Basic Principles of Biological Chemistry Lecture Notes 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.