CH 2: Chemicals and Biology Biology is multidisciplinary science Ex: use of formic acid by ants to maintain devils garden Key

ey concepts 2.1 matter consists of elements in pure form and combination called compounds 2.2 element properties depend on atomic structure 2.3 influence of chemical bonding on molecules formation and function 2.4 Chemical reactions make and break chemical bonds All known matter is composed of elements, including organisms Element- substance that cant be broken down any more by chemical reactions Compound- substance with 2 or more elements in a fixed ration 118 elements known, 94 occur naturally A chemical compound is combination of 2 or more elements held together by chemical bonds In a chemical bond, trace elements may not have original properties, but a gain new characteristics -Ex: Hydrogen is combustible and a non-fueling element to combustion, Oxygen is non- combustible but a fueling element. Combined make water, non combustible nonfueling About 20-25% elements are essential to life Oxygen, carbon, hydrogen, nitrogen (96% of living matter), trace elements Na, K, Ca, S., etc. Very important element is carbon (talk about later on) In biochemistry, trace elements are called micronutrients, trace elements must be taken in because organisms cant produce them and are essential to growth, development, etc. Some elements can be toxic; arsenic Some species can adapt to harsh chemicals: serpentine communities Each element consists of unique atoms- smallest unit of matter that makes up and element Atoms are composed of subatomic particles -neutrons () -protons (+) -electrons (-) Electron form electron cloud around nucleus Elementary particles: Leptons, quarks, hadrons Mass -1.67261027 kg protons -9.111031 kg electron -1.661027 kg neutron Atoms vary in different number of subatomic particles -an elements number is the number of protons in its nucleus Neutron and proton (nucleus) make up atomic mass, measured in Daltons

Concept 2.1: Matter consists of elements in pure form and combination called compounds

Elements of Life

Case Study: evolution of tolerance to toxic elements C 2.2: element properties depend on atoms structure

Atomic number and atomic mass

Isotopes

There is a flexibility of electrons in the same element Radioactive decay spontaneously give of particles and energy Application -fossil dating -diagnose medical disorder -tracing atom threw metabolic process Electrons in orbitals determine an atoms chemical property Ion- atom or group of that lost 1or + electrons, giving a net positive charge (cation), or gained 1 or + electron giving a net negative charge (anion)ion is pretty much anything that doesnt have a neutral charge Isotope- atoms with same atomic number but different neutron number(thus different mass) Energy is capacity to cause change Potential energy is energy that matter has because of its location or structure Higher energized electrons are back more, an switch of electrons to levels cause spectral lines, color of substance, and creation of ions Electron shell- electrons state of potential energy Pull on outermost electrons from nucleus are weakest and determines elements valence electron Elements full of valence electrons are chemically inert Orbital of the 3d space where electrons can be found 90% of the time Each electron shell consists of specific number of orbitals s=2 p=6 d=10 f=14

Energy levels of electrons

Electron orbitals

C2.3 the formations and function of molecules depend on chemical bonding between atoms Bond Types

atoms with incomplete valence shells can share or transfer valence electrons with certain other atoms Interactions usually end up staying close, held by attractions- chemical bond

-Covalent bond- sharing of electrons. 2 types: -Nonpolar (similar electro negativities) -Polar (dis-similar electro negativities) -Ionic bond -Weak chemical bonds- Hydrogen bonds & Van der Walls interactions Covalent bond- share an electron (nonpolar vs polar) In cov. Bond, shared electron count as part of each atoms valence shell A molecule consists of 2 or more atoms held together by covalent bonds In single cov bond, or single bond, is sharing of one pair of valence electrons In double cov bond, or double bond, is shareing of two pairs of valence electrons Cov. Bond can form between same element of

Covalent bond

Bonding details

different Bonding capacity is called the atoms valence Atoms in a molecule attract electrons to varying degrees based on the atoms electronegativity -the more electronegative an atom, the stronger the attractions of shared electron to self In nonpolar cov bond, the atoms share the electron equally In polar cov bond, one atom is more electronegative, and atoms do not share electron equally Unequal sharing of electron caused partial - or + charge for each atom or molecule Atoms sometimes strip electron from their bonding partner -Ex: transfer of an electron from sodium to chlorine -after transfer on an electron, both atoms have charges called ions Ionic compounds are called salts Salts hydrolyze to produce hydroxide ions (basic) or hydronium ions (acid) when dissolved in water Strongest bond in organisms are covalent bonds that form in cells molecules Weaker chemical bond (ionic and hydrogen bonds) reinforce shapes of large molecules and help molecules adhere to each other Hydrogen bond forms when hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom Temporary dipoles created when electrons are lopsided When electrons move randomly, sometimes they get closer to each other, the uneven concentration causes one side to be negatively charged than the other. Explains how non-polar molecules can have attractive forces. Molecules shape is very important to its function, usually. Shape determined by -position of valence orbitals -hybridization between s and p orbitals to create specific molecular shapes Biological molecules recognize & interact with a specifity based on molecular shape Molecules with similar shape can have similar biological effect Similar enough to work (endorphin and morphine) Chemical reaction are making and breaking chemical bonds The starting molecules are called reactants, final molecule is called products Photosynthesis: sunlight power to convert carbon dioxide and water to glucose and oxygen Some chemical reactions go to completion: all reactants are converted to products All chemical are reversible Chemical equilibrium is reached when forward and reverse reaction are equal 1 identify four major elements 2 distinguish between the following pairs: neurons and protons, atomic number and mass number, atomic weight and mass number 3 Distinguish between and discuss the biological importance of the following nonpolar covalent bonds, polar covalent bonds, ionic bonds, hydrogen bonds, and van der Waals interactions

Electronegativity and bond polarity

Ionic bond

Weak bond

W. bond- Hydrogen Bond

W. bond- Van der Waals interaction

Molecular shape and function

C: 2.4 Chemical reaction make and break bonds

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