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Advanced Cell Bio Exam 1 Study Guide!

by: Izabella Nill Gomez

Advanced Cell Bio Exam 1 Study Guide! BCMB 311

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Hey guys, so with the first exam coming up, I've compiled all of the notes from lecture and the textbook to provide a detailed and vocab-based study guide for the first exam! Good luck, happy study...
Advanced Cellular Biology
Dr. Barry Bruce, Dr. J. Park
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This 32 page Study Guide was uploaded by Izabella Nill Gomez on Monday February 8, 2016. The Study Guide belongs to BCMB 311 at University of Tennessee - Knoxville taught by Dr. Barry Bruce, Dr. J. Park in Spring 2016. Since its upload, it has received 57 views.


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Date Created: 02/08/16
Advanced Cell Biology Notes! Chapter 1 Cells: small, membrane enclosed units filled with an aqueous solution of chemicals and the ability to create copies of themselves (simplest forms of life). Cell Biology: study of cells and their structure, function, behavior. -Cells vary in shape and size and chemical requirements, but have similar basic chemistry internally. Genetic information inside cells is carried in DNA molecules. In every cell, DNA polymer chains are made from the same set of monomers, nucleotides. Information is encoded in DNA and transcribed to RNA, which is translated to protein--central dogma. The appearance and behavior of a cell is dictated by its protein molecules, which serve as structured supports, chemical catalysts. Proteins are built from amino acids; all organisms use the same set of 20 amino acids to make proteins. Amino acids are linked in different sequences for a different 3D shape (conformation). -Protein is a single functional unit of architecture and functional properties in a cell. How a cell organizes this machinery? Cells function as aggregates, tissues. Properties above and beyond individual properties. Common features of all cells? Cell expansion and cell division. Protein composition affects polarization of cell walls and connected membranes (all surfaces are slightly different). -Viruses are chemical zombies; inert and inactive outside host cells, but can exert malign control over a cell once they can gain entry. -Mutations in a cell can create offspring that are malignant, benign or beneficial. Principles of genetic change and selection, applied repeatedly over billions of cell generations are the basis of evolution--process by which living species become gradually modified and adapted to their environment in more sophisticated ways. Evolution offers a compelling explanation as to why present day cells are similar in fundamentals: all inherited genetic instructions come from the same common ancestor. The ancestral cell existed between 3.5 and 3.8 billion years ago; developed into different types of cells through the long process of mutation and selection. A cell’s genome--the entire sequence of nucleotides in an organism’s DNA; provides genetic program that instructs the cell how to behave. For cells of plant and animal embryos, the genome directs growth and development of an adult organism with hundreds of different cell types. Can be varied; developed during embryonic growth from one fertilized egg cell. Different cells express different genes depending on the internal state and cues from surroundings. -Cells were made visible in the 17 century when the microscope was invented. Light microscopes use visible light to illuminate specimens and allowed biologists to see the structure that underpins living things. Electron microscopes (1930s) use beams of electrons to be the source of illumination. Extended the ability to see details of cells. Using the light microscope, Robert Hooke identified the first cells. The birth of cell biology occurred after 2 publications: Schleiden in 1838 and Schwann in 1839. Documented the results of systematic investigation of plant and animal tissues with light microscopes. The cell theory was eventually developed. Louis Pasteur then confirmed that cells do not arise spontaneously but originate from other cells. The theory of evolution by Charles Darwin explained divergence and similarities of different organisms. -In a section of tissue, divided into thousands of small cells, compacted or separated by extracellular matrix, made of protein fibers in a polysaccharide gel. Each cell is about 5-20 μ m in diameter. The inside of the cell is transparent, mostly colorless--seen by staining cells or using optical techniques. Inside the cell, the nucleus is in the middle. The cytoplasm surrounding is transparent. Fluorescence microscopes use sophisticated methods: electron image processing o see fluorescently labeled cell components in finer detail: can push limits to identify even a ribosome (which is a large macromolecular complex that is composed of proteins and RNA molecules). Electron microscopy has the highest resolution/magnification. Tissue must be fixed (preserved by solution) supported by embedding in resin/wax, sectioned into thin slices and stained before viewed. Cell components can then be organized into organelles--substructures with specialized functions. Plasma membrane is separate cell interior from exterior environment. Membranes surrounding organelles are internal. Transmission electron microscopy can look at thin sections of tissue, transmitting beams of electrons through the sample. Scanning electron microscopy scatters electrons off the surface of the sample to look at surface detail of cells. None of these can visualize individual atoms of the biological molecules (use X-ray crystallography). -Bacteria have the simplest structure of all cells. Essentially contain no organelles- no nucleus. Eukaryotes are organisms that contain a nucleus. Prokaryotes do not have. Prokarya often have a tough coat on the cell wall surrounding the plasma membrane, which encloses single compartment with cytoplasm and DNA. Most live as single-celled organisms, although chains/clusters can form. Chemically most diverse and inventive of cells. Exploit many different habitats. -Organelles are subcomponents within the eukaryotic cell (contain 2 double membranes). When cells engulf bacteria, vesicles and lysosomes consume via a hydrolytic process. Mitochondria are thought to have evolved from aerobic bacteria that lived inside of anaerobic eukaryotes. Almost any carbon-containing source is used for nutrient-- even CO2 (inorganic). Some prokaryotes can perform photosynthesis; others derive energy from chemical reactivity of inorganic substances in the environment. Other living things depend on the organic compounds that these cells generate from inorganic materials. Plants (using photosynthesis) also depend on bacteria to capture N2 from the atmosphere. Chloroplasts evolved from photosynthetic bacteria that once found a home inside of a plant ancestor. -2 domains of prokarya- bacteria and archaea. Archaea are found in extreme inhospitable habitats, resembling from primitive Earth. -Eukaryotes are generally bigger, more elaborate than bacteria and archaea. The nucleus is usually the most prominent organelle; enclosed within two membranes that form a nuclear envelope. Contains more molecules of DNA--long polymers with genetic information of the organism. Chromosomes are compact versions of this information before the cell divides. Mitochondria are present in almost all eukaryotic cells, among the most conspicuous organelles in the cytoplasm. Seem to be worm-shaped structures with branching networks. Individual mitochondria is enclosed in 2 separate membranes--with inner membrane formed into folds that project into interior of organelles. Mitochondria are generators of chemical energy for the cell by harnessing energy from oxidation of food molecules like sugars to produce ATP to power cell activities. Because mitochondria consumes oxygen and produces CO2 in the course of the activity, it’s called cellular respiration--breathing on a cellular level. Without it, organisms would be unable to use oxygen to extract the energy they need form food molecules. Mitochondria contain their own DNA information to divide in two (resembling bacteria). Chloroplasts are large, green organelles found only in the cells of plants and algae. More complex than mitochondria: possess internal stacks of membranes with pigment chlorophyll. Carry out photosynthesis-trapping energy of the sunlight in chlorophyll molecules in the process. Photosynthesis is the fundamental metabolism--most far-reaching energy source is solar radiation. Chloroplasts release oxygen as a byproduct. Plant cells can store the sugar for use and oxidize in mitochondria. Chloroplasts have their own DNA. In plant cells, they have water transporters that stores in vacuole that has hydrostatic pressure that fills up but continues to keep a certain shape in leaves (thanks to cellulose microfibers--resists Turgor pressure). The cell wall, chloroplasts, vacuole, Golgi move around in plant cells. Plastids--plasticity in form and function--pigmentation granules/pigments are accumulated from chloroplasts. Chlorophyll membranes are packaged in discs (grana) in chloroplasts. Thylakoids are where photosynthesis proteins are. Photosynthesis is membrane process. Chloroplasts and mitochondria were once considered prokarya. -Compartmentalization is the hallmark of eukarya. 1 place for DNA, many places for proteins--stamped with zipcode to correct organelle--if trafficked, causes problems (like in Alzheimer’s). -The ER is an irregular maze of interconnected spaces enclosed by a membrane site where most cell-membrane components as well as materials destined for export are made. Enlarged in cells that specialize in secretion of proteins and contiguous with the nuclear envelope--contents are regulated. Assembly site for many parts of the cell, secretion proteins, lipids, transportation site. Made on ribosomes attached to the ER. Stacks of flattened membrane-enclosed sacks are Golgi apparatus, which modifies and packs molecules made in ER for transportation. The Golgi is attached by the Golgi matrix (glue). Specialized is vesicularization, formed by pinching off. No mixing of contents, fusion is as precise as fission. Cis Golgi faces the ER, trans Golgi faces away (towards membrane)--functionally distinct compartments. Lysosomes are small irregular shaped organelles in which intracellular digestion occurs, breaking down unwanted molecules by recycling or excreting from cells. Peroxisomes are small membrane-enclosed vesicles that provide a safe environment for a variety of reactions in which HO5 (Hydrogen Peroxide) is used to inactivate toxic molecules. **Continual exchange of materials takes place between the ER, Golgi, lysosome and the outside of the cell, mediated by transport vesicles that pinch from membrane of one organelle and fuse with another, like tiny soup bubbles making big ones. Endocytosis carries products from outside the cell, exocytosis takes out. The cytosol is part of the cytoplasm is not contained within intracellular membranes (the largest single compartment)--behaves like water-based cells. Eukaryotic cells cytosol criss-crossed by long, fine filaments. Filaments anchored to one end to the plasma membrane or radiate out from a central site adjacent to the nucleus-- cytoskeleton--composed of actin filaments (abundant in muscle cells), microtubules (form hollow tubes) are the thickest, help align chromosomes in replication. Intermediate filaments which strengthen the cell--gives shape, ability to move, strength. The cytoskeleton’s function in cell division is most ancient--separates internal components into 2 daughter cells during cell division. The cytosol is a dynamic jungle of protein ropes are continually strung together and taken apart. Motor proteins use ATP to move along these cables, carrying organelles/proteins through the cytoplasm. Large and small molecules that fill the free space are swept by thermal motion. -According to a theory, ancestral eukaryotes were predators that fed by capturing other cells. Requires large size, flexible membrane, and a cytoskeleton to help the cell move and eat. The nuclear envelope could have developed to keep DNA function in a physical/chemical lifestyle. Most likely engulfed free-living bacteria. Partnership endued with oxygen-rich levels. Protozoans are free-living, motile microorganisms that prey on other cells. Ex: Didinium. Swims at high speed by beating its cilia/ releases darts from the snout to paralyze, then attaches and swallows/ Protozoans can be photosynthetic, carnivorous, motile or sedentary. They can be intricate and versatile. Model organisms contribute to our knowledge of biology through scientific research and expand our understanding of how cells work. -E.coli is a small, rod-shaped cell that normally lives in the gut of vertebrates. This model organism has taught the fundamental mechanisms of life. Yeast is a simple eukaryote, single-celled fungus with a rigid cell wall, immobile, with mitochondria but no chloroplasts. Carries out basic task of eukaryotes. Arabodopsis is a model plant, a small weed that gives insight into the development and physiology of crop plants and evolution of other species. Plants, animals and fungi diverged 1.5 billion years ago and bacteria, archaea, eukarya 3 billion years ago. Multicellular animals account for the majority of all named species of organisms, and the majority are insects and Drosophila is used to study genetics and modes of inheritance. Valuable model for studying human development and disease. The nematode is also studied for developmental processes that occur in other organisms. Ex: known apoptosis, programmed cell death by which surplus cells are disposed of--special for cancer research. Zebrafish (vertebrate--transparent for the first 2 weeks of life) are also studied for developmental processes. The mouse is also used to study mammalian genetics, developmental immunology, cell biology--for human disease. -At the molecular level, evolutionary change is slow. Evolutionary conservatism provides the foundation on which the study of molecular biology is built. Advanced Cell Bio Chapter 2 Notes! Chemistry of life is based on carbon compounds (organic chemistry); depends on chemical reactions that take place in aqueous solutions and in the narrow temperature ranges on Earth. Enormously complex, dominated and coordinated by polymeric molecules, chains of chemical subunits linked end-to-end whose unique properties enable cells/organisms to grow and reproduce and do all things characteristic of life. Tightly regulated by cell mechanisms. -Matter is made of combinations of elements that cannot be broken down or interconverted by chemical means. The smallest particle of an element that still retains distinctive chemical properties is an atom. Characteristics of substances other than pure elements including materials from living cells depend on which atoms they contain and the way they are linked to form molecules. An atom has a center of positively charged nucleus, surrounded by negatively charged electrons held by electrostatic attraction. Subatomic particles are protons and neutrons. The number of protons determines the atomic number (hydrogen is the lightest element). The electric charge of the proton is equal and opposite to the charge of the electron. Atomic number dictates the chemical behavior. Neutrons contribute to structural stability of nucleus--if too many/few, the atom can disintegrate by radioactive decay--does not alter the chemical properties. Isotopes are physically distinguishable but chemically identical forms of elements (different number of neutrons). Can occur naturally. Atomic weight of an atom or molecular weight of a molecule is mass relative to a 23 Hydrogen atom. Equal to P+N--specified in daltons. Avogadro’s number ( 6∗10 ) atoms allows to relate the quantity of chemicals to numbers of atoms/molecules. If a substance has a molecular weight of M, M grams of the substance contain 23 6∗10 molecules (mole). Organisms are made of only a small selection of elements (C,H,N,O)--constitute 96% of an organism’s weight. Composition is very different from inorganic environments. -In living tissues, electrons are the only parts of atoms that undergo rearrangements. Laws of movement dictate electrons can exist in certain orbits, 2 per energy level (electron shell). Electrons closest to the nucleus are held more tightly--innermost can hold only 2 electrons, 2 ndcan hold eight, 3 can hold eight, 4/5 --18. Electrons are most stable when electrons occupy innermost shells first. An outermost field shell makes the atom stable--chemically unreactive. -Atoms with incomplete outer shells have a strong tendency to react with other atoms. Ionic bonds are formed when electrons are donated by an atom and gained by another, covalent bond formed when 2 atoms share a pair of electrons. H atoms commonly form bonds with C,N,O,P and S. The number of electrons an atom must acquire or lose to fill an outer shell determines the number of bonds. H 2 Molecule: cluster of atoms held by covalent bonds ( ). The shared electrons form a cloud of negative charge that is densest between 2 positively charged nuclei. Attractive and repulsive forces are in balance when nuclei are separated by a distance of bond length. When an atom forms covalent bonds with others, multiple bonds have definite orientations of the shared electrons. Bond angles then form, as well as lengths and energies. Double bonds are shorter and stronger than single bonds and have an effect on 3D geometry--less flexible. Covalent bonds in which electrons are shared unequally are polar covalent bonds. Polar structure is one in which the positive charge is concentrated toward the end of the molecule (positive pole) and the negative charge to the negative pole. O and N atoms attract electrons strongly, H not so much. Bond strength is measured by the amount of energy that must be supplied to break the bond, measured in kcal/mole or kJ/mole. Kcal is the amount of energy to raise the temperature of 1 L of H2O by 1 degree Celsius. **1 kcal= 4.2 kJ. The typical covalent bonds are resistant to being pulled apart by thermal energies/motions, and are broken during specific chemical reactions controlled by enzymes. When water is present, covalent bonds are much stronger than ionic. When an electron (in ionic bonds) jumps from ex: Na to Cl, both atoms become electrically charged ions (Na loses, Cl gains). Because of opposite charges, Na and Cl attract each other and form an ionic bond (called salts)--highly soluble in H2O (polar). Cations=+, anions= --. Associations of transient interactions between molecules are mediated by noncovalent bonds, normally weak, but energies can sum to create an effective force between 2 molecules. Ionic bonds in NaCl are a form of noncovalent bond--electrostatic attraction. Strongest when atoms are fully charged---weaker ones are polar covalent bonds (allow the molecule to interact through electric forces). Any large molecules with polar groups have a pattern of +/- charges on the surface, accompanied by complimentary set of charges, matches with a second molecule. H2O has 2 H-O bonds, with unequal distribution of electrons, with preponderance of + charge on the 2 H atoms and - charge on the O. When + region of H atom comes close to a separate O, electrical attraction can cause a weak hydrogen bond. Much weaker than covalent bond and easily broken by thermal motion--but the combined effect of weak bonds allows water to be liquid at room temperature (constantly breaking and reforming)--without h bonds, life as we know it cannot exist. H bonds can occur in other instances (such as with a large molecule) and help fold into a particular shape. Hydrophilic molecules can dissolve readily in water due to polar bonds (includes sugars, RNA, DNA and many proteins). Hydrophobic molecules are uncharged and form few/no H bonds; do not dissolve in H2O. Hydrocarbons are important hydrophobic cell constituents. H atoms covalently linked to C atoms by nonpolar bonds. Because of no + charge, can’t form good H bonds--helps create lipid molecules for cell membranes. -When a molecule in a highly polar covalent bond dissolves with H, the electron is given up as a proton (H+) is released. The proton is attracted to partial negative charge on the O2 atom of an adjacent H2O molecule; the H+ can dissociate from the original and associate with H2O to form an H3O+ hydronium ion--the reverse reaction takes place readily--back and forth occurs often to find an equilibrium state. Substances that release protons when dissolving in water to form H3O+ are acids. The higher the concentration of H3O+, the more acidic the solution. Concentration of H+ is the pH scale. Strong acids lose protons easily to water--weak ones give up less easily. Sensitivity to changes in pH affect cell function. Acids tend to give up H+ more readily if the concentration is low and accept if high. The opposite of an acid is a base, which includes any molecule that accepts a proton when dissolved in water. Bases raise the concentration of hydroxyl ions (OH-) by removing a proton from a water molecule (becoming alkaline/basic--NaOH is a strong base because it dissociates into Na+ and OH- easily). Weak bases have a weak tendency to accept protons--more important in cells--like NH2 by generating OH-. Increase in OH- concentration decreases H+. Buffers are mixtures of weak acids/bases that adjust proton concentrations to pH 7 and keep the cell neutral. Carbon is outstanding among all elements to form large molecules. An a tom is small and has 4 electrons and 4 vacancies in the outer shell; can form 4 bonds. Can form stable covalent C-C bond for chains and rings and create long/complex molecules. Carbon compounds made by cells are organic molecules. Other molecules, even H2O, are inorganic. Methyl (CH3), Hydroxyl (OH), Carboxyl (COOH), 2−¿ Carbonyl (CO), phosphoryl ( PO ¿ ), amino (NH2) groups occur repeatedly in 3 organic molecules. Each chemical group has distinct chemical and physical properties that influence the behavior of the molecule in which the group occurs, including if it tends to gain/lose electrons and which molecules interact. Small organic molecules of the cell are Carbon compounds with weights between 100-1000 that can have 30 or 50 C atoms. Usually found free in the cytosol and have different roles--some as monomers to construct macromolecules--proteins, nucleic acids, large polysaccharides. Others as energy or potential subunits. Small th organic molecules are less abundant than macromolecules (1/10 ). 4 major families of small organic molecules: sugars, fatty acids, amino acids and nucleotides-- ¿ account for a large fraction of the cell’s mass. Sugars: monosaccharides (CH2O n --n=3, 4, 5, or 6. Larger molecules of sugars (carbs)--depending on the orientation of -OH groups, sugars can be converted into others and have 2 forms, D and L forms, mirror images of each other. Sets of molecules with the same chemical formula but different shape are isomers, and mirror images are optical isomers. Monosaccharides can be linked by covalent bonds (glycosidic) to form larger carbs. 2 monosaccharides make di, 3 tri, so forth. Larger sugars are oligosaccharides (2-10 subunits), and polysaccharides (100eds of subunits). The bond between an -OH on one sugar and -OH on another by condensation reaction, in which molecules of H2O are expelled. Other subunits use the same form--can be broken by hydrolysis, in which one H2O is consumed. Sugar polysaccharides can be branched and large-- arrangement is difficult to know. Glucose has a central role as an energy source for the cell; broken down to smaller molecules by reactions--can be stored as glycogen/starch. Also used for mechanical supports--ex: cellulose (plants), chitin (fungi, insects). Simple oligosaccharides can be linked to proteins to form glycoproteins and lipids for glycolipids (for membranes). Protect cell’s surface and help cells stick to one another. Different in types of cell surfaces: sugars are for blood groups. A fatty acid has a long hydrocarbon chain (hydrophobic) and hydrophilic head. Almost all fatty acids in a cell are covalently linked by carboxylic heads-- amphipathic. -Hydrocarbon tail of palmitic acid is saturated: no 2x bonds between C bonds and a max number of H. Some other like olcic acid have unsaturated tails. With 1 or more 2x bonds along length, creating kinks that inhibit the ability to pack together-- different between head (unsaturated) and soft (saturated) margarine. Many different fatty acids in cells differ only by cell length--serve as concentrated food reserve and can be broken down to use 6x as much energy as glucose. Stored in cytoplasm as fat triglycerol molecules---3 fatty acids joined. Can be broken down into 2 C subunits--identical to glucose. Lipids constitute fatty acids, insoluble in water but soluble in fats/organic solvents (ex: benzene). Can have multiple linked aromatic rings (steroids). Can form lipid bilayer, basis for cell membranes-- composed mostly of phospholipids--glycerol joined to 2 fatty acids, not 3. Leftover -OH links to hydrophilic phosphate group, then is attached to small hydrophilic compounds like choline. Strongly amphipathic. Membranes also have other lipids, such as glycolipids (sugar instead of phosphate). Form a monolayer, phobic tails in air and philic heads in water. 2 layers make a bilayer. Amino acids are small organic molecules that possess a carboxylic acid and amino group both linked to an alpha- Carbon atom. Also has a side chain to alpha-C. Cells use amino acids to make proteins--polymers made of amino acids, joined head to tail in a long chain that folds in a unique 3D shape. Covalent bond between 2 amino acids is a peptide bond; chain is a polypeptide. Always NH2 (N-terminus) and COOH (C terminus) at either end of the chain. Has structural polarity/directionality. 20 types of amino acids--can exist as optimal isomers in D and L forms (only found in proteins). 5/20 can have side chains to form ions and carry a charge (others are uncharged). Amino acids can be polar/nonpolar--philic/phobic. DNA/RNA built from nucleotides. Nucleosides are made of N-ring compound linked to 5-C sugar (ribose/deoxyribose). Nucleotides have nucleoside with 1 or more P groups to sugar--2 forms--rib/deoxyribonucleotides. The N-rings are bases; can bond H proton in acidic conditions to increase OH concentration (C,T,U,G,A). Nucleotides can act as short term carriers of energy--ATP (ribonucleotide) participates in the transfer of energy, 3 P’s linked in series by 2 phosphoanhydride bonds--breaking releases energy. Terminal P is frequently split by hydrolysis. Nucleotides also have a role in storage and retrieval of biological information. Serve as building blocks for construction of nucleic acids--long nucleopolymers linked by phosphodiester bonds between P group to sugar of one nucleotide and hydroxyl to sugar of the next nucleotide. Nucleic acid chains are synthesized from energy-rich nucleoside triphosphates by condensation reaction that releases inorganic pyrophosphate during phosphodiester bond formation. 2 types of nucleic acids--ribonucleic acids (based on sugar ribose) and deoxyribonucleic acids (based on deoxyribose). The based deoxyribonucleic has a hydroxyl at the 2’ position of ribose Carbon ring replaced by H. RNA is usually in a single-stranded polynucleotide, DNA double stranded. Linear sequence of nucleotides in DNA/RNA encodes genetic information. DNA is more stable with H bond helices, long term storage for hereditary information. RNA is the more transient carrier of molecular instructions. On a basis of weight, macromolecules are by far the most abundant of organic molecules in the living cell--principal building blocks from which a cell is built and confer the most distinctive properties of living things. Macromolecules are constructed simply by covalently linking organic monomers/subunits into long chains/polymers. Proteins are especially versatile and perform thousands of distinct functions in cells many proteins act as enzymes that catalyze the chemical reactions that take place in cells. -In nucleic acids, polysaccharides and proteins, each polymer grows by the addition of a monomer onto one end of the polymer down via a condensation reaction, in which a molecule of water is lost with each subunit added. In all cases, catalyzed by specific enzymes. Most macromolecules, although built predictably, are made from a set of monomers slightly different form one another--ex: proteins are built from 20 different amino acids. Polymer chains are not assembled randomly; have a sequence. Sequence is incredibly important for distinction of function. Most of the single covalent bonds that link subunits allow rotation of atoms, giving great flexibility, allows for multiple conformations (affected by thermal energy motions). Shapes highly constrained by weaker noncovalent bonds too--ensures preference to one conformation--determine chemistry/activity. 2 types of noncovalent bonds--electrostatic attractions--weak in water because of partially charged polar groups in attraction are shielded by H2O/inorganic interactions--helps enzyme to substrate guide certain chemicals to place. Hydrogen bonds are important in folding of the polypeptide chain and holding together strands of DNA. Van der Waals attractions are a form of electrical attraction by fluctuating charges when 2 atoms come within a short distance of each other. Weaker than H bonds, hydrophobic interaction expulse hydrophobic molecules form polar ones (like H2O and oil). Creates bonds in hydrophobic molecules. Gathered noncovalent bonds makes it possible for proteins to be enzymes, stabilize associations between macromolecules--can be used for larger structures. Advanced Cell Bio Chapter 4 Notes! Proteins are the main building blocks form which cells are assembled and constitute most of a cell’s dry mass. Provide the cell with shape and structure; proteins execute nearly all its functions. Enzymes promote intracellular chemical reactions by providing intricate molecular sugars, contoured with bumps/crevices that cradle/exclude specific molecules. Proteins in the plasma form channels/pumps controlling nutrient passage; can also carry messages from one cell to another. Protein molecules are made from a long chain of amino acids, held together by covalent peptide bonds. Proteins are referred as polypeptides, and amino chains as polypeptide chains. In each type of protein, amino acids are present in a unique order (amino acid sequence)--same from one molecule of protein to the next. Each polypeptide has a backbone with a side chain--polypeptide backbone is formed form repeating a sequence of core atoms (-N-C-C-C-). The two ends of each amino acid are chemically different. The N-terminus carries an amino group (NH3+, NH2). C- terminus has carboxyl group (COO-, COOH). Projecting form the backbone are amino acid side chains--part of the amino acid that is not included in making peptide bonds. Give unique properties--can be nonpolar, hydrophobic, negatively/positively charged chemically reactive, etc. Long polypeptides are very flexible, as many peptide bonds that link C allow free rotation. The shape of folding is constrained by weak noncovalent bonds that form within proteins. Involve atoms in the backbone and side chains. Include H bonds, electrostatic attraction, Van der Waals. It takes many nthcovalent bonds to hold two regions of a polypeptide chain tightly together. The 4 weak intersection is hydrophobic, also has a central role in determining the shape a protein. In In an aqueous solution hydrophobes involving non-polar side chains tend to be formed together to minimize their disruptive effect on the H-bonded network of H2O. Important factor to folding of any protein is the distribution of polar/nonpolar amino acids. Nonpolar side chains (leucine, phenylalanine, valine, tryptophan) tend to fold to interior/polar side chains (arginine, glutamine, histone) interact to form H bonds. When polar amino acids inside protein, usually H bonded to other polar amino acids or the peptide chain backbone. Conformation: folded structure of polypeptide chain determined by what folding minimizes free energy (G)--releases heat and increases disorder (energetically favorable). Protein can be denatured by treatment with solvents that disrupt noncovalent interactions; converts protein into flexible polypeptide that’s lost its natural shape. Under conditions where the solvent is removed, folding occurs spontaneously (renaturation). Each protein normally folds into one stable conformation, but changes slightly with molecular interaction. Change of shape is crucial to function. When folded incorrectly, sometimes forms aggregates that damage cells (can cause neurodegenerative disorders--sheep (scapie)--(mad cow) cattle--(Jakob disease) human--caused by misfolded proteins--prions. Prions can convert good proteins to bad ones--considered infectious. Protein folding is usually assisted by chaperone proteins by shaping through energetically favorable pathways or through “isolation chambers” in which single polypeptides are few without the risk of forming aggregates in the crowded cytoplasm--chaperones make folding more efficient/reliable, but shape is specified by amino acid sequence. Proteins are the most structurally diverse in the cell-normally 50-2000 amino acids long. Hpr (bacterial transport cell) is 88 amino acids long, facilitates the transport of sugar into bacterial cells. Backbone model of protein illustrates the overall organization of protein; ribbon emphasizes folds, wire shows possible amino acids involved in activity; space filling reveals what amino acids are on the surface. Alpha-helix folding pattern was discovered in alpha-keratin (for skin, hair, etc.). Beta sheet is found in fibroin, a major component of silk. Both result from H bond from N- H and C-O groups in the backbone. Because the amino acid side chains are not involved, alpha-helices and beta sheets can be generated from different amino acid sequences. Causes repeating pattern to form. A helix is a regular structure resembling a spiral staircase. Generated by placing many similar subunits next to another in a strict repeating form. Depending on the twist, the helix can be right/left handed. The alpha helix is made when a single polypeptide chain turns around to form a cylinder. H bonds are made between every 4 amino acid, linking C-O of one bond to N-H of another. Gives rise to regular right-handed helix. Short regions of alpha helix are abundant in proteins embedded in cell membranes, such as transporters/receptors. Sometimes 2/3’s alpha helices wrap around one another to form a stable coiled-coil structure. Forms when alpha helices have most hydrophobic side chains on one side to twist around each other with side chains facing inward to minimize contact with the cytosol (ex: keratin, myosin). Beta sheet is made when H bonds form between segments of polypeptide chain that lie side by side. When neighboring segments run in the same orientation (like N to C terminus) structure is parallel beta sheet; if opposite, anti-parallel beta sheet. Both types produce rigid pleated structure and form one of many proteins. Beta sheets give silk its tensile strength; permit formation of amyloid fibers, an insoluble aggregate related also to Alzheimer’s. These structures are formed from abnormally folded proteins, stabilized by beta sheets that stack tightly with sides that chain like the teeth of a zipper. The primary structure of a protein is its amino acid sequence. The secondary includes alpha and beta sheets that form within the segments of the polypeptide chain. Tertiary is the 3D form (alphas, betas, random coils, any other loops between the N and C terminus). Quaternary involves a complex of more than 1 polypeptide. Protein domain is a level of organization; any segment of a polypeptide that can fold independently into a compact, stable structure (40-350 amino acids folded in alpha’s, beta’s, etc.)--molecular unit from which larger proteins are constructed. Different domains associate with different functions (ex: CAP< small domain to DNA, large to cyclic AMP). Larger proteins can have dozens of domains, connected by unstructured lengths of chain. These intrinsically disordered sequences are often found as short stretches of linking domains in otherwise ordered proteins--have lack of folded structure, do not form protein crystals. Unstructured sequences can wrap around one or more target proteins by binding with high specificity and low affinity--provide flexibility while increasing encounters between domains. Can help scaffold proteins bring together proteins in intracellular signal pathways. Also give proteins like elastin the ability to 20n form rubberlike fibers (recoiling after stretch). possible polypeptide chains possible from n amino acids. But a fraction are present due to stability and need for “behaved” ( no unwanted interactions=no aggregates) functional proteins. Protein families--one in which each family member has an amino acid sequence and 3D conformation that closely resemble the others. Ex: serine proteases (family of protein cleaving enzymes) include digestive enzymes, elastase, enzymes involved in blood clotting. Portions of their sequences are almost the same size--3D conformations are alike too. But enzymatic/cleaving activities affect different proteins. The same noncovalent bonds that allow specific protein also allow proteins to bind to each other to produce larger structures in the cell. A surface on a protein that interacts with another molecule through noncovalent bonds is a binding site. If the binding site recognizes the surface of a second protein, tight binding of 2 folded polypeptides will create a larger protein, one whose quaternary structure geometry is precise. Each polypeptide in this protein is a subunit that can have more than 1 domain. IN a simple case, 2 identical, folded chains from symmetrical copies of 2 protein subunits (dimer) are held by binding sites (ex: CAP protein). Other proteins do not have identical polypeptides (hemoglobin). Globular proteins are polypeptides that fold into a complex shape like a ball with irregular surface. Enzymes tend to be globular. Fibrous proteins generally have an elongated #D structure (when needed to span a large distance). One class ex: keratin filaments-- extremely stable. Alpha-keratin is a dimer with long alpha-helices forming coiled- coils capped at either end by globular domains with binding sites to assemble into ropelike intermediate filaments, Fibrous proteins are especially abundant outside the cell (extracellular matrix--binds cells to form tissue)--collagen is the most abundant--bound (overlapped together, they form collagen fibrils--extremely strong). Elastin is another fibrous protein, but loose and unstructured to form elastic fibers for lungs, skin, arteries to stretch and recoil. Many proteins are either attached to the membrane or secreted as a part of the extracellular matrix. To maintain structure, polypeptide chains are stabilized by covalent cross-linkages--can tie 2 amino acids in the same polypeptide or join many polypeptides in a large complex (ex: cell fibrils, elastic fibers). Most common covalent cross links are S-S bonds (disulfide bonds) formed before a protein is secreted by an enzyme in the ER that links 2 SH groups from cysteine side chains adjacent in folded proteins. They do not change conformation but act as an “atomic staple” to reinforce the most favored conformation. Ex: lysozyme retains antibacterial activity because it is stabilized by disulfide links. Generally do not form in cytosol--mild conditions. -Biological properties of a protein are determined by physical interaction with other molecules. All proteins stick/bind to other molecules in a specific manner. Sometimes tight/sometimes weak/short-lived. Binding has great specificity--any substance bound by protein is a ligand. The ability to bind selectively and with high affinity due to a set of weak, noncovalent interactions--requires many simultaneous bonds to hold--possible only if the surface contours of the ligand fit closely to the protein. When molecules match poorly, few noncovalent interactions occur, and the 2 molecules dissociate as rapidly as they come together. At the other extreme, noncovalent interactions occur and persist for a long time (ex: ribosome). Region of protein that associated with the ligand (binding site) belong to amino acids widely separated on linear polypeptide chain brought together when the protein folds. Other binding sites help regulate protein activity. Parts like alpha helices may be required to attract or attach a protein to a part of the cell. Antibodies are immunoglobin proteins produced by the immune system in response to foreign molecules, especially those on the surface of invading microorganisms. Each antibody binds to a particular target molecule extremely tightly, either inactivating it or marking it for destruction. Antibody recognizes the target--antigen with high specificity. Antibodies are Y-shaped molecules with 2 identical antigen binding sites, each complimentary to part of the antigen surface. Antigen binding sites are formed from several loops of the polypeptide chain that protrude from the ends of 2 closely juxtaposed protein domains. The amino acid sequence loops can vary greatly without altering the basic structure of the antibody. AN enormous diversity of antigen-binding sites can be generated by changing only the length of the amino acid sequence of loops (how a variety of antibodies are formed). Enzymes are responsible for nearly all of chemical transformations that occur in cells--proteins that need ligand binding as a first step for function. Enzymes bind to one or more ligands (substrates) and convert them into chemically modified products--enzymes speed up reactions without being changed (catalyst)--permit cells to make/break covalent bonds. Each enzyme is highly specific, catalyzing only a specific type of reaction. Ex: hexokinase adds a phosphate group to D-glucose but not to optical isomer L-glucose. Enzymes often work in tandem, with the product of one enzyme becoming a substrate for the next. Result is elaborate metabolic pathways. Lysozyme is an enzyme that acts as a natural antibiotic in egg white, saliva, tears, other secretions. Severs polysaccharide chains that form the cell walls of bacteria. Because of the bacterial cell being under osmotic pressure, a small number of polysaccharide chains that are cut ruptures the cell wall, bacteria bursts and lyses. The reaction catalyzed by lysozyme is hydrolysis--adds one molecule of H2O to a single bond between two sugar groups in a polysaccharide, causes the bond to break. The reaction is energetically favorable because free energy of the severed polysaccharide is lower than the free energy of the intact chain. There are energy barriers for catalyzed reactions, called activation energy. For colliding H2O molecules to break the bond linking the two sugars, the polysaccharide has to be distorted into a transition state in which atoms around the bond have altered geometrically and electron distribution is changed. Requires random molecular collisions for energy input. In aqueous solution at room temperature, the energy of collision almost never exceeds activation energy; therefore, hydrolysis occurs extremely slowly. This is where the enzyme comes in; binding site (active site) that cradles substrate. Because substrate is a polymer, lysozyme’s active site is a long groove that holds 6-linked sugars in the polysaccharide at the same time. As soon as the enzyme-substrate complex forms, the enzyme cuts the polysaccharide by catalyzing the addition of H2O to one sugar-sugar bond. Severed chain is released for further cleavage--active site of the enzyme contains precisely positioned chemical groups that speed up the reaction by altering the distribution of electrons in substrates. Binding to the enzyme also changes the shape of the substrate, bending bonds to drive to a certain transition state. Then, a brief covalent bond between substrate and amino acid side chain occurs in the active site. The final reaction leaves the enzyme unchanged. Many drugs used to prevent illness inhibit enzymes. Ex: cholesterol-lowering statins inhibit CoA reductase, involved in producing cholesterol. Some proteins need more than just amino acids to do its job; they employ non- protein molecules to aid. Ex: photoreceptor protein rhodopsin detects light by retinal (attached to the protein by covalent bond to the lysine side chain. Retinal changes shape to absorb a photon, leads to electrical signal by rhodopsin to the brain). Another ex: hemoglobin with 4 heme groups to pick up O2. Enzymes also use non- proteins (ex: biotin for enzymes--classified as vitamin, not found in body). Most proteins are regulated in coordination to maintain in optimal state--energy in cell not depleted. Regulation: 1. Amount of protein in a cell (regulates gene expression and degradation rate) 2. Control of enzymatic activities by confining enzymes in certain membranes 3. Protein level switches. Regulatory sites at enzymes alter the rate of the enzyme-substrate conversion. Feedback inhibition (negative regulation--prevents acting) has an enzyme acting early in the reaction inhibited by the late product in a pathway. In positive regulation, the enzyme is stimulated to produce. Active/regulatory site communicates to allow events at the active site to be influenced by binding at the regulatory site. Interaction between sites depends on the conformational changes in the protein. Many proteins are allosteric: can adopt 2 or more slightly different conformation and activity is regulated by the shift from one to another. Enzymes are regulated solely by the binding of small molecule. Another method of regulation is via phosphate groups, that causes major conformational change due to 2 negative charges by attracting positive side chains from somewhere in the same protein, affecting ligand binding. Reversible protein phosphorylation is used to control many proteins, can be caused by signaling intracellular/extracellularly. Involves the enzyme-catalyzed transfer of terminal phosphate group of ATP to hydroxyl group on a serine, theonin or tyrosine side chain of the protein; catalyzed by protein kinase. Reverse (dephosphorylation) catalyzed by protein phosphatase. Phosphorylation can either stimulate or inhibit protein activity. Phosphorylation can do more than control activity; can create a docking site where other proteins can bind. Promoting larger complexes. Phosphorylation is not the only form of covalent modification that can affect protein location/activity--can be affected by the addition of an acetyl group/lysine side chain. The addition of fatty palmitate to cysteine side chains drives protein to associate with the cell membrane. Ubiquitin can activate degradation. Eukaryotes have a second way of regulation for protein activity via P- addition/removal. P not enzymatically transferred, but part of guanine nucleotide-- GTP--bound tightly to types of GTP-binding proteins. These act as molecular switches--active when GTP bound, but can hydrolyze to GDP (removing a P) and inactivate. The process is reversible: conformational charges enable certain specific proteins to divide movements of cells and components=motor proteins generate the forces responsible for muscle contraction and most other movements. Also power intracellular movements of organelles/macromolecules (help move chromosomes and organelles). Many move via ATP hydrolysis to drive orderly conformational changes--can be rapid. From small, single-domain proteins to large proteins of many domains, functions that can be performed are elaborate. The most complex are carried out by assemblies formed from many molecules. DNA replication, gene transcription, protein synthesis, etc--catalyzed by highly coordinated linked set of many proteins---protein machines. Hydrolysis of ATP-GTP drives an ordered series of conformational changes in some of the individual protein subunits, enabling coordinated movement of proteins. In this way, enzymes can carry out successive reactions in order. Cell employ proteins machines to produce more efficient tasks products--better than doing it individually. To study, proteins are now isolated from lab-grown cells-“tricked” into making large quantities of protein using genetic engineering--the first step to the purification process is to break open the cells and release its contents--the result is cell homogenate/extract--a physical disruption followed by the initial fractionation procedure to separate the class of molecules of interest--ex: all soluble proteins. The job then is to isolate the desired protein. Involves purifying through chromatography steps that separate the mixture into fractions based on properties (sit, shape, electric charge). The most efficient is to separate the protein by the basis to bind to specific molecules--affinity chromosomes. Can also be separated by electrophoresis. Here, a mix of proteins is loaded onto a polymer gel and subjected to an electric field polymerase migrates on gel depending on size and net charge. If too big, can use 2D electrophoresis. To determine the amino acid sequence of a protein--can be done by directly analyzing amino acids ain the protein. First, protein is broken down due to a smaller process by using selective protease. Then countless amino acids determined chemically. First protein sequenced--insulin. Faster way is through mass spectrometry--determined the exact mass of every peptide in a purified protein, which allows the protein to be identified from a database that has a list of every protein though to be encoded by the genome of the organism in question. To perform mass spectrometry, peptides are derived from digestion with trypsin and are blasted with a lasers. Heats peptides, becoming electronically charged and ejected as a gas. Accelerated by the power of the electric field, peptide ions fly towards the detector, and the time is takes to arrive is related to the mass and charge. (larger-slower, les s mass, more charge). The masses of protein fragments are produced by trypsin cleavage serve as fingerprint to identify the protein and gene from databases. For more complex mistrusted, increased resolution can be found via tandem mass spectrometry--broken down by first mass spectrometer, then 2 nd3D conformation can be found via X-ray crystallography, nuclear magnetic resonance spectroscopy (NMR). With genetic engineering/biochemistry, mass production of proteins can be done and now proteins can be made to do unusual tasks, not as efficient as naturally occurring enzymes, but getting close. Advanced Cell Bio Chapter 7 Notes! DNA does not synthesize DNA by itself, but acts like a manager, delegating tasks to workers. When a protein is needed, the nucleotide sequence is copied form an RNA segment called a gene, and the resulting RNA copies are used to make a protein. The central dogma of molecular biology is DNA to RNA to protein. Transcription/translation is a means by which cells read out or express instructions in their genes. Many identical RNA copies ca be made by the same gene, and each RNA can direct synthesis of the same protein. Successive amplification allows cells to synthesize large amounts of protein whenever necessary. Cell can regulate the expression of each of its genes according to reads. The first step to expression of genes is to copy nucleotide sequence to RNA (transcription). RNA is a linear polymer made of 4 different nucleotide subunits, linked by phosphodiester bonds. Differs from DNA--contains U instead of T, contains sugar ribose. The structure is dramatically different--DNA has 2x helix, RNA single--can fold into many shapes (like a polypeptide). Some RNAs have structural, regulatory or catalytic functions unlike DNA. Transcription begins by opening and unwinding a small portion of DNA to expose the bases on each DNA strand. 1 of 2 then acts as a template for synthesis of RNA. Ribonucleotides are added one by one to RNA chain, determined by complimentary base pairing. When a match is made, incoming ribonucleotides are covalently linked to the growing RNA by RNA polymerase. RNA chain--RNA transcript is elongated. TO leave DNA , RNA strand is displaced and DNA helix reforms-- doesn’t stay H bonded to DNA--also much shorter than DNA. RNA polymerase catalyzes the formation of phosphodiester bonds that link nucleotides together and form sugar-phosphate backbone of RNA chain. RNA polymerase moves stepwise along DNA, unwinding the helix to expose a new region of template strand for copying (5’-3’)--ATP, GTP, CTP, UTP provide energy needed for the reaction. RNA polymerase catalyzes basically the same reaction as DNA polymerase, but uses ribonucleotides. Can start replication without a primer. Likely evolved because transcription need not be as accurate as DNA replication--RNA not used for 4 permanent storage--so mistakes have minor consequences-- 10 nucleotides per 1 mistake. RNA that directs synthesis of proteins is mRNA. Usually carries information transcribed form just one gene to one protein. In bacteria, adjacent genes can be transcribed and consecutive proteins synthesized. rRNAs form structural and catalytic core of ribosomes, which translate mRNAs into protein, and tRNAs act as adaptors that select specific amino acids and hold them in place on a ribosome for incorporation into protein. miRNAs serve as key regulators of eukaryotic gene expression. Gene expression refers to the process by which information in DNA is translated into product that affects a cell/organism. When RNA polymerase collides randomly with a DNA molecule, enzyme sticks weakly to 2x helix and slides rapidly along its length. RNA polymerase latches on tightly only after it finds gene region promoter, which has specific sequence of nucleotides that is immediately upstream of starting point for RNA synthesis. Once bound tightly, RNA polymerase opens helix to expose nucleotides--one side acts as a template. Chain elongation until terminator found--transcribed onto new RNA. In bacteria, sigma factor is responsible for recognizing promoter--seen because of unique factors lying outside of the helix so no need to open helix to find it. Polarity of promoter helps determine what side of the helix RNA polymerase will use for transcription. Because RNA polymerase can only synthesize in the 5’-3’ direction on the enzyme bound, must use strand with 3’-5’ direction as template. Direction of transcription varies from gene to gene (typically one promoter/each). Eukaryotic RNA polymerases have different types-- I, II, III responsible for transcribing different types of genes. I and II for tRNA, rRNA, etc. II transcribes most genes, including those for proteins and miRNA. In eukarya, RNA polymerase needs general transcription factors which must assemble at each promoter, along with polymerase before transcription; mechanisms of transcription initiation is more elaborate--regulation can be aided by regulatory DNA sequences, DNA packed into nucleosomes. GTFs (accessory proteins) assemble on the promoter, where they position RNA polymerase and pull apart DNA double helix to expose template strand--like sigma factor. Assembly starts with TFIID to a segment of DNA helix composed mostly of T and A nucleotides (TATA box). Upon binding, TFIID causes a distortion in DNA double helix, landmark for assembly of other proteins. TATA is key in many promoters for RNA II polymerase. Usually 25 nucleotides upstream. TFIID+TATA=RNA polymerase +nTFs--transcription initiation complex--assembly order differs from one position to next. Liberation of RNA polymerase from GTFs is the addition of P groups to RNA polymerase tail--initiated from TFIIH (with protein kinase). Once transcription begins, TFs dissociate from DNA, waiting to be reused. When RNA polymerase is released after transcription, P groupsare taken from the tail by phosphatases; polymerase then ready to find a new promoter. Only dephosphorylated form of TNA polymerase can initiate transcription. Bacterial DNA is exposed in the cytoplasm with ribosomes close for protein synthesis--unlike bacteria, eukaraya must undergo RNA processing in the cytoplasm--includes capping, splicing, polyadenylation. Enzymes that are responsible ride on phosphorylated tail of RNA polymerase II and process the transcript as it emerges from polymerase. Those destined to be mRNA--undergo RNA capping which modifies the 5’ end of the transcript, the end that is synthesized first. Capped by adding atypical nucleotide Guanine with methyl group attached to 5’ end of RNA--occurs after RNA polymerase produces 25 nucleotides--before finishing. Polyadenylation provides new mRNA with special structure at the 3’ end--unlike bacteria, mRNA trimmed by enzyme that cuts RNA at a certain number of nucleotides, transcript is finished off by 2denzyme that adds repeated (A) nucleotides to cut end--poly-A tail.--Both cap and polyadenylation increases mRNA stability, mark identification and allow export to the cytoplasm. Introns are noncoding/intervening sequences--expressed/coding sequences are exons--usually shorter. RNA splicing removes intron copies from pre-mRNA and stitches exons together. Poly-A occurs after splicing/sometimes before. After splicing, mRNA is ready. Cues in introns allow for correct splicing--found near each end of an intron, same or similar in all introns. Splicing machine cuts out in “lariat” structure, formed by reaction of “A” nucleotide. Splicing carried out largely by RNA molecules--snRNAs--packaged with addition proteins to form snRNPs (small nuclear ribonucleotide proteins)--recognize splice site sequences via complimentary base- pairing between RNA components and sequences in pre-mRNA. Together, sNRPS form spliceosome--large assembly of RNA and protein molecules that carries out RNA splicing in the nucleus. Splicing can be alternative to produce distinct proteins from the same gene. TO transport only good mRNA, selection is high in the nucleus via macromolecules--“waste” degraded in nucleus and parts reused. Amount of time that mature mRNA persists in the cell affects the amount of protein it produces. Each mRNA is eventually degraded by ribonucleases (RNAses) present in the cytosol, but lifespan varies depending on nucleotide sequence of mRNA nad the type of cell. In bacteria, usually degraded rapidly (lifespan=3 minutes). In eukarya, persist longer (sometimes 10 hrs-B-globin; or 30 minutes). Lifespan contributed by 3’ untranslated region, between 3’ end of coding sequence and poly- A tail. Process of transcription universal: all cells use RNA polymerase and complimentary base-paring--RNA splicing seems to mark fundamental difference between pro/eukarya. Splicing allows for a variety of protein --but need for larger genome and must discard a large fraction of synthesized RNA without using it. Early cells might have had introns lost in prokarya during evolution--allowing for faster reproduction. Yeasts (eukarya) have few introns. Other theory is that some introns are originally parasitic mobile genetic elements that invaded early eukarya. Translation is the conversion of information in RNA to protein. Genetic code is ruled by which nucleotide sequence of a gene through mRNA is translated into the amino acid sequence of a protein. The sequence of RNA is read in groups of 2. 64 possible combinations of 3 nucleotides , but only 20 different amino acids. Code is redundant. Group of 3 nucleotides in RNA is called a codon, which specifies one amino acid. The same genetic code is used in all organisms, with slight differences in mRNA of mitochondria in fungi and protozoa. ** Mitochondria have their own DNA replication, transcription, protein-synthesis machinery (ribosomes) independent of the rest of the cell. In principle, mRNA sequences can be translated in any one of the 3 different reading frames, depending on where decoding begins. However, only 1/3 of the reading frames in mRNA specifies the correct protein. Codons in mRNA do not directly recognize the amino acids they specify, group of 3 nucleotides do not bind directly to amino acids. Adaptor molecules recognize, bind to codon at one site and amino acid at another site (tRNAs)--each about 80 nucleotides in length. RNA typically fold into 3D structures by forming base pairs between different regions--if extensive, will fold back into a 2x helix--tRNA a good example--cloverleaf structure. Undergoes further folding to form compact, L-shaped structure held by H bonds. 2 regions of unpaired nucleotides are situated at either end crucial to function of tRNAs in protein synthesis. One of these regions forms anticodon, set of 3 consecutive nucleotides that bind to complimentary codon in mRNA. Some amino acids have more than one tRNA, and some tRNAs are made so they can “wobble” at the 3 position of codon and tolerate a mismatch. The number of kinds of tRNAs differ from one species to the next. rRNA must be charged to carry out role with the correct amino acid--recognition and attachment dependent on aminoacyl-tRNA synthetases, which covalently couple each amino acid to the appropriate set of tRNA molecules. In most organisms, different synthetase/amino acid (20 in all). Each recognizes specific nucleotides in both anticodon and amino acid arm of the correct tRNA. Synthesis is a catalyzed reaction that attaches the amino acid to the 3’ end of the tRNA--is one of many reactions in cells coupled to the hydrolysis of ATP. Recognition of a codon by an anticodon on tRNA depends on the same recognition as base-pairing used in DNA replication/transcription. Ribosome--large complex made from small ribosomal proteins and rRNAs--millions in a eukaryotic cell. Eukaryotic/Prokaryotic ribosomes are similar in structure and function. 1 large/small subunit (mass is over 1 million Daltons). Small ribosomal subunit matches the tRNAs to codons of the mRNA, while the large catalyzes the formation of peptide bonds that covalently link amino acids together into a polypeptide chain. Both come together on mRNA near the 5’ end to start synthesis, then pulled like a long piece of tape. As mRNA moves forward in the 5’-3’ direction, ribosome translates. Each eukaryotic ribosome adds about 2 amino acids/sec. Bacteria even faster=20/sec. 3 binding sites for an mRNA , A, P, E site. First charged tRNA enters the A site by base pairing with the codon, amino acid then linked to the chain in the P site, exits via E. Ribosome is a ribozyme--one of the largest and most complex structures in the cell-- composed of 2/3 RNA, 1/3 protein by weight. rRNAs are responsible for overall structure and ability to choreograph/catalyze protein synthesis. rRNAs are folded into highly compact, precise 3D structures that form the core of ribosome. Ribosomal proteins fill the surface to fill gaps of folded RNA-main role is to stabilize the RNA core while permitting changes in RNA conformation. The 3 tRNA binding sites are formed primarily by rRNA--but site for catalytic peptide-bond formation made by 23s rRNA of the large subunit. Catalytic site--peptidyl transferase similar to protein enzymes--highly structures--orients elongating polypeptide and charged tRNA. Ribozymes are RNA that have catalytic activity. Initiator tRNA is a special tRNA used to start translation, carries methionine--N- terminus synthesized first (always). Usually removed later by specific protease. Loaded onto P site along with other translation initiation factors--along with initiator tRNA only one able to bind tightly to P site without the large subunit. Then, small subunit binds to 5’ end of mRNA, moves to find AUG--with tRNA bound, factors dissociate to make way for large subunit and complete assembly. In bacteria, ribosome sequences on mRNA allow for binding/start upstream of AUG. as long as binding site precedes start on mRNA, prokaryotic ribosome can bind directly to start codon in interior of mRNA--allows mRNA to be polycistronic--encode different proteins from the same mRNA. Stop codons signal the end of translation--release factor protein binds to any stop codon that reaches A site on the ribosome-- catalyzing the addition of H2O instead of amino acid to phosphorylated-tRNA--finds carboxyl end of polypeptide chain form attachment to tRNA--released, ribosome dissociates. **Most proteins require chaperone proteins to fold correctly in the cell. Synthesis of most protein molecules takes between 20 seconds and several minutes. Multiple ribosomes bind usually to each mRNA being translated. Multiple rib


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