Quiz 2 Flashcards
Protein
Chain of amino acids
Describe the structure of an amino acid?
Amino group
Carboxyl group
Side chain
Where is the side chain of amino acid attached to?
Core carbon
Peptide bond
Covalent bond that links amino acids together
Polypeptide backbone
Repeating series of atoms along core
N-terminus
Beginning of sequence; carries free amino group (NH3+)
C-terminus
End of sequence; carries free carboxyl group (COO-)
20 side chains fall into one of four groups:
- Acidic amino acids
- Basic amino acids
- Polar amino acids
- Nonpolar amino acids
Describe polar amino acids.
- Hydrophilic
- Make up outer portion of folded protein
In primary structure, the peptide chain is held together by ______ bonds between two amino acids
Covalent
Secondary structure
alpha-helix and beta-sheet
What is the structure of an alpha-helix and how is it held together?
- Spiral structure
- Held together by hydrogen bonds between carbonyl oxygen and amide hydrogen of every fourth amino acid residue of a polypeptide chain
Describe the structure of a beta-sheet.
Zigzag polypeptide structure
What additional chemical reactions occur to help the polypeptide fold into the tertiary structure?
- Hydrophobic forces
- Ionic bonding
- Disulfide bridges
Tertiary structure
final 3D functional form of proteins
Quaternary structure
Two or more polypeptide chains combine from tertiary structure
Quaternary structure can be ______ or ______.
Heteromeric or homomeric
Native conformation
Three-dimensional structure of a protein
Explain the process of protein folding
- Peptide chain folds in alpha-helices and beta-sheets through hydrogen bonding
- Hydrophobic side chains come together
- Polypeptide is packed into folded intermediate with hydrophobic core
- Polar residues on surface make additional hydrogen bonds and ionic interactions
- Adjacent cystines form covalent disulfide bonds
What happens when protein have multiple cysteines?
protein disulfide isomerase enzyme catalyzes rapid exchange of thiol groups
What are the two categories most proteins fall into?
- Globular
- Fibrous
Describe globular proteins and list examples.
Intracellular
Water-soluble
E.g., enzymes, transcription factors
What are some types of structures in globular proteins?
Filaments
Multimeric complexes
Quaternary structures
Describe fibrous proteins.
Located in extracellular matrix
Provide structure
Composed of either alpha helices or beta sheets
Hydrophobic amino acids on outer surfaces
Give two examples of fibrous proteins and what they are composed of.
Collagen - composed of alpha-helices
Fibroin - composed of beta-sheets
Hydrophobic amino acids on _______; charged and polar amino acids on _______.
Inside; outside
What is the function of the proteasome?
Degrade misfolded proteins
What are misfolded proteins?
proteins folded into incorrect shapes
What are enzymes?
biological catalysts that accelerate reaction rates without being consumed
Enzymes are typically ________.
Proteins
What are enzymes located?
- cytoplasm
- organelles
- cell or organelle membranes
Enzymes function ________ or are secreted ________.
Intracellularly; extracellularly
What two things are required for enzymes to work at peak efficiency?
Specific temperature and specific pH
What is a substrate?
reactants that bind to active sites on enzymes
What is an active site?
region on enzyme where reactions occur
Enzymes catalyze the conversion of ________ into _______.
Substrates; products
What are examples of cofactors?
Non-protein molecules (e.g., vitamins, metal ions, ATP)
Enzyme kinetics
studies rates of enzyme-catalyzed reactions
Reaction velocity ________ at low substrate concentrations.
Increases
Reaction velocity ______ at higher substrate concentrations.
Plateaus
What is Vmax and what does it signify?
- Vmax - maximum velocity
- Enzyme is completely saturated with substrate
What is enzyme affinity?
measures how strongly or weakly an enzyme binds its substrate
Enzyme affinity is quantified by __________.
Michaelis constant (Km)
What is Michaelis constant (Km)?
Equal to substrate concentration when rate is 50% of Vmax
What does a small Km represent?
enzyme has high substrate affinity
What does a large Km represent?
enzyme has low substrate affinity
Requires higher substrate concentration
What is activation energy (Ea)?
difference in free energy between substrates in ground state and high-energy transition state
Transition state has ______ energy than reactants or products.
Higher
What happens when substrates bind to their enzyme?
- Activation energy decreases
- More reactants convert into products
- Increases rate of enzyme-catalyzed reaction
What is one way enzymes speed up reaction rates?
Stabilizing transition state by:
1. Positioning substrate in proper orientation
2. Providing appropriate chemical environments (e.g., charge or pH)
What causes proteins to stay in abnormal shapes?
Inadequate cellular overnight, such as nonfunctioning chaperones or proteasome
Accumulation of amyloid fibrils has been found in certain neurodegenerative disorders, such as:
- Alzheimer’s disease
- Parkinson’s disease
Accumulation of amyloid fibrils has been found in prion diseases, such as:
- Creutzfeldt-Jacob (humans)
- Bovine spongiform encephalopathy (Mad Cow Disease)
What is PRP and how does it form amyloid fibrils?
- PRP - neural membrane protein
- Misfolded PRPs convert normal PRPs into abnormal shapes
- Misfolded PRPs contain beta sheets and tend to aggregate and form amyloid fibrils
Amyloid formation from misfolded PRPs is associated with _______________.
Fatal neurodegeneration
Provide examples of how amyloid fibrils can be beneficial?
- Some bacteria use amyloid fibrils on their surfaces to create protective biofilms
- Eukaryotes build reversible amyloid fibrils to pack and store secretory proteins until the cell needs to release them
What is an example of an amino acid with a simple nonpolar side chain?
Glycine
What is are examples of amino acids with a complex nonpolar side chain?
Tryptophan and proline
Aspartic acid and glutamic acid both have side chains with a ______.
Carboxyl group
Secondary structures are formed when amino acids make _______ bonds with their neighbors.
Hydrogen
