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The Chemical Level of Organization - Coggle Diagram
The Chemical Level of Organization
Basic Chemistry
Matter
anything that has mass and takes up space
solid, liquid, gas
Elements
any substance that cannot be broken down into another substance
Carbon (C), Hydrogen (H), Oxygen (O), and Nitrogen(N) make up 96% of our body mass
Atoms
the smallest particles of an element that retain the elements properties
protons+, neutrons, electrons-
atomic number
the number of protons in the atom, this number will never change in the same element
atomic mass
number of neutrons and protons in the nucleus
isotope
an atom of a particular element with a different number of neutrons
radioactive isotope
an unstable isotope that spontaneously emits subatomic particles, used in PET scans
electron shells
3D regions around the nucleus where electrons are found. 1st shell:2 electrons 2nd shell: 8 electrons
valence shell
the outer most shell of an atom
valence electron
electrons found in the outermost ring
determine the chemical properties of the element
If the valence shell is not full, the atom is considered unstable. It will interact with the valence electrons of other atoms in a way that will completely fill the outermost shell.
Molecules and Compounds
molecule
: 2 or more atoms bonded together
compound
: a molecule composed of more than one element
chemical bonds
ionic bonds
created by the electrical attraction between a cation and an anion
cation
-an ion with a positive charge, lost an electron
anion
- an ion with a negative charge, gained an electron
covalent bonds
formed when atoms share an electron in their valence shells
nonpolar covalent bonds
covalent bond between atoms that share electrons equally
polar covalent bonds
unequal sharing of electrons between atoms of different electronegativity
creates polar molecules, water for example
hydrogen bonds
form when polar molecules are in close proximity
form between water molecules
Chemical Reactions
chemical bonds are formed or broken during chemical reactions
Decomposition Reaction
break a molecule down into smaller fragments
hydrolysis
a type of decomposition reaction that requires water
catabolism
decomposition reactions that occur within a cell
Synthesis Reaction
smaller molecules are used to create larger molecules
dehydration synthesis
a type of synthesis that releases water
anabolism
synthesis of new molecules in the cell
Enzymes and Activation Energy
activation energy
- the amount of energy needed to start a reaction
enzymes
speed up chemical reactions by lowering the activation energy
catalysts
speed up reactions without being permanently altered or changed
Inorganic and Organic Molecules
Inorganic Compounds
small molecules that may contain either carbon or hydrogen, but not both
Organic Compounds
much larger molecules that contain both carbon and hydrogen, four major classes: carbohydrates, proteins, lipids, nucleic acids
Water
water is a
polar
molecule formed by
covalent bonds
hydrogen bonds
form between water molecules
dissociation
- when inorganic molecules like salt dissolve in water, their ionic bonds break
Water has a very high heat capacity, water has the ability to absorb and retain heat
Water is an excellent solvent, and it can dissolve a variety of molecules (called solutes), creating a solution
Water is an essential reactant in the chemical reactions of living systems
Acids, Bases, Salts, pH and Buffers
Dissociation of Water
When water molecules break down they produce one H+ and one OH- (hydroxide ion) from one H2O
The concentration of H+ is
reported as the pH of the solution
Acids
substances that release hydrogen ions (H+) when they dissociate in water, pH<7
weak acids
- partially dissociate in a solution
strong acids
- completely dissociate in a solution
An acid is a proton (H+) donor. Acidic solutions have
high H+ concentrations.
Base
substances that dissociate in water, releasing hydroxide ions (OH-) OR take up (accept) hydrogen ions (H+), pH>7
strong bases
- completely dissociate in a solution
weak bases
- partially dissociate in a solution
A base is a proton (H+) acceptor. Basic solutions have
low H+ concentrations.
Salts
A salt is an ionic compound consisting of any cation except H+ and any anion except OH-.
An acid and a base react to form a salt and water.
Acid + Base → Salt + Water
electrolyte
an inorganic compound that dissociates into ions when placed into a solution
pH
pH is a measure of H+ in a solution, and it indicates the acidity of a solution
Physiological pH
Most body fluids and blood is pH 7.35-7.45
Acids: pH<7 [H+] > [OH-]
Neutral: pH=7 [H+] = [OH-]
Base: pH>7 [H+] < [OH-]
A change in pH by 1 unit = a 10 times change in [H+]
buffer
a substance that helps minimize the change in the pH of a solution when acids or bases are added
When pH increases (that is, [H+] decreases), buffers release H+
When pH drops (that is, [H+] increases), buffers absorb H+
Biomolecules
organic molecules (containing both hydrogen and carbon) in living organisms
monomer
- the smaller molecules that make up biomolecules
carbohydrates: monosaccharides
protein: amino acids
nucleic acid: nucleotides
polymer
- many monomers strung together
Biomolecule Synthesis
Monomers are strung together to form polymers through dehydration or condensation reactions. In a
dehydration synthesis
reaction enzymes remove water by taking -OH from the end of one monomer and H from the end of the other monomer
Biomolecule Hydrolysis
Polymers are broken down into individual monomers through hydrolysis reactions. In a hydrolysis reaction enzymes add water to break apart polymers into monomers.
Carbohydrates
Three Types:
Monosaccharides
(simple sugars)
ex: glucose, ribose, fructose, galactose
Disaccharides
(chain of 2 monosaccharides)
ex: maltose, lactose, sucrose
Polysaccharides
(complex carbohydrates)
ex: glycogen, cellulose, starch
disaccharides and polysaccharides are formed through dehydration reactions
Primary Function
The primary role of carbohydrates is to provide energy for all the cells in the body. They are necessary to make ATP.
Additional Functions
Act as building blocks for cellulose and deoxyribose for DNA, long-and short term storage, carbohydrates are also added to structures within organisms to change, tag, or mark that molecule
Lipids
Functions of Lipids
-energy storage
-build cells
-cushion and protect
-hormones
Types of Lipids
-fatty acids
-fats
-phosopholipids
-steroids
fatty acids
have 2 parts; a hydrophilic carboxyl group on one end and a hydrophobic hydrocarbon tail
saturated fatty acids
only contain single bonds and are solid at room temperature
unsaturated fatty acids
have a carbon double bond and are liquid at room temperature
fats
Triglycerides contain three fatty acid chains attached to a glycerol molecule. They are attached to the glycerol molecule by dehydration synthesis.
biological role of fats
- energy reserve, insulation, and cushioning our organs
phospholipids
main component of biological membranes, made of a glycerol molecule, two fatty acid chains, and a nonlipid group linked to a phosphate group.
The nonlipid portion is polar (hydrophilic) and dissolves in water, whereas the fatty acid chains are nonpolar (hydrophobic) and are not soluble in water.
Because phospholipids have both hydrophilic and hydrophobic portions, when placed in an aqueous environment, they form
phospholipids bilayers
steroids
lipids that do not contain fatty acid chains, they consist of four fused carbon rings
cholesterol
makes up 30% of our cell membranes and is the precursor molecule for many hormones such as hormones produced by the adrenal cortex as well as the sex hormones testosterone and estrogen
Proteins
Major functions of proteins include
Support (structure)
Movement (contraction)
Transport (hemoglobin transports O2)
Buffering (prevent changes in pH)
Metabolic regulation (enzymes)
Control (hormones)
Defense (antibodies)
denaturation
if a protein unfolds and loses its shape, it also loses its function, typicalled caused by a change in pH or temperature
amino acids
the monomers of protein containing a central carbon, one amino group, one carboxyl group, one hydrogen atom, and
one variable r group
Amino acids are linked by the
dehydration reaction.
These reactions create
peptide bonds
between the amino acids.
Amino acids polymerize to form long chains called
peptides
. Two amino acids joined by a peptide bond form a
dipeptide
, larger chains of amino acids (less than 100) are called
polypeptide
, and a peptide with 100 or more amino acids becomes a protein.
Protein Structure
Primary
: sequence of amino acids
Secondary
: local structures (coils and folds in peptide chain)
Tertiary
: overall 3-dimensional shape (folding of the polypeptide)
Quaternary
: organization of the subunit
enzymes
the most important proteins in the body, they act as catalysts to speed up chemical reactions
substrates
reactants in the chemical reaction
active site
the region of the enzyme where the substrates will bind
product
the molecule produced by the enzymatic reaction. It is released from the active site following formation
Nucletides
nucleic acids
are biomolecules built from atoms of carbon, hydrogen, oxygen, nitrogen and phosphorous,
nucleic acids are polymers
and the monomers of nucleic acids are the nucleotides
a nucleotide has 3 components
sugar
phosphate
nitrogenous base
Bases in DNA
:
adenine (A)
guanine (G)
cytosine (C)
thymine (T)
Bases in RNA
adenine (A)
guanine (G)
cytosine (C)
uracil (U)
there are two classes of nucleic acids:
DNA
(deoxyribonucleic acid)
RNA
(ribonucleic acid)
RNA
involved in protein
synthesis as directed by DNA
DNA
stores genetic information, double helix shape
ATP
the primary source of the energy for activities in the cell
