Module 1B - Biomolecules & Enzymes Flashcards
Structurally complex and functionally sophisticated
molecules.
Proteins
The shape of protein is specified by its:
Amino acid sequence
Protein structure is made of:
Long unbranched chain of amino acids/Polypeptides
Repeating sequence of atoms along the core of polypeptide chains
Polypeptide backbone
Gives the amino acids their unique properties
Side Chains
Amino acids with negative side chains:
Aspartic Acid and Glutamic acid
Amino acids with positive side chains:
Arginine, Lysine, Histidine
Amino acids with uncharged polar side chains:
Asparagine, Glutamine, Serine, Threonine, Tyrosine
Amino acids with non-polar side chains:
Alanine, Glycine, Valine, Leucine, Isoleucine, Proline, Phenylalanine, Methionine, Tryptophan, Cysteine
Causes protein folding:
Weak non-covalent bonds
Non-covalent bonds of protein:
Hydrogen bonds, electrostatic attractions, and Van der Waals
The force that causes hydrophobic molecules to be forced together within an aqueous environment to reduce the disruptive effects of water molecules on the hydrogen bonded networks.
Hydrophobic clustering forces
Proteins form into a conformation of:
Lowest Energy
Class of proteins that assist in protein folding or unfolding
Molecular chaperones
Contains all the information needed for specifying the three dimensional shape of a protein.
Amino acid sequence
The 3D structure of protein has the ability to
Denature and Renature
Two regular folding patterns of protein are found within proteins:
α-Helix and β sheet
The protein folding structure takes shape due to the result of hydrogen bonding between the:
N-H and C=O groups in the polypeptide chain groups
Polypeptide chain pattern that forms from the neighboring segments of the polypeptide backbone that runs in the same orientation/direction.
Parallel chains
Polypeptide chain pattern that folds back and forth upon itself with each section of the chain running in the direct opposite direction of its immediate neighbors.
Anti-parallel chains
Folding patter that generate when a single polypeptide chain twists around itself to form a rigid cylinder.
α-Helix
Hydrogen bonds linking C=O of one peptide bond to N-H of another occurs between every:
4th peptide
Forms when two or more α-Helix chains that coil have most of their non-polar side chains on one side.
Coiled-coil
Stage of protein structure that only comprises the sequence of amino acids:
Primary protein structure
Stage of protein structure where the occurrence of hydrogen bonding in the polypeptide backbone of the protein structure that causes amino acids to fold into a repeating pattern. Appearance of α-Helix and β sheets.
Secondary protein structure
Stage of protein structure where full 3D folding of the protein structure occurs due to polypeptide chain interactions.
Tertiary protein structure
Stage of protein structure where the protein molecule forms a protein complex consisting of more than one amino acid polypeptide chain.
Quaternary protein structure
How many protein coding genes does the human genome have?
21,000 protein-coding genes
Proteins can be classified into families based on their:
Amino acid and 3D conformation
___% of our protein coding genes to known protein structure belong to ____ different families.
40, 500
The structure of proteins (such as arrangement of atoms and the interactions and dynamics of proteins at the atomic level) and their classifications are identified using:
X-ray crystallography and Nuclear Magnetic Resonance (NMR)
Basic units of protein that can fold, function, and evolve independently. They easily integrate into other proteins.
Protein domains
Process of creating new novel combinations of gene functional domains. Can be readily linked in series to form extended protein structures.
Domain shuffling
What are protein modules?
The subset of protein domains, mobile during evolution.
___% of human protein domains are vertebrate specific.
7%
A specialized function of a protein domain.
Major Histocompatibility Complex (MHC)
Vertebrates have inherited majority of their protein domains from:
Invertebrates
Given rise to many novel combinations of protein domains during the evolution of vertebrates.
Domain shuffling
Allows protein to bind to each other to create/produce structures in the cell.
Weak non-covalent bonds
Any region in the protein’s surface that can interact with other molecules.
Binding site
Formation of a symmetric complex of two protein subunits(dimer).
“Head to head” arrangement
A symmetrical arrangement of two identical α-globin subunits and two identical β-globin
subunits.
Hemoglobin
A long chain of identical protein molecules can be constructed if:
Each molecule has a binding site complementary to another region on the surface of the same molecule.
Long helical structures produced from many molecules of the protein actin.
Actin filament
An elongated three-dimensional protein structure.
Fibrous protein
Main component in long lived protein structures.
Keratin filaments
A dimer of two identical subunits.
α-keratin
Rope-like protein structures that is the important component of the cytoskeleton.
Intermediate filaments
What are the dimension of a collagen molecule?
300 nm x 15 nm
This type of protein is abundant outside of the cell and is the main component for the gel like consistency of the extracellular matrix.
Fibrous protein
Consists of three long polypeptide chains, each containing that non-polar amino acid glycine at every 3rd position.
Collagen
Type of protein with a highly disturbed polypeptide chain and also dominant within the extracellular matrix.
Elastin
Relatively loose and unstructured polypeptide chains that are covalently cross-linked to produce a rubber-like elastic meshwork that can be reversibly pulled from one conformation to another.
Elastin
Why are disordered polypeptide chain proteins so frequent naturally?
- Serves as a “tether” to hold two protein domains in close proximity
- Form specific binding sites for other proteins that have high specificity
- They restrict diffusion
- Trigger cell signaling events
Proteins that are secreted extracellular are often stabilized by:
Covalent cross-linkages
A sample of covalent cross-linkages that does not change the conformation of a protein but instead act as atomic “staples”
Sulfur-sulfur bonds/disulfide bonds
What type of reaction causes the formation of covalent cross-linkages?
Oxidation Reduction
In the proteins secreted extracellular, oxidation reduction reaction forms ___________ that stabilizes those proteins.
Covalent cross-linkages
The advantages of using protein molecules as subunit of large structures:
- Requires only a small amount of genetic information.
- Assembly and disassembly can readily be controlled.
- Errors in the synthesis of the structure can easily be avoided.
Structure made from hundreds of identical protein subunits that encloses and protects the viral nucleic acid.
Protein coat/Capsid of viruses
Cell subunit that is capable of spontaneous assembly into the final structure under appropriate conditions.
Purified subunits
Organisms or structures that are capable of self assembly:
Tobacco mosaic virus (TMV) and bacterial ribosomes
Guides the construction of complex biological structures but does not take part in the final assembled structure.
Assembly factors
Self propagating stable β-sheet protein aggregates that are released from dead cells that can kill cells and damage tissues.
Amyloid Fibrils
Accumulation of protein aggregates from dead cells:
Amyloid
Most severe amyloid pathologies:
Neurodegenerative diseases (Alzheimer’s and Parkinson’s)
A subclass of amyloid, caused by misfolded, aggregate form of a particular protein called prion protein (PrP).
Prions
Acts as vesicles containing peptides and hormones.
Secretory granules that consists of amyloid fibrils
Determines the BIOLOGICAL properties and function of a protein.
Physical interaction with other molecules.
Characteristic of a protein that allows it to bind to just ONE or FEW MOLECULES out of a THOUSAND.
Specificity
Substance that is BOUND by the PROTEIN.
Ligand
The specificity and affinity of a protein to a ligand is determined by:
Formation of a set of weak non-covalent bonds plus- favorable hydrophobic interactions.
Determines the CHEMISTRY of a protein molecule:
Surface conformation
The region of a protein that ASSOCIATES WITH a LIGAND.
Binding sites
Different types of PROTEIN-PROTEIN INTERACTION:
- Surface-string interaction
- helix-helix interaction
- surface-surface interaction
Association of two or more alpha-helix strands that are common to the secondary structure in proteins.
Helix-helix interaction
Occurs when specific regions on the surface of one protein binds to a complementary region on a surface of another protein:
Surface-surface interaction
Catalysts that cause chemical transformation that make or break covalent bonds in cells.
Enzymes
A complex that forms when a substrate binds with an enzyme.
Enzyme-substrate complex (ES)
Protein that binds to a target molecule (antigen), causing its inactivation or making it for destruction.
Anti-body or immunoglobins
Speeds up the reaction time in cells, they act as catalysts.
Enzymes
Standard formula for enzyme catalyzed reactions:
E + S = ES —> EP —> E + P
The formula for enzyme catalyzed reactions:
E + S = ES —> EP —> E + P
What is the main function of an enzyme?
Lower the activation energy required for a reaction
The maximum rate of reaction divided by the enzyme concentration:
Turnover number
Unstable intermediate state of an enzyme-substrate reaction:
Transition state
The free energy required to attain the transition state:
Activation energy
True or False. Enzymes are capable of using an Acid and a Base Catalysis simultaneously.
True
Enzymes contains precisely positioned atoms that alter the electron distribution of atoms that participate directly in:
Making and breaking covalent bonds
Addition of a water molecule to a single bond between two adjacent sugar groups in the polysaccharide chain, causing the bond to break:
Hydrolysis
Addition of a water molecule between two bonded molecules, causing the bond to break:
Hydrolysis
Presence of a _____________ associated on an enzymes binding site assists with the catalytic function of the enzyme.
Small molecule/Metal atom
Proteins that require specific small molecules to function properly:
Rhodopsin and hemoglobin
A large assembly of multiple proteins/enzymes; it allows the passage of product from enzyme a directly towards enzyme B and so on:
Multi-enzyme complex
A product produce by enzyme catalysis inhibits an enzyme that acts earlier within the pathway to stop the reaction:
Feedback inhibition
When a molecule binds to an enzyme that changes the conformation of its binding site that prevents another substrate binding:
Negative feedback/Negative regulation
A regulation where a molecules binds to an enzyme that stimulates its activity rather that shutting the enzyme down:
Positive feedback/Positive regulation
A type of enzyme that contains two binding sites on its surface; an active site that recognizes the substrate and a regulatory site that recognizes regulatory molecules:
Allosteric enzyme
Allosteric came from these Greek words:
allos = “other”
stereo = “solid” or “3D”
The interaction between separated sites on a protein:
Conformational change
Phenomena that occurs on multimeric enzymes, where each subunit of the protein has its own ligand-binding site:
Cooperative allosteric transition
Transfer of the terminal phosphate group from an ATP molecule to the hydroxyl group:
Protein phosphorylation
A protein that selectively modifies other proteins by covalently adding phosphates to them (phosphorylation).
Protein kinase
Enzyme that causes the removal of phosphate from proteins (dephosphorylate).
Protein phosphatases
Addition and removal of phosphate regulates the state (active or inactive) of the this protein.
GTP-binding proteins
GTP-binding proteins is hydrolyzed causing the loss of one phosphate group in a reaction catalyzed by the protein itself. What is the inactive state of GTP-binding proteins?
GDP-bound state
Responsible for generating the forces responsible for muscle contraption and the crawling and swimming of the cells:
Motor proteins
Proteins that produce large movement in the cells:
Motor proteins
Coupling one of the conformational changes to the hydrolysis of an ATP molecule that is tightly bound to the protein:
Unidirectional conformation changes
Membrane bound transporter that functions to export hydrophobic molecules from the cytoplasm:
ABC transporters
Composes of a linked set of 10 or more proteins that catalyzes DNA replication, protein synthesis, vesicle budding, or transmembrane signaling.
Protein machines
Protein binding sites for multiple proteins.
Scaffold proteins
