Biology by Robert Brooker, Eric Widmaier, Linda Graham, Peter Stiling

January 8, 2016
Publisher: McGraw-Hill Education
ISBN: 978-1259188121

Notes

  • Genomes - all the genes an organism has (the storage unit of life).
  • Proteomes - all the proteins encoded by those genes (the functional unit of life). In any particular individual, the genes in a human skin cell are identical to those in a human nerve cell. However, their proteomes are different.
  • Photosynthesis - a process of harnessing light energy by plants, algae, and certain bacteria to produce nutrients.
  • Evolutionary change occurs by two mechanisms: vertical descent with mutation and horizontal gene transfer. In some cases, horizontal gene transfer can occur between members of different species.
  • Hypothesis - a proposed idea. A hypothesis is never really proven.
  • Theory - an established set of ideas that explains a vast amount of data and offers valid predictions that can be tested. Like a hypothesis, a theory can never be proven to be true. Theories are viewed as knowledge.
  • Inorganic chemistry - the nature of atoms and molecules, with the exception of those that contain rings or chains of carbon.
  • Organic chemistry - the nature of molecules that contain rings or chains of carbon.

 

  • The atomic mass scale indicates an atom's mass relative to the mass of other atoms. By convention, the most common type of carbon atom, which has six protons and six neutrons, is assigned an atomic mass of exactly 12. Atomic mass is measured in units called daltons. One Dalton (Da), also known as an atomic mass unit (amu), equals 1/12 the mass of a carbon atom, or about the mass of a proton or a hydrogen atom.
  • A mole of any substance contains the same number of particles as there are atoms in exactly 12 g of carbon. 1 mole of any element contains the same number of atoms - 6.022 x 1023. This number is known as Avogadro's number.
  • Isotopes vary in their number of neutrons. The length of time the isotope persist is measured in half-live - the time it takes for 50% of the isotope to decay.
  • Four elements account for the vast majority of atoms in living organisms: oxygen, carbon, hydrogen, and nitrogen. All living organisms require trace elements such as iron or copper.
  • Two or more atoms bonded together make up a molecule.
  • Covalent bonds join atoms through the sharing of electrons. Covalent bonds are strong chemical bonds, because the shared electrons behave as if they belong to each atom.
  • Atoms tend to be most stable when their outer shells are filled with electrons.
  • Atoms are electrically neutral because they contain equal numbers of negative electrons and positive protons. If an atom or molecule gains or loses one or more electrons, it acquires a net electric charge and becomes an ion. Ions that have a net positive charge are called cations. Ions with a net negative charge are anions. The ions are relatively stable when the outer electron shells of the ions are full.
  • An ionic bond occurs when a cation binds to an anion.
  • Salt is the general name given to compounds formed from an attraction between a positively charged ion (a cation) and negatively charge ion (an anion).
  • Ionic bonds are easily broken in water - the environment of the cell.
  • The three-dimensional, flexible shape of molecules contributes to their biological properties.
  • Free radicals are a special class of highly reactive molecules. A molecule containing an atom with a single, unpaired electron in its outer shell is known as a free radical. Free radicals can react with other molecules to "steal" an electron from one of their atoms, thereby filling the orbital in the free radical. In the process, this may create a new free radical in the donor molecule, setting off a chain reaction. Free radicals can be formed in several ways, including exposure of cells to radiation and toxins. Free radicals can do considerable harm to living cells - for example, by causing a cell to rupture or by damaging the genetic material.
  • Protection from free radicals is afforded by molecules that can donate electrons to the free radicals without becoming highly reactive themselves. Examples of such protective compounds are certain vitamins known as antioxidants (for example, vitamins C and E), found in fruits and vegetables, and the numerous plant compounds known as flavonoids. This is one reason why a diet rich in fruits and vegetables is beneficial to our health.
  • Heat energy causes atoms and molecules to vibrate and move, a phenomenon known as Brownian motion.
  • A catalyst is a substance that speeds up a chemical reaction.
  • Substances dissolved in a liquid are known as solutes, and the liquid in which they are dissolved is the solvent. Solutes dissolve in a solvent to form a solution.

Carbon

  • One of the properties of the carbon atom that makes life possible is its ability to form four covalent bonds with other atoms, including other carbon atoms. This occurs because carbon has four electrons in its outer shell, and it requires four additional electrons for its outer shell to be full.
  • Carbon bonds may occur in configurations that are linear, ringlike, or highly branched.
  • The ability of carbon to form both polar and nonpolar bonds contributes to its ability to serve as the backbone for a variety of biologically important molecules.
  • Carbon-containing molecules may exist in multiple forms called isomers. Two structures with an identical molecular formula but different structures and characteristics are called isomers.

Some organic molecules are composed of thousands or even millions of atoms. Such large molecules are formed by linking together many smaller molecules called monomers and are known as polymers. The structure of polymers depends on the structure of their monomers, the number of monomers linked together, and the three-dimensional way in which the monomers are linked.

Organic molecules and macromolecules fall into four broad categories:

Carbohydrates

  • Sugars are carbohydrate monomers that may taste sweet.
  • Polysaccharides are carbohydrate polymers that include starch and glycogen.
  • Cellulose accounts for up to half of all the carbon contained within a plant, making it the most common organic compound on Earth.

Lipids

  • Lipids account for about 40% of the organic matter in the average human body and include fats, phospholipids, steroids, and waxes.
  • In organisms such as mammals, some fatty acids are necessary for good health but cannot be synthesized by the body. Such fatty acids are called essential fatty acids, because they must be obtained in the diet; an example is linoleic acid.
  • Stearic acid is an abundant saturated fatty acid in animals, whereas linoleic acid is an unsaturated fatty acid found in plants.
  • Saturated fats have high melting points and tend to be solid at room temperature.
  • Animal fats contain a high proportion of saturated fatty acids.
  • Certain types of fats used in baking are called shortenings. They are solid at room temperature. Shortenings are often made from vegetable oils by hydrogenation process.
  • Fats high in unsaturated fatty acids usually have low melting points and are liquids at room temperature. Such fats are called oils.
  • Olive oil contains high amounts of oleic acid, a monosaturated fatty acid with a melting point of 16C.
  • Linoleic acid, found in soybeans and other plants, melts at -5C.
  • Of particular importance to human health are trans fatty acids, which are formed by a synthetic process in which the natural cis form is altered to a trans configuration. This gives the fats that contain such fatty acids a more linear structure and, therefore, a higher melting point. Although this process has been used for many years to produce fats with a longer shelf-life and with better characteristics for baking, it is now understood that trans fats are linked with human disease.

Proteins

  • Proteins are polymers of amino acids.
  • Proteins have a hierarchy of structure.

Nucleic acids

  • Nucleic acids are polymers made of nucleotides.
  • Molecules of nucleic acids are extremely important because they are responsible for the storage, expression, and transmission of genetic information
  • The two classes of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)

All living organisms display seven common characteristics:

  • Organisms maintain an internal order that is separated from the environment. The simplest unit of such organization is the cell.
  • Organisms need energy to maintain internal order. Energy is used in chemical reactions known as metabolism.
  • Organisms react to environmental changes that promote their survival.
  • Organisms regulate their cells and bodies, maintaining relatively stable internal conditions, a process called homeostasis.
  • Growth produces more or larger cells, whereas development produces organisms with a defined set of characteristics. Development is a series of changes in the state of a cell, tissue, organ, or organism.
  • To sustain life over many generations, organisms must reproduce. All living organisms contain genetic material of DNA (deoxyribonucleic acid). Due to the transmission of genetic material, offspring tends to have traits like their parents.
  • Populations of organisms change over the course of many generations. Evolution results in traits that promote survival and reproductive success.

Living organisms can be viewed at different levels of organization

  • Atoms
  • Molecules and macromolecules
  • Cells
  • Tissues
  • Organs
  • Organism
  • Population
  • Community
  • Ecosystem
  • Biosphere 

The cell theory states that:

  • All living organisms are composed of one or more cells.
  • Cells are the smallest units of life.
  • Cells come from pre-existing cells by cell division.

All forms of life can be placed into three large categories (or domains):

  • Bacteria
  • Archaea
  • Eukarya - once subdivided into four kingdoms: protists, plants, fungi, and animalia

Bacteria and Archaea are microorganisms that are also termedprokaryotic. A defining distinction between prokaryotic and eukaryotic cells is that eukaryotic cells have a cell nucleus whereas prokaryotic cells lack a membrane-enclosed nucleus. Eukaryotic cells are compartmentalized by internal membranes to create organelles.

Mitochondria and chloroplasts contain their own genetic material and divide by binary fission (splitting in two).Mitochondria and chloroplasts are derived from ancient symbiotic relationships.

We can view a eukaryotic cell as a system of four interacting parts:

  • Nucleus - the nucleus houses the genome.
  • Cytosol - the cytosol is the region that is enclosed by the plasma membrane but outside of the organelles.
  • Endomembrane system - the endomembrane system includes the nuclear envelope, endoplasmic reticulum, Golgi apparatus, lysosomes, vacuoles, peroxisomes, and plasma membrane.
  • Semiautonomous organelles - semiautonomous organelles include the mitochondria and chloroplasts.