Modern States - Biology, Module 1

Matter

Anything that takes up space and has mass, made of elements

Elements

Cannot be broken down to other substances; each of these have unique atoms

Atoms

Smallest unit of matter with element’s properties

Compound

2+ different elements combined in a fixed ratio

Molecule

2+ same or different elements combined in a fixed ratio

Electrons

Negatively-charged particle of an atom (-) found orbiting in shells

Valence electrons

Electrons in the valence shell of an atom who can only interact with another

Chemical Bonds

Attractions that keep atoms close together; protons and electrons attract like magnets

Covalent bond

Sharing pair of electrons, strong bonds

Nonpolar bond

Covalent bond where sharing is equal

Polar bond

Covalent bond where sharing is unequal, which creates partial charges (poles)

Ionic bond

One atom steals electron while the other loses electrons, strong bonds

Anion

Atom of an ionic bond which steals electron

Cation

Atom of ionic bond which loses electron

Hydrogen bond

Form between poles of H and O in water molecules, weak bonds

Chemical Reactions

Make and break chemical bonds

Products

Part of chemical reaction who get produced as a result of the reactants reacting together

1st Law of Thermodynamics

Energy cannot be created or destroyed

2nd Law of Thermodynamics

Reactions tend to increase disorder (make energy less available for cells)

Endothermic reactions

Take energy

Exothermic reactions

Release energy

Water

Only molecule to exist in all three states: solid, liquid, and gas

Ice (solid water)

Less dense than liquid water

Adhesion

Water molecules will stick to molecules other than water very well

Cohesion

Water molecules stick to each other very well

Surface tension

It’s difficult to break the surface of water

Universal solvent

Liquid where everything dissolves in

High specific heat

It takes longer to increase of one unit of this liquid one degree than it takes for a lot of other molecules

Evaporative cooling

Evaporation of a liquid helps lower temperature of something else

Acids

Dissolves in water and increases relative H+ ion concentration in the solution

Bases

Dissolves in water and decreases the H+ ion concentration in the solution

pH scale

Shows relative amount of H+ ion concentration; smaller number means more acidic, larger number means more basic, and 7 is the neutral level

H+

Hydrogen ions

Organic Molecule

Any molecule containing carbon, though it can also contain other molecules like oxygen, hydrogen, nitrogen, etc.

Monomers

Building blocks of organic molecules

Polymers

Many monomers linked together in an organic molecule

Carbohydrates

First class of organic molecules made only of carbon, oxygen, and hydrogen

Monosaccharide

Carbohydrate monomer, example is glucose

Polysaccharide

Carbohydrate polymer, example is starch

Lipids

Second class of organic molecules group together because of their hydrophobic properties: waxes, fats, phospholipids, and steroids

Proteins

Third class of organic molecules who form most of the enzymes, antibodies, and muscle fibers in your body

Amino acid

Protein monomer

Polypeptide

Protein polymer; these bonds hold amino acids together

Nucleic acids

Fourth class of organic molecules whose primary function is information storage

Nucleotide

Nucleic acid monomer with five variations made of a nitrogen base, a sugar, and a phosphate group: adenine (A), thymine (T, only in DNA), uracil (U, only in RNA), cytosine (C), and guanine (G)

Adenine

A

Thymine (found only in DNA)

T

Uracil (found only in RNA)

U

Cytosine

C

Guanine

G

Between two strands of DNA, via a hydrogen bond

Nitrogenous bases in nucleotides and nucleic acids are joined together—

“Backbone”

Barriers of the DNA molecule made from sugar and phosphate found in a nucleotide’s nitrogen base

Base pair

Pairs of nucleotides such that DNA and RNA strands are complimentary: A-T or A-U, and C-G, where they are joined in the center by hydrogen bonds

T and U

The nucleotide A can only form base pairs with—

A

The nucleotides T and U can only form base pairs with—

G

The nucleotide C can only form base pairs with—

C

The nucleotide G can only form base pairs with—

3.5 million years ago, from fossil evidence

Life evolved—

Bacteria and Archaea found in deep sea vents, hot springs, and tide pools

The first living things probably were—

Simple organic molecules

Start of evolution, where they then started to be able to replicate

Membranes

Formed spontaneously in the evolution of life with the rise of cell division

Metabolism

Conversion of food into energy

Cell membranes, metabolism, DNA, and fossils

Types of evidence for all common ancestry includes—

Tree of Life

Has patterns of evolution from simple to complex

Membranes

Selectively permeable boundary—phospholipid bilayer—between the inside of the cell and its surroundings which includes proteins, other lipids, and hybrid molecules

Phospholipid bilayer

Two layers of phospholipids: a hydrophobic layer on the inside and a hydrophilic layer on the outside

Selective Permeability

Membranes regulate cell traffic by only allowing some things to pass freely

Passive transport

Membrane allows things to pass through by themselves which requires no energy but needs a “doorway” protein in membrane

Active transport

Membrane requires energy and “doorway” protein to pass through; useful for moving molecules against their concentration gradients

Diffusion

Movement of molecules from higher to lower concentrations where each molecules moves randomly and no energy is required; spontaneous, type of passive transprt

Osmosis

Diffusion of water across membrane from higher to lower concentrations

Facilitated Diffusion

Diffusion with help of “doorway” protein

“Doorway” protein

Specific type of protein inside membrane which serves as a tunnel, allowing certain molecules to go through it

Bulk transport

Type of active transport for large molecules that can’t pass through the membrane; the cell creates a pinched-off area forming a “vessel” transporting the molecule through the membrane

Exocytosis

Leaving cell via bulk transport through vesicles

Endocytosis

Entering cell via bulk transport through vesicles

Prokaryote

Type of unicellular body who are the most ancestral living things and the most abundant living things on the planet with a cell membrane, a cell wall, a cytoplasm, and/or locomotor structures but no nucleus and organelles

Eukaryote

Type of uni- or multicellular body that evolved from prokaryotes who have internal organelles and DNA, with some even having cell walls or locomotor structure

Animals, plants, fungi, etc.

Examples of eukaryotes include—

Activation Energy

Initial energy barrier required to pass before any chemical reaction (Ea) which determines rate of reactions

Existing chemical bonds must be broken before new bonding can occur

Activation energy exists because—

Enzymes

Proteins that act as catalysts; ex. lactase and lactose

Catalysts

Make reactions happen faster by lowering Ea without actually being changed themsellves

Their bodies do not have the lactase enzyme; therefore, the Ea for lactose is higher and the chemical does not break down

People are lactose intolerant because—

Substrate

Molecule enzyme interacts with

Active site

Location where enzyme interacts with subtrate

Enzyme-Substrate Complex

Enzyme and substrate fit together like hand in glove in the active site, where the enzyme will then either release the bond(s) of the substrate or join the two substrates together into one molecule

Denaturation

Shape of enzyme active site is changed (temperature, pH) by the environment, forcing it to stop working

Induced Fit

Theory of Enzyme-Substrate binding which states that as the enzyme and substrate come together, their interaction causes a mild shift in the structure of the enzyme that confirms an ideal binding arrangement between the enzyme and the transition state of the substrate

Competitive inhibition

Inhibitor molecule competes with the substrate for active site binding

Noncompetitive inhibition

Inhibitor molecule binds to enzyme somewhere other than the active site, which changes the enzyme’s shape and makes catalyzing a reaction less effective

Cofactor

“Helper” molecule who bonds to enzymes’ active site to optimize process and help form enzyme-substrate complex

Feedback inhibition

Cells use reaction product to regulate its own further production, which may inhibit the enzymes that catalyzed their production

Coenzyme

Organic cofactors, commonly vitamins

Cosubstrate

Type of coenzymes which are detachable

Prosthetic Group

Type of coenzymes which are permanent

Inhibition

The slowing down or blocking of a reaction

Inhibitors

Molecules that compete with substrates for enzymes’ active sites

Sit in active site and block it such that enzyme and substrate cannot interact, or attach themselves to an enzyme outside active site and then change shape of the active site

To perform inhibition, inhibitors will either—

a2-antiplasmin

Type of inhibitor which stops enzymes from dissolving blood clots; helpful for treating bleeding disorders like hemophilia