BY 330: MACROMOLECULES
28 Cards in this Set
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General size of macromolecules
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10,000 to 1 million Da (100-1000X larger than small molecules)
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T/F
Macromolecules are assembled from low molecular weight subunits.
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True, small molecules have low molecular weights
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How are chains in macromolecules held together?
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strong covalent bonds
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types of non-covalent weak bonds/interactions used to make macromolecules
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1. Hydrogen bonds - attraction b/t H and O
2. Ionic bonds - ions, ex. Na+/Cl-
3. Van der Waals forces - very transient, momentary interactions when positive and negative charges attract each other
4. Hydrophobic interactions - a characteristic which causes things to be pushed tog…
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Which type of bond, covalent or non-covalent gives functionality? Structure?
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Functionality = non-covalent
Structure = covalent
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AMINO ACIDS:
1. # common?
2. 4 broad characteristics
3. Can any form covalent bonds?
4. 2 Forms
5. Average protein has ___ a.a.
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1. 20
2. polar, non-polar, acidic, basic
3. yes
4. Globular - R groups interact, winding up to avoid environment; Fibrous - unwound chain, R groups want to interact with environment
5. 300
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Two properties for a functional protein.
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1. Stable conformation (low energy) - high energy will not stay folded
2. Flexibility - weak bonds break and reform over time, proteins are not static structures
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Levels of protein structure
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Primary = string of a.a. bound tog. with peptide bonds
Secondary = forms α helix and β pleated sheets stabilized by H-bonds **formed by R group interactions
Tertiary = polypeptide strand, interactions between α helices and β pleated sheets
Quarternary = 2+ polypeptide strands int…
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Multimeric protein and example
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protein with multiple subunits
ex. hemoglobin
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What is a dimer?
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two polypeptide strands (3°) bound together
Homodimer = 2 identical 3° structures bound together
Heterodimer = 2 different 3° structures
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T/F
One strand of polypeptides has many individual 2° structures, and a protein must consist of both α-helices and β-pleated sheets.
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False,
A protein is made up of many 2° structures, but it is possible for a protein to be made up of only α-helices or only β-pleated sheets
ex. protein that needs to go through membranes may be made of only α-helices
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1° structure is held together with ____
99% of 2°, 3°, and 4° structues held together with ____
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covalent bonds
weak bonds
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T/F
Most 1°, 2°, 3°, and 4° structures fold spontaneously without any enegy or help when in the correct solution
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True
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What are chaperones?
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proteins that assist new proteins in folding into their final functional form
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What are domains?
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clusers of interacting 2° structures, a discrete portion of the larter polypeptide
--often make up very important functional components (i.e. binding sites)
--very distinct
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Functions of Proteins given in class: (4)
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1. Interaction factors - cell signaling
2. Elongation factors
3. Structural components - skeleton like to maintain shape (ex. globular or fibrous)
4. Enzymes
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Properties of enzyme proteins: (3)
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1. Binding site to bind with substrate
2. R-groups are arranged specifically in binding pocket to ineract with ligand
3. Proteins can have multiple binding sites, and some sites act as regulators for the remaining binding sites
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anyting that binds to protein
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Ligand
ex. ion, small molecule, macromolecule, or another protein
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Discuss difference in high affinity and low affinity of ligand and binding site
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high affinity = good matchup b/t ligand to binding site (like a strong magnet)
low affinity = poor matchup of ligand to binding site
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All bonds between R groups of binding pocket on enzyme and ligand are _____
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hydrogen bonds (weak bonds) - this is a characteristic of functionality of R groups
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Discuss and example of multiple binding sites which can act as regulators for a protein
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The first oxygen to bind to hemoglobin is the most difficult/has the lowest affinity. The shape changes after the first O binds, which increases the affinity of the rest of the biding sites to oxygen.
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Theories of Ligand binding (old and new)
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1. Lock and key (OLD) - must have perfect match b/t ligand and binding site
2. Induced fit (CURRENT) - ligand is roughly the same shape as binding site, shape conforms to fit even more closely after binding
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How does affinity of enzyme to substrate affect rate of product production?
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Enzyme does not degrade as it converts substrate to product, so high affinity = rapid production and low affinity = slower rate of production
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What changes in substrate cxn velocity graph in non-competitive example
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Km (concentration of substrate at 1/2 max. velocity)
High affinity = low Km
Low affinity = higher Km
**vmax stays the same
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What changes in competitive example of substrate cxn and velocty graph
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max velocity changes, so we can measure the change in the 1/2 max velocity where Km stays the same
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Define allosteric in terms of enzyme
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enzyme has multiple binding sites, something binds to a regulatory site which changes the affinity of the substrate to the binding sites/changes the shape of the enzyme
ex. hemoglobin/oxygen
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Difference in competitive and non-competitive allosteric binding
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Non-competitve - regulatory protein not competing for same site as substrate, Km changes
Competitive - regulatory protein and substrate are competing for same site, changes vmax
--In competetive enzyme is no longer functional when binding of inhibitory protein is irreversible
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Name some environmental factors that affect rate of protein production
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pH, temperature, pressure (altitude), inhibitors
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BY 330: SMALL MOLECULES