Biochem Sheet 24 PDF 2024

24 Nahla Ayad & Obadah mahafzah Waqar Alfaqeer Nafiz Abutarboush 1  Immunoglobulins (antibodies) The immune system plays a major role in the body's defense mechanisms against pathogens that enter the body. This mechani...

24 Nahla Ayad & Obadah mahafzah Waqar Alfaqeer Nafiz Abutarboush 1  Immunoglobulins (antibodies) The immune system plays a major role in the body's defense mechanisms against pathogens that enter the body. This mechanism is represented by defense lines in our body: A) Non-specific (Innate): 1.First line: which are barriers and there are two types of barriers 1-Physical barriers such as: skin, hair, mucous membranes. 2-Chemical barriers such as: sweat, tears, saliva, stomach acid, urine. These barriers prevent the body from external pathogens, whoever if the pathogens get through the barriers and get through the blood a second line of defense takes place: 2. Second line: here after the pathogens enter the circulation phagocytic white blood cells take action with anti microbial proteins with making an inflammatory response. B) Specific (acquired): Third line: here lymphocytes and antibodies are acquired to fight against pathogens. Acquired (specific) immunity: lymphocytes have 2 types: 1- T-lymphocytes: are what make cell-mediated immunologic process. These are involved in graft rejection, hypersensitivity reactions and they are involved in defense against many malignant cells and viruses. 2 *in AIDS cell-mediated immunologic process is what is distrubted* T-lymphocytes are matured in the thymus. 2- B-lymphocytes: are matured in the bone marrow, after maturing they form plasma cells, which produce antibodies there for making humoral immunity. Plasma cells are specialized B cells that synthesize and secrete immunoglobulins into plasma in response to exposure antigen. Antibodies have 5 types:(IgG, IgM, IgA, IgE, IgD). -There is a specific cell to produce every antibody type. - when we have a genetic deficiency therefor recurrent infections are caused. Immunoglobulins and antigens Immunoglobulins (antibodies): are glycoproteins that contain 4 polypeptide chains, 2 light and 2 heavy chains, bonded together by a disulfide bond, therefore forming a quaternary structure. They are synthesized by plasma cells and bind to foreign molecules (even if not encountered before) acting as a line of defense. Antibodies are Y shaped molecules and antigens bind on the tips of the Y molecule so it binds to 2 identical antigens. Effects of antibody binding to antigen: 1.acts as a physical barrier by preventing it from binding to another molecule ( prevents the foreign body – toxin- from affecting on the body) 3 2.since it is binding to the tips, the ending( the stalk) may be bound to Tcell, macrophage or compliment proteins where it may cause an immune response within the cell. Antibodies have high specificity and high affinity which make them fit for there function and they are present in huge numbers of different kinds approximately 10^8. There synthesize is stimulated by having an immunogen and they induce the effector functions causing inactivation, degredation or lysis of the foreign molecules. Antigen: Foreign molecules to which Igs bind. Antigens should be rather big to elicit an immune response, big antigens are called Immounogen and these cause the antibodies formation. Small foreign molecules are called haptens and they cannot elicit an immune response. How are cells recognized as foreign? There should be protein markers on the surface which determine the antigen, there could be more than one, which are called epitopes ( antigenic determinant). Each epitope is recognized by a different antibody. Immunoglobins structure -All contain a minimum of 2 identical light chains ( 25 kDa) (214 AAs.) and 2 identical heavy chains ( 50 kDa) (446 AAs.) , the total size of antibodies ~150KDa. Linked by inter and intra chain disulfide bonding 4 *disulfide bonding is formed highly as we want the structure to be static and conserved to adhere with the high variability of antibodies. Y- shaped: binding of antigen at both tips. Each chain has specific domains: *domains are a specific part of protein where they are a specialized structure responsible for a specific function * 1.light chain( L): we have 2 domains: 1. Variable ( in amino acid )domain (vl) which is in the amino half of the chain. 2. Constant ( amino acid) domain (Cl) which is found on the carboxyl half of the chain. 2. Heavy chain( H): there are 4 domains, only one(1/4) is variable domain (VH) in the amino part and 3(3/4) constant domains (CH1, CH2, CH3) which are in the carboxyl half. *variable means that there are amino acids that are changing not constant* -antigen binds VH and vl domains Antibodies are classified into two pieces 1. Fab: antigen binding fragment and there are 2 Fab regions 2. Fc: crystallizable fragment, if it is cut and out alone it will crystallize. Only 1 region. Papain and pepsin are proteolytic enzymes that are able to cut the amino acid sequence in the antibodies however each one is specific for a region. -papain: cuts in the hinge region making an output of 2 antigen- binding fragments ( Fab) and one crystallizable fragment (Fc) since the disulfide bonds are not involved. 5 -pepsin: cuts under the hinge region causing an output of 1 Fab fragment made from the 2 Fab regions connected together by disulfide bond as they are involved here and one crystallizable fragment (Fc). -Hinge region (CH1 & CH2 domains):connection between Fab and Fc fragment which is through a structure that is looped to allow flexibility and independent movement to accommodate to antigen size and shape -Fc and hinge regions differ in different classes of antibodies. Light chain: around 110 AA are variable and from 111-214 are similar. Heavy chain: around 113AA are variable and from 114-446 are similar The red lines in the variable regions of light and heavy chains are 3 stretches where they are hyper variable in the rest of the region variability is less. There are about 7-12 Amino acids in each stretch. Immunoglobulin interactions: With antigen: (infinite): electrostatic, hydrogen bonds, Van der Waals and hydrophobic interactions. Here the (Fab)2 fragment can detect, bind and precipitate the antigen, it can block the active sites of toxins therefore no toxins released and block interactions between host and pathogen. With other cells and molecules binding is through the Fc portion (finite): here the (Fab)2 fragment cannont activate the inflammatory 6 functions that are associated with cells, of complement proteins and cannot activate intracellular cell signaling molecules. Domain structural variation of immunoglobulins constant region: Structure of heavy chain= 1 variable and 3 constant regions (may be 4 in some antibodies). In the constant region sequence of amino acids is constant and we have 5 different genes that are responsible for synthesize of 5 different types of antibodies Alpha=IgA. Delta=IgD. Epsilon= IgE. Gamma= IgG. Miu=IgM These are responsible for synthesizing the constant region in heavy chain. As for the light chain there are 2 domains variable and constant. Constant have 2 types kappa and lambda, in the same antibody you cannot have a mixture either both light chains lambda or both kappa. The L chains and H chains are synthesized separately. Antibodies are glycoproteins so they are attached to carbohydrates and location of carbohydrate binding is on the 7 sliceable fragment, which is the region responsible for binds to immune cells or compliment proteins to make the interaction sticky. The immunoglobulin folds:the characteristic structural motif of all Ig domains: Each domain is made out of beta sheets that adopts a structure of Beta barrel (like the shape of an empty cylindrical barrel) of 7 Cl or 8 Vl polypeptide strands connected by by loops and arranged to enclose a hydrophobic interior. When the beta barrel is unfolded it shows beta sheets with a disulfide in the middle that controls its structure. Unfolded VL region showing 8 antiparallel β-pleated sheets connected by loop. Genes involved & diversity: “one gene, one protein” concept is not valid: Immune system can generate around 10^8 antibodies and the human genome contains around 25000 genes( rearrangements of these genes make infinity numbers of antibodies(. The light chain is a product of at least 3 genes which are: 1. Variable gene( Vl): 40 genes 2. Joining region gene( J): 5 genes 8  3. Constant region gene Cl : kappa or lambda The heavy chain is a product of at least 4 genes: 1. Variable region gene VH: 51 genes 2. Diversity region gene D: 27 genes 3. Joining region gene J: 6 genes 4. Constant region gene CH : 5 genes Variable region: No 2 variable regions in different humans are identical. L chains have 3 hyper variable regions while H Chain has 4 and they are present on the loops of the beta barrel making them be on the tips of Y shape. Hyper variable regions comprise the antigen binding site and dictate the amazing specificity of antibodies. Hypervariable regions: complementarity- determining regions CDRs Each region is made out of 7-12 amino acids each one contributes to the antigen binding site. CDRs are located on small loops of variable domains. 9 There is also a framework regions: the surrounding polypeptide regions among the hyper-variable regions Variability in terms of proteins as how much amino acids change is if the change is less than 20-30% meaning that there is no high degree of variability, if more than that meaning there is a high degree of variability. To prove variability take other group of proteins and compare antibodies to it. Cytochromes C( all proteins with heme C) has different types and they have a change of amino acids groups, to test the degree of variability and as shown in the graph there is almost no variability. While for antibodies it is very high. These we called them as stretches complemantarity determining regions. antigen ‫يعني يحددوا كيف يكون متطابق مع ال‬ CDRs interaction with antigens: The antigen- antibody interactions is based on mutual complementarity between surfaces. If the antigen is large it will interact with all of the CDRs of the antibody therefore eliciting an immune response, but small antigens(hapten) interact with only one or a few CDRs form a pocket or a groove in the antibody molecule, 10 and they won’t elicit an immune response unless they are bound to a larger molecule( macromolecules) ‫الدكتور رمز عهاي المعلومة "إذا اجاكوا سؤال‬ "hapten ‫باالمتحان عن‬ Immunoglobulin classes- overview Igs are classified based on the nature of their heavy chain. IgG is the only one that crosses the placenta and is the one that is highly available. IgG and IgM can bind to compliment system and elicit an immune response. IgG gives immunity to fetus, for the newborn IgG also in the circulation from the mother from before being born until it can create its own antibodies. Domains in different classes ( H – chain) Three of them IgA , IgD and IgG have 3 constant domains and one variable domain , while IgE and IgM have another constant domain is replaced the hinge region which limits the movement of hinge region so these have 4 constant domains and one variable domain. 11 ‫تمت كتابة هذا الشيت عن روح والدة زميلنا عمرو رائد من دفعة تيجان‬ ‫دعواتكم لها بالرحمة والمغفرة‬ ‫‪Thank you‬‬ ‫‪12‬‬