Biology Chapter 3: Protein Structures and Functions
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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
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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
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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
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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
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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
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*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?
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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
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Proteins that catalyze reactions;
often end in -ase. - Lock and Key Model
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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
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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?
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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).