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CH 2: Chemicals and Biology

 

Biology is multidisciplinary science

Ex: use of formic acid by ants to maintain “devil’s garden”

Key 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

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

All known matter is composed of elements, including organisms

Element- substance that can’t 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 non- fueling

Elements of Life

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 can’t produce them and are essential to growth, development, etc.

Case Study: evolution of tolerance to toxic elements

Some elements can be toxic; arsenic

Some species can adapt to harsh chemicals: serpentine communities

C 2.2: element properties depend on atom’s structure

Each element consists of unique atoms- smallest unit of matter that makes up and element

Atoms are composed of subatomic particles -neutrons (Ø) -protons (+) -electrons (-)

 

Electron form electron cloud around nucleus

Elementary particles: Leptons, quarks, hadrons

Atomic number and atomic mass

Mass -1.6726×10−27 kg protons -9.11×10−31 kg electron -1.66×10−27 kg neutron

Atoms vary in different number of subatomic particles -an element’s number is the number of protons in its nucleus

Neutron and proton (nucleus) make up atomic mass, measured in Daltons

number is the number of protons in its nucleus  Neutron and proton (nucleus) make up
 

There is a flexibility of electrons in the same element

Isotopes

Radioactive decay spontaneously give of particles and energy

Application -fossil dating -diagnose medical disorder -tracing atom threw metabolic process

Electrons in orbitals determine an atom’s 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 doesn’t have a neutral charge

Isotope- atoms with same atomic number but different neutron number(thus different mass)

Energy is capacity to cause change

Energy levels of electrons

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- electron’s state of potential energy

Pull on outermost electrons from nucleus are weakest and determines element’s – valence electron

Elements full of valence electrons are chemically inert

Orbital of the 3d space where electrons can be found 90% of the time

Electron orbitals

Each electron shell consists of specific number of orbitals

s=2
s=2

s=2

p=6

d=10

f=14

atoms with incomplete valence shells can share or transfer valence electrons with certain other atoms

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

Interactions usually end up staying close, held by attractions- chemical bond

-Covalent bond- sharing of electrons. 2 types:

Bond 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

Covalent bond- share an electron (nonpolar vs polar)

In cov. Bond, shared electron count as part of each atom’s 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 atom’s valence

Atoms in a molecule attract electrons to varying degrees based on the atom’s electronegativity -the more electronegative an atom, the stronger the attractions of shared electron to self

Electronegativity and bond polarity

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

Ionic bond

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

Weak bond

Strongest bond in organisms are covalent bonds that form in cell’s molecules

Weaker chemical bond (ionic and hydrogen bonds) reinforce shapes of large molecules and help molecules adhere to each other

W.

bond- Hydrogen Bond

Hydrogen bond forms when hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom

W.

bond- Van der Waals

Temporary dipoles created when electrons are lopsided

interaction

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.

Molecular shape and function

Molecule’s 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)

C: 2.4 Chemical reaction make and break bonds

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

You should now be able to

1 identify four major elements

2 distinguish between the following pairs: neurons and protons, atomic number and mass

number, atomic weight and mass number

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

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