polypeptide chain

Antibodies (Human)

  • The ‘foot’ (bottom) of the antibody is known as the Fc fragment - binds to cells, binds to complement = effector function (kills or removes antigen)
  • The top (antigen binding) is the Fab fragment
  • Chains are held together with disulphide binds
  • Associated molecules allow intracellular signalling 
  • Normally 3X constant heavy chain domains per chain and a hinge region (except μ and ε which have 4 and no hinge region)

Classes of Immunoglobulins

The five primary classes of immunoglobulins are IgG, IgM, IgA, IgD and IgE,  distinguished by the type of heavy chain found in the molecule. 

  • IgG - gamma-chains
  • IgMs - mu-chains
  • IgAs - alpha-chains
  • IgEs - epsilon-chains
  • IgDs - delta-chains.

Differences in heavy chain polypeptides allow different types of immune responses. The differences are found primarily in the Fc fragment. There are only two main types of light chains: kappa (κ) and lambda (λ), and any antibody can have any combination of these 2 (variation).

IgG 

  • monomer
  • Gamma chains
  • 70-85% of Ig in human serum. 
  • secondary immune response 
  • only class that can cross the placenta - protection of the newborn during first 6 months of life
  • principle antibody used in immunological research and clinical diagnostics
  • 21 day half life
  • Hinge region (allows it to make Y and T shapes - increasing chance of being able to bind to more than one site)
  • Fc strongly binds to Fcγ receptor on phagocyte - opsono-phagocytosis
  • Activates complement pathway

IgM

  • Serum = pentamer 
  • Primary immune responses - first Ig to be synthesised
  • complement fixing 
  • 10% of serum Ig 
  • also expressed on the plasma membrane of B lymphocytes as a monomer - B cell antigen receptor
  • H chains each contain an additional hydrophobic domain for anchoring in the membrane
  • Monomers are bound together by disulfide bonds and a joining (J) chain.
  • Each of the five monomers = two light chains (either kappa or lambda) and two mu heavy chains.
  • heavy chain = one variable and four constant regions (no hinge region)
  • can cause cell agglutination as a result of recognition of epitopes on invading microorganisms. This antibody-antigen immune complex is then destroyed by complement fixation or receptor mediated endocytosis by macrophages.

In humans there are four subclasses of IgG: IgG1, IgG2, IgG3 and IgG4. IgG1 and IgG3 activate complement.


IgD 

  • B cell receptor
  • <1% of blood serum Ig
  • has tail pieces that anchor it across B cell membrane
  • forms an antigen specific receptor on mature B cells - consequently has no known effector function (don’t kill antigens, purely a receptor) (IgM as a monomer can also do this)

IgE 

  • Extra rigid central domain
  • has the most carbohydrates
  • IgE primarily defends against parasitic invasion and is responsible for allergic reactions.
  • basophils and tissue mast cells express very high affinity Fc receptors for IgE - mast cells then release histamine
  • so high that almost all IgE is bound
  • sensitizes (activates) mucosal cells and tissues 
  • protects against helminth parasites

IgE’s main purpose is to protect against parasites but due to improved sanitation these are no longer a prevalent issue across most of the world. Consequently it is thought that they become over activated and over sensitive while looking for parasites and start reacting to eg pollen and causing allergies.

IgA

  • Exists in serum in both monomeric (IgA1) and dimeric (IgA2) forms (dimeric when 2 Fcs bind via secretory complex)
  • 15% of the total serum Ig.
  • 4-7 day half life
  • Secretory IgA2 (dimer) = primary defense against some local infections
  • Secreted as a dimer in mucous (e.g., saliva, tears)
  • prevents passage of foreign substances into the circulatory system


Isotype: class of antibody (IgD, IgM etc)

Allotype: person specific alleles 

Idiotype: (hyper) variable region - antibody specificity 

AP BIO Study Guide- Water, Carbon, & Macromolecules

Water

H2O = two hydrogen ions bonded* to an oxygen ion

*bond = “polar covalent”: the molecule has opposite charges on opposite ends; this is due to the electronegativity difference between the H’s and O, causing the H’s to have partial negative charges and the O to have a partial positive one; strong bond that keeps the water molecule together

H2O molecules bond to each other by “hydrogen bonding”: these are weaker bonds that are able to be broken and reformed frequently; this allows water its many emergent properties and to be the key to life

Four emergent properties:

1)      Cohesion/Adhesion- This is the ability of water molecules to stick to one another due to hydrogen bonding as well as to other surfaces, respectively. This is what allows transpiration up the plant xylem and out the leaves to occur (this is also due to the difference in water concentrations between inside the plant and in the atmosphere, as water wants to go from a high concentration to a low concentration). Also, surface tension is considered a subtopic of this property.

2)      Moderation of Temperature- Due to water’s high specific heat, it is able to absorb heat from the environment (breaking bonds) or release heat to it (forming bonds), without more than a slight change in its own temperature. This allows water to regulate to temperature of the environment around it and to make sure it is habitable enough for life. Water also has a high heat of vaporization. This results in “evaporative cooling”: as a surface is heated (heat is absorbed), the hydrogen bonds between water molecules break, and water changes from its liquid form to a gas, and is evaporated. This allows water to stabilize the temperatures of organisms and bodies of water.

3)      Expansion upon Freezing- When water freezes and changes to its solid form, the H2O molecules form a crystal lattice, where the hydrogen bonds keep each water molecule a certain distance away from each other. Due to this further apart spacing, ice is less dense than liquid water. Therefore, ice floats on top of liquid water. This allows ice to insulate what is below it, and helps regulate life.

4)      Versatility as a Solvent- Due to the partial pos. and partial neg. charges within an H2O molecule, when a solute is introduced into water, as long as that solute has charged ions, the H’s and O’s will be attracted to the oppositely charged ions, creating a hydration shell around the ions and pulling them away from the solute’s molecules, dissolving it (WATER IS PRETTY CLOSE TO A UNIVERSAL SOLVENT.)

Acids/Bases:

An “acid” is any substance that increases the hydrogen ion concentration of a solution.

A “base” is any substance that reduces the hydrogen ion concentration of a solution.

pH = “percent (%) hydrogen”

[H+] and [OH-] have an inverse relationship. This means as one goes up in concentration, the other goes down. Their relationship always has a constant of 10 ^ -14.)

(In a neutral solution, pH is 7, which means [H+] = 10 ^ 7, and [OH-] = 10 ^ 7.)

*Know how to do a Mol equation/set-up*

Carbon

Carbon can create up to four bonds with many different elements due to its “tetravalence” (has 4 valence electrons, and needs 4 more)

Ability to create long chains, often with hydrogen, resulting in organic molecules

Despite some organic molecules being isomers (same molecular formula), the variation in their carbon skeletons (brancing, double bonds, etc.) is what makes them completely different molecules.

Macromolecules

Monomers are the “building blocks” of macromolecules, which, when linked together, create polymers.

Monomers are bonded together using “dehydration synthesis” (the removal of water molecules), and broken apart by “hydrolysis” (the addition of water molecules).

Carbohydrates

Carbohydrates are sugars that provide fiber and a quick source of energy for your body. The monomer of carbohydrates is called a monosaccharide. Glucose is most common monosaccharide.

The type of links within carbohydrates are called “glycosidic linkages”. Two monosaccharides linked together creates a disaccharide. For example, two glucose molecules bonded together would create maltose.

Many monosaccharides linked together creates a polysaccharide. In aqueous solutions they form rings.

Carbohydrates are used for many different purposes, such as energy storage in plants (starch) and animals (glycogen), as well as for structure within plants (cellulose, forms cell wall) and animals (chitin, forms exoskeletons).

Carbohydrates contain a carbonyl group

Carbs contain “alpha” or “beta” links. We are unable to digest beta links.

Lipids

Lipids are not considered polymers because they are made up of a few monomers they are not made up of many. Usually lipids consist of a glycerol and three fatty acids (triglyceride). There are three types of lipids: fats, phospholipids, and steroids, but they all have one thing in common: they are hydrophobic. This is due to them being nonpolar and having no charge (fatty acids are basically really long chains of hydrogen and carbon with no charge).

The types of links within lipids are called “ester linkages”.

Saturated fats have a straight molecule and are solid at room temperature. These are bad for you, such as butter.

Unsaturated fats are “kinked” due to a carbon double bond and are liquid at room temperature. These are good for you, such as different types of oils.

Phospholipids contain a hydrophilic head (this is due to it actually having a charge due to its phosphate group’s neg. charge) and a hydrophobic tail. They make up the cell membrane of animal cells.

Steroids are made up of 4 carbon rings. One common type of steroid is cholesterol.

Proteins

Amino acids are the building blocks, made from the ribosomes of cells. They can either be nonpolar, polar, electrically charged, or etc. There are 20 different amino acids in existence, but they can make up countless proteins.

Amino acids consist of an alpha carbon, a hydrogen, an R group/side chain, a carboxyl group (COOH), and an amino group (N3H+). The “R” group is the variable that makes the specific amino acid unique. All amino acids are distinguishable by their “N-C-C” backbone.

The types of bonds present between amino acids are called peptide bonds, and the polymers of amino acids are called “polypeptides” (proteins).

Amino acids sequences are controlled by DNA/genetics. Even one amino acid being out of place can cause serious issues.

There are 4 levels of conformation to creating a protein. CONFORMATION = STRUCTURE.

Primary structure consists of the unique amino acid sequence. Secondary structure is the “backbone” of a protein, where the curves and folding of polypeptide chains are created through the attraction of hydrogen bonding. Tertiary structure by the interactions (Ex: types of bonds) between the “R” groups. Quaternary structure is the creation of a macromolecule through two or more polypeptides.

Some examples of quaternary structures are collagen (found in hair) and hemoglobin (found in the blood, in RBC’s).

Nucleic acids

Monomers are called nucleotides.

They make up your genes.

There are two types, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).

They consist of a phosphate group, a pentose sugar, and a nitrogenous base.

Molecule of the Day: Tetracycline

Tetracycline (C22H24N2O8) is a yellowish powder that is used as a broad-spectrum antibiotic. It has a remarkable tetracyclic core, which is shared with a related group of compounds which also have antibiotic activity, collectively called the tetracycline antibiotics.

It is produced naturally by the bacterium Streptomyces via the following pathway:

It is used to treat many bacterial infections such as Lyme disease, and does so by inhibiting protein synthesis in prokaryotes. It binds to the A site of the large ribosomal subunit, preventing the aminoacyl-tRNA from entering the A site to lengthen the growing polypeptide chain. Interestingly, even though it inhibits both the 70S prokaryotic ribosome and the 80S eukaryotic ribosome, it is highly selectively disrupts prokaryotic protein translation, as human cells do not have a mechanism to pump tetracycline into the cytosol, whereas bacterial cells do.

Tetracycline is also used as a selective agent in cell cultures; cells containing the tetracycline resistance gene, tetR, will be able to survive in a medium containing it, whereas those which do not, or have an insertionally inactivated tetR gene, will not survive. This enables for the selection of recombinant cells or cells which have uptaken a desired plasmid.

As an antibiotic, tetracycline suffers from some drawbacks; it can stain teeth yellow, grey, or brown, and cause headaches, fevers, and rashes. 

Neurofilaments are the 10 nanometer or intermediate filaments found in neurons. They are a major component of the neuronal cytoskeleton, and are believed to function primarily to provide structural support for the axon and to regulate axon diameter. Neurofilaments are composed of polypeptide chains or subunits which belong to the same protein family as the intermediate filaments of other tissues such as keratin subunits, which make 10 nm filaments expressed specifically in epithelia.

Image: Rat brain cells grown in tissue culture and stained, in green, with an antibody to neurofilament subunit NF-L, which reveals a large neuron. The culture was stained in red for alpha-internexin, which in this culture is found in neuronal stem cells surrounding the large neuron.

GPCRs/7-transmembrane receptors (7TM receptors)

G-protein-coupled receptors (GPCRs) are the largest and most diverse group of membrane receptors in eukaryotes. 

Structure

  • single polypeptide chain comprising of seven transmembrane α-helices
  • extracellular N-terminal domain of varying length, 
  • intracellular C-terminal domain.
  • length of the extracellular N terminus and the location of the agonist binding domain determines family.
  • The long, third cytoplasmic loop couples to the G-protein 
  • Usually particular receptor subtypes couple selectively with particular G-proteins
  • For small molecules, such as noradrenaline, the ligand-binding domain of class A receptors is buried in the cleft between the α-helical segments within the membrane. Peptide ligands bind more superficially to the extracellular loops

G protein system

GPCRs interact with G proteins in the plasma membrane when an external signaling molecule binds to a GPCR, causes a conformational change in the GPCR.  G-proteins comprise a family of membrane-resident proteins
whose function is to recognise activated GPCRs and
pass on the message to the effector systems that generate
a cellular response. 

  • G proteins are specialized proteins with the ability to bind the nucleotides guanosine triphosphate (GTP) and guanosine diphosphate (GDP). 
  • The G proteins that associate with GPCRs are heterotrimeric, (alpha beta and gamma subunits)
  •  alpha and gamma are attached to the plasma membrane by lipid anchors 
  • Trimer in resting state 
  • activated alpha monomer and beta/gamma dimer

Guanine nucleotides bind to the α subunit, which has enzymic activity, catalysing the conversion of GTP to GDP. The β and γ subunits remain together as a βγ complex. All three subunits are anchored to the membrane through a fatty acid chain, coupled to the G-protein through a reaction known as prenylation.

  • G-proteins are freely diffusible so a single pool of G-protein in a cell can interact with several different receptors and effectors 
  • When GPCR is activated by an agonist, a conformational change causes it to acquire high affinity for αβγ (G protein)
  • bound GDP dissociates and is replaced with GTP, which in turn causes dissociation of the G-protein trimer, releasing α-GTP and βγ subunits - the ‘active’ forms of the G-protein
  • which diffuse in the membrane and can associate with various enzymes and ion channels
  • Signalling is terminated on hydrolysis of GTP to GDP through the GTPase activity of the α subunit.
  • resulting α–GDP dissociates from the effector, and reunites with βγ
  • Attachment of the α subunit to an effector molecule increases its GTPase activity
  • GTP hydrolysis is termination –> activation of the effector tends to be self-limiting

Second messenger targets for G proteins

Main targets:

  • Adenylyl cyclase (responsible for cAMP formation)
  • Phospholipase C (inositol phosphate and diacylglycerol (DAG) formation)
  • Ion channels, particularly calcium and potassium channels
  • Rho A/Rho kinase (system controlling the activity of many signalling pathways for cell growth and proliferation, smooth muscle contraction, etc.)
  • Mitogen-activated protein kinase (MAP kinase) system controlling cell functions eg division.

(notes on these coming soon)

Electron Transport Chain
  • Situated in the inner mitochondrial matrix
  • produces most eukaryotic ATP
  • a chain of proteins that move electrons from higher to lower energy levels
  • electrons are provided by FADH2 or NADH
  • terminal electron acceptor is oxygen
  • as electrons move to from high to lower energy levels, the energy is used to pump H+ against its concentration gradient out into the intermembrane space
  • this established concentration gradient drives the phosphorylation of ADP to ATP
  • oxidative phosphorylation

electrons flow from protein to protein spontaneously 

  • due to the relative electron affinities of the proteins
  • this tendency is known as redox potential

Click read more for detailed step by step

Keep reading

Rough Endoplasmic Reticulum
  • Rough ER (RER) is involved in some protein production, protein folding, quality control and despatch
  • Called ‘rough’ because studded with ribosomes
  • Smooth ER (SER) is associated with the production and metabolism of fats and steroid hormones
  • Smooth because no ribosomes and is associated with smooth, slippery fats.

STRUCTURE

  • Continuous membrane of flattened sacs (cisternae) and network tubules, touching nuclear membrane. 
  • Membrane bound ribosomes firmly attached to the outer cytosolic side of the RER
  • However these are constantly being bound and released - will only bind when specific protein-nucleic acid complex forms in cytosol 

FUNCTION

  • Proteins are made by the ribosomes on the surface of the RER - translation
  • Then (some) are threaded inside RER to be modified and transported
  • RER working with membrane bound ribosomes takes polypeptides and amino acids from the cytosol and continues protein assembly including, at an early stage, recognising a ‘destination label’ attached to each of them. 
  • Proteins are produced for the plasma membrane, Golgi apparatus, secretory vesicles, lysosomes, endosomes and the ER. 
  • Some  proteins into the lumen (inside) of the RER; others are processed in RER membrane itself
  • Lumen: some proteins have sugar groups added to form glycoproteins; some have metal groups added
  • EG: in RER four polypeptide chains are brought together to form haemoglobin.

Protein folding unit
lumen of the rough ER: proteins folded to produce biochemical architecture which will provide ‘lock and key’ and other recognition and linking sites.

Protein quality control section

  • Lumen: incorrectly formed or incorrectly folded proteins rejected
  • Rejects stored in the lumen or sent for recycling for eventual breakdown to amino acids. 
  • A form of cystic fibrosis = missing single amino acid, phenylanaline, in a particular position in the protein construction. Quality control section spots the error and rejects, however individual would have been better off with poor product than none at all

From Rough ER to Golgi
In most cases proteins are transferred to the Golgi apparatus for ‘finishing’. They are conveyed in vesicles or possibly directly between the ER and Golgi surfaces. After ‘finishing’ they are delivered to specific locations.