Amino Acids

Functions
Amino acids have interconnections with other biochemical processes of the body. They can be used for energy (ketogenic), or be converted to glucose (glucogenic). Ketogenic amino acids can convert directly to acetyl CoA, while glucogenic amico acids can convert to intermediate molecules in the Krebs cycle, which can contribute to the synthesis of glucose.

Amino acids also contribute to the formation of nucleic acids, spingolipids, hormones, peptides, and other molecules.

Mnemonics
Essential 10
"Private Tim Hall" (Phe Val Thr Trp Ile Met His Arg Leu Lys).

Purely ketogenic
Only leucine and lysine are not glucogenic.

Both glucogenic and ketogenic
"Tip" ([Thr Tyr Trp] Ile Phe).

The remaining amino acids are purely glucogenic.

Excretion
Excess amino acids are not stored, so they are used as energy or converted into other molecules. In this conversion, the -NH₂ groups are removed (by transamination), transported, and excreted as urea:

1. By transamination, 2-ketoglutarate transfers its oxygen to the amino acid while removing and taking on the -NH₂ group to form glutamate. (2-ketoglutarate is a Kreb's cycle intermediate, and a nitrogen transporter).
2. Glutamate travels to the liver and releases ammonia (oxidative deamination) to the urea cycle. In the process, glutamate changes back to 2-ketoglutarate. 

Lipids

Fatty acid synthesis and oxidation 
The synthesis and breakdown of fatty acid chains are due to repetitive cycles that add and remove two carbons each time. Synthesis occurs in the cytosol while oxidation occurs in the mitochondrion. In the breakdown cycle, energy molecules NADH, FADH₂ and acetyl CoA are produced, which results in 17 ATPs for each two-carbon loss.

Hormonal controls
When blood sugar is low, epinephrine, norepinephrine and glucagon stimulate lipase in fat cells to break down triglycerides. The glycerol can then be used to produce more glucose.

In contrast, insulin promotes the transport of glucose into cells, where glucose is converted and stored as triglyceride. Insulin also inhibits lipid breakdown through several mechanisms and increases synthesis of glycogen, fatty acids, triglycerides and proteins.

Ketones
In states of starvation, fatty acid breakdown results in the four-carbon acetoacetyl CoA. Acetoacetyl CoA can break down further to acetyl CoA, be used for synthesis of cholesterol, or change to ketones. Ketones may be used for fuel by the brain as a last resort.

Lipids 
Fatty acids are stored on the three-carbon glycerol, forming glycerides. Triglycerides are the main storage molecules, which can revert to fatty acids and glycerol - to be used for cellular energy (glycerol to glycerol 3-P to glyceraldehyde 3-P). Acetyl CoA from the energy pathways with glycerol can form triglycerides. Therefore, excess sugar from the diet goes into glycerol to fatty acids (via acetyl CoA) to triglycerides, which are stored in fat cells.

Phosphoglycerides
Glycerol can also form phosphoglycerides when attached to phosphate attached to serine, ethanolamine, choline or inositol. Compared to triglycerides, phosphoglycerides are esters of only two fatty acids, and are important membrane components.

Prostaglandins
Prostaglandins are fatty acids synthesized throughout the body, having hormone-like effects.

Sphingolipids 
These molecules contain two fatty acids and a third group linked to the three-carbon serine. They are found in the nervous system.

Cholesterols
Cholesterol is ingested, but also synthesized from acetyl CoA, which transforms to isoprene. Isoprenes are the five-carbon building block forming isoprenoid molecules, or cholesterols. Cholesterol may then become bile acids and salts (mainly produced and exported by the liver), or form various steroid hormones.

Steroidogenesis by David Richfield and Mikael Häggström

Carbohydrates

An energy source
The pentose phosphate pathway, or the hexose monophosphate (HMP) shunt, is a way to produce energy in the form of NADPH from the oxidation of six carbon sugars. It is an alternative to glycolysis, but its primary role is anabolic rather than catabolic: the transformation of sugars with the release of CO₂ produces the five carbon ribose, which can be used for DNA and RNA synthesis. Also, if there is a need for NADH, FAD or CoA, ribose can be converted to glyceraldehyde 3-phosphate used in glycolysis.

The PPP is found throughout the body, in fat and liver cells, which use NADPH for fatty acid synthesis and (in liver) for cholesterol synthesis. Red blood cells lacking mitochondria use this pathway as an important source of energy.

Carbohydrate storage / Glycogen breakdown
Steps of glycogen formation:

1. Glucose 
2. Glucose 6-P
3. Glucose 1-P
4. UDP-glucose (addition of ribose sugar UTP)
5. Amylose (unbranched)
6. Glycogen (branched)

Enzymes of glycogen breakdown:

1. Phosphorylase breaks apart glucose units, but cannot break 1-6 branching. Glucose units are phosphorylated to become glucose 1-P. 
2. Debranching enzyme breaks down branched residue, producing more glucose 1-P. 
3. Salivary and pancreatic amylase can break down starch directly to maltose, which can then split to glucose by maltase. 
4. Lysosomal alpha-glucosidase, found throughout the body, converts glycogen directly to glucose. 

Note that glycogen can only be broken down to glucose or glucose 1-P. Unlike glucose, glucose 1-P does not easily cross membranes, so it is preferred by cells in the muscle or liver.

Cellular Energy

Energy molecules
ATP is the body's main energy molecule. Energy is stored in forms of glycogen or triglyceride, which can be broken down to regenerate ATP. Some high-energy molecules include:

1. ATP, UTP, GTP: donators of phosphoryl group.
2. NADH, FADH₂: donators of electrons or hydrogen.
3. Biotin: donator of carboxyl group.
4. Acetyl CoA: donator of acyl group.
5. Others: THF-C, Thpp, S-Adenosylmethionine, UDP-Glucose.

A note about enzymatic biochemistry reactions
Enzymes and substrates of a reverse reaction are usually found in a different area of the body, so forward and reverse reactions do not compete. If a two-way reaction is found in the same area, then negative (or positive) feedback of enzymes prevent a "futile cycle" (competition within two-way reactions).

ATP production
Glycolysis occurs in all organ cells, producing two pyruvates per glucose. Pyruvate is converted to acetyl CoA, which can enter the Krebs cycle. Besides glycolysis, acetyl CoA can also be formed through fatty acid degradation or by transformation of certain amino acids.

Glycolysis (cytosol)
Produces 2 pyruvate, net 2 ATP and 2 NADH per glucose.

Anaerobic glycolysis (cytosol)
The Krebs cycle needs O₂ to run, otherwise anaerobic glycolysis will occur. It is like glycolysis with an extra step: cycle the 2 NADH to replenish 2 NAD⁺ via transformation of 2 pyruvate to 2 lactate. Net 2 ATP.

Pyruvate decarboxylation (mitochondria)
Produces 2 acetyl CoA and 2 NADH per glucose.

Krebs cycle and Oxidative phosphorylation (mitochondria)
Including pyruvate decarboxylation, the Krebs cycle produces 1 ATP, 1 GTP, 8 NADH, and 2 FADH₂ per glucose. In the electron transport chain, phosphorylation (ATP production) is coupled with oxidation (requiring O₂ at the end).

Based on newer sources, 2.5 ATP are generated per NADH in the mitochondria. 1.5 ATP are generated per NADH in the cytosol, and per FADH₂. This is a total of 30-32 ATP per glucose in aerobic respiration. 

Note that the presence of ADP stimulates oxidation, and the lack of ADP (and abundance of ATP) slows the rate of oxidation.

Cell Respiration by RegisFrey

Connections to other processes
Glyceraldehyde 3-P (halves of glucose) can be directed back towards gluconeogenesis, or towards acetyl CoA and the Krebs cycle. Amino acids can be transformed into acetyl CoA or other molecules in the Krebs cycle, and vice versa. Acetyl CoA is also used to generate lipids (lipogenesis). Succinyl CoA can be used to produce heme molecules, while other molecules from the Krebs cycle can be used to make purines and pyrimidines for DNA synthesis.

T Cell Education in the Thymus

Intrathymic T Cell Differentiation by Wilson Savino

T cells mature in the thymus after being tested for tolerance induction (negative selection) and MHC restriction (positive selection). This ensures that T cells (and B cells) do not recognize self antigens as dangerous, and that T cells recognize only antigens presented by self MHC.

Process of T cell education

1. Immature T cells from the bone marrow enter thymus via blood. T cells are "nude" and have no expression of Fas, CD4, CD8 or TCR. 
2. T cells migrate to the cortex, the outer region of the thymus, and proliferate. 
3. Some T cells start to encode α and β chains, and CD3 of the TCR complex. Later, they express both CD4 and CD8, and high levels of Fas, which receives apoptosis signals. 
4. MHC restriction: Using the Fas apoptotic scheme, cortical epithelial cells test positive selection for MHC recognition in T cells. (If MHC binding is too weak, then the T cell dies).
5. Central tolerance induction: T cells pass to the medulla (central thymus) and test tolerance for self using negative selection. Thymic DCs that have migrated from the bone marrow present self peptides to T cells. Medullary thymic epithelial cells also test tolerance for tissue-specific peptides. (If peptide binding is too strong, then the T cell dies). T cells are now single positive for either CD4 or CD8. 

Secondary Lymphoid Organs

Secondary lymphoid organs include lymph nodes, spleen and mucosa-associated lymphoid tissue (MALT). These structures are passages for blood and lymphatics, and possess distinct areas where T cells and B cells proliferate.

Lymph node

Structure and Histology of a Lymph Node by OpenStax College

B cells, T cells and dendritic cells enter and exit the lymph node through the afferent and efferent lymphatic vessels, or through the blood vessels. In contrast to DCs, follicular dendritic cells (FDCs) reside within secondary lymphoid organs, and present antigen to B cells.

B cells and FDCs are found in the cortex. T cells and DCs are found in the paracortex (not labeled) towards the center of the lymph node. The cortex contains lymphoid follicles (shown in red), also known as primary lymphoid follicles. Active lymphoid follicles are called secondary lymphoid follicles or germinal centers where B cells proliferate and grow.

B cell proliferation

1. In the lymphoid follicle, FDCs take in opsonized antigen. Both complement proteins and antibodies are recognized by the FDC.
2. FDCs cross-link B cells and the few B cells that recognize a presented antigen stay and proliferate. 
3. Proliferated B cells are apoptotic unless activated Th cells migrate to the lymphoid organ and provide costimulation (CD40L).
4. B cell activation. The B cell also costimulates the T cell (B7) and present antigen. 
5. Some B cells become plasma B cells and leave to the blood. Others undergo somatic hypermutation and cycle the lymphoid follicle again.

The germination center has a "light zone" where step 5 occurs, and a "dark zone" where steps 3 and 4 occur. It is so named because proliferated B cells move toward the edge to be nearer to Th cells, forming a darker region.

High endothelial venule
Found in the venules, where lymphocytes exit the blood into the lymph (except in the spleen). T cells return to the lymph node via the HEV to be restimulated, proliferate, and stimulate any rare B cells.

Chemokines
FDCs produce CXCL13 to attract naive B cells. B cells that have found their antigen upregulate receptor CCR7 to migrate towards the edge of the germinating center, where they will receive help from Th cells. Likewise, activated Th cells upregulate receptors to migrate towards this same region.

Peyer's patch (MALT)
This is a MALT found in the intestine, with M cells that uptake antigen into the lymphoid organ. There is no incoming lymphatic vessel.

Spleen (blood filter)
There are no lymphatics. Everything from the blood can enter and pass.

B Cell

B cell activation
T cell dependent

1. B cell receptors (BCRs) cluster by recognizing epitopes of a pathogen. To promote clustering, complement receptor type 2 (Cr2) on the B cell can anchor invaders that are opsonized by C3b, bringing the pathogen closer to the BCRs. This is an example of how the innate immune system identifies the invaders for the adaptive.
2. CD40L of T cells ligate CD40 of B cells, providing the signal for cell activation. (Therefore, APCs activate T cells activate B cells).

T cell independent (faster activation, recognizes a range of antigen other than protein)

1. Repeated epitopes cluster BCRs, which substitutes for CD40L costimulation.
2. Battle cytokines, such as IFN-γ, fully activate B cells.

What is clustering?
When BCRs are brought close together, internal signaling proteins are concentrated enough to begin an enzymatic chain reaction.

Activated B cells

Fully activated B cells have the choice to undergo class switching (from IgM) or somatic hypermutation.

Class switching
Changes of the gene encoding the tail or heavy chain of the antibody affect the antibody type. This is done by the cutting and pasting of constant region segments. Remember that "VJC" is the light chain, and "VDJC" is the heavy chain.

Somatic hypermutation
"VDJ" gene segments undergo mutation at a high rate to create and circulate more fine-tuned B cells.

Antibodies

IgG/IgE isotype

IgM

• First evolved aB. 
• Appearance of five IgGs stuck together.
• Good at fixing complement. C1 proteins bind to the Fc region. Two C1 clusters activate the complement cascade to form C3b. This allows the complement system to direct an attack on any bacteria, even those that resist complent protein attachment.

IgG

• Unique in that it passes the placenta. 
• Longest lived aB. 
• Abundant in blood. 
• Can fix complement with at least two IgGs, but not well. 

IgA

• Most abundant in body, in mucosal linings.
• Secreted in milk. 
• Has a clip that holds together two IgGs at the tail region. The clip helps transport IgA in and out of the intestine, and makes IgA resistant to acid and enzymes. 
• Does not fix complement.

IgE

• Loaded onto mast cells when the body is first exposed to an allergen. 
• Degranulates mast cells upon second exposure where IgE binds to the same allergen. This causes an allergic reaction. 

T Cell

Antigen Presenting Cell (APC)
Dendritic cells deal with first encounters of a pathogen. Macrophages support the immune response with continued antigen presentation to T cells. B cells have a late but effective response; they are also prepared in case of a second encounter.


Helper/Killer T cell activation by APC

Antigen presentation by Sjef

1. The T cell comes in contact with an APC by weak adhesion molecules as TCR binds MHC. 
2. T cell upregulates CD40L, which binds CD40 on APC. 
3. This stimulates MHC and B7, or other costimulating molecules, on the APC. (B7 ligates CD28). 
4. Costimulation amplifies the TCR signal. This is important for naive T cell activation, whereas costimulation is not needed in activated T cells. 
5. More efficient T cell activation. 

(Not shown in image). CD4 or CD8 also act like a "clip" to strengthen the adhesion of the TCR and MHC. With cytotoxic T cells, CD8 binds MHC I. With helper T cells, CD4 binds MHC II. 

αβ T cell signaling

TCR Complex by Anriar

This describes the TCR of the most common T cell type. The components of the signaling complex are: 

TCR made of α and β chains, for antigen recognition. The TCR comes into contact with antigen-loaded MHC molecules. 

CD3 made of four peptide chains: γ, δ and ε associate with the TCR; the ζ-chain generates an intracellular activation signal. 

Th cytokines

Helper T cells respond specifically to a pathogen by producing cytokines. 

Th1 (classical subset against viruses and bacteria)

• IL-2, the growth factor of CTL and NK cells. Therefore, when many CTLs are needed in a viral infection, the Th cell controls the strength of the cytotoxic T cell response. 
• IFN-γ, which primes macrophages and influences IgG class switch in B cells. 
• TNF, which activates macrophages and NK cells. 

Th2 (parasitic or mucosal subset)

• IL-5, which encourages B cell IgA production. 
• IL-10, which downregulates Th1 cytokines and enhances B cell survival and proliferation. 
• IL-4, a B cell growth factor; influences IgE class switch in B cells. 

Innate Immune System, Abridged

Leukocyte extravasation
Neutrophils, eosinophils and mast cells exit the blood and enter tissues by extravasation. This begins when endothelial cells of the blood vessel express surface proteins selectin (SEL) and intercellular adhesion molecule (ICAM) in response to local cytokines IL-1 and TNF, which are produced by macrophages at the site of inflammation.

Extravasating immune cells possess ligands selectin ligand (SLIG) and integrin (INT). INT is expressed in response to inflammatory signals (for the neutrophil, the signals are LPS and complement protein C5a).

1. SEL and SLIG contribute to rolling adhesion. 
2. ICAM and INT is a strong interaction, causing the immune cell to stop rolling. 
3. Extravasation to the battle site. 

Major histocompatibility complex
MHC class I molecules are found on non-immune cells, which present cellular proteins to killer T cells. MHC class II molecules are found on immune cells, which present foreign proteins to helper T cells.

Macrophage hyperactive state 
Inputs
IFN-γ received from Th cells or NK cells prime the macrophage to upregulate MHC II molecules. This lets the macrophage become an active antigen presenter to Th cells. A primed macrophage becomes hyperactive when it detects the presence of LPS or mannose.

Outputs
Hyperactive macrophages produce alarm signals IL-1 and TNF, and NK cell-activating IL-12.

• TNF kills tumor cells and virus-infected cells, and activates immune cells, including the macrophage to produce IL-12. 
• Neutrophils also produce TNF, as they are one of the first responders to inflammation. 

Natural Killer cell
Inputs
The detection of LPS causes NK cells to produce IFN-γ; the production of IFN-γ is increased by signals IL-12 and TNF. TNF also influences the upregulation of IL-2R in NK cells.

Outputs
NK cells produce the growth factor IL-2. When there is an increase of IL-2 receptors, NK cells will proliferate. 

• NK cells destroy virus-infected cells if a combination of signals exists: MHC I and an unusual surface protein or carbohydrate. However, if there is a high balance of MHC I, the NK cell determines that the cell is healthy and does not destroy the cell. 

Dendritic cell
Inputs
DC cells become activated in response to TNF or antigen recognition by their toll-like receptors (TLR). Chemokines encourage extravasation.

• The activated DC cell uptakes tissue antigens to load onto MHC II molecules, and expresses MHC II on the cell surface. When it travels to the nearest lymph node, it upregulates surface protein B7 and MHC I (in the event the DC cell may be infected). 
• In the lymph node, DC cells act as antigen presenters and T cell activators. B7 pairs with CD28 on the T cell, and MHC pairs with T cell receptors (TCRs).  

Complement pathways

Alternate (non-discriminate binding)

1. C3 made by liver to blood. 
2. Spontaneous: C3 → C3a + C3b
3. C3b binds to cell surface. 
4. C3b + B → C3bB
5. C3bB + D (cleaver) → C3bBb
• Propagation: C3 + C3bBb (cleaver) → C3b → → C3bBb
6. C5 + C3bBb (cleaver) → C5b
7. C5b + C6 + C7 + C8 + C9 → MAC

Classical (occurs with two units of IgG or IgM; only the pathogen is targeted)

1. Antibody binds antigen. 
2. Two activated subunits C1s form a C1 complex at the Fc tail. 
• C2 + C1s (cleaver) → C2a + C2b
• C4 + C1s (cleaver) → C4a + C4b
3. Forms on pathogen surface: C4b + C2b → C4b2b
4. C3 + C4b2b (cleaver) → C3a + C3b
5. Step 3 of Alternate. 

Lectin (MBL only binds pathogenic carbohydrate)

1. MBL made by liver to blood. 
2. MBL + MASPs
3. MBL/MASP complex binds to pathogen surface. 
4. C3 + MASP (cleaver) → C3a + C3b 
5. Step 3 of Alternate.