BIO140 DOYLE JMU FINAL

Atom

the basic unit of a chemical element.

Ions

charged atoms

Cation

A positively charged ion

Anion

A negatively charged ion

Mass Number

the sum of the number of neutrons and protons in an atomic nucleus

Atomic Number

the number of protons in an atom

Valence Electrons

electrons in the outermost shell

Shells

the orbits of electrons around the nucleus in certain energy levels

Orbitals

regions around the nucleus in which given electron or electron pair is likely to be found

Bohr Model

model of an atom that shows electrons in circular orbits around the nucleus

Rows of periodic table

periods

columns on the periodic table

groups

significance of carbon

major element of organic compounds

Covalent Bonds

sharing of electrons

Polar Covalent Bonds

unequal sharing of electrons

Non-Polar Covalent Bonds

equal sharing of electrons

Non-covalent bonds

Weak bonds, does not involve the sharing of electrons.

Ionic Bonds

transfer of electrons

Hydrogen bonds

weak attraction between a hydrogen atom and another atom

Hydrophobic forces

Hydrophobic groups interact with each other to exclude water molecules

Van der waals forces

intermolecular forces of attraction

2 unique properties of water

1. Expands as a solid
2. universal solvent

pH scale

measurement system used to indicate the concentration of hydrogen ions (H+) in solution; ranges from 0 to 14

pH scale: acidic

0-6

pH scale: neutral

7

pH scale: basic

8-14

pH equation

pH=−log[H+]

Calculating hydrogen ion concentration

Calculating pH

1. Determine the concentration of H+ ions in the solution.
2. Plug the concentration of H+ ions into the pH equation: ⁡pH=−log[H+].
3. Calculate the negative logarithm of the H+ ion concentration using a calculator to find the pH of the solution.

Calculating the fold difference

To calculate the fold difference between two values, you simply divide one value by the other.
The fold difference represents how many times larger or smaller one value is compared to the other.

Peptide bonds

Bonds between amino acids

Macromolecules

A very large organic molecule composed of many smaller molecules

Monomers and Polymers

Monomers are the smaller units that join together to form polymers.

Proteins

Chains of amino acids linked by peptide bonds

Nucleic acids (DNA and RNA)

DNA which contains the code for replication
RNA used in transfer and as a messenger

Lipids

any of various organic compounds that are insoluble in water

Sugars

generic term for any disaccharides and monosaccharides

Carbohydrates

J.B.S Haldane and Alexander Oparin

Believed that organic molecules could be formed from abiogenic materials in the presence of an external energy source

Darwin and Joseph Hooker

theory of evolution by natural selection

Harold Urey and Stanley Miller

Discovered deuterium; a stable isotope of hydrogen with a mass approximately twice that of the usual isotope.

Requirements of the Cell

1. A way to encode/transmit information
2. A membrane separating inside from out
3. ENERGY

Metabolism

building up and breaking down of carbon sources

Catabolism

the set of metabolic processes that break down large molecules

Anabolism

a biochemical process in metabolism where the simple molecules combine to generate complex molecules.

Kinetic vs. Potential energy

Kinetic is the energy in motion, potential is the stored energy

ATP

Adenosine Triphosphate

ATP contains energy in its chemical bonds that can be used to perform the work of the cell

First law of thermodynamics

Energy is neither created nor destroyed - it changes form

Second law of thermodynamics

In the universe, the degree of disorder can only increase

Entropy

Measure of disorder

Chemical reactions

Occur when molecules interact

Gibbs free energy (ΔG)

Energy available to do work (usable or good energy)

Non-spontaneous (endergonic)

Energy is required

Spontaneous (exergonic)

Energy is not required

H

Enthalpy

G

free energy

S

Entropy

Energetic Coupling

linking energetically favorable and unfavorable reactions together to drive the unfavorable reaction using the energy released by the favorable reaction.

GOAL IS TO HAVE AN OVERALL NEGATIVE ΔG

Enzymes

substrate interactions stabilized by non-covalent(weak) interactions

Substrate

the surface on which an organism lives or the substance on which an enzyme can act

Active site

the part of the enzyme where substrate molecules bind and a chemical reaction takes place

Allosteric site

other, or second, site

Enzyme activators

increase activity of enzymes

Irreversible inhibitors

form covalent bonds

Reversible inhibitors

form weak bonds, can come off

Competitive inhibitors

compete with the substrate for binding at the active site

Non-Competitive inhibitors

bind at an allosteric (other, or second) site - change the shape of the active site.

Feedback inhibition

Molecules from the end of a pathway bind to an enzyme at the beginning of thepathway, and turn off that enzyme (and therefore flow through the pathway)
Uses allostery to reduce enzyme activity

Griffith's experiment

DNA acts as the carrier of genetic information.

Avery, MacLeod, and McCarty

discovered that DNA was responsible for the genetic exchange of information.

James Watson and Francis Crick

discovered the three-dimensional structure of DNA.

Purines

Adenine (A)
Guanine (G)

Pyrimidines

Thymine (T)
Cytosine (C)

Nucleosides

Sugar molecule bonded by a nitrogenous base (A, G, T, or C)

Nucleotides

Nucleoside bonded to one or more phosphate groups

Phosphodiester bonds

Covalent bonds that connect nucleotides to each other.

Hydrogen bonding

Attraction between partial charges.

Histones

Many positively charged amino acids

Nucleosomes

DNA and histones

Chromatin

the complex of genomic DNA with proteins called histones

Epigenetics

Study of heritable phenotype changes that do NOT involve changes to the DNA sequence

Epi = over, outside of, or around

Centromeres

Allows one copy of each duplicated chromosome togo to each daughter cell inmitosis

Telomeres

Repeated sequences at tips
Required for complete replication of chromosome

Telomeres role-playing in aging

Add telomeres = extend lifespan

RNA world hypothesis

RNA likely evolved first (before protein and DNA)

Transcription

using PARTS of the DNA sequence as a template for RNA

Initiation

where initiator AUG is recognized

Enhancer sequence

regulatory DNA sequences that enhance the transcription of an associated gene.

General transcription factors

needed at every promoter

Enhancers/transcriptional activators

vary for each promoter, Enhancers are DNA, transcriptional activators are protein

RNA polymerase

Enzyme that synthesizes RNA.

RNA processing

Editing and modifying RNA molecules.

5' cap

Modified nucleotide at mRNA's beginning.

Poly A tail

String of adenine nucleotides in mRNA.

Introns

intervening sequencings (spliced out)

Exons

Expressed sequences (made into protein)

Splice out introns (RNA splicing)

Removing introns from pre-mRNA.

Alternative splicing

Connect exons together in different combinations - more than one protein per gene

Termination

ending of transcription

Transcription in prokaryotes

DNA copying to RNA in bacteria.

Template strand

what is copied

Daughter Strand

newly synthesized