Download CB098-008.22_Biochemistry

Biochemistry
(The Chemistry of Life)
The Units of Matter
Atom – The smallest
unit of matter that
retains the
properties of an
element.
Element – A
substance that
cannot be broken
down to other
substances by
chemical means.
Molecule – A group of two or more atoms held together by
covalent bonds. A molecule is any 2 or more atoms
joined together. Examples: H2, CO2, O2 and H2O.
Compound – A substance contain two or more different
elements in a fixed ratio. Compounds have different
elements present. All compounds are molecules.
Examples: CO2 and H2O
Proton – A subatomic particle with a single positive
electrical charge, found in the nucleus of an atom.
Neutron – An electrically neutral particle found in the
nucleus of an atom.
Electron – A subatomic particle with a single negative
electrical charge. One or more electrons move around
the nucleus of an atom.
Nucleus – An atom’s central core, containing protons and
neutrons. Not to be confused with the nucleus of a cell.
Ion – An atom that has gained or lost one or more electrons,
thus acquiring a charge.
Ionic Bond – A chemical bond resulting from the attraction
between oppositely charged ions.
METHANE
Covalent Bond – An
attraction between
atoms that share one
or more pairs of outershell electrons;
symbolized by a
single line between
the atoms.
The Milieu of Life
When unequal electron
sharing occurs in a
covalent bond, we end
up with polar covalent
bonds. One end of the
molecule is more
negative and the other is
more positive. This
occurs in water (H2O).
The oxygen atom hogs
the electrons and that
end becomes more
negative. Thus, the
hydrogens become more
positive. We end up with
a polar molecule.
Water, a polar molecule
Nonpolar covalent bonds
occur when electrons are
shared equally like in methane.
Methane is a nonpolar
covalent molecule.
Water, a polar molecule, has a negative end and a positive
end. When a hydrogen atom is part of a polar covalent bond,
its partial positive charge allows it to share attractions with
other electronegative atoms such as oxygen or nitrogen.
These weak but important bonds (Hydrogen Bonds) cause
water molecules to be attracted to other water molecules.
Hydrogen bonds are bonds between different water
molecules. Polar molecules are attracted to polar molecules
because hydrogen bonds form between polar molecules.
Each water molecule can hydrogen-bond to as many as four
water partners.
Hydrogen
bonds are
indicated by
the dashed
lines between
different water
molecules.
Solvent – A dissolving agent. Water is the solvent of life.
Solute – A substance that is dissolved.
Solution – A liquid consisting of a uniform mixture of 2 or
more substances. An aqueous solution is one in which
water is the solvent.
If you put table salt, NaCl (a solute) into water (a solvent),
you will have salt water (a solution).
Water Molecules
Hydrophilic – “Water-loving”; pertaining to polar, or
charged, molecules (or parts of molecules) that are
soluble in water.
These will readily dissolve in water. These are polar
molecules. They usually have nitrogen and/or oxygen
present. Water can dissolve polar molecules and ionic
substances.
Hydrophobic – “Water-fearing”; pertaining to nonpolar
molecules (or parts of molecules) that do not dissolve
in water.
These avoid water and will not dissolve in water. These
are nonpolar molecules. Nonpolar molecules are made
mostly of carbon and hydrogen, thus also often called
hydrocarbons.
Oil is hydrophobic. Oil and water do not mix. Try to mix
corn oil and water and watch what happens.
Acids Donate—and Bases Accept—Hydrogen Nuclei
The pH scale is from 0 to 14.
7 is neutral. 7 is pure water. At 7, there is the
same number of hydrogen (H+) and hydroxide
ions (OH-) present. H+ plus OH- = H2O
As you increase from 7, the solution is more
alkaline or basic. You will have more
hydroxide ions or hydroxyls present.
As you decrease from 7, the solution is more
acidic. You will have more hydrogen ions.
Since you have more hydrogen ions present,
you will have more hydroniums present.
Hydronium is water with an extra hydrogen.
Each unit of change is a tenfold change in
concentration. A solution of ph 4 is 10 times
more acidic than a solution of ph 5. A solution
of ph 3 is 100 times more acidic than a solution
of ph 5.
The Substance of Life
Organic Compound – A chemical compound containing the
element carbon and usually synthesized by cells. The
below macromolecules are examples of organic
compounds.
Macromolecules (Biomolecules) – A giant molecule in a
living organism formed by the joining of smaller
molecules. The major macromolecule groups are
Carbohydrates, Lipids, Proteins and Nucleic Acids.
Carbohydrates
Carbohydrates are the sugars
(the saccharides). They have
a roll of energy, storage and
structure in plants.
Monosaccharides (single-unit
sugars) generally have a
molecular formula that is
some multiple of CH2O.
Many sugars end in “ose.”
Examples include fructose,
glucose, and sucrose.
Polysaccharides are long
chains of sugar units. This
includes starch, glycogen,
pectin, and cellulose. Pectin
and cellulose are important
components of cell walls of
plants.
Cellulose
Lipids
Lipids are insoluble in water. They
are for the most part hydrophobic
(nonpolar) oil-soluble substances.
Fats are lipids that are mostly energystorage molecules.
Phospholipids and glycolipids make
up the membrane of plant cells. Their
heads are hydrophillic and their tails
are hydrophobic.
Here is a a membrane. There are many phospholipids
present. Can you see the head and tail structure of a
phospholipid? The tails are hydrophobic and they are
facing inwards to other tails where water is not present.
Membrane - A thin, soft,
pliable sheet; specifically a
limiting surface within or
surrounding a cell, formed by
phospholipids, glycolipids, or
other hydrophobic
compounds. Membranes
surround many organelles
within cells.
Proteins are made
from amino acids
linked by peptide
bonds. Twenty
different amino acids
are found in proteins.
All amino acids have
the same backbone
but each has a
different side chain
attached to the
central carbon.
Proteins
Amino Acid Structure
Proteins have diverse shapes and functions and are 3dimensional. Large protein complexes give form to the cell,
direct movement within the cell, or provide a scaffold for
chemical reactions.
All enzymes which catalyze the chemical reactions of the cell
are proteins.
Nucleic Acids
DNA
DNA and RNA are nucleic acids. DNA is the Genetic
material that organisms inherit from their parents. Gene (a
characteristic) is a segment of DNA molecule that carries
the instructions for amino acid sequence of proteins.
DNA is made of nucleotides. Each nucleotide consists of 3
parts (a Phosphate, Sugar (Deoxyribose) and a Nitrogen
containing base. The nitrogen containing base is one of
the following within each nucleotide: Cytosine (C),
Guanine (G), Adenine (A), or Thymine (T). To give DNA
its double helix nature, complementary bases are
connected by hydrogen bonds. A always connects with T
and C always connects with G. This nucleotide sequence
of DNA determines genes.
Replication of a DNA Molecule
DNA Replication
Double Helix untwists and DNA molecule separates
New nucleotides line up next to old ones.
Result in 2 new strands of DNA
RNA is made from a single strand of nucleotides. RNA is
involved in using genetic information to synthesize proteins.
BIO 141 Botany with Laboratory
•
This product is sponsored by a grant awarded under the President’s Community-Based Job Training Grants as implemented
by the U.S. Department of Labor’s Employment and Training Administration. The information contained in this product was
created by a grantee organization and does not necessarily reflect the official position of the U.S. Department of Labor. All
references to non-governmental companies or organizations, their services, products, or resources are offered for
informational purposes and should not be construed as an endorsement by the Department of Labor. This product is
copyrighted by the institution that created it and is intended for individual organizational, non-commercial use only.