BIOMG 1350 Lecture Notes - Lecture 3: Protein Kinase, Threonine, Conformational Change

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maroongiraffe649

28 Feb 2018

School

Cornell University

Department

Molecular Biology and Genetics

Course

BIOMG 1350

Professor

All

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Document Summary

Regardless of its strength, the binding of a protein to other biological molecules always shows great specificity: each protein molecule can bind to just one or a few molecules out of the many different molecules it encounters. Any substance that is bound to a protein is a ligand for that protein. The ability to bind selectively is due to weak, noncovalent interactions hydrogen bonds, electrostatic attractions, and van der waals attractions, plus favorable hydrophobic forces. Binding site= region of a proteins that associates with a ligand. There are billions of different antibodies, each with a different binding site. Antibodies immunoglobulin proteins produced by the immune system in response to foreign molecules, esp. those on the surface of an invading microorganism. Antigen the target molecule of antibodies. Antibodies are y-shaped with 2 identical antigen-binding sites, complementary to a small portion of the antigen molecule. Responsible for nearly all of the chemical transformations that occur in cells.

Related Questions

Why do nonpolar molecules, such as cholesterol, repelwater?

	Theyhave an even distribution of electrons.
	Thecovalent bonds of lipids create a small charge that repels watermolecules.
	Theirelectrons tend to cluster around the carbon atoms within themolecule.
	Theycontain many hydrogen bonds.

What determines whether or not a beta-sheet or an alpha helixforms in a polypeptide chain?

	Thesize of the Van der Waals forces in the molecule
	Thebond angles between amino acids
	Thepolarity of the molecule
	Thenumber of disulfide bonds

Nonessential amino acids of a human aredefined as

	thosethat may be synthesized by human cells
	thosethat can not be synthesized by human cells
	thosethat must be present in the human diet
	thosethat are not required by humans

What allows a protein to bind a ligandwith a high degree of specificity?

	Van derWaals forces
	Sugarresidues, such as glycosylated proteins
	Noncovalentchemical interactions
	Covalentchemical bonds

A modulator that increases protein function by binding to a proteindistant from the binding site is called what?

	Cofactors
	Allostericactivator
	Competitiveinhibitor
	Allostericinhibitor

turquoiseelk931

16.Globular proteins fold up into compact, spherical structures that have uneven surfaces. They tend to form

multisubunit complexes, which also have a rounded shape. Fibrous proteins, in contrast, span relatively large

distances within the cell and in the extracellular space. Which protein is not classified as a fibrous protein?

(a)elastase (b)collagen (c)keratin (d)elastin

17.You have two purified samples of protein Y: the wild-type (nonmutated) protein and a mutant version with a

single amino acid substitution. When washed through the same gel-filtration column, mutant protein Y runs through

the column more slowly than the normal protein. Which of the following changes in the mutant protein is most likely

to explain this result?

(a)the loss of a binding site on the mutant protein surface through which protein Y normally forms dimers

(b)a change that results in the mutant proteinâs acquiring an overall positive instead of a negative charge

(c)a change that results in the mutant proteinâs being larger than the wild-type protein

(d)a change that results in the mutant proteinâs having a slightly different shape from the wild-type protein

18.Which of the following statements is true?

(a)Disulfide bonds are formed by the cross-linking of methionine residues.

(b)Disulfide bonds are formed mainly in proteins that are retained within the cytosol.

(c)Disulfide bonds stabilize but do not change a proteinâs final conformation.

(d)Agents such as mercaptoethanol can break disulfide bonds through oxidation.

19.Proteins bind selectively to small molecule targets called ligands. The selection of one ligand out of a mixture of

possible ligands depends on the number of weak, noncovalent interactions in the proteinâs ligand-binding site. Where

is the binding site typically located in the protein structure?

(a)on the surface of the protein (b)inside a cavity on the protein surface

(c)buried in the interior of the protein (d)forms on the surface of the protein in the presence of ligand

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1. Select which of the following are mechanisms used by pathogens to avoid host defenses and to successfully colonize the host.

A. Producing siderphores to obtain iron from the host for growth

B. producing adhesins for damaging host cells

C. Avoiding IgA proteases for avoiding secretory IgA

D. Avoiding secretory IgA by rapid turnover of pili

E. Producing toxic substances to suppress host responses

2. People considered obese have a different normal flora in the gastrointestinal tract compared to people who are considered lean.

A. true

B. false

3. Which of the following is NOT a mechanism used by pathogens for avoiding or surviving phagocytosis?

A. Killing macrophages and neutrophils

B. Colonizing the phagocyte

C. inhibiting opsonization

D. Inhibiting phagocte chemotaxis

E. these are all methods of avoiding or surviving phagocytosis

4.Which of the following immune responses is best suited to prevent a virus from infecting a cell?

A. complement cascade

B. inflammation

C. Virus-specific antibodies

D. Fever

E. phagocytic cells

5. Which of the following is NOT a method used by pathogens for penetrating skin or mucous membranes?

A. Injection of effector proteins that induce endocytosis

B. Exploiting antigen-sampling processes

C. these are all mechanisms for penetrating skin or mucous membranes

D. Exploiting an injury

E. Production of endotoxin

6. Antibodies, which are produced as part of the adaptive immune response, can sometimes be damaging rather than beneficial. People suffering from an autoimmune disease called antiphospholipid antibody syndrome (APS) make antibodies that bind to phospholipids. Some of the signs and symptoms affected individuals experience are blood clots, stroke, heart attack, and kidney damage. What is the likely cause of these symptoms?

A. the anti-phospholipid antibodies cuse immune complexes that lodge in the affected organs

B. The person fails to make protective antibodies

C. The anti-phospholipid antibodies weaken certain organs that contain fat

D. the person makes antibodies that bind inappropriately to bacterial capsules, preventing phagocytosis of these cells

E. Cell damage caused by binding of these antibodies initates inappropriate coagulation events which inferfere with blood flow in affected organs.

7. Only Gram-positive bacteria produce exotoxins

A. true

B. False

8. Which of the following members of the normal microbiota inhibit the growth of Candida albicans?

A. Lactobacilus species

B. Staphylococci species

C. E. coli

D. Neisseria species

E. Propionibacterium species

9. Would an antibody response against the B subunit of an A-B toxin protect against the effects of the toxin?

A. yes. if antibodies bind to the B protion, the toxin can no longer bind to target cells and will thus not affect those cells

B. No, even if antibodies bindto the B portion of the toxin, it is the A portion that actually causes damage to the cell

C. This question cannot be answer. The immune system does not mount a strong response against proteins, so this situation is unlikely to occur.

D. Yes, if antibodies bind to the B protein, that portion of the toxin does not become activated, and thus does not damage the host cell

E. No, even if antiibodies bind to the B portion of the toxin, the toxin is still taken into the host cell by phagocytosis, damaging that cell

10. Please select the correct definition of balanced pathogenicity.

A. A host-parasite relationship in which the parasite persists in the host, causing maximal harm. The pathogen becomes more virulent while the host becomes increasingly susceptible.

B. A mechanism that allows bacteria to transfer gene products directly into host cells, inducing changes such as altering the cell's cytoskeleton structure

C. A generated balance in the microbiome that may be caused by taking antimicrobial medication. it generally helps the host maintain optimal health

D. A situation in which an abnormally high number of T-helper cells are stimulated, causing a massive release of cytokines.

E. A host-parasite relationship in which the parasite persists in the host while causing minimal harm. The pathogen becomes less virulent while the host becomes less susceptible

11. Bacteria may survive phagocytosis by

A. preventing encounters with phagocytes AND preventing fusion of two pathogosomes

B. avoiding recognition and attachment of lymphocytes AND lysinf the phagosomes

C. preventing fusion of the lysosome with the phagosome AND mimicking host molecules

D. lysing the phagosome AND mimicking host molecules

E. preventing fusion of the lysosome with the phagosome AND lysing the phagosome

BIOMG 1350 Lecture Notes - Lecture 3: Protein Kinase, Threonine, Conformational Change

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