Matter consists of chemical elements in pure form an in combinations called
compounds.
Elements – Substances that cannot be broken down to other substances.
Compounds – Substance composed of two or more elements.
Matter – Anything that takes up space.
*An Element’s properties depend on the structure of its atoms
Atom – Smallest unit of matter that still retains the properties of an element
Proton (+), Neutrons (no charge), and Electrons (-) are subatomic particles.
Isotope – A different atomic form of an element (# of neutrons change)
Energy – The capacity to cause change
Electron Shell – An energy level of electrons at characteristic average
distance from the nucleus of an atom
*The formation and function of molecules depend on chemical bonding between
atoms
Chemical Bonds – Attraction between two atoms results from sharing of
outer shell electrons or the present of opposite charges on atoms
*The strongest chemical bonds are covalent and ionic.
Covalent bonds – STRONG chemical bonds in which 2 atoms share 1 or
more pairs of valence electrons.
*Valence equals the # of unpaired electrons required to complete the atom’s
outermost shell.
Polar Covalent Bond – Electons NOT shared equally
Nonpolar Covalent Bond – Electrons shared equally
Ion – Charges Atom, (+) = Cation, (-) = Anion
Ionic Bond – Chemical bond resulting from the attraction between
oppositely charged ions
Ionic Compounds – Compound resulting from formation of ionic bonds
(Salts)
Hydrogen Bonds – WEAK chemical bonds formed when slightly (+)
hydrogen atoms of a polar covalent bond in one molecule is attached to the
slightly (-) atom of a polar covalent bond in another molecule (Water has
hydrogen bonds)
*Chemical Reactions make and break chemical bonds
*96% of all living matter is made of carbon, hydrogen, nitrogen and oxygen
The polarity of water molecules result in hydrogen bonding.
Polar Molecule – Two ends of a molecule have opposite charges (polar loves
water)
*Water is the solvent of Life
Hydrophilic – Water loving, dissolves in water
Hydrophobic – Water fearing, doesn’t dissolve in water
Aqueous Solution – Solution where water is the solvent.
*Acidic and Basic conditions affect living organisms
Acid – Substance that increases the hydrogen concentration of a solution
Basic – Reduces the hydrogen ion concentration of a solution
pH Scale – Ranges from 0 – 14 (0 = acidic, 7 = neutral, 14 = basic)
Buffer – Substances that minimize changes in the concentration of H+
(acidic) and OH- (basic) solutions
*Accepts H+ ions when solution is too acidic
*Donates H+ ions when solution is too basic
Carbon is the backbone of life
*What carbon can build is unlimited
*Organic Chemistry is the study of carbon compounds
*Carbon Atoms can form diverse molecules by bonding to four other atoms
Isomers – Compounds that have the same # of atoms of the same elements
but different structure and different properties
Hydrocarbons – Organic molecules consisting of only carbon and hydrogen.
*A Small # of chemical groups are key to the functioning of biological molecules
Functional Groups – A specific configuration of atoms commonly attached
to the carbon skeletons of organic molecules and usually involved in
chemical reactions
Adenosine Triphosphate (ATP) – An adenine + ribose sugar + three
phosphates that releases energy when its phosphate bonds are hydrolyzed
(broken off): This energy is used to drive chemical reactions
Macromolecules – A giant molecule formed by joining of smaller molecules, usually
by a condensation reaction. Polysaccharides, proteins and nucleic acids are
macromolecules
Polymer – Long molecule consisting of many similar or identical building
blocks linked by covalent bonds
Monomer – The repeating units that serve as building blocks
Condensation Reaction – 2 molecules become covalently bonded to each
other through the loss of water (Aka dehydration reaction)
Hydrolysis – When polymers are disassembled to monomers. Reverse of
above
Enzymes – Specialized macromolecules that speed up chemical reactions in
cells.
Substrate, Active Site, Product
Enzymes change shape using a Phosphate
*Carbohydrates serve as fuel and building material
Carbohydrates – Both sugars and polymers of sugars
Monosaccharides – Simplest Carbs
Disaccharides – 2 monosaccharides joined
Polysaccharides – 100 to 1000’s of monosaccharides joined together
Starch in plants
Glycogen in animals
*Lipids are a diverse group of hydrophobic molecules
*Triglycerides/Phospholipids/Steroids
*Phospholipids make up cell membranes
*Steroids are a group of hormones made from cholesterol
*Triglycerides – Saturated, Unsaturated, Trans Fat, Omega 3 Fatty
Acids
*Proteins have many structures, resulting in a wide range of functions (repair,
catalyze, provide structural support…)
Monomers - amino acids
Polymers – polypeptides
4 levels of structure (Primary, Secondary, Tertiary, Quaternary
*Denaturing Proteins – Protein wears down/becomes inactive
High temperatures, low pH
*Cellular Organelles
Ribosomes - Serve as “Protein factories” of the cell
Mitochondria – Site of cellular respiration (Powerhouse of the cell),
produces ATP aerobically
Lysosome – Produces Digestive enzymes
Peroxisome – Breaks down Hydrogen Peroxide/ Catalase
Golgi Apparatus – Vesiculation and Glycosylation
Centrioles – Helps in cellular division by dividing the cells
Rough Endoplasmic Reticulum – Stores Calcium, Helps in Protein Synthesis
Smooth Endoplasmic Reticulum – Stores Calcium, Produces Triglycerides,
Phospholipids and Steroid Hormones
*The plasma membrane of the cell exhibits selective permeability
*Phospholipids and proteins move laterally within the membrane
*Membrane Proteins
Integral Proteins – Trans membrane protein with
hydrophobic regions that extend into and often span the
hydrophobic interior of the membrane and the hydrophilic
region in contrast with the aqueous solution on either side of
the membrane
Peripheral Proteins – A protein loosely bound to the surface
of a membrane or to part of an integral protein and not
embedded in the phospholipid bilayer
*Membrane structure of the cell, results in semi-permeable or selective permeability
*A cell must exchange molecules and ions with its surrounding, a process controlled
by the plasma membrane
*Hydrophobic substances can pass through the cell’s lipid bilayer rapidly.
*To cross a cell’s membrane substances generally require transport proteins.
*Passive Transport is diffusion of a substance across a membrane that DOES NOT
require energy
Diffusion – The movement of molecules of any substance from high
concentration to low concentration, so that they spread out evenly into
available space.
Passive Transport – The diffusion of a substance across a biological
membrane
Osmosis – The diffusion of water across a semi-permeable membrane
*Active Transport USES ENERGY to move solutes against their concentration
gradient, from low concentration to high concentration.
Primary – Movement of one type of substance at a time across the
membrane
Secondary – Movement of two types of substances at a time across the
membrane. Symport/Antiport
*Metabolism – The totality of an organism’s chemical reactions, consisting of
catabolic and anabolic pathways, which manage the material and energy resources
of the organism
*Aerobic Respiration – A catabolic pathway that consumes oxygen and organic
molecules, producing ATP.
*Cellular Respiration has 3 stages
Glycolysis – Splitting of glucose into pyruvate (occurs in the cytoplasm and
is anaerobic)
Citric Acid Cycle – Completes the metabolic breakdown of glucose molecules
begun in glycolysis by oxidizing pyruvate to carbon dioxide (occurs in the
mitochondria and is aerobic)
Oxidative Phosphorylation – The production of ATP using energy derived
from an electron transport chain. Uses NAD and FAD carriers of Hydrogen
(Occurs in the mitochondria and is aerobic)
*DNA is the genetic material
*Four nitrogenous bases in DNA
Adenine (A)
Thymine (T)
Guanine (G)
Cytosine (C)
*These nitrogenous base pairs in a DNA double helix are held together by hydrogen
bonds. Base pairs are complementary:
*Adenine bonds with Thymine
*Guanine bonds with Cytosine
*A chromosome consists of a DNA molecule packed together with proteins
*Nucleic Acids store and transmit hereditary information
*2 types: DNA and RNA
DNA: (deoxyribose) (C, G, A, T) (Double-Stranded)
Stores all hereditary information
RNA: (Ribose) (C, G A, U) (Single-Stranded)
*Nucleic Acids carry protein-coding instructions from DNA to protein synthesizing
machinery.
*Nucleus contains most of the genes in the cell
*Nuclear envelope encloses the nucleus
Chromosomes – Units of DNA that carries the genetic information
Gene Expression – The process by which DNA directs the synthesis of proteins (or
in some cases, just RNAs)
*Genes specify proteins via the processes of TRANSCRIPTION and TRANSLATION
Transcription – The synthesis of RNA under the direction of DNA (occurs in
the nucleus)
Translation – The synthesis of a polypeptide, which occurs under the
direction of mRNA and a ribosome (occurs in the cytoplasm)
*Genetic information is encoded as a sequence of non-overlapping base
codons. A codon in messenger RNA either is translated into an amino acid or
serves as a stop signal. Codons must be read in the correct order
*In RNA uracil (U) takes the place of thymine (T)
*RNA is modified after transcription
RNA Processing – Modification of RNA transcripts, including splicing out
introns, joining together exons, and adding a methylated cap and a poly A
tail
Introns – A non-coding, intervening sequence within a primary
transcript that is removed from the transcript after RNA polymerase
reads the mRNA; also refers to the regions of DNA from which this
sequence was transcribed
Exons – Coding regions. A sequence within a primary transcript that
remains in the RNA after RNA processing; also refers to the region of
DNA from which this sequence was transcribed
*More on Translation
*A cell translates mRNA message into protein using tRNA. After binding up
specific amino acids, tRNA lines up via their anticodons at complimentary
codons on mRNA. Ribosomes help facilitate this coupling with binding sites
for mRNA and tRNA
*Point mutations can affect protein structure and function
*A point mutation is a change in one DNA base pair, which may lead to
production of a non-functional protein. Base-pair substitutions can cause
missense or nonsense mutations. Base-pair insertions or deletions may
produce frameshift mutations
*Mutagens – A chemical of physical agent that can interact with DNA and
cause mutation such as Benzene found in gasoline