BIOL 150 Lecture 2 2024 - Biological Chemistry PDF

BIOL 150 LECTURE 2 Basic Principles of Biological Chemistry (review)  The Chemical Context of Life Chemical elements and Compounds Matter consists of chemical elements in pure form and in combinations called compounds Life requires about 25 chemical elements Jus...

BIOL 150 LECTURE 2 Basic Principles of Biological Chemistry (review)  The Chemical Context of Life Chemical elements and Compounds Matter consists of chemical elements in pure form and in combinations called compounds Life requires about 25 chemical elements Just 4 of these natural elements make up 96% of living matter – C, O, H and N  Atoms and Molecules Atomic structure determines the behaviour of an element Atoms combine by chemical bonding to form molecules Weak chemical bonds play important roles in the chemistry of life A molecules biological function is related to its shape Chemical reactions make and break chemical bonds Basic Principles of Biological Chemistry Definitions, definitions, definitions! Review of atomic structure Types of bonds Matter Something that occupies space and can be perceived by one or more sense Physical body Physical substance Universe as a whole  Matter Something that has mass Solid, liquid, gas, or plasma http://gal2.piclab.us/key/States%20of%20Matter Elements Something that can not be broken down into a simpler substance by a chemical reaction Examples include Hydrogen, Helium, Lithium, Beryllium, Boron, Carbon etc. Most commonly occurring element on Earth is iron Second most commonly found element on Earth is hydrogen https://upload.wikimedia.org/wikipedia/commons/3/39/Periodic_table_large.png Essential Elements Essential elements are those that an organism needs to live or grow. These vary somewhat between organisms (i.e. they are differences for bacteria vs. plants vs. mammals), There are several common essential elements including Carbon, Oxygen, Nitrogen, Phosphorous, Sulphur and Hydrogen. Trace Elements In analytical chemistry, a trace element is an element in a sample that has an average concentration of less than 100 parts per million (ppm) measured in atomic count, or less than 100 micrograms per gram (µg/g). In biochemistry, a trace element is a dietary mineral that is needed in minute quantities for the proper growth, development, and physiology of the organism. often referred to as a micronutrient Iron, Magnesium, Potassium, Cobalt, Selenium etc. Compounds A chemical compound is a substance consisting of two or more different chemical elements. These can be separated into simpler substances by chemical reactions. Chemical compounds have a defined chemical structure consisting of a fixed ratio of atoms that are held together by chemical bonds (covalent, ionic etc.). Mixtures A mixture is a substance consisting of two or more substances mixed together – not in fixed proportions and with no chemical bonding. In a mixture, each substance keeps their own properties and the amounts of each substance in a mixture can vary. Mixtures can be homogenous (uniform throughout– think salt water) or heterogeneous (like soil or oil & water). Review of Atomic Structure Atom In chemistry and physics, an atom is the smallest unit of matter that retains the chemical properties of an element. An atom consists of a dense nucleus of positively-charged protons and electrically-neutral neutrons, surrounded by a much larger electron cloud consisting of negatively-charged electrons.  Atom PROTON NEUTRON ELECTRON http://education.jlab.org/qa/atom_model.html Atom An atom is electrically neutral if it has the same number of protons as electrons. The number of protons in an atom defines the chemical element to which it belongs, while the number of neutrons determines the isotope of the element.  Atom PROTON http://education.jlab.org/qa/atom_model.html Protons A proton is a subatomic particle found in the nucleus of all conventional atoms. The proton has a positive charge, which balances out the negative charge of the electrons in atoms. If an atom has an imbalance of protons or electrons, it is no longer neutral and becomes a charged particle, also known as an ion. Protons The properties of atoms are defined by the number of electrons, neutrons and protons they have, but the number of protons is the most significant variable. The number of protons in the nucleus of an atom is referred to as the atomic number, and atoms are named based on the number of protons they have. Atoms with low atomic numbers are the most prevalent in the universe, because they are the easiest to form (Hydrogen and Helium).  Atom ELECTRON http://education.jlab.org/qa/atom_model.html Electrons An electron is a subatomic particle. Carrying a negative charge, an electron orbits an atom’s nucleus in a cloud and is bound to it by electromagnetic forces. An electron has a mass that is minuscule in comparison with even the smallest of atoms, coming in at about one thousandth the size of the tiniest atom. The electron is a basic unit of nature, meaning it cannot be broken down into smaller units. Electrons The electron plays a critical role in many of the interactions we see on a daily basis. Lightning  Lightning https://www.facebook.com/KingstonPolice/photos/pcb.10155273069789972/10155273064134972/?type=3&theate r  Atom NEUTRON http://education.jlab.org/qa/atom_model.html Neutrons A neutron is a tiny subatomic particle that can be found in practically all forms of conventional matter. The only stable exception is the hydrogen atom (i.e. hydrogen doesn’t have any). The neutron’s home is in the atomic nucleus, where it is bound closely with the protons through the strong nuclear force, which is one of the strongest forces in nature. Neutrons The neutron is so named because it is electrically neutral. A neutron’s mass is slightly larger than the mass of a proton. In general, atoms have a balanced number of protons and neutrons in their nucleus. Helium = two protons and two neutrons Sodium = 11 protons and 11 neutrons. When this balance is broken, the atom is referred to as an isotope. Atomic Number # PROTONS = ATOMIC # In other words, each element has a unique number that identifies how many protons are in one atom of that element. Atom of hydrogen (H) one proton = atomic number of 1 Atomic Number Atom of carbon (C) six protons = atomic number of 6. Atom of oxygen (O) 8 protons = atomic number of 8. The atomic number of an element never changes, meaning that the number of protons in the nucleus of every atom in an element is always the same. ATOMIC NUMBER 6 C Carbon 12.011 Atomic Mass The mass number is the same as the atomic mass. All atoms have an atomic mass which is derived as follows: # NEUTRONS + # PROTONS = ATOMIC MASS  6 ATOMIC MASS C Carbon 12.011 Atomic # vs. Atomic Mass 1. An element's or isotope's atomic number tells how many protons are in its atoms. 2. An element's or isotope's mass number tells how many protons and neutrons in its atoms. # of protons 6 # of protons + # of neutrons C Carbon 12.011 Ions & Isotopes Ions are atoms that are either missing or have extra electrons. Atoms do not lose protons. An atom that is missing or has an extra neutron is called an isotope. An atom is still the same element if it is missing an electron. The same goes for isotopes. Ions & Isotopes Isotopes of an element interact chemically with other atoms in the same way so cells can use any isotope. There are a lot of carbon atoms in the universe. Normal = carbon-12. 6 neutrons. Carbon isotope = Carbon-14 8 neutrons (2 extra compared to normal) Ions & Isotopes The atomic mass of an element is rarely an even number This is due to isotopes. Example: In carbon, there are a lot of C-12, a couple C- 13, and a few C-14 atoms. When you average out all of the masses, the average atomic mass = 12.011. Since you never really know which C atom you are using in calculations, you should use the mass of an average C atom. Radioactive Decay Radioisotope is an isotope that has an unstable nucleus and becomes more stabilized by spontaneously emitting energy and particles. Radioactive Decay is the loss of neutrons over time from an unstable isotope. Isotope C-14 does not last forever. Eventually it loses those extra neutrons and becomes C-12. Decay happens regularly like a clock. For carbon, the decay happens in a couple of thousand years. For P-32, decay happens in days to weeks. Common half life elements Energy Levels of Electrons An ELECTRON’S ENERGY LEVEL is the amount of energy required by an electron to stay in orbit. Just by the electron’s motion alone, it has kinetic energy. The electron’s position in reference to the nucleus gives it potential energy.  Energy Levels of Electrons An energy balance keeps the electron in orbit and as it gains or loses energy, it assumes an orbit further from or closer to the center of the atom. http://www.fastbleep.com/biology-notes/40/1089 Energy Levels of Electrons The electrons cannot choose any orbit they wish. They are restricted to orbits with certain energies. Electrons can jump from one energy level to another, but they can never have orbits with energies other than the allowed energy levels.  Energy Levels of Electrons http://www.fastbleep.com/biology-notes/40/1089 Electron Orbitals Electrons are found in clouds that surround the nucleus of an atom. Those clouds are specific distances away from the nucleus and are generally organized into shells or orbitals. The higher the atomic number, the more electrons and shells an atom will have.  Electron Orbitals The cloud that is found closest to the nucleus is called the 1s orbital. Slightly further away from the nucleus is the 2s orbital. So, the 1s orbital with its 2 electrons is the first “shell.” http://www.chem.fsu.edu/chemlab/chm1046course/orbitals.html Electron Orbitals After the 2s orbital comes the 2p orbital. Unlike the s orbitals, p orbitals are shaped like two opposite pointing balloons. 3 different 2p orbitals: 2px, 2py, and 2pz. Each 2p orbital holds 2 electrons. The 2s orbital and the three 2p orbitals contain 8 electrons. (The second “shell.”)  Electron Orbitals Next comes the 3s orbital. Similar in shape to the 1s and 2s orbitals, and also holds 2 electrons. Next comes 3p orbitals: 3px, 3py, 3pz. As we keep going, it gets goofy, so we’ll leave that for your chemistry class. http://www.chem.fsu.edu/chemlab/chm1046course/orbitals.html Electron Orbitals Electron Shells and Orbitals The Octet Rule: In general, atoms are most stable when they have 8 electrons in their outer-most shell. (That’s the s+p orbitals) The exception is the first shell which is most stable with TWO electrons (1s orbital). If you know the Atomic Number and Mass Number of an element and the maximum number of electrons in each electron shell you can draw a diagram of the element, and figure out whether electrons fill s or p orbitals. Electron Shells and Orbitals Example: Sodium (Na) Atomic # = 11 Mass # = 23 11 Protons and therefore 11 electrons. Protons + Neutrons is 23, and there are 11 Protons there must be 12 Neutrons. 2 electrons in the 1s orbital (1st shell), 2 electrons in the 2s orbital, 6 electrons in the 2p orbitals (2nd shell), and 1 electron in the 3s orbital.  Electron Shells and Orbitals http://hyperphysics.phy-astr.gsu.edu/hbase/chemical/eleorb.html Practice Question Chlorine has a Mass Number of 35.5 and an Atomic Number of 17. This means an atom of Chlorine has x Protons and therefore x electrons. Since the number of Protons + Neutrons is 35 and there are x Protons there must be y Neutrons. Draw the orbitals.  Answer 1s Atomic # = # of protons 2s 17 protons Energy 17 electrons 2p 2p 2p Atomic Mass = # of protons + # of neutrons 3s 18 Neutrons 3p 3p 3p Chemical Bonds Principles for Atoms to Interact An atom will not react with other atoms when its outermost electron shell is completely full. This atom is inert. An atom will react with other atoms when its outermost electron shell is partially full. This atom is reactive. Types of Chemical Bonds Intramolecular (within a molecule) Covalent Ionic Intermolecular (between molecules) Hydrogen ionic vs covalent vs hydrogen Ionic and covalent bonds are intramolecular bonds, (they exist inside the molecule. These bonds deal with the exchange of electrons. Hydrogen bonds are intermolecular bonds, meaning they bond two separate molecules. Covalent Bonds Chemical bonds formed by the sharing of one or more electrons (typically a pair) between atoms. Covalent bonds are the strongest type of chemical bond and are created between atoms with similar electronegativity. Electronegativity is a measure of the tendency of an atom to attract a bonding pair of electrons.  Covalent Bonds In general electronegativity increases as you move to the right of the periodic table and up the periodic table. http://edtech2.boisestate.edu/kilnerr/502/jigsaw.html Covalent Bonds Each electron shell has a maximum number of electrons, and each atom "wants" to max out its electrons in each shell. Noble gases are the most stable elements because their electron shells all carry the maximum number of electrons. They don’t easily form covalent bonds with other atoms. Helium (He), Neon (Ne), Argon (Ar), Krypton (Kr), Xenon (Xe), Radon (Rn) Fluorine is the most electronegative element. Covalent Bonds When two or more atoms have the same electronegativity, a true covalent bond is formed. Whenever two atoms of the same element bond together, a non-polar covalent bond forms Example - H2 When one of the atoms is just a bit more electronegative than the other, a polar covalent bond is formed. This means that the electrons spend a little bit more time around the more electronegative atom than the other, resulting in a slightly negative charge at one end, and a slightly positive charge at the other. Example - H20 Covalent Bonds A molecule of water (H2O) Covalent Bonds Covalent bonds are not as common within the processes of life because it takes a lot of energy to break them apart, making them too inefficient to work with. Depending on the number of shared electron pairs, a covalent bond is characterized as a single bond, a double bond, triple bond, etc. Ionic Bonds Ionic bonds are a type of electrostatic bond between two atoms that are weaker than covalent bonds, but usually stronger than hydrogen bonds. Electronegativity plays a big role here. Ionic bonds are an association between two ions that have opposing charges. Typical participants in an ionic bond are a metal and a non-metal, such as sodium and chlorine. Sodium and chlorine combine to create sodium chloride, or common table salt. Ionic Bonds Electron shells "want" to have the maximum number of electrons. That's when they're at their most stable energy state. When an atom missing only a single electron from its top orbital comes into contact with an atom that only has one electron in its top orbital, the "wanting" atom "steals" an electron from the other atom, thereby stabilizing its orbital. The orbital of the other atom is stabilized too, as it no longer has a lone electron in it’s outer orbital  Ionic Bonds http://www.nicerweb.com/bio1152/Locked/media/ch02/ionic_bond.html Ionic Bonds The consequence is that it now has one more electron than it has protons, making it negatively charged. The "victim" of the stolen electron correspondingly has a positive charge. In electromagnetic theory, opposites attract, so the atoms are forced to hang around each other until they get broken up by a force such as heat. Ionic compounds dissolve easily in water and other polar solvents. In solution, ionic compounds easily conduct electricity. Ionic vs Covalent bonds Hydrogen Bonds Polar molecules, such as water molecules, have a weak, partial negative charge at one region of the molecule (the oxygen atom in water) and a partial positive charge elsewhere (the hydrogen atoms in water). Molecules that H-bond: H2O NH3 HF Alcohols Any molecule in which H is attached directly to a very electronegative atom that has a lone electron pair. Hydrogen Bonds and Water When water molecules are close together, their positive and negative regions are attracted to the oppositely-charged regions of nearby molecules. The force of attraction, shown here as a dotted line, is called a hydrogen bond. Each water molecule can hydrogen bond to four others. http://macrotomicro.blogspot.ca/2011/04/hydrogen-bonding.html Hydrogen Bonds The hydrogen bond has only 5% or so of the strength of a covalent bond. However, when many hydrogen bonds can form between two molecules (or parts of the same molecule), the resulting union can be sufficiently strong as to be quite stable. Multiple hydrogen bonds: hold the two strands of the DNA double helix together hold polypeptides together in such secondary structures as the alpha helix and the beta conformation help enzymes bind to their substrate help antibodies bind to their antigen Chemical Reactions The reaction of two or more elements together results in the formation of a chemical bond between atoms and the formation of a chemical compound. Chemical Equations When a chemical reaction occurs, it can be described by an equation. This shows the chemicals that react (called the reactants) on the left-hand side, and the chemicals that they produce (called the products) on the right-hand side. The chemicals can be represented by their names or by their chemical symbols. Chemical Equations For example, hydrogen gas (H2) can react with oxygen gas (O2) to form water (H20). The chemical equation for this reaction is written as:  Chemical Equilibrium Because atoms are neither created nor destroyed in a reaction, a chemical equation must have an equal number of atoms of each element on each side of the arrow (i.e. the equation is said to be “balanced” or in EQUILIBRIUM). http://www.mikeblaber.org/oldwine/chm1045/notes/Stoich/Equation/Stoich01.htm Next Lecture…. The Structure and Properties of Water