BIOL 4374 Lecture Notes - Lecture 4: Activation Energy, Electrophoresis, Western Blot

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magentafly481

26 Jan 2017

School

University of Houston

Department

Biology

Course

BIOL 4374

Professor

Frigo Daniel

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Document Summary

Lecture 4- 1/26/2017: proteins can bind to molecules known as ligands. Affinity with which proteins bind to these ligands is quantified by kd or km. The lower the value the higher the affinity. To selectively bind, many interactions must take place with the binding site and the ligand. Binding site: allow protein to interact with only certain ligands: makes it specific. Antibodies: have highly developed binding: very important to recognize body"s own cells vs invader cells, immunoglobins have heavy and light chains. Held together by disulfide bonds: located between heavy and light chains, and also within the heavy and light chains. They also have variable regions with hyper- variable loops. Enzymes: work in tandem to form pathways. This is where antigens bind: bind to ligands substrates, convert ligands to chemically modified products. Are not themselves altered or changed during the reaction: ex: lysozyme distorts chemical bonds to reduce activation energy for hydrolysis.

Related Questions

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. The pre-B-cell receptor provides an important signal that induces transition of pro-B cells to pre-B cells. An important characteristic of this receptor is that:
A. It signals without binding to an extracellular ligand.
B. It is composed of immunoglobulin heavy chains and the VJ region of a rearranged gamma light chain.
C. It is expressed at very high levels on the surface of the pro-B cell.
D. It signals without requiring association with B-cell receptor signaling subunits, Igalpha and Igbeta

2. The vaccine to Haemophilus influenzae type b is called a conjugate vaccine. It is composed of the tetanus toxoid protein conjugated to the capsular polysaccharide of the H. influenzae type b bacteria. When used to vaccinate infants, the antibody response generated by this vaccine would include:
A. Antibodies to the bacterial polysaccharide and the tetanus toxoid
B. Antibodies to the tetanus toxoid only
C. Antibodies to the bacterial polysaccharide only
D. Antibodies that only bind to the protein-polysaccharide conjugate in the vaccine
E. Antibodies that recognize the polysaccharide capsule
when shed by the bacteria
E. It signals without requiring the B-cell receptor signaling kinase, BTK.

3. CXCR5 is the receptor for the chemokine CXCL13, secreted by follicular stromal cells and follicular dendritic cells in the B cell zones (i.e., lymphoid follicles) of secondary lymphoid organs. A conditional knockout mouse in which CXCR5 was specifically deleted only in T cells would have:
A. No defects in any type of antibody response
B. Defects in the initial activation of all B cells
C. A lack of discrete B cell and T cell zones in the
lymphoid organ
D. A defect in T cell-dependent antibody responses
E. An increased number and size of germinal centers

rosemole174

True / False Questions

01. _____ Antibody is composed of 2identical long heavy chains and 2 identical shorter lightchains.

02. _____ Variable (V) and constant(C) regions are part of both heavy and light chains.

03. _____ Variable regions for heavyand light chains from the same antibody molecule are alwaysidentical.

04. _____ Variable region of lightchains are encoded by the DNA sequences that contain rearranged V,D, and J segments.

05. _____ Fc part of the antibody isnot important, F(abâ)₂ fragment has the same binding andeffector capacity.

06. _____ Fab fragments are generatedby alternative splicing.

07. _____ J chain is used as asurrogate light chain during pre-B cell receptor testing forsuccessful V(D)J rearrangement.

08. _____ Binding of the antigen byantibody is stabilized by disulfide bonds.

09. _____ RAG1/2 are always expressedin B cells at high level, because B cells need RAG1/2 to constantlyrearrange their V regions.

10. _____ âNâ (non template)nucleotides are added by TdT.

11. _____ The 12/23 rule is appliedduring class switching.

12. _____ For B cells, V(D)Jrecombination occurs only in the bone marrow.

13. _____ The process of somatichypermutation helps to improve specificity of the antibody.

14. _____ In late pro-B cells, Vsegment is rearranged with DJ segments.

15. _____ Failure to eliminateself-reactive B cells may lead to serious autoimmune diseases.

16. _____ Mature, naÃ¯ve B cellsexpress IgD and any of the other classes of antibody (IgM, IgG,IgA, or IgE) on their surfaces.

17. _____ B1 cells are present in theperitoneal cavity, pleural spaces and brain.

18. _____ AID (activation inducedcytidine deaminase) is expressed only in B cells and it canintroduce breaks in double stranded DNA.

19. _____ Different classes (isotypes)of antibodies have different effector functions, which aretriggered by special receptors expressed by a variety of cells.

20. _____ Plasma cells are terminallydifferentiated cells that produce large quantities ofantibodies.

21. _____ Repeated exposure to thesame antigen eventually leads to immunological exhaustion and lackof immunity, because there is no room for new plasma cells in thebone marrow.

22. _____ Germinal centers arespecialized sites within the bone marrow where Ig genes ofactivated B cells undergo affinity maturation.

23. _____ B cells can present antigensto T helper cells.

24. _____ Co-stimulatory molecules arerequired for efficient generation of memory B cells.

25. _____ Lymphocytes migrate to thelymphoid tissues in response to chemokines.

26. _____ Class switching duringgerminal center reaction is a random process.

27. _____ T cell independent responsescan generate strong and long lasting B cell memory.

28. _____ Fc receptors that arepresent on many different cell types are crucial for removal of thepathogens.

29. _____ The ideal vaccine should bedesigned to mimic the natural course of infection without causingsymptoms of the disease.

30. _____ The protective immunity canbe generated against any pathogen because there is virtuallyunlimited number of possible V regions, thus any antigen can berecognize by an antibody.

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BIOL 4374 Lecture Notes - Lecture 4: Activation Energy, Electrophoresis, Western Blot

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