Topic 3 - Biological Macromolecules: Proteins Flashcards
Why is carbon important?
It provides the framework for all biological molecules. Biological molecules are hydrocarbon skeletons (C and H only) with attached functional groups.
List the functional groups and their properties.
- Hydroxyl (polar)
- Carbonyl (polar)
- Carboxyl (polar, acidic)
- Amino/Amine (polar, basic)
- Sulfhydryl (polar, only found in proteins as sulfide bridges with other sulfhydryl)
- Phosphate (polar, acidic, only found in nucleic acids)
- Methyl (nonpolar)
Describe the structure of hydroxyl
O bonded to H and R group
R-OH
Describe the structure of carbonyl
Carbon bonded to O in a double bond with two R groups
R-(C=O)-R’
Describe the structure of carboxyl
Carbon bond to O in a double bond, with an R group bond and OH bond
R-C(=O)-OH
Describe the structure of amino/amine
Two H bond to N, with an R group bond
R-NH2
Describe the structure of sulfhydryl
R group bonded with S, H bonded with S
R-SH
Describe the structure of phosphate
P bonded to O in a double bond, a second O bonded to P with an R group bonded to O, and two OH bonded to P
R-O-P(=O)(OH)2
Describe the structure of methyl
CH3 bonded to an R group
R-CH3
Monomers
Subunits/building blocks of polymers
Polymers
Larger molecules formed from monomers
What are the four major macromolecules (polymers) and their monomers?
- Carbohydrates - monosaccharides
- Lipids - triglycerides
- Proteins - amino acids
- Nucleic acids - nucleotides
How do polymers form?
Dehydration synthesis
Dehydration synthesis
(also, condensation)
Reaction that links monomer molecules, releasing a water molecule for each bond formed
How do polymers disassemble?
Hydrolysis
Hydrolysis
Reaction that causes breakdown of larger molecules into smaller molecules by utilizing water
True or false: dehydration synthesis requires the removal of water
True
True or false: hydrolysis requires the addition of water
True
Protein
Biological macromolecule comprised of one or more amino acid chains
What are the components of amino acids?
Amino, carboxyl, R groups and H attached to a central carbon (alpha carbon)
R-CH(NH2)-COOH
What properties does an R group determine?
Nonpolar
Polar
Charged
Aromatic/aliphatic
Special function
What are the nonpolar, aliphatic amino acids?
Glycine
Alanine
Leucine
Valine
Methionine
Isoleucine
Proline
What are the nonpolar, aromatic amino acids?
Phenylalanine
Tyrosine
Tryptophan
What are the polar, uncharged amino acids?
Cysteine
Serine
Asparagine
Threonine
Glutamine
What are the positively charged amino acids?
Histidine
Arginine
Lysine
What are the negatively charged amino acids?
Glutamate
Aspartate
What are the four levels of protein structure?
Primary, secondary, tertiary, quaternary
Primary structure
A chain of amino acids linked by strong covalent bonds known as peptide bonds - AKA a polypeptide chain
This level is stable and can be broken by enzymes.
Peptide bond
Covalent bond between two amino acids formed by a dehydration reaction
(Remember: dehydration reactions form polymers)
Secondary structure
Formed by hydrogen bonds between C=O and N-H of the amino acid; the local folding of the polypeptide in some regions gives rise to secondary structure.
α-helix - coils
β-strands - pleated sheets
This level is sensitive to changes in temperature and pH.
Tertiary structure
A protein’s three-dimensional shape, formed by interactions among R groups (side chains)
1. Weak bonds - hydrogen bonds, ionic bonds, van der Waals forces, hydrophobic forces are all weak bonds that are easily disrupted.
2. Strong disulfide bridges - made between adjacent sulfhydryl functional groups; strong covalent bonds
This level is sensitive to changes in temperature and pH.
Quaternary structure
Interactions of two or more polypeptide subunits; held together by weak and strong interactions
1. Fibrous - fiber-like strings
2. Globular - spherical, three-dimensional blobs
What is an example of primary structure?
Insulin - two polypeptide chains linked together by disulfide bonds
What is an example of secondary structure?
Keratin - α-helix
What is an example of tertiary structure?
Myoglobin
What is an example of quaternary structure?
Hemoglobin
What is the importance of weak bonds in a protein?
- A protein’s shape is flexible because of the weak bonds that hold it together. This allows it to change shape which can aide its function.
- This flexibility also means that proteins can lose their function if their shape changes too much. The right pH, temperature and salt concentrations are all essential for protein function.
Chaperonins
Special proteins that help refold proteins whose shape has changed
Motifs
Common shapes that are found in many different proteins. These shapes can give clues about the function of a protein.
β barrel - may be found in a membrane pore protein
β-α-β nucleotide binding side - usually NAD indicates a protein, may be a dehydrogenase
Helix-turn-Helix - DNA binding site (two α-helixes)
Domains
Independent “chunks” of protein, often coded by different exons - may be “mixed and matched” through evolution
What are the different types of proteins?
Enzymes, transport, structural, hormones, defense, contractile, storage
Denaturation
Loss of shape in a protein as a result of changes in temperature, pH, or chemical exposure
Enzymes
Catalysts in a biochemical reaction that are usually a complex or conjugated protein
True or false: all enzymes are proteins, but not all proteins are enzymes
True
Activation energy
Energy necessary for reactions to occur
Fill in the blank: enzymes are catalysts that _______ activation energy.
Lower
Induced fit model
Dynamic fit between the enzyme and its substrate, in which both components modify their structures to allow for ideal binding
Substrate
Molecule that will undergo a reaction
Active site
Region of the enzyme that binds to the substrate
Fill in the blank: an enzyme’s function depends on its _______
Shape
What bonds maintain three-dimensional structure?
Covalent, ionic, hydrogen, van der Waals
What factors can change an enzyme’s function?
- Temperature
- enzyme activity may be increased with increasing temperature up to the optimal level
- temperatures above the optimum can denature an enzyme - pH
- acids increase H+ which interfere with ionic and hydrogen bonds
- bases increase OH- which interfere with ionic and hydrogen bonds
What helps refold an enzyme?
Chaperonin/heat shock proteins
Inhibitors
Molecules that bind to an enzyme to decrease enzyme activity
Competitive inhibitors
Inhibitors that compete with the substrate for binding to the same active site
Allosteric enzymes…
- exist in either an active or inactive state
- possess an allosteric site where molecules other than the substrate bind
Noncompetitive inhibitors
Inhibitors that bind to sites other than the active site
Allosteric inhibitors
Inhibitors that bind to the allosteric site to inactivate the enzyme
Allosteric activators
Bind to the allosteric site to activate the enzyme
What are the advantages of multienzyme complexes?
- the product of one reaction can be directly delivered to the next enzyme
- the possibility of unwanted side reactions is eliminated
- all of the reactions can be controlled as a unit
Negative feedback inhibition
The end product of a biochemical pathway is an inhibitor of an earlier enzyme in the pathway; occurs when the product of a biological reaction stops the reaction from continuing to occur.
