Ch.4 - Protein Struc/Func Flashcards
Amino acids have directionality. What does this mean?
Directionality - two ends of ea AA are chem diff:
- one w amino group (NH3+, also NH2);
- End carrying amino group is called amino terminus (N-terminus).
- other w carboxyl group (COO–, also COOH)
- End carrying free carboxyl group is carboxyl terminus (C-terminus).
What feature of a peptide bond permits polypeptide chains to bend and fold?
Peptide bonds are single, covalent bonds b/w the carboxyl C (C-terminus) of one AA and the amino N (N-terminus) of another AA.
- If peptide bonds were double covalent bonds, the polypeptide chain wouldn’t be able to bend/fold into necessary conformation.
Which three types of noncovalent bonds help proteins fold and maintain their shape?
H-bonds, electrostatic attractions, and vdw interactions help proteins fold/maintain shape (provide stability)
- Individually weak, but combine to provide stability.
- Hydrophobic forces also involved, but not considered a “bond”.
How do hydrophobic forces contribute to protein shape?
Hydrophobic forces are the result of nonpolar molecules (e.g. nonpolar side chains) being expelled fr the H-bonded network of an aq environ
- I.e. tendency to minimize disruptive effect on H-bonded network.
- As a result, nonpolar side chains tend to cluster in interior of folded protein → avoid contact w aq cytosol.
- Similarly, polar side chains tend to arrange themselves near outside of folded protein → form H bonds w water/other polar molecules.
- Not technically considered a noncovalent bond.
T/F: the same AA side chain can make multiple H-bonds.
True
A single AA side chain can make multiple H-bonds.
How are energetic considerations factored into the final conformation adopted by a polypeptide chain? How does entropy change?
Proteins typ fold into a shape in which its free energy (G) is minimized, i.e. folds into most energetically favorable shape.
- Folding process is energ fav → releases heat, increases entropy of universe.
Consider a protein denatured via treatment w solvents, i.e. noncovalent interactions are disrupted and polypeptide loses its natural shape. When the solvent is removed, the protein spontaneously regains its original conformation. What does this spont renaturation indicate wrt folding info?
Spontaneous renaturation implies that all info necessary to specify 3D shape is contained w/i the AA seq itself.
Urea (shown) disrupts the H-bonded network of an aq environ, like cytosol. Why might high concentrations of urea unfold proteins?
Urea functions both as an efficient H-bond donor (thru amino groups) and an efficient H-bond acceptor (thru carbonyl group).
- Squeezes b/w H-bonds that stabilize proteins and thus destabilizes.
- At high concens of urea, H-bonded network of water becomes disrupted and hydrophobic forces expelling protein fr water are significantly diminished.
- As a result, proteins unfold in urea due to disruption of H-bonding and hydrophobic forces.
Describe how prions affect protein folding.
Prions (proteinaceous infectious particles) are infectious agents that can cause abnormal protein folding.
- Misfolded prion form of a protein can convert properly folded version (typ in brain) into abnormal conformation → allows misfolded prions, wh tend to form aggregates (amyloid fibrils), to spread rapidly fr cell to cell and causing death.
- Incorrect folding - proteins sometimes form aggregates that can damage cells and even whole tissues.
Describe how chaperone proteins assist protein folding.
Chaperones merely make folding process more efficient and reliable. Final 3D struc of protein still specified by AA seq.
- Some chaperones bind to partly folded chains → help fold along most energ fav pathway.
- Others form “isolation chambers” → single polypeptide chains fold w/o risk of forming aggregates in crowded cytoplasm.
T/F: chaperone proteins help correct misfolded proteins.
False
Chaperone proteins only make the initial folding process more efficient and reliable; not involved in fixing misfolded proteins.
Describe the alpha-helix protein folding pattern.
α helix - Single polypeptide chain twists around itself to form a rigid cylinder stabilized by H bonds b/w every fourth AA.
- Complete turn every 3.6 AAs
- Short regions of α helix are partic abundant in proteins embedded in cell mems, e.g. transport proteins and receptors
- Polyp backbone (hphilic) is H-bonded to itself in α helix → shielded fr hphobic lipid environ of mem by protruding nonpolar side chains.
Describe the beta-sheet protein folding pattern.
β sheet - neighboring regions of polypeptide chain associate side by side thru H bonds to give rigid, flattened structure.
What makes the alpha helix and beta sheet such common folding patterns?
Partic common folding patterns bc result fr H bonds b/w N–H and C=O groups in backbone, i.e. secondary structure.
- AA side chains not involved in forming these H bonds → α helices and β sheets can be generated by many diff AA seqs.
The α helix results fr a single polypeptide chain twisting around itself to form a rigid cylinder stabilized by H bonds. Describe the structure formed by 2-3 α helices twisting around ea/o.
Coiled-coil - partic stable struc formed by 2-3 α helices wrapped around ea/o.
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Form when α helices have most of their nonpolar side chains on one side → twist so side chains face inward (min contact w aq cytosol).
- I.e. driven/stabilized by hydrophobic forces.
- Long, rod-like coiled-coils form struc framework for many elongated proteins.
- α-keratin - forms IC fibers; reinforce epidermis.
- myosin - motor protein → muscle contraction
β sheets form via H bonding b/w segments of polypeptide chain that lie side by side. What region of proteins do β sheets typ form?
β sheets form rigid structures at the core of many proteins.
- Confer extraordinarytensile strength, e.g. silk fibers.
- Stabilize amyloid fibers: insoluble protein aggregates (recall: prions).
- Note: infectious bacteria can use amyloid fibers to help form biofilms → colonize host tissues; other types of filamentous bacteria use amyloid fibers to extend filaments into air → disperse spores. I.e. not always disruptive.
Which common folding pattern typ helps stabilize misfolded protein aggregates?
The beta sheet helps/stabilizes misfolded protein aggregates; permits formation of amyloid fibers.
Briefly summarize the four levels of protein structure.
- Struc begins w AA seq → primary struc.
- α helices and β sheets w/i polypeptide chain → secondary struc.
- Full 3D conformation formed by entire polypeptide chain (incl α helices, β sheets, random coils, other loops/folds b/w N- and C-termini) → tertiary struc.
- If multi proteins combine to form complex → quaternary struc.
Which level of protein structure does not involve covalent bonds?
Secondary struc (alpha helices/beta sheets) does not involve covalent bonds; only H-bonds.
- Secondary struc involves backbone-backbone interactions.
- Tertiary struc involves side chain interactions, wh can include disulfide bridges (covalent).
What are protein domains?
Protein domain - Segment of polyp chain that can fold into compact stable struc and typ carries out specific function.
- Typ 40-350 AAs folded into α helices, β sheets, other elements of 2nd struc
- Modular unit fr wh many larger proteins are constructed.
- Diff domains typ = diff func.
What term refers to the modular unit fr wh many larger proteins are constructed?
Protein domains are the modular unit fr wh many larger proteins are constructed
Large proteins typ contain several dozen protein domains connected by __________.
Large proteins typ contain several dozen protein domains connected by unstructured regions.
What are intrinsically disordered sequences?
Intrinsically disordered seqs - seqs w/o definite 3D struc; typ found as short stretches linking domains in otherwise highly ordered proteins; comprise unstructured regions.
- 1/3 of all euk proteins likely have long unstruc regions in polypeptide chain (30+ AAs in length).
- Continually flex/bend → can wrap around 1+ target proteins like a scarf, binding w both high specificity and low affinity (tethering).
- IDPs - entire proteins w/o definite 3D struc; serve similar roles.
How do intrinsically disordered/unstruc seqs contribute to protein struc?
Intrinsically disordered/unstrucseqs:
- Can flex/bend → wrap around 1+ target proteins like a scarf, binding w both high specificity and low affinity → tethering.
- Flexible tethers b/w compact domains provide flexibility while ↑ freq of encounters b/w domains.
- Help scaffold proteins bring t/g proteins in IC signaling pathway → facilitate interactions.
- Give proteins ability to form rubberlike fibers (like elastin) → tendons/skin can recoil.
- Ideal substrates for addition of chem groups that control how many proteins behave.
Many present-day proteins can be grouped into _________, in wh ea member has a similar AA seq/3D conformation.
Many present-day proteins can be grouped into protein families, in wh ea member has a similar AA seq/3D conformation.
- Struc modified thru evolution to adopt new funcs.
What type of bonds allow proteins to bind to ea/o to produce larger structures?
Weak, noncovalent bonds allow proteins to bind to ea/o to produce larger structures.
- Protein-protein binding sites.
- Ea protein considered a subunit.
What are binding sites?
Binding site - any region on protein’s surface that interacts w another molecule thru sets of noncovalent bonds.
- Protein can have binding sites for variety of molecules.
What term refers to a symmetrical complex of two identical, folded polypeptide chains (subunits)?
Dimer - symmetrical complex of two identical, folded polypeptide chains (subunits).
- Tetramer - 4 symmetrical, identical subunits.
- Other protein complexes are formed of > 1 subunits, but still symmetrical, e.g. hemoglobin (2x2 diff subunits)
Filaments, sheets, and spheres are protein structures formed via complementary ___________.
Filaments, sheets, and spheres are protein structures formed via complementary binding sites.
- Ea protein is identically bound to neighbor → often forms helix, extends either direction (bilateral).
- Partic useful for protein filaments like actin/tubulin (recall: dynamic instability).
- Also critical to protein capsid (coat) of viruses.
Enzymes are typ globular in shape, containing > 1 subunit. Which protein shape(s) is/are partic common in the extracellular matrix?
Fibrous proteins are partic common in ECM.
- ECM helps bind cells t/g, i.e. form tissues.
- Proteins are secreted → assemble (in ECM) into sheets or long fibrils.
- E.g. Collagen: most abundant fibrous EC protein in animal tissues.
- Typ have regular, repeating struc → permits coiled-coil and fibrils that connect end-to-end.
- Can also form cross-linked networks, e.g. elastin.
- Elasticity is due to ability of individual proteins to uncoil reversibly whenever stretched.
Many proteins are either attached to EC-side of pmem or secreted as part of ECM. As a result, these proteins are exposed to EC conditions. Describe how cross-linkages contribute to protein stability in such environ.
Covalent cross-linkages:
- Linkages either tie t/g 2 AAs in same chain or many chains in large complex, e.g. collagen/elastin.
-
Disulfide (S-S) bond - most common covalent cross-link.
- Formed before protein secreted by enzyme in ER.
- Links two sulfhydryl (-SH) groups fr adj cysteine side chains.
- Don’t change protein’s conform; act as reinforcement of favored conform.
- Typ don’t form in cytosol bc high concen of reducing agents → convert S-S back to cysteine–SH groups; also, reinforcement not req’d in relatively mild conditions in cytosol.
Why don’t disulfide bonds typ form in the cytosol?
Disulfide bonds are covalent cross-links that act as reinforcement of a protein’s favored conformation.
- Typ don’t form in cytosol bc high concen of reducing agents → convert S-S back to cysteine–SH groups.
- Also, reinforcement not req’d in relatively mild conditions in cytosol.
Selective binding w high affinity to a ligand is due to what types of forces?
Selective binding w high affinity to a ligand is due to weak, noncovalent interactions (H bonds, e-static, vdWs) and hydrophobic forces.
T/F: interior atoms of a protein w no direct contact w ligand have no effect on binding of the ligand.
False
Interior atoms of protein have no direct contact w ligand, but provide essential scaffold and elicits chem props.
Changes to interior atoms/AAs can still drastically affect 3D shape/func.
What are antibodies, and what make them unique in terms of binding sites?
Antibody - Immunoglobulin protein produced in response to foreign molecules/invading orgs, partic those on surface. Binds to invader (antigen) v tightly → inactivates or marks for destruction.
- Limitless possible ligands; ea antibody has diff binding site, i.e. remarkable specificity.
How are enzymes classified?
Enzymes are grouped into functional classes based on the partic chem rxn catalyzed.
- Partic focus in BIO 301: kinases and phosphatases → adding and removing P gr, resp.
What are lysozymes?
Lysozyme - Relatively small, stable enzyme that severs the polysacch chains that form cell walls of bacteria (hydrolysis); found in many secretions incl saliva/tears.
- In short, lysozymes digest polysacchs.
- Catalyzes hydrolysis of adj sugars in polysacch:
- Lysozymes contort polysacch into transition state via noncovalent bonds, i.e. stabilizes transition state, thereby decreasing activation energy.
- Rxn is energ fav bc free energy of severed polysacch chain is lower than that of intact chain (exergonic; spont .)
How do enzymes catalyze chemical reactions?
Enzymes catalyze chem rxns by stabilizing the transition state → decrease activation energy.
- Active site contains precisely positioned chem groups → speed up rxn by altering distribution of electrons in substrates as well as changing its shape (into transition state).
Describe how small, non-protein molecules bind and contribute to protein function?
Proteins/enzymes often bind small, non-protein molecules to perform funcs that would otherwise be v slow or impossible.
-
Small molecule often forms transient, covalent bond w substrate, wh helps hold substrate in active site long enough for rxn to occur.
- E.g. retinal, hemoglobin, biotin, other vitamins.
In regard to enzymes, what is feedback inhibition?
Feedback inhibition - Form of metabolic control; end product of enzymatic rxn chain ↓ activity of enzyme earlier in pathway.
- Large qty of final product begins to accumulate → product binds to an earlier enzyme → catalytic action ↓ by limiting further entry of substrates.
- Where pathways branch or intersect, typ mult points of control by diff final products, ea wh works to regulate its own synth.
Many enzymes have two conformations, ea stabilized by binding of diff ________.
Many enzymes have two conformations, ea stabilized by binding of diff ligands.
- E.g. feedback inhibition: inhibitor binds at regulatory (allosteric) site → protein struc changes → active site (elsewhere) becomes less accessible to substrate.
T/F: Most enzymes are allosteric.
True
Most enzymes are allosteric, i.e. can adopt 2+ slightly diff strucs → activity regulated by changing b/w strucs.
- Ea ligand will stabilize the struc (transition state) that it binds most strongly → at high enough concens, ligand will tend to “switch” proteins to favored struc
Describe how phosphorylation can control protein activity.
Protein phosphorylation - euk cells can regulate protein activity via phosphorylation: covalently attaching a P group to 1+ AA side chains (via kinases).
-
Ea P group carries two neg charges → enzyme-catalyzed phosphorylation can cause major struc change (e.g. attracting cluster of pos charged AA side chains fr other site on same protein) → can affect ligand binding or other activity.
- Terminal P gr typ transferred fr ATP to OH gr of AA side chain.
- Reversible, i.e. dephosphorylation via phosphatases.
- Can act as “docking site” for other molecules or distort protein struc b/w active/inactive conformations.
What are GTP-binding proteins?
GTP-binding protein - IC signaling protein whose activity is det by its assoc w either GTP or GDP.
- Incl both trimeric G proteins and monomeric GTPases, such as Ras.
- Molecular switches, i.e. active conformation when GTP is bound, but can hydrolyze this GTP to GDP → releases P → protein flips to inactive conformation.
- Reversible, i.e. active conformation restored by dissoc of GDP and binding of new GTP—often in response to EC signal.
Describe how ATP hydrolysis allows motor proteins to produce directed movements in cells.
ATP hydrolysis and motor proteins:
Unidirectional movement (req’d by motor proteins) is achieved by making a step irreversible, partic by coupling one conformational change to hydrolysis of ATP (bound to protein).
- Hence, motor proteins are also ATPases.
- Large amount of free energy is released when ATP is hydrolyzed → v unlikely that protein will undergo rev rxn—as req’d for moving backward.
- Energ unfav to phosphorylate ADP to ATP (rev rxn) → protein instead moves steadily forward.
