carried by motor proteins using energy 0 Flagellum and cilia OO Cilia is found in some protists ciliates and in our respiratory tract Flagellum is found in some protists and human sperm 0 Have 92 arrangement of microtubules 9 outer pairs 2 central microtubules O Centriole and basal body have 90 arrangement of microtubules found inside of cilia and agellum 9 outer tripelets No central microtubule 0 What is outside of animal cell 0 Extracellular matrix Organizes cells in tissues Supports plasma membrane Communicates with cytoskeleton Composed of fibrous proteins glycoproteins and proteoglycans 0 Collagen and elastin fibrous proteins 0 Fibronectin glycoprotein 0 Proteoglycans proteins with 1 or more polysaccharide chains 0 Junctions Between Cells 0 Tight junction anchoring and communicating junctions found ONLY in animal cells Tight junction I connects the plasma membranes of adjacent cells in a sheet preventing the movement of material between them 0 EX Digestive tract Anchoring junction I connects the cytoskeleton of one cell with cytoskeleton of another cell with the help of proteins 0 Cadherin I proteins that help with junctions 0 Can be found where tissues stretch Communicating junction gap junction I involves the formation of gap between plasma membranes of 2 adjacent cells 0 Made of proteins called connexins 0 Allows animal cell to pass ions sugars and amino acids 0 Outside of Plant Cells 0 Plants have primary and secondary cell walls which are made up of cellulose 0 Plant Cells Communicate via Plasmodesmata O Plasmodesmata cytoplasmic connections between two neighboring plant cells 0 Function similar to gap junctions in animal cells
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