Lecture 1 Flashcards
Gram-Negative Bacteria
Outer membrane and a thinner peptidoglycan layer. Do no stain
Gram-Positive Bacteria
No outer membrane and have a thicker peptidoglycan layer. Do stain
Bacteria Ribosomes
smaller than eukaryotic. Protein synthesis from an RNA message.
Bacteria Nucleoid
Contains a single, simple, long circular DNA molecule
Pili
Provide points of adhesion to surface of other bacteria cells
Flagella
Propel cell through its surroundings
Nucleus
contains the genes (chromatin)
Nuclear envelope
segregates chromatin (DNA + protein) from cytoplasm
Nucleolus
site of ribosomal RNA synthesis
Plasma membrane
separates cell from environment, regulates movement of materials into and out of the cell
Mitochondrion
oxidizes fuels to produce ATP
Rough ER
Has ribosomes attached and is site of much of the protein synthesis.
Smooth ER
site of lipid synthesis and drug metabolism
Golgi complex
processes, packages, and targets proteins to other organelles or for export. Cis part is closest to the ER. Trans is where vesicles leave
Transport vesicles
shuttles lipids and proteins between ER, Golgi, and plasma membrane
Lysosome
degrades intracellular debris in a very acidic environment
Cytoskeleton
supports cell, aids in movement of organelles
Peroxisome
oxidizes fatty acids. Take long chain fatty acids and make them into medium length fatty acids, which are then taken to the mitochondria.
Eukaryotic Ribosomes
protein-synthesizing machines. Can be attached to the ER or can be free floating.
Phototrophs
get energy from light
Chemotrophs
get energy from oxidation of chemical fuels
Covalent bonds
sharing of electrons
Stereoisomers
molecules with same chemical bonds but in different configurations
Geometric isomers
cis-trans. differ in the arrangement of their substituent groups with respect to a non rotating double bond.
Chiral carbon
carbon atom with 4 different substituents is asymmetric
Enantiomers
stereoisomers that are mirror images of each other
Diastereomers
stereoisomers that are not mirror images of each other
Two ways enzymes speed up reactions
change the reaction by coupling to a fast reaction. Lower activation barrier by catalysis
Endergonic
metabolic reaction that requires energy
Positive Gibbs Free energy
thermodynamically unfavorable. Because creating order requires work and energy
Exergonic
metabolic reaction that releases energy often as a result of a breakdown
Negative Gibbs Free energy
Thermodynamically favorable.
Energy Coupling
chemical coupling of exergonic and endergonic reactions allow otherwise unfavorable reactions to proceed (ATP is used a lot)
Phosphorylation
when the phosphate group from an ATP goes onto an enzyme or substrate
Adenlyation
when an AMP or ADP is put onto an enzyme or substrate
Catalyst
compound that increases the rate of a chemical reaction. Do not alter Gibbs free energy, but rather lower activation energy.
Catalyst offers 3 things
acceleration under mild conditions
high specificity
possibility for regulation
Metabolic Pathway
produces energy or valuable materials
Signal Transduction Pathway
transmits information
Positive Feedback regulation
rate of processes increases as the concentration of the product increase
Negative Feedback inhibition (regulation)
controls the rate of the processes when the product starts to accumulate
Types of non-covalent interactions
Ionic, Dipole (Hydrogen), Van der Waals, and Hydrophobic Effect
Ionic Bonding
Electrostatic interactions between permanently charged species, or between the ion and a permanent dipole
Dipole Interactions
Electrostatic interactions between uncharged, but polar molecules.
includes hydrogen bonding
Van der Waals Interactions
Weak interactions between all atoms, regardless of polarity
Attractive ( London dispersion) and repulsive (steric) component
Hydrophobic Effect
complex phenomenon associated with the ordering of water molecules around non-polar substances
Acid
Proton donor
Base
Proton acceptor
Hydrogen Bonds
strong dipole-dipole and charge-dipole interaction that arises between and acid and base
Van der Waals attraction
(london dispersion). the forces depends on the polarizability. Attraction dominates at longer distances
Van der Waals repulsion
(Steric repulsion) depends on the size of the atoms.
Dominates at shorter distances
Water is a good solvent for
charged and polar substances, such as: amino acids, peptides, small alcohols, and carbohydrates
Water is a poor solvent for
nonpolar substances, such as: non polar gases, aromatic moieties, and aliphatic chains
Amphipatic
both polar and nonpolar
Hydrophobic effect
the association of non-polar molecules in an aqueous solution. Brought together by entropy
Entropy
Measure of disorder
Positive entropy
More disordered, thus spontaneity more favorable
Negative entropy
Less disordered, thus spontaneity less favorable
Micelles
Allow for all hydrophobic groups to be sequestered from water. Leading to increase in entropy, thus more favorable
Hydrophobic Effect plays major role in… (4)
1) Protein Folding
2) Protein-Protein association
3) Formation of lipid micelles
4) Binding of steroid hormones to their receptors
