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43 Cards in this Set

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Describe the assumptions of Miller's famous experiment
Assumed the early atmosphere was full of high energy molecules when chemical evoution occured, making redox reactions possible.
Describe the set-up of Miller's experiment
The microcosm of the atmosphere contained CH4, NH3, and H2, which were carried by water vapor through the cycle; elecric impulses sparked chemical evolution
Name some of the problems later found with Miller's chemical evolution experiment
Volcanic gases would have had lowe energy forms (CO2 and CO) which are less reactive; Chemical evolution may take place in the ocean, not atmosphere
Describe the basic structure of the 20 protein-forming amino acids
1st bond- NH2 the amino func. group
2nd bond- COOH the carboxyl group
3rd bond- H atom
4th bond- the 'R' group (side chain); distinguishes the amino acids from each other
What happens to amino acids in water?
The concentration of proteins causes the amino acids to act like bases, forming NH3+ and COO-.
Describe the difference hydrophobic and hydrophilic R groups
Hydrophobic- Non-polar side chains that cannot form H bonds in water
Hydrophiliac- Polar side chains that interact with water and dissolve easily
Describe the reaction patterns of side chain composed of mostly C and H atoms
These R groups rarely react chemically.
Explain the importance of R groups containing S
These R groups help link larger proteins.
Isomers
Molecules that have different structures, but the same molecule formulas.
Describe the 3 types of isomers
1. Structural Isomers- same atoms, different order due to covalent bonds
2. Geometric Isomers- differ in ring or double bond
3. Optical isomers- carbon atoms with 4 different groups attached
T/F in cells, the 'left handed' isomer is interchangable with the 'riight handed' version
False- the right handed version causes malfunctions.
Monomer
A molecular subunit such as a sugar, amino acid, or a nucleotide.
Polymer
The result of several monomers linked together.
Polymerization
The process of linking monomers.

(Amino Acids polymerize to form proteins)
Protein
The linear macromolecule of linked amino acids monomers.
Why are proteins technically not expected to form spontaneously?
Complex and highly organized molecules are not expected to form spontaneously because they result in decreased entropy; Delta G is positive for all temperatures.
Condensation Reactions (Dehydration Reactions)
A reaction in which the new molecule reults in the loss of a water molecule.
Hydrolysis
A reaction that breaks polymers apart by adding water molecule; dominates because it increases entropy and is energeticallt favorable.
How do polymers escape hydrolysis?
Adsorption to mineral particles protects polymers from hydrolysis.
Peptide Bond
A bond that forms between the carboxyl group of one amino acid and the amino group of another vi a condensation reaction.
Describe a polypeptide
*Side chains extend out from the-
*Backbone, which has direction and flexibility (due to single bonds); the peptide is always N terminus to C.
How are amino acids referred to in a polypeptide?
The amino acids are referred to as residuals.
Primary Structure
The sequence of amino acids of a protein; each protein has a unique sequence and structure ( Fred Sanger & insulin).
Secondary Structure
This structure is created by the H bonds that form between carboxyl and amino groups in the backbones ONLY; either alpha helices or beta pleated sheets.
Tertiary Structures
This structure is responsible for the overall shape of the protein; results froom interacts between R groups and backbones.
What are some of the possible interactions at the tertiary level?
1. Covalent bonds can form between the S atoms (disulfide bridges)
2. In H2O, hydrophobic regions form vn der Waals interactions; inc. stability and create glob structure
3. Ionic bonds can form between ionized amino and carboxyl groups
4. H bonds
Quaternary Structures
Not present in every protein; this structure is due to the combination of polypeptide subunits.
Why is folding both spontaneous and important?
Folding is spontaneous because van der Waals interactions make folded proteins more energetically stable, releasing free energy; folding is essential for protein function.
How is a denatured protein different from regular proteins?
Denatured proteins are unfolded.
Molecular Chaperones
Molecules that facilitate protein folding which belong to a group of proteins known as heat shock proteins.
Heat Shock Proteins
Proteins that are produced in large quantities in a cell after the cell experiences high temps. or other situation that make them lose 3rd struc.
Prions
Infectious proteins that are improperly folded forms of regualr proteins; they differ in shape and can induce normal proteins to change as well (fatal disease).
What are the 6 main functions of proteins?
1. Defense (antibodies), 2. Movement (motor/ contractile proteins), 3. Catalysis (enzymes), 4. Signaling (peptide hormones bind to receptors), 5. Structure (mechanical support), 6. Transport (carry compounds through body/ allow enterance into cells)
Catlalyst
A substance that lowers the activation energy of a reaction and increases the rate of the reaction; it is not consumed in the reaction.
Enzymes
Proteins that catalyze reactions;
often end in -ase.
Lock and Key Model
Enzymes are ridgid structures analogous to a lock; substrates bind to this lock and react;
However, enzymes are really flexible.
Activation Sites
The locations on the enzymes where the substrates bind to and react.
Describe the process of catalyzing an enzyme
1. Initiation- Reactants bind to the activation sites in a specific orientation
2. Transition Site- Activation energy lowered by the interaction between the enzyme and substrate
3. Termination- Products have lower affinity for activation sites and are released; enzyme remains unchanged.
Enzyme Cofactor
Atoms or molecules that are not part of the enzymes primary structure; they are either metal ions or coenzymes.
Competitive Inhibition
Catalysis is inhibited when a molecule similar in shape and size to the substrate competes for the enzyme activation site.
Allosteric Regulation
Molecule changes enzyme shape to activate/inactivate it.
Enzyme Kinetics
The rate of enzyme action; at a certain point, the rate tapers off because all of the enzyme is being used; affected by pH and temperature ( and population).
How do endergonic reactions take place?
1. Most reactions are endergonic
2. Adding a phosphate group (PO4 3-) adds 2 negative charges and adds enough free energy for polymerization -- phosporization occurs (exergonic).