BIOL 100 (copy)

Science

a system of thought that is based on reasoning logic and evidence

The Scientific Method

used within science to try to figure out how things work and to gain new knowledge/insight

What are the two types of Science?

• induction-based science

• hypothesis-based science

Induction-based science

makes prediction based on past experience

Induction

predictive generalizations that are based on a large number of observations

Hypothesis-based science

uses hypothesis as the basis for most formulations of the scientific method and uses deductive reasoning

Hypothesis

a tenative explanation for an observation

Deduction

reasoning from more general statements to a conclusion that must be true

Hypothetico-deductive method

involves hypothesis testing; hypotheses are tested by the use of experiments

Testable hypothesis

hypothesis which can be provide testable predictions for outcomes of experiments

Non-testable hypothesis

a hypothesis which cannot provide testable predictions

What are the two types of controls in an experiment?

• negative controls

• positive controls

Negative controls

always part of experimental designs (e.g., in algal example, the negative control was the breaker to which nothing was done)

Positive controls

aren’t always a part of experimental designs (e.g., you are testing a new type of plant fertilizer, and you want to see if the new fertilizer is a good as the existing fertilizer —> you would need two controls → positive control (w/ existing fertilizer), negative control (w/ no fertilizer) & treatment (w/ new fertilizer))

Scientific progress

due to rejected/falsified hypotheses; old ideas are rejected, and new ones formulated

Powerful hypotheses

means that they have a great deal of explanatory power; the greater the amount of explanatory power, the more important the hypothesis

Scientific theories

hypotheses that attempt to explain a large variety of phenomena

Replication

being able to repeat the same results under similar conditions

Reproducibility

if an experiment is repeated, the results should be the same

Occam’s razor

if several explanations are compatible with the evidence at hand, the simplest should be considered the most likely

Atom

basic building blocks of matter

What is an atom composed of?

• nucelous —> protons + neurons

• electrons in orbitals around the nucleus

The atomic number

number of protons

The mass number

number of protons and number of neutrons

Isotopes

have the same number of protons but different number of neutrons (i.e., different mass numbers)

What are the bonds between atoms based on?

electrons —> there are possibly single, double or triple bonds between two atoms

Chemical bond

 based on a pair of electrons, one electron provided by each atom

Why is C important in biology?

C always has 4 bonds, therefore, at minimum it must have bonds to at least two other atoms

What are the smallest atoms (from smallest to least smallest)?

• hydrogen

• helium

Ions

atoms or molecules in which the number of protons ≠ the number of electrons

Cations

positively charged ions; more protons than electrons

Anions

negatively charged ions; fewer protons than electrons

Bohr diagrams

indicate how many electrons fill each principal shell

Covalent

the electrons in the bonds are shared

Polar

there is an unequal sharing of electrons

Non-polar

there is equal sharing of electrons

Electronegativity

the ability of an atom to attract electrons to itself; higher EN means a greater ability to attract electrons

Polar covalent bonds

bonds between atoms that have a moderate difference in EN

What happens when the electrons in a bond are shared unequally?

the electrons shifted toward the atom with the higher EN

What happens in a bond when electrons have a negative charge?

negative charge shifted towards the atom with the higher EN and away from the atom with lower EN

Non-polar covalent bonds

bonds between like atoms (e.g., X-X) which have the same EN, but also occur between non-like atoms that have similar EN values

Ionic bond

the electrons in the bond are not shared but actually taken by the atom with larger EN

Is there sharing of electrons in ionic bonds?

No, ionic bonds form between atoms with very different EN

What is a weak bond and why are they weak?

weak bonds are constantly breaking and re-forming due to polar covalent bonds containing H

Water

solvent of life

Solvent

a substance that dissolves a solute

Properties of Water (polar covalent bond):

polar covalent bonds containing H lead to possibility for H-bonding → H bonds are weak due to polar covalent bonds containing H → H-bonding in water causes it to be a liquid at room temperature

What does water exhibits cohesion mean?

water molecules are attracted to each other and stick to each other due to H-bonding

What does water exhibits adhesion mean?

water is attracted to large polar/charged molecules and will stick to those molecules even though the molecules are too large to be dissolved

Hydrophilic

like water; molecules are polar/charged and exhibit mutual attraction with water molecules

Hydrophobic

dislikes water; molecules are composed of nonpolar covalent bonds (e.g., fats/oils) and exhibit mutual repulsion with water

Why are hydrophobic molecules hydrophobic?

because they are composed of largely non-polar covalent bonds and those do not have partial charges, or have relatively few partial charges

What effect does molecule size have on water solubility?

the solubility of polar molecules decreases as the molecules get larger

Why are molecules with mainly C-H and C-C bonds not water soluable?

these molecules do not have partial or full charges, and do not interact with water; they are hydrophobic and are not water soluble (e.g., vegetable oil)

C-based molecules play a role in:

• structural roles in cells

• play metabolic roles in cells

• has moderate to low EN

C can form:

• polar covalent bonds (C-H and C-C)

• non-polar covalent bonds (C-O and C-N)

• single, double and triple bonds

• always have four bonds

How to interpret chemical structures?

• end of every stick is C

• C atoms always have bonds to at least two other atoms

• if carbon at end of stick does not have 4 bonds, you keep adding hydrogen until you have 4 bonds

Isomers

molecules that have the same molecular formula but different structure

What are the 3 types of isomers?

• structural isomerism

• cis/trans isomerism

• enantiomers

Structural isomerism

have a different covalent arrangement of atoms

Cis/trans isomerism

have a different arrangement of atoms around a double bond

Enantiomers

are non-superimposable mirror images of each other

Macromolecules

very large biological molecules composed of many monomer subunits synthesized by condensation synthesis (e.g., carbohydates, proteins and nucleic acids)

Large biological molecules

biological molecules not quite as big as macromolecules, but still pretty big (e.g., lipids)

Monomers

one unit that can exist on their own and are also the building blocks of polymers (e.g., glucose in blood sugar)

Polymer

a molecule composed of linked monomers that are linked by covalent bonds

Condensation reaction (dehydration reaction)

formation of a covalent bond with the loss of a water molecule

Condensation synthesis (dehydration synthesis)

several to many rounds of condensation reactions, leading to the formation of small polymers, all the way to large biological molecules or macromolecules (depends on how many rounds of condensation reactions)

Hydrolysis

breaks apart a bond via the addition of water

Why do hydrolysis on macromolecules?

to remove damaged macro molecules or macromolecules that are no longer needed; the monomer subunits of the macromolecules can be recycled to produce new macromolecules

4 major groups of large biological molecules/macromolecules:

• carbohydrates

• proteins

• lipids

• nucleic acids

Monosaccharide

a sugar monomer (e.g., glucose, fructose, and galactose)

Cellular roles for monosaccharides:

• form parts of other molecules

• energy metabolism

Oligosaccharides

short chain of 2 or more sugar monomers

Disaccharides

oligosaccharides composed of only 2 subunits (e.g., maltose, lactose, sucrose)

Polysaccharides

many (hundreds to thousands) of linked monomer subunits and are a product of condensation synthesis

Polysaccharides that are polymers of glucose include:

• starch

• glycogen

• cellulose

Subgroups of lipids are:

• fats

• phospholipids

• steroids

Proteins

composed of linear sequence of amino acids (held together by peptide bonds - carboxyl group of one amino acid is linked to the incoming amino acid’s amino group)

Structural roles of proteins

• cellular cytoskeleton are composed of protein

• multicellular animals has a lot of extracellular collagen

• catalytic role (cellular metabolism run by enzymes which are proteins)

• transport proteins

Carbohydrate

composed of monomers and small polymers

Protein

composed of polymers of amino acids

Lipid

composed of large biological molcules rather than macromolecules

Nucleic acid

polymers of nucleotides

Fat

used as energy storage molecules

Phospholipids

form the basis of biological membranes (have both hydrophobic and hydrophilic parts on the molecule)

Steroid

play two major roles in hormones and are components of biological membrane and influence the fluidity of the membrane

Levels of Structure in Proteins:

• primary

• secondary

• teritary

• sometimes quaternary

Primary structure

sequence of a chain amino acids

Secondary structure

hydrogen bonding of the peptide backbone causes the amino acids to fold into a repeating pattern

Tertiary structure

three-dimensional folding pattern of a protein due to side chain interactions

Quaternary structure

protein consisting of more than one amino acid chain

What happens when an alteration is made in an amino acid in hemoglobin?

this changes the shape of a protein

Polypeptide *has two very different definitions

• subunit of a protein that has 4 degree structure

• a string of 10+ linked amino acids; typically a signaling molecule in an organism

Peptide

2-10 linked amino acids typically a signaling molecule; smaller than D#2 of polypeptide (e.g., there are peptide hormones)

Oligopeptide

a string of 10+ linked amino acids typically signaling molecule in an organism; equivalent to D#2 of polypeptide

Native conformation of proteins

the three dimensional shape of the functional protein

Protein denaturation

a change in confirmation away from the native conformation

Denaturation

a change in the three dimensional structure of a protein away from the native conformation due to a change in the environment of the protein (e.g., high temperature (i.e cooking an egg) typically results in irreversible denaturation)

Nucleic acids

represent genetic information and also play other roles related to information processing