BIO PDF - Covalent and Non-Covalent Bonds

What does a covalent bond result in? increased stability Why do covalent bonds form? To achieve a filled outer (valence) electron shell What is a noncovalent bond? Weak interactions between atoms or molecules where no chemical reaction takes place. What are characteristics of non-covalent bonds Prof...

What does a covalent bond result in? increased stability Why do covalent bonds form? To achieve a filled outer (valence) electron shell What is a noncovalent bond? Weak interactions between atoms or molecules where no chemical reaction takes place. What are characteristics of non-covalent bonds Profoundly influenced by temperature and pH, doesn't involve chemical reactions or require enzymes, vary in affinity (binding strength), and greatly influenced by concentrations of interacting molecules What is electronegativity? an affinity for electrons What does electronegativity determine? If the sharing of electrons is equal or unequal What is the saying for memorizing the four relative electronegativities, from greatest to least? "Obviously Not Crazy Hard" Oxygen (3.5), Nitrogen (3.0), Carbon (2.5), and Hydrogen (2.1) What happens in a covalent bond between atoms of the same element? The electrons are shared equally because the two atoms have the same electronegativity. What is a non-polar covalent bond? When electrons are shared equally between two atoms of similar electronegativity. The atoms have no charge. What are the conditions of both non-polar and polar covalent bonds in an aqueous environment? They are very strong and stable What is a polar covalent bond? Occurs when there is an unequal sharing of electrons that results in atoms having partial positive and negative charges What describes the location of a polar covalent bond? Close to the nucleus of an atom What kind of molecule is water? Polar What bonds do polar covalent bonds allow? Hydrogen bonds What kind of bond is located within the water molecule? Polar covalent bond What charges do the hydrogen and oxygen atoms have in water? hydrogen atoms- partial positive; oxygen atom - partial negative What overall charge does a water molecule have? Neutral How many other water molecules can a water molecule bond with? Four water molecules that are bonded by hydrogen bonds What makes a water molecule polar? The unequal sharing of electrons What are ionic bonds? Attraction between ions of opposite charge Why do molecules form ionic bonds? So the bonds can achieve a full valence electron shell What does a full valence shell mean in terms of stability for the molecule? The stability is increased; therefore, things will move closer to a molecule in which the stability has increased. What type of bond is an ionic bond? non-covalent bond What are ions? An atom or group of atoms that has gained or lost one or more electrons, thus acquiring a charge. What happens when two atoms are so unequal in their attraction for valence electrons? The more electronegative atom strips an electron away from its partner. What are the conditions of ionic bonds under aqueous conditions Not strong What does gaining or losing electrons do in an ion? Allows for increased stability What is an ion? The charged form of an atom, when protons and neutrons aren't equal What bonds are formed between water molecules? Hydrogen bonds What are hydrogen bonds dependent on? Atoms being in a polar covalent bond Are hydrogen bonds covalent? NO Do hydrogen bonds occur in a large number? Yes What are hydrogen bonds? Weak chemical bonds are formed when the slightly positive hydrogen atom is attracted to the slightly negative oxygen atom of a polar covalent bond in another molecule or another region of the same molecule. The atom that is more electronegative has what kind of charge? A negative charge The atom that is less electronegative has what kind of charge? A positive charge What are Van der Waals interactions? Interactions of electrons of nonpolar substances What does hydrophobic mean? Weak interactions between nonpolar substances in a polar environment What is an example of something that is hydrophobic? Oil in water; the molecules don't distribute or dissolve easily, they coalesce What is a polymer? A long molecule consisting of many similar or identical monomers linked together by covalent bonds. What is a real world example of a polymer? A train consisting of a chain of boxcars What are the functions of proteins? Communication (involves signals and receptors), defense, enzymes act as catalysts, movement, and structure What affects protein structure and function? The fact that opposite charges attract and same charges repel. The lack of charges affects fusion across the cell membranes. How many polypeptide chains could one protein molecule have? 2 or 3 What is a protein? They are polymers of amino acids, and they are extremely diverse in terms of function. What is a peptide? A short polymer of amino acids (12-24) What is a polypeptide? A full-length polymer that could have hundreds or thousands of amino acids What are the seven functional groups? hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, methyl Hydroxyl -OH Carbonyl -C=O Carboxyl -COOH Amino -NH2 Sulfhydryl -SH Phosphate -OPO3^2- Methyl -CH3 What is a dehydration reaction? A reaction that removes a water molecule and forms a new bond. What occurs in a hydrolysis reaction? When a water molecule is added and a bond is broken. This reaction consumes a water molecule What is a dehydration reaction the reverse of? Hydrolysis What is required to build things, but not break things? Cell energy What are the two acidic amino acids? Aspartic acid (Asp or D) and Glutamic acid (Glu or E) What are the three basic amino acids? Lysine (Lys, K), Arginine (Arg, R), and Histidine (His, H) Which functional group acts like an acid? Phosphate, loses hydrogen ions to surrounding solution Where do things move towards? Their lowest energy state What occurs when a bond is hydrophilic? When oxygens and nitrogens are bonded to elements with lower electronegativity What bond is classified as hydrophilic? A polar covalent bond What can polar covalent bonds form? Hydrogen bonds What can one single change in an amino acid being hydrophobic or hydrophilic result in? Sickle cell anemia What is residue? Any polymer that is made up of many repeating units When looking at nonpolar covalent side chains, what atoms will you only see? Carbon and hydrogen atoms What is the primary structure of a protein? The primary sequence of amino acids of polypeptide chains. It is not a 3-D shape What is secondary structure of a protein? It is a 3-D shape and consists of both an alpha-helix and beta-sheet model, which are commonly observed structures What is an alpha-helix model? It is the coil of a polypeptide and it is found in many different proteins, but not all Why do we see a alpha-helix and beta strand models? We see it because of regular repeating hydrogen bonding and because the side groups are pointed outwards What is a beta sheet? It is composed of two or more beta strands How are the side groups in a beta sheet composed? They aren't pointed inward, up, or down where they will disrupt the helical structure. How will beta sheets form? Within 1 polypeptide or different polypeptides What strands form a beta sheet? Parallel and antiparallel strands Why would a protein adopt an alpha helix or beta sheet model? Because of its environment, lowest energy state, sequence, or connections to something that is most stable What is the tertiary structure of a protein? The overall 3-D shape of a single polypeptide chain What is the quaternary structure of a protein? two or more polypeptide chains joined; the overall structure of a protein composed of more than 1 polypeptide chain What is a glycoprotein? Any class of proteins that have carbohydrate groups attached to the polypeptide chain What are two proton denaturing agents? Urea and mercaptoethanol What determines the structure of a polypeptide chain? The sequence and side chains of a protein What does dialysis provide? Information for separating small and large molecules and for diluting out urea and mercaptoethanol Where is the info for protein structure found? In the sequence of polypeptide chains What does the word prokaryotic mean? before nucleus What organisms of which domains are classified under prokaryotic cells? Bacteria and Archaea Where is the DNA concentrated in a prokaryotic cell? In a region that isn't membrane-enclosed (nucleoid) Which is smaller, a prokaryotic or eukaryotic cell? Prokaryotic What does the word eukaryotic mean? True nucleus What organisms of which domain are classified as being eukaryotic? Eukarya (protists, fungi, animals, and plants) Where is the DNA in a eukaryotic cell? In the nucleus and bounded by a double membrane Which cell is larger, an animal or plant? plant cell Do animal cells have a cell wall? No Does an animal cell have many vacuoles? Yes Where is the nucleus located in a plant and animal cell? Plant (on the side) animal (in the center) What contains the cytoskeleton Both the animal and plant cell What is the first thing we use to observe the inside of a cell? Centrifuge What does a centrifuge do? It pellets dense components, first encountering the nucleus Are cytoplasm and cytosol the same thing? NO What is cytoplasm? Everything within the plasma membrane, except for the nucleus What is cytosol? The fluid portion of the cytosol in which gel-like fluid compartments are suspended. Where are cytoskeleton proteins found and where do they extend to in cell division? They are found in cytosol and extend into the nucleus What is light microscopy (LM)? It is a special kind of microscopy that is based on fluorescence What is fluorescence? Molecules emit light energy (at a lower level) and omit light energy, which results in a loss of energy transformations What best describes the color component of fluorescence? The color that is emitted is different from the color that is omitted (what we only can see) What are fluorescent dyes? Small molecules that are fluorescent and have an affinity for a special biological molecule of interest What was the first naturally discovered protein? Green Fluorescent Protein (GFP) What is immunofluorescence microscopy? Almost all cell biologists use this tool, and it uses antibodies as a scientific tool in research What are microtubules? They are membrane-bound compartments and are involved in separating chromosomes, structural and directional movement rates (organelle to cell surface), and the movement of cilia and flagella Does the nucleus have microfilaments? NO How long can microtubule filaments span in the cell? They can span the entire length of the cell What is a microtubule? Millions of polypeptide chains that form an alpha and beta tubulin. How many amino acids does an alpha and beta tubulin each contain? 500 amino acids What are the characteristics of both an alpha and beta tubulin? They are complimentary in shape and chemistry, connect and associate with one another through non-covalent associations, and are NOT identical What is a characteristic of microtubule filaments at their different ends? They have directional polarity, which is a result of structural/directional polarity. They have positive and negative ends; however, this is not in relation to charge. What are characteristics of the motor proteins in a microtubule? They move cargo directionally along microtubules and use ATP What special contraption is located in microtubules, what is their function, and what direction do both structures move? Kinesin (moves toward the positive end) and dynein (moves toward the negative end) and they transport organelles Microtubules rapidly from and decay. What is the scientific term for this characteristic? Polymerization (rapidly forming) and depolymerization (rapidly decaying) What is a characteristic of mictrobules that allows chromosomes to move during mitosis? Dynamic instability What are microfilaments? Filamentous structures that are made up of thousands or millions of polypeptide monomers that associate with one another and are involved in contraction. Microfilaments work with motor proteins; therefore, what is this motor protein called? Myesin True or false, microfilaments have directional movement and support? True What are intermediate filaments? The skeleton through the cell that is involved in linking junctions from one cell to another, and they are crucial for keeping cells together in tissue How do intermediate filaments form? They occur when 2 polypeptides of an intermediate filament coil around each other, forming this structure In terms of diameter, of the three cytoskeletal filaments, what is the order in least to greatest? microfilaments, intermediate filaments, and microtubules What are intermediate filaments used in both structural and directional support? No, they are only used in structural support In intermediate filaments, what are actin? Fingerlike projections in individual cells (microvilli) How do microfilaments form? When two of the dimers associate with one another in opposite orientations, it forms a tetramer, and thousands of tetramers form a microfilament Why would some of our cells have fingerlike projections in the plasma membrane? To increase surface area and for absorption in the intestine Where does directional polarity have to be in the protein? All along the length of the protein What are lipids? An organic compound that is insoluble in water, nonpolar, and hydrophobic What does amphipathic mean? a molecule that has both hydrophilic and hydrophobic parts What part of the cell membrane lipid is hydrophilic? the head What part of the cell membrane lipid is hydrophobic? the tails What is the cell membrane's most stable and lowest energy state? The hydrophobic tails What would pure membrane lipids with added water form? Closed spherical compartments, which resemble cells What three characteristics do cell membranes have? Flexibility, fluidity, and freedom of movement (however, they don't flip or cartwheel) How are membrane lipids linked together? By hydrophobic, non-covalent interactions From top to bottom, what is the order of materials found in a phospholipid head group? Polar or charged group Phosphate Glycerol Are lipids symmetrical or asymmetrical? Asymmetrical Do all membrane lipids contain phosphate groups? No, but most do What are glycoproteins and glycolipids? Proteins and lipids that have sugar covalently linked What is phosphatidylinositol? A polar head group that gets cleaved off and acts as a signaling molecule throughout the cell, structural and cell communication role. What is a phosphatidylserine? It is exclusively within the intracellular leaflet side on cytosolic face. What are the functions of a phosphatidylserine? It acts a signal when cells undergo death, membranes are disrupted, asymmetry is lost, and for other cells to recognize and engulf or break it down In cell membranes, what is a kink the result of? A double-double carbon bond What type of fat occurs when double bonds are present? Unsaturated fats What are trans isomers? An isomer in which the functional groups are located on opposite sides of the bonds, resulting in a linear chain What are cis isomers? An isomer in which the functional groups are located on the same side of the bond, resulting in a kink in the chain Which isomer configuration is in our membrane lipids? The cis configuration, which are formed for the purpose of introducing a kink; they are formed by enzymes What kind of permeability does a lipid bilayer with no unsaturated fatty acids have? Lower permeability What kind of permeability does a lipid bilayer with many unsaturated fatty acids have? Higher permeability What kind of permeability will occur if a phospholipid has short tails? High permeability What are the characteristics of kinks? They are more permeable to certain substances, more fluid, and they affect the length of the tail What are the characteristics of non-kinked? They are less fluid and permeable What does fluidity mean? Molecules are exchanging places, referred to as the "fluid mosaic model" What does permeability mean? How readily do molecules diffuse across the lipid bilayer How does cholesterol influence the permeability of our membranes? It decreases the permeability, reduces membrane fluidity at moderate temperatures, and hinders solidification at low temperatures What is the affect on fluidity when having cholesterol in our membranes when temperatures are high? The membrane is less fluid What is the affect on fluidity when having cholesterol in our membranes when temperatures are low? The membrane is more fluid What does cholesterol act like in a cell membrane? It acts as a buffer, preventing any extreme solidness or fluidness in the cell membrane What influences permeability of a cell membrane? Whether or not something is charged, has a partial charge, or no charge, and the size of the molecule that wants to enter the cell Where is there a difference in permeability? In ions How do small solutes that don't readily diffuse across a pure lipid bilayer move across the cell membrane? They move across the cell membranes frequently and in large numbers. What are integral (transmembrane) proteins? They span the lipid bilayer, anchored in the membrane, their side chains are hydrophobic, and they span the lipid bilayer once or many times What are peripheral membrane proteins? They are associated with the membrane, but they don't span the membrane; they are located on the outside of it What are lipid-linked membrane proteins? They are proteins that are covalently linked to the lipid What kind of interaction does a single fatty acid tail have with a membrane? They have a stable interaction and they keep the protein at the membrane What is passive transport of proteins? When solutes move downhill and with the gradients; no energy is required What is active transport of proteins? When things move uphill and against gradients; energy is required What kind of transport do channels fall under? Passive transport, and they move ions as the solute Channels in membranes help with diffusion. What is diffusion and what is it a result of? Diffusion is the net movement from high to low concentration. It occurs as a result of random movement (thermal energy) and it has a net change that is more towards disorder What are ion channels? They move their solutes the fastest by many orders of magnitude; they can move up to tens or hundreds of millions of ions per second. What do ion channels allow? They allow movement, which results in an open structure What happens when ion channels are open? Molecules can fly through without changing What does a ligand-gated channel control in an ion channel? Whether the channel is open or closed. Without a ligand-gated channel, the channel is closed What can bind into a ligand-gated channel? A small molecule or a protein What kind of change does an ion channel NOT undergo? A conformational charge What influences the diffusion of water across a membrane? The movement of solutes What is osmosis? The diffusion of water across a selectively permeable membrane What does hypertonic mean? There is a higher concentration of solutes located on the outside of the cell, resulting in the shrinking of a cell because water follows the solutes What does hypotonic mean? There is a lower concentration of solutes located on the outside of a cell, resulting in the swelling or bursting of a cell because water follows the solutes What does concentration mean? It is the number of molecules in a given volume What are the common causes of diarrheal diseases that cause them to be fatal? Contaminated drinking water with microorganisms or bacteria, which disrupt the water flow What do protein toxins in contaminated water do? They bind to cells, enter and modify protein channels and lock them in an open state What are characteristics of uniporters? They are not nearly as fast as ion channels, but they can move hundreds or thousands of solutes per second. They also go through conformational change in association with each of the solutes What kind of transport does a uniporter fall under? Uniporters are passive transport; they can only facilitate diffusion What are symporters? When driving solutes go in the same direction What are antiporters? When driving solutes go in the opposite direction What kind of transport are symporters and antiporters? Active transport Why do symporters and antiporters exist? To move 1 particle of solute against a gradient, which requires energy. This energy comes from the other solute moving with its gradient (one thing goes downhill and another goes uphill) Where do gradients come from? ATP driven pumps, which move 1 or multiple solutes against their gradients What does ATP being broken down do? It drives many pumps Where are sodium potassium pumps? In the membrane of most cells How many sodium and potassium ions go in and out of the cell? 3 sodium ions go out of the cell and 2 potassium ions enter the cell In relation to the number of sodium and potassium ions outside and inside of the cell, what does this result in? A change in distribution, meaning that there is a positive charge outside of the cell and a negative charge is left behind inside of the cell Where is a potassium leak channel at and what is it's function? They are located in the nerve cells in the same membrane, and they are always open. When the potassium leaks out, the outside of the cell is more positive and the inside is more negative What are electrochemical gradients? They influence the movement of potassium and are competing forces in the movement of potassium What two things aid in the absorption of water? Glucose and sodium When dehydrated, what is a better solution than pure water? Water that contains glucose and sodium What is bulk transport? The movement of large molecules, such as proteins, in and out of the cell What is phagocytosis and where does it occur? It is the uptake of the largest molecules in the cells and a limited number of cells carry out this process. It occurs in neutrophils and macrophages (white blood cells). It is very important for internalizing microbial cells (yeast and bacterial) What is pinocytosis? It is cell drinking and refers to the taking in of the plasma membrane and whatever is in the fluid phase of the cell. What happens if something enters the cell membrane by phagocytosis and pinocytosis? It is not in the cytosol, but separated by a membrane What is the process of something leaving the cell through a membrane transport protein? It goes from cytosol to extracellular fluid What happens when a solute enters a cell through a channel, pump, symporter, or antiporter? It enters from extracellular fluid to cytosol What is receptor-mediated endocytosis? The infolding of a protein, and when the cells regulate what they take up for their environment, and it brings in cell-surface receptors and things bound to those receptors. What is included in metabolism? Cellular respiration and photosynthesis What releases energy? Breaking and forming bonds, new bonds which are more stable than they ever were before What is the Gibbs Free Energy Formula? Delta G= Delta H - T (Kelvin) Delta S How do you calculate Delta G? The difference between the value of products and the value of reactants What does free energy mean? the ability to do work What does it mean to be a spontaneous reaction? These reactions result in products that have less free energy than the reactants, resulting in a delta g value that is negative (exergonic) How can we identify favorable reactions? When products have more capacity to do work than reactants, results in a delta g value that is positive (endergonic, not spontaneous or occurring without something releasing energy) What kind of reaction is hydrolysis of ATP? A spontaneous reaction What kind of reaction is a polymer being hydrolyzed? Spontaneous reaction What kind of reaction results when the delta g has a value that is negative? Exergonic reaction and favorable reaction What kind of reaction results when the delta g has a value that is positive? Endergonic reaction and not spontaneous reaction What influences delta g? Delta h (enthalpy), which is the heat content or potential energy in chemical bonds What is included in delta h? Exothermic (releasing heat) and endothermic (absorbing heat) What does a decrease in enthalpy from reactant to product result in? A release of heat If a reaction is exothermic, what is the sign of delta h? Negative In an exothermic reaction, how does the negative delta h sign affect delta g? Delta g is also negative If a reaction is endothermic, what is the sign of delta h? positive In an endothermic reaction, how does the positive delta h sign affect delta g? delta g is also positive An exothermic reaction contributes to a reaction being what? exergonic An endothermic reaction contributes to a reaction being what? endergonic What does delta s stand for? entropy (disorder) What value do delta s and delta g have when products have more entropy or disorder? delta s has a positive value and delta g has a negative value What value do delta s and delta g have when products have less entropy or disorder? delta s has a negative value and delta g has a positive value Where do things move more towards, things that are more ordered or disordered? Things that are more disordered because they have more energy What is found in a sodium gradient? Potential energy in that gradient that moves toward equilibrium and does work in concentration glucose What does gradient and lack of gradient mean? Gradient means order and lack of gradient means disorder What process is downhill? A spontaneous process What process is uphill? Not spontaneous As oil droplets come together, what happens to the surface area? The surface area decreases (bringing something together decreases the surface area) What kind of transport is endocytosis? Active transport because it requires energy What should you do to revise the energy of a molecule? Add a phosphate group What do hydrolysis reactions result in? More stable bonds What happens when you break something? Order is moving to more disorder, which contributes to hydrolysis being a favorable reaction How do we move against gradients? Coupling an exergonic process to endergonic reaction or process What are the steps in building a polymer? Linking things together; the pieces that get added have to have their free energy level raised before they can be added