BIO 166 Test 1

Chapters 1-5

Inductive reasoning

a form of logical thinking that uses related observations to arrive at a general conclusion

ex: you can be brought to the general conclusion that spoiled food makes you sick

deductive reasoning

a form of logical thinking that uses a general principle to forecase future events

ex: tomorrow, the sun will travel from east to west

hypothesis

a testable solution, a general statement about the natural world

The Scientific Method

1. Make an observation and ask a question

2. Form a hypothesis

3. Make a predicition to test the hypothesis

4. Design an experiment that tests this prediction

5. Analyze the results

Scientific Theory

a general hypothesis that has been heavily tested several times by many scientists; they may be refuted in the future

independent variable

the factor that the experimentor chose to change during the experiment

• it is not dependent

bacteria

small organisms found everyywhere. Most are harmless to humans, but a few can cause diseases (pathogenic)

The Characteristics of Life

1. Order or Organization

2. Response to Stimuli

3. Reproduction

4. Regulation

5. Energy Processing

6. Evolution

What does a branch in a phylogenitc tree represent?

lineage (the length of a branch is proportional to the length of time elasped since the split

What does each node in a phylogenic tree represent?

a divergence event, a time where scientists believed a common ancestor diverged into two species

species

group of living organisms that, under normal conditions, will breed and have healthy viable offspring with others within that group; two _______ are more related if they share a common ancestor

mass

the amount of material in an object

matter

anything that occupies space and has a mass

element

a substance that cannot be broken down into other substances by ordinary means; they have specific chemical and physical properties

What are the 4 elements that make up 96% of matter?

Oxygen (O)

Carbon (C)

Hydrogen (H)

Nitrogen (N)

atom

the smallest unit of matter that still retains the properties of an element; composed of a nucleus and an electron cloud

orbitals

a cloud of electrons

atomic number

number of protons in an atom

isotope

the nucleus has the same number of protons but a different number of neutrons

mass number

determined by protons and neutrons; the calculated mean of all the element’s naturally occuring isotopes

radioisotopes

isotopes that emit subatomic particles to reach a more stable atomic configuration

electron shells

“n” are the energy levels

1n is the first level which is closest to the nucleus

octet rule

with the exception of the innermost shell, atoms are more energetically stable when the valence shell has eight electrons

covalent bonds

an electron is shared between the atoms; this is the strongest bond

ionic bonds

atoms gain or give up electrons; attractive forces between oppisitely charged ions

hydrogen bond

weak bonds formed when a hydrogen atom that is attracted to an element becomes attracted to a different electronegative element

polar covalent bonds

electrons are unequally shared by the atoms and attracted more to one nucleus than the other

polar molecule

a molecule in which the distribution of electrical charges is unequal, resulting in regions of partial negative or partial positive charges (hydrophilic)

nonpolar covalent bonds

electrons are equally shared by the atoms

nonpolar covalent molecules

a molecule in which the distribution of electrical charges is equal; there is no electrical charge (hydrophobic)

chemical reactivity

the ability for elements to combine and to chemcially bond with each other

periodic table columns

represent the potential shared state of the elements (whether they are more likely to take or share an electron)

periodic table

groups elements according to chemical properties

molecules

when two or more atoms are chemically bonded to each other

key properties of water

• Changes densities at different temperatures

• High heat capacity

• “Universal solvent”

• Cohesion and adhesion

• Participates in critical chemical reactions

pH

a way to measure the concentration of hydrogen ions in a solution

acidic

solutions with a higher [H+] (<7); can donate H+

basic/alkaline

lower [H+] (>7); can receive H+, often giving OH- in exchange

Why is carbon so important?

• Can form double or single bonds

• Can form linear, branched, or ring-shaped molecules

• It can share 4 of its electrons with other molecules, can form up to 4 covalent bonds

macromolecules

subset of organic molecules; any carbon-containing liquid, solid, or gas; especially importatn for life

ex: proteins, nucleic acids (RNA and DNA), carbohydrates, and lipids

hydrocarbons

organic molecules consisting entirely of carbon and hydrgoen

ex: methane

hydrocarbon chains

successive bonds between carbon atoms form hydrocarbon chains; they may be branched or unbranched

• prefix for two hydrocarbons: “eth”

• suffixes “-ane,” “-ene,” and “-yne” refer to the presence of single, double, or triple bonds, respectively

• double and triple bonds change the molecule’s geometry: single bonds allow rotation along the bond’s axis; whereas double bonds lead to planar configuration (one atom is in the center that the others rotate around) and triple bonds lead to a linear one

aliphatic hydrocarbons

linear chains of carbon atoms; sometimes they can form rings with all single bonds

aromatc hydrocarbons

closed rings of carbon atoms with alternating single and double bonds

isomers

molecules that share the same chemical formula but differ in the placement (structure) of their atoms and/or chemical bonds

strucutral isomers

differ in the placement of their covalent bonds but differ in how these bonds are made to the surrounding atoms, especially in carbon-to-carbon double bonds

geometric isomers

similar placements of their covalent bonds but differ in how these bonds are made to the surrounding atoms

cis configuration

when the carbons are bound on the same side of the double bond; these make a bend on the carbon backbone

trans configuration

when they are on opposite sides of a double bond; the carbons form a more linear structure

unsaturated fats

fats with at least one double bond between carbon atoms; they remain liquid at room temprature

saturated fats

triglycerides without double bonds between carbon atoms, meaning that they contain all the hydrogen atoms possible; these are solid at room temperature

trans fats

triglycerides with trans double bonds that have relatively linear fatty acids that are able to pack tightly together at room temprature and form solid fats

functional groups

in an organic macromolecule, the groups of atoms directly involved in chemical reactions

hydrocarbons

organic molecule consisting entirely of carbon and hydrogen, such as methane

hydrocarbon chains

successive bonds between carbon atoms; may be branched or unbranched

monomers

repeating units

polymers

what monomers make after combining withe each other using covalent bonds

dehydration synthesis

two monomers are linked to form a polymer; a water molecule is formed as they are linked by a covalent bond

hydrolysis

breaking down a monomer into polymers; water serves as a reactant; this reaction produces energy

monosaccharides

• cannot be broken down into smaller sugars

  • Glucose

  • Galactose

  • Fructose

• usually have 3-7 carbons

  • trioses - three carbons

  • pentoses - five carbons

  • hexoses - six carbons

• five and six carbon monosaccharides exist in equilibrium between linear and ring forms

glucose

the main source of energy for your cells

disaccharides

form when two monosaccharides are linked in a dehydration reaction; two monomers are joined by a glycosidic bond

polysaccharides

• long chain of monosaccharides joined by glycosidic bond

• may be branched or unbranched

• may consist of multiple types of monosaccharides

• different kinds:

  • Starch

  • Glycogen

  • Cellulose

lipids

a diverse group of hydrophobic molecules made from different molecular building blocks; are not polymers made from repeating monomers

Different kinds

• Fats and Oils (triglycerides)

  • Contain two main components:

    • Glycerol

    • Fatty acids

  • Phospholipids

  • Steroids

Omega-3 fats

an essential type of fats our body is incapable of creating

phospholipids

composed of:

• glycerol

• fatty acids

• phosphate group: may be modified by the addition of charged or polar chemical groups

they are amphipathic, when dropped into water they form a phospholipid bilayer (heads out, tails in)

amphipathic molecules

a molecule with a hydrophilic region and a hydrophobic region

steroids

• Have a closed ring structure made of four linked fused carbon rings

• Testosterone: the male hormone

• Estrogen: the female hormone

cholesterol

a key component of cell membranes and the “base steroid” from which our body produces other steroids

proteins

• Polymers made of amino acid monomers

  • Common structure:

  • Central carbon atom

  • Amino group

  • Carboxyl group

  • Hydrogen

• Are used to make hair and horns, transport materials, control gene expression, and facilitate chemical reactions

• Contractile function: they contract your muscles, allowing you to move

amino acids

• Combine to form proteins

• Represented by a single upper case letter or three letters

  • Valine = V or Val

  • Aspartic acid = D or Asp

• Linked via peptide bond formation (dehydration synthesis)

polypeptide

a chain of amino acids joined together in peptide linkages; a functional protein is one or more polypeptides precisely twisted, folded, and coiled into a unique shape

denaturation

changes in protein structure that leads to changes in function

protein shape

based upon four levels of structure:

• Primary: amino acid sequence

• Secondary: folding of the polypeptide

• Tertiary: the unique three-dimensional structure of a polypeptide due to chemical interactions between R-groups on amino acids

• Quaternary: interacttion between several polypeptides that make up a protein

nucleic acids

macromolecules that store informaiton (DNA) and privde the instructions for building proteins (RNA)

DNA

the instructions for every possible protein you body will ever need

RNA

messenger RNA, holds specific instructions on how to make one protein

nucleotides

monomers that make up DNA and RNA

consists of three parts:

• Nitrogenous base

• Pentose sugar

• One or more phosphate groups

ester bond

What bond is formed when the phosphate group attached to the sugar on one nucleotide forms bond with the sugar of the next nucleotide?

types of nitrogenous bases

Pyrimidines - cytosine (C), thymine (T), and uracil (U)

Purines - Adenine (A), Guanine (G)

structure of DNA

• double stranded

• Nucleotides contain:

  • Deoxyribose (sugar)

  • Adenine

  • Guanine

  • Cytosine

  • Thymine

DNA pairing

• phosphate is attached to Carbon 5 (C5)

• The phosphodiester bond between 2 nucleotides attach the phosphate on C5 to the C3 carbon

• One DNA strand is oriented from 5’ to 3’

• Opposed strand is oriented 3’ to 5’

• A-T

• G-C

strucutre for RNA

• single stranded

• Nucleotides contain

  • Ribose (sugar)

  • Nitrogenous bases

    • Adenine

    • Guanine

    • Cytosine

    • Uracil

  • A-U

  • G-C

cell theory

cells are the basic unit of all organisms

3 tenents of cell theory

1. All living things are composed of cells

2. A single cell is the smallest unit that exhibits all the characteristics of life

3. All cells only come from preexisting cells

light microscopes

• uses glass lenses and visible light to form images

• the smallest detail that can be seen is about 0.2 micromeers in diameter

• Living cells can be imaged using this, but if a stain is used it usually kills the sample

electron microscopes

• uses an electron beam focused by magnets to illuminate a specimen and produce and image on screen

• the size limit for an electron microscope is 0.1 nanometer

• specimens need to be preserved and stained with heavy metals, so living cells cannot be visualized

all cells

• have a plasma membrane separating the outside from the inside of the cell

• the components insidue the cell are called the cytoplasm

• all cells have genetic material (DNA)

• all cells have ribosomes (protein factories)

prokaryotes

• more “primitive”; mostly single-celled organisms

• internal environment of cell is not divided into membrane-bound compartments (organelles)

• do not have a nucleus

eukaryotes

• internal environment is divided into organelles

• mostly multicellular organisms

• have a nucleus

characteristics of prokaryotic cells

• always unicellular

• consists of

  • plasma membrane

  • rigid cell wall containing peptidophycans (sugars mixed with peptides)

  • cytoplasm internal cell contents

  • genetic material is not enclosed by a membrane

  • no membrane-bound organelles

  • chromosomal DNA is located in a nucleoid

  • ribosomes are in the cytoplasm

  • the other strucutres may be present in some, not all, bacterial structures

characteristics of eukaryotes

• contain human and all other animals, plants, fungi, and protists

• cell structure consists of:

  • plasma membrane

  • nucleus

  • cytoplasm

  • organelles

nucleus

membrane-bound genetic material

cytoplasm

internal cell contents, exluciding the nucleus

organelles

variety of membrane-bound strucutres within the cytoplasm with specialized functions

plasma membrane

a phospholipid bilayer with embedded proteins

• the heads are hydrophilic while the tails are hydrophobic (tails in, heads out)

• has glycoproteins, glycolipids, peripheral and integral proteins, and cholesterol

separates the cell from its environment

is selectively permeable

enables transfer of information between environment and cell

selectively permeable

permits movement of some substances in and out of the cell, but blocks others

central dogma of biology

genetic information only flows in one direction

genetic information —> instructions to make a protein —> proteins, the workhorse of the cell

nucleus function

contains the genetic information (DNA) of the cell

controls the activities of the cell

nuclear envelope

double-layered membrane (two membrane, each is a phospholipid bilayer for a total of four phospholipid bilayers)

nuclear pores