Module 1B Biomolecules and Enzymes (Proteins) Flashcards
structurally complex and functionally sophisticated molecules.
Proteins
What specifies the shape of a protein?
amino acid sequence
How many amino acids make up proteins?
20
What type of chain are proteins made of?
long, unbranched chains of amino acids.
What is the term for a chain of amino acids in a protein?
Polypeptides
It is the repeating sequence of atoms along the core of the polypeptide chains.
polypeptide backbone
What gives each amino acid its unique properties?
side chains
influenced by weak noncovalent bonds: hydrogen bonds, electrostatic attractions, and van der Waals forces.
protein folding
What is protein folding influenced by? (3)
weak noncovalent bonds:
- hydrogen bonds
- electrostatic attractions
- van der Waals forces
They force hydrophobic molecules, including nonpolar side chains, together in an aqueous environment to minimize disruption of the hydrogen-bonded network of water molecules.
hydrophobic clustering forces
What are the two types of groups based on solubility found in proteins? (2)
Hydrophobic (nonpolar) and polar groups.
Into what structure do proteins fold?
into a three-dimensional structure of lowest energy.
__ is when a protein loses its structure; __ is when it regains it.
- Denaturation
- renaturation
What contains all the information needed for the three-dimensional shape of a protein?
amino acid sequence
What assists in the folding of proteins?
Molecular chaperones
What are the two common folding patterns found within proteins? (2)
- α helix
- β sheet
They result from hydrogen-bonding between the N-H and C=O groups in the polypeptide chain.
- α helix
- β sheet
α helix and β sheet result from hydrogen-bonding between the __ and __ groups in the polypeptide chain.
- N-H
- C=O
form from neighboring segments of the polypeptide backbone that run in the same orientation.
parallel chains
form when the polypeptide backbone folds back and forth, with sections running in opposite directions.
antiparallel chains
generated when a single polypeptide chain twists around itself to form a rigid cylinder.
α helix
How often do hydrogen bonds form in an α helix?
form between every fourth peptide, linking the C=O of one peptide bond to the N-H of another.
formed from two or more α helices with most of their nonpolar side chains on one side.
coiled-coil structure
What is the primary structure of a protein?
amino acid sequence
Structure of protein: Hydrogen bonding of the peptide backbone, forming helices and β sheets.
secondary structure
Structure of protein: The full three-dimensional organization of a polypeptide chain.
tertiary structure
Structure of protein: A protein molecule formed as a complex of more than one polypeptide chain.
quaternary structure
How can proteins be classified? (2)
- based on their amino acid sequence; and
- three-dimensional conformation.
What is an example of a protein family?
Serine proteases, which are protein-cleaving (proteolytic) enzymes.
Which has been more conserved in protein families, structure or amino acid sequence?
structure
Give an example of two regulatory proteins in the homeodomain family. (2)
- yeast α2 protein
- Drosophila engrailed protein.
How many amino acid residues are identical in the yeast α2 protein and the Drosophila engrailed protein?
only 17 of 60 amino acid residues.
How are protein families identified in a sequenced genome?
when the genome of an organism is sequenced.
Approximately how many protein-coding genes are in the human genome?
about 21,000 protein-coding genes.
What percentage of human protein-coding genes relate to known protein structures?
About 40%, spanning 500 different families.
What techniques are used to study protein structure? (2)
- X-ray crystallography
- nuclear magnetic resonance (NMR).
- the basic units of proteins that can fold, function, and evolve independently.
- can be easily integrated into other proteins and linked in series to form extended structures.
protein domains
the process of creating new combinations of gene functional domains.
domain shuffling
a subset of protein domains that are mobile during evolution.
Protein modules
What is an example of a domain with a specialized function?
Major Histocompatibility Complex (MHC) antigen-recognition domain, found only in humans.
Where have most vertebrate protein domains been inherited from?
invertebrates
What percentage of identified human protein domains are vertebrate-specific?
7%
What has domain shuffling during vertebrate evolution resulted in?
many novel combinations of protein domains.
bonds that allow proteins to bind to each other to produce structures in the cell.
Weak noncovalent bonds
any region of a protein’s surface that can interact with another molecule.
binding site
The “head-to-head” arrangement forms a symmetric complex of two protein subunits, known as a __.
dimer
The __ arrangement forms a symmetric complex of two protein subunits, known as a dimer.
“head-to-head”
What subunits make up hemoglobin?
- two identical α-globin subunits; and
- two identical β-globin subunits
symmetrically arranged.
How can a long chain of identical protein molecules be constructed?
By having each molecule with a binding site complementary to another region of the surface of the same molecule.
Give an example of a long helical structure formed by protein molecules.
The actin filament, formed from many molecules of the protein actin.
In a chain of identical subunits, the only way they fit together is rarely in a straight line, resulting in a __, which resembles a staircase. This is a common structure in biology.
helix
- A protein that have an elongated three-dimensional structure.
- abundant outside the cell, where they form the main component of the gel-like extracellular matrix.
fibrous proteins
What is the main component in long-lived structures composed of fibrous proteins?
keratin filaments
- a type of keratin with a dimer of two identical subunits.
- a fibrous structural protein, meaning it is made up of amino acids that form a repeating secondary structure.
α-keratin
ropelike structures that are important components of the cytoskeleton.
intermediate filaments
A protein molecule that consists of three long polypeptide chains, each containing glycine at every third position.
collagen
an abundant protein in the extracellular matrix (ECM) with highly disordered polypeptide chains. These chains are covalently cross-linked to create a rubberlike, elastic meshwork that can stretch and return to its original shape.
elastin
Intrinsically disordered regions are common because they serve multiple functions such as forming specific binding sites for other proteins with __.
high specificity
What is one function of intrinsically disordered regions in proteins?
can trigger cell signaling events
intrinsically disordered regions assist in protein structure because they can act as “__” to hold two protein domains in close proximity.
tethers
What role do intrinsically disordered regions play in molecular movement?
help restrict diffusion within cellular structures.
provide stability for proteins secreted extracellularly, preventing degradation.
Covalent cross-linkages
What type of bond commonly stabilizes extracellular proteins?
Disulfide bonds, or sulfur-sulfur (S-S) bonds.
Do disulfide bonds change the conformation of a protein?
No, disulfide bonds do not change the protein’s conformation but act as atomic “staples” for stability.
disulfide bonds act as atomic “__” for stability.
staples
What are the advantages of using protein molecules as subunits for large structures? (3)
- Requires only a small amount of genetic information
- Allows controlled assembly and disassembly through multiple low-energy bonds
- Errors in the synthesis of the structure can be more easily avoided
What shapes can protein subunits form when assembled? (often enclose specific RNA or DNA molecules) (3)
- tubes
- spheres
- capsids
They are made of hundreds of identical protein subunits that enclose and protect the viral nucleic acid.
protein coats or capsid in viruses
What are examples of a structure in cells that can self-assemble? (2)
- tobacco mosaic virus (TMV)
- bacterial ribosomes
It is the process by which purified subunits spontaneously form into the final structure without additional cellular machinery.
self-assembly
It guides the construction of complex biological structures but are not part of the final assembled product.
assembly factors
Do all cellular structures self-assemble through noncovalent bonds?
No, some require assembly factors for proper formation.
What is an example of a process involving assembly factors in protein formation?
Proteolytic cleavage is involved in the assembly of insulin, where specific segments are removed to form the active structure.
involved in the assembly of insulin, where specific segments are removed to form the active structure.
Proteolytic cleavage
are self-propagating, stable β-sheet aggregates that can form from many proteins.
Amyloid fibrils
__ may be released from dead cells and accumulate as amyloid, which can kill cells and damage tissues.
Protein aggregates
Protein aggregates may be released from dead cells and accumulate as __, which can kill cells and damage tissues.
amyloid
What are some severe amyloid pathologies? (2)
neurodegenerative diseases, such as Alzheimer’s and Parkinson’s disease.
- Disease caused by a misfolded, aggregate form of a particular protein called PrP (prion protein), which forms infectious amyloid fibrils.
- transmissible, untreatable, and fatal brain diseases of mammals
Prion diseases
Give examples of prion diseases:
- in sheeps; (1)
- humans; and (2-3)
- cattles. (4)
1) scrapie
2) Creutzfeldt-Jakob disease (CJD) - leads to dementia
3) Kuru
4) bovine spongiform encephalopathy (BSE) - “mad cow disease”
- consist of amyloid fibrils and act like vesicles containing peptides and hormones.
- membrane-bound vesicles that store biologically active substances, including peptide hormones and proteins.
- Some of these can contain amyloid fibrils, which allow for dense packing of hormones like insulin and glucagon.
- Upon signaling (e.g., changes in blood glucose), this undergo exocytosis, releasing their contents into the bloodstream. The amyloid fibrils dissociate upon release, ensuring that the hormones become active and functional.
specialized “secretory granules”
In this organisms, amyloid structures secrete proteins that form long amyloid fibrils projecting from the cell exterior, which help bind their neighbors to biofilms. What organism is this?
bacteria
In bacteria, amyloid structures secrete proteins that form __ projecting from the cell __, which help bind bacterial neighbors to __.
- long amyloid fibrils
- exterior
- biofilms (a community of microorganisms attached to an inert or living surface)
help bind bacterial neighbors together, contributing to the formation and stability of biofilms.
amyloid fibrils
A protein molecule’s biological properties are determined by its __ with other molecules.
physical interaction
refers to a protein molecule’s ability to bind just one or a few molecules out of many thousands.
specificity
the substance that is bound by a protein.
ligand
What types of noncovalent bonds facilitate a protein’s binding to a ligand? (4)
- hydrogen bonds
- electrostatic attractions
- van der Waals attractions
- along with favorable hydrophobic interactions.
How does the surface conformation of a protein influence its chemistry? (2)
1) the interaction of neighboring parts of the polypeptide chain may restrict the access of water molecules to that protein’s ligand-binding site
2) the clustering of neighboring polar amino acid chains can alter their reactivity
What are the three types of interfaces through which proteins bind to other proteins? (3)
- surface-string interactions
- helix-helix interactions
- surface-surface interactions.
- bind tightly to a specific target molecule (antigen), inactivating it directly or marking it for destruction.
- Y-shaped molecules with two identical binding sites that are complementary to a small portion of the surface of the antigen molecule.
Antibodies (immunoglobulins)
Antibodies are __-shaped molecules with __ identical binding sites that are complementary to a small portion of the surface of the antigen molecule.
- Y-shaped
- two
powerful and highly specific catalysts that cause the chemical transformations that make and break covalent bonds in cells.
enzymes
What is the equation representing the enzyme-catalyzed reaction sequence?
E + S → ES → EP → E + P
indicates the maximum rate of reaction that a single enzyme molecule can process in a given time, calculated as the maximum rate of reaction divided by the enzyme concentration.
turnover number
Enzymes achieve extremely high rates of chemical reactions by ______ and greatly increasing the local concentration of substrate molecules at the catalytic site.
selectively stabilizing transition states
an unstable intermediate state that occurs during the conversion of substrates to products.
transition state
the free energy required to attain the transition state in a chemical reaction.
activation energy
Enzymes __ the activation energy required to reach the transition state, facilitating faster reaction rates.
lower
Enzymes can bind tightly to a __ and contain precisely positioned atoms that alter electron distributions in the atoms that participate directly in the making and breaking of __
- transition state
- covalent bonds
It is a mechanism where enzymes use both acid and base catalytic actions simultaneously to stabilize transition states and enhance reaction rates.
acid-base catalysis
an enzyme that catalyzes hydrolysis, adding a water molecule to break the bond between two adjacent sugar groups in a polysaccharide chain.
Lysozyme
These small molecules or metal atoms assist enzymes in their catalytic function by enhancing the enzyme’s reactivity and specificity.
coenzyme
Give examples of proteins that require small molecules to function properly. (2)
- Rhodopsin requires retinal
- hemoglobin requires a heme group
- a large protein assembly that allows the product of one enzyme to be passed directly to the next enzyme, increasing metabolic efficiency.
- It speeds up metabolism by facilitating the direct transfer of intermediate products between enzymes in a pathway.
multienzyme complex
Cell regulate the number of enzyme molecules produced by regulating the __ of the __ that encodes the enzyme.
- expression
- gene
One way cells control enzymatic activity spatially is by confining sets of enzymes to specific __ within the cell.
- compartments
A process where a product produced late in a reaction pathway inhibits an enzyme that acts earlier in the pathway.
feedback inhibition
It is a type of regulation that prevents an enzyme from acting/creating more products.
negative regulation
Involves a regulatory molecule stimulating an enzyme’s activity instead of inhibiting it.
positive regulation
- Enzymes with at least two binding sites: an active site for substrates and a regulatory site for regulatory molecules.
- Greek words __ meaning “other”, and __ meaning “solid” or “3D”
- allosteric enzymes
- allos
- stereo
The conformational change in an allosteric enzyme is because of the Interaction between the enzyme’s __ site and the __ site, often due to binding of a __.
- active
- regulatory
- regulatory molecule
When two ligands with coupled binding sites interact on a protein, they reciprocally affect each other’s binding, where a ___ caused by one ligand can alter the __ for the other.
- conformational change
- affinity
Describe an example of negative regulation due to conformational coupling between two binding sites.
If glucose binding causes a shape change that decreases a protein’s affinity for molecule X, the binding of X will also decrease the protein’s affinity for glucose.
It is a phenomenon in multimeric proteins where each subunit has its own ligand-binding site, allowing the protein to undergo a coordinated allosteric change when a ligand binds.
cooperative allosteric transition
In what type of protein structure does cooperative allosteric transition commonly occur?
multimeric proteins with multiple subunits
The transfer of the terminal phosphate group of an ATP molecule to a protein’s hydroxyl group.
protein phosphorylation
It phosphorylates proteins by adding a phosphate group.
protein kinase
They remove phosphate groups from proteins, a process called dephosphorylation.
protein phosphatases
- Proteins that use the guanine nucleotide GTP
- they regulate cellular processes by switching between active (GTP-bound) and inactive (GDP-bound) states.
GTP-binding proteins
GTP-binding proteins become __ by hydrolyzing GTP to GDP, with the loss of a phosphate group, a reaction catalyzed by the protein itself.
inactive
They produce forces for processes like muscle contraction and cell movement (crawling and swimming).
motor proteins
Proteins produce __, by coupling conformational changes to the hydrolysis of a tightly bound ATP molecule.
unidirectional conformational changes
export hydrophobic molecules from the cytoplasm and are associated with chemotherapy resistance in tumor cells when overproduced.
ATP-binding cassette (ABC) transporters
consist of 10 or more proteins that coordinate essential cellular processes like DNA replication, protein synthesis, vesicle budding, and transmembrane signaling.
Large protein complexes, or “protein machines”
have binding sites for multiple other proteins, linking specific sets of interacting proteins and positioning them at specific cellular locations.
Scaffold proteins
