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Antibodies

Proteins with high specificity for ligands- protein binding specificity

Antibodies (immunoglobulin) are proteins produced 
by the immune system, bind to antigen

Antigen: foreign substance that elicits production of an antibody

In some cases antibody can distinguish between proteins that differ by a single amino acid


1

T & B Cells

T cells recognize antigen and attach infected cells, killin the cells and the virus within

T cells also activate B cells which are memory cells (remember invading agents, remember the shape of the proteins on cell wall). They produce antibodies that bind to the antigens

2

Antibody structure

•  Antibody 
has 
4
 subunits(polypeptides: 2
 heavy 
&
 2
 light
 chains


•  Chains 
are 
held
 together 
by
 S‐S 
bonds

•  Each 
polypeptide
 chain 
can 
be 
divided
 into 
2
 domains:


–  Variable
 domain 
VL
&
VH

–  Constant 
domain 
CL
&CH


•  the variable domains interact with the antigen- Variable sites are on the tips. Every antibody has a different variable region. A lot of beta pleated sheets

The binding site is where the variable regions for the heavy and the light regions come together

3

Influenza
 Virus

Proteins protruding from the virus (hemagglutinin), binding site and transmembrane region

4

CDR

The variable domains contain the complementarity‐determining region (CDR)

CDR contains 6 highly variable loops that form the antigen binding sites, interacts with antigen

5

Epitope

Epitope: region of antigen that is recognized by the antibody

Interaction between antibody and epitope of antigen is complimentary

Fits like a glove

6

Antivenom

Inject horse with genome, they generate antibodies to combat the venom. Those antibodies are removed and put into humans. Not possible to be completely purified so its possible that the human would get sicker

7

Protein folding

When proteins are first being translated they can be "sticky"- Energetically unstable- hydrophobic patches that are exposed

Sometimes proteins denature, but can denature with help of other proteins

8

The role of molecular chaperones

Facilitate proper folding in the cell

Bind and stabilize partially or unfold proteins and prevent interactions with other proteins

Ex: mRNA, chaperone hsp70 either folds into a native polypeptide or puts in in chaperonin hsp60 which folds it into its native state. Then release into the cytosol

9

Chaperonins

Multiple of the same subunits. Hsp10 (groES) makes the cap, 60 (groEL)makes the two barrels

Substrate goes into substrate binding cavity

Uses 14 ATP- 7 to bring it in, 7 to eject i

15 seconds

10

Types of Protein modifications

Often essential for the function of a proteinase the regulation of protein activities

Different modifications:
Methylation
acetylation
Phosphorylation
Hydroxylation
Ubiquitination
Glycosylation
Proteolitic processing
Disulfide bond formation, and cleavage

11

Protein modification

Amino acids often modified after translation

Modification can affect regulatory function

Can affect structural features

12

Methylation

Addition of methyl group

Regulation of gene expression

13

Acetylation

Affects about 80 percent of all proteins

Done by N- acetyltransferases

Transfers the acetyl groups from acetyl CoA

Important in gene regulation

14

Protein phosphorylation

Addition of a phosphate group to the hydroxyl of serine, threonine, or tyrosine (sometimes histidine)

Phosphorylation/dephosphorylation (kinase/phosphatase) provides a quick mechanism for alterin protein activity

15

How many modifications per protein?

Not limited to one

Ex: Histone octamer. Some things can be methylated phosphorylated etc

16

Hydroxylation

Hydroxyl groups can be added to lysine or proline

17

Glycosylation

Often occurs in ER(further modification in the Golgi) found in secrete proteins or those on the outside of the cell

Addition of carbohydrates can be added to Asn, Ser, or Thr

18

Adding a lipid group

A protein may be anchored to the membrane if it is attached with lipid molecules such as farnesyl group, palmitate, or myristate groups

Integral proteins anchored by lipid groups

19

Proteolytic processing

Removal by protease- reducing environment

Activation and transportation

Seen commonly in proteins that's are in response to conditions (hormones), in response to a region (proteases), or transported to mitochondria and chloroplasts. this requires the removal of the signal peptide

Removal of n terminal methionine

20

Proteolytic cleavage to activate a protein

Many proteins are synthesized as larger precursors that need to be cleaved to become active

Ex: chymotrypsinogen is synthesized in the pancreas and the secreted into the small intestine

Become active enzyme chymotripsin after trypsin cleaves its proform

21

Uniquitination

Proteins marked for degradation linked covalently to ubiquitin

Brings it into the proteosome which breaks it down

22

Proteolysis

Hydrolysis process in which peptide bonds of protein is cleaved into small peptides or individual AA

Why are proteins degraded?
-no longer needed by the cell
-Proteins are damaged
-misfolded protein
-too much energy to repair a damaged/misfolded protein