12 Maha AbuAjamieh Tamara Wahbeh Mamoon Ahram -
- Go to this sheet s last page for definitions of the words with an asterisk above them (*) - You should memorise the 3-letter abbreviations, of all the amino acids we are going to study, You should know their main characteristics, general structures and names, too. - Refer to the slides for photos. Lipids Lipid component of biological membranes Lipid bilayers are large assemblies of molecules. A cell membrane is made of phospholipids assembled into an orderly formation called a bilayer. Phospholipids are amphipathic, the polar group (phosphate heads/ backbone) extends outward and is in contact with the intracellular/ extracellular aqueous environment (watery fluid). The nonpolar (fatty acid tails) are found in the interior of the membrane, orienting themselves away from the watery fluid inside and outside the cell. Thus the lipid bilayer is composed of two leaflets. - The inner leaflet - The outer leaflet They differ in their phospholipids components, - The outer: phosphatidylcholine, sphingomyelin, and glycolipids*. - The inner: phosphatidylethanolamine, phosphatidylserine, and phosphatidylinositol*. Fatty acids of phospholipids, 1- Saturated -fully reduced, only single bonds- (the fatty acids in the membrane are packed, which contributes to membrane s rigidity) 2- Unsaturated -there are carbon carbon double bonds in the chain, usually in the cis configuration*, the fatty acids are less packed, this makes the membrane fluidic/ highly viscous) The presence of saturated and unsaturated fatty acids differ from one cell to another, for example, the highly packed endothelial (epithelial) cells have high amounts of saturated fatty acids, but rod cells (which are found in the eye) have more unsaturated fatty acids than unsaturated, to let the signalling molecules move quickly and enable us to see.. With heat, ordered bilayers become less ordered; bilayers that are comparatively disordered become even more disordered.
Melting (transition) temperature, it is the temperature required to induce a change in the lipid physical state from the ordered phase, where the hydrocarbon chains are fully extended and closely packed, to the disordered liquid phase, where the hydrocarbon chains are randomly oriented and fluid. All lipids have this characteristic temperature at which they undergo a transition (melt) from the solidlike to liquid phase. The transition temperature (the change is relatively fast, refer to the slides to see the sudden, fast change in fluidity that is shown in the MembraneFluidity-Temperature diagram). At lower temperature the membrane is solidlike, as the temperature gets higher, it becomes more fluidic. It depends on the presence of saturated fatty acids, the membranes with greater amounts of saturated fatty acids are the ones with higher transition temperatures. Cholesterol is the characteristic steroid* alcohol of animal tissues, it is distributed equally in both leaflets in animal s cells (not plants or prokaryotes) as a result, animal membranes are less fluid (more rigid) than plant membranes. On the other hand, plants have sterols (that look like cholesterol) and prokaryotes are totally different in this term. What is the effect of cholesterol on the fluidity of the membrane? It has dual effect, it protects the membrane from both very high temperatures and very low temperatures - at very high temperature, the electrons of the atoms will have a high kinetic energy, causing a lot of movement in the fatty acids of the phospholipids, the presence of cholesterol between fatty acids will prevent the membrane from collapsing. - at very low temperature, low kinetic energy, the fatty acids of phospholipids are static, the presence of cholesterol prevents the packing of the fatty acids and reduces the rigidity of the membrane, it keeps it fluidic. How does cholesterol interact with phospholipids? - We should remember that cholesterol is amphipathic, its hydrophilic portion is the hydroxyl group (OH), and the rest (the fused-ring structure) is hydrophobic - Its hydrophilic part (the hydroxyl group) interacts with the hydrophilic portion of the phospholipid (the head), and its hydrophobic part interacts with the hydrophobic portion of the phospholipid (the tails). Protein component of the membrane Proteins in a biological membrane can be associated with the lipid bilayer in either of two ways as peripheral proteins on the surface of the membrane or as integral proteins within the lipid bilayer. Structures differ in terms of how these proteins are inserted and localised in the membrane, we have different types of membrane proteins: 1. Peripheral proteins (not embedded within the membrane). - Peripheral proteins are associated with the membrane by electrostatic interactions (not covalent), this is why they are not strongly bound to the membrane and can be
removed without disrupting the membrane structure by treatment with mild detergent. 2. Lipid-anchored (they are peripheral) they do not interact with phospholipids, but these proteins are covalently attached to lipids embedded within the cell membrane. 3. Integral membrane proteins (the hydrophobic part (non-polar amino acids) is found inside the membrane, the other part is projected outward). o o o Integral proteins are embedded more solidly in the membrane. there are different ways by which these proteins become integral Single trans domain Multiple trans membrane domain, most common is seventransmembrane domain in which the chain loops seven times through the thickness of the cell membrane. Examples on the multiple are: Signalling proteins such as G-protein Some channels (in a circular way) to allow transport of ions (for example). The membrane integral domains (transmembrane domain) are: Single or multiple Can be made of alpha helix or beta -sheet #Note: Some embedded proteins (integral) have no extracellular/ intracellular parts, some have extracellular/ intracellular (exposed to both sides) some have a part that is exposed to one side (either extracellular or intracellular) Functions of proteins Transport - Membranes are impermeable barrier - Proteins can be carriers or channels Signaling - a ligand (such as hormones, cytokines...) binds to a protein receptor, the receptor changes, leading to the movement of the signal inside the cell, so the ligand does not directly move the signal to the inside of the cell, but it induces changes to receptor, which in turn moves the signal to the inside, Catalysis - Enzyme-linked receptors.
Amino acids Amino acids are the basic subunits of proteins, There are twenty kinds 20 of amino acids found in proteins, depending on the side chains varying in Size (small/ large) Shape (amino acids of different shapes: ( branched/ chains/ cyclic/ ringed/ double ringed..) Charge & Polarity - ( negatively charged/ positively charged) - ( polar / non-polar) Hydrogen-bonding capacity (hydrogen bond donors/ acceptors/ others don t form hydrogen bonds) Hydrophobicity character (hydrophobic/ hydrophilic) Chemical reactivity (highly reactive / not chemically reactive). Amino acids general structure is: 1. A central carbon ( called the alpha carbon) which is -generally- chiral (attached to 4 different groups), because they are chiral we can get either an L amino acid or D-amino acid In our body, we have L-amino acids, The amino acids that occur in proteins naturally are all of the L form.. BUT D -sugars are more abundant naturally. 2. The four groups that are attached to the alpha carbon are: a. H group b. Carboxyl group c. Amino group d. R group (the side chain) which determines the characteristics of the different amino acids because it differs from one amino to the other, Thus depending on their sidechain characteristics, certain amino acids cluster together to exclude water (hydrophobic effect), whereas others participate in hydrogen bonding. Cysteine can form disulfide bonds, whereas charged amino acids can form ionic bonds. #Note: the free amino acids exist as zwitterions ions*, in which the amino group is positively charged, and the carboxylate group is negatively charged How to name the carbons in the R group (designation of carbons) A. Beta carbon β (directly attached to the alpha carbon) B. Gamma carbon γ (attached to beta) C. Delta δ D. Epsilon ε E. Omega the terminal carbon ( omega is the last in the sequence). Omega is the last letter in the Greek alphabet. REMEMBER: The omega system of nomenclature is based on numbering the double bonds from the last carbon in the fatty acid instead of the carbonyl group [the delta system].
There are many criteria to which we can refer when classifying amino acids one way is according to: Charge and polarity of R groups o Non polar o Polar o Positively charged (basic) at physiologic ph. o Negatively charged (acidic) at physiologic ph. #Note: the amino acids orders in the slides are according to their complexity. Here are the four main groups of amino acids which are found in proteins: Glycine (Gly) is the simplest amino acid, and it does not fit well into any classification because its side chain is just a hydrogen atom. 1) The only amino acid that is achiral. 2) The smallest amino acid because its R group is just a hydrogen atom 3) It is polar with a non-polar R group, the hydrogen atom does not have a great effect on the charges of the amino acid 4) Its R group causes the least amount of steric hindrance when found in a protein Non- polar amino acids In terms of structural features, the following amino acids would be classified into (aliphatic, cyclic, aromatic) Aliphatic (forming open chains, not rings) 5) Alanine (Ala) - R group: methyl group ( CH3) - The methyl group reduces the effect of the amino acid charges ( +, amino group / -, carboxyl group) 6) Valine (Val) 7) Leucine (Leu) 8) Isoleucine (Ile) - Valine, Leucine, Isoleucine These are essential* amino acids, they are branched, when they are found in a protein, these branches effects would be obvious in a protein because of the different interactions, Although it is true that if we replace one of these amino acids in the protein with another one of them, the newly formed protein would not be different from the previous one, because we are replacing a branched non-polar with a branched non-polar amino acid. The effect would be slight.
- Leucine and isoleucine only differ in the position of the branching point, in Leucine the branching is at the Gamma carbon, while the branching in Isoleucine is at the Beta carbon 9) Methionine (Met) - although it contains a sulfur group, it is a nonpolar amino acid with a large bulky side chain that is hydrophobic. Cyclic Proline (imino acid)* - This rigid ring causes a kink in the peptide backbone that prevents it from forming its usual configuration (It prevents the protein from being flexible ) - It contains a secondary amino group, we call it an alpha-amino group (bound to two carbons) the nitrogen is not only linked to the alpha carbon (as in all amino acids), but also to the R group.. - Proline shares many properties with the aliphatic group, this is why they are found in the same category in many sources. (See Figure 1 ) Aromatic amino acids o Phenylalanine (Phe) Its structure is an alanine that is linked to a benzene ring. (The R group is a benzyl group) It is highly hydrophobic o Tryptophan (Trp) The largest amino acid, because it is a double ringed structure that is (Indole ring) Although one of the rings contain a nitrogen, its overall structure shows that it is a hydrophobic amino acid, the nitrogen s effect would not be great. However, this nitrogen can contribute to its reactivity, it can form hydrogen bonds. Electrically neutral polar amino acids Aromatic Polar o Tyrosine (Tyr) The same structure as phenylalanine with an extra hydroxyl group (OH) on the benzene ring, this is why it is polar and highly reactive. Aliphatic Polar o Serine (Ser) o Threonine (Thr)
- Both Ser and Thr contain a hydroxyl group (OH) in their structures this is why they are, polar and reactive - How are their structures? o Cysteine (Cys) Serine is the same as Alanine, but we removed one H from the methyl group and replaced it with a hydroxyl group Threonine is the same as Valine, but we have replaced the methyl group with a hydroxyl group 1. Its structure contains a terminal thiol group (sulfur), this is why it is polar, highly reactive and if it was a part of a protein, it would have great implications in its structure, (the only amino acid that can form disulfide bridges o Asparagine (Asn) o Glutamine (Gln) Both names end with (n), they both contain a nitrogen in their amide group. They can form hydrogen bonds with other molecules (hydrogen-bond acceptors) Asparagine and Glutamine are both derived from other amino acids, Aspartic acid (Asp) and Glutamic acid (Glu) respectively. Positively charged amino groups This group has basic side chains, and the side chain in all three following amino acids is positively charged at or near neutral ph. o Lysine (Lys) the side-chain amino group is attached to an aliphatic hydrocarbon tail. It has two amino groups ( the one which is connected to the alpha carbon and the side-chain primary amino group (in the R group)). o Arginine (Arg) It has a positively charged R- group because of the guanidino group (H 2 NC(=NH)NH ) which is found at the end of the side chain Itts positive charge alternates between the two amino groups, this positive charge is stabilized by resonance) o Histidine (His) It is a very important amino acid, physiologically. It has an imidazole (ring) group The nitrogen in its imidazole ring could be either neutral or positively charged -as shown below-
Histidine can be found in the protonated or unprotonated forms in proteins, and the properties of many proteins depend on whether individual histidine residues are or are not charged. Negatively charged Amino acids They both have a terminal negatively charged carboxyl group o Aspartate (Asp) It is in its ionized form, its protonated form is called (Aspartic acid) o Glutamate (Glu) It is in its ionized form, its protonated form is called (Glutamic acid) #Notes: - As previously mentioned, (The amidations of aspartate and glutamate can produce Asparagine and Glutamine) - The negatively charged acidic amino acids (aspartate and glutamate) form ionic (electrostatic) bonds with positively charged molecules, such as the basic amino acids (lysine, arginine, and histidine)
Figure 1
Some examples on how we are gonna be asked about amino acids in the exam? Which amino acid contain a phenyl group in its structure? - Answer: Phenylalanine. What are the two amino acids that contain sulfur? - Answer: Methionine / Cysteine Which amino acid is achiral? - Answer: Glycine Which amino acid that contain only a methyl group in its structure? - Answer: Alanine Which of group of amino acids contain non-polar branched side chains - Answer: Valine, Leucine, Isoleucine Which amino acids are negatively charged? - Answer: Aspartate/ Glutamate Which amino acid has a double ring in its R group? - Answer: tryptophan What are the amino acids that can participate in hydrogen bonding? - Answer: a. Uncharged polar amino acids: serine, threonine, tyrosine, asparagine, and glutamine. b. The acidic and basic amino acid side chains also participate in hydrogen bonding Definitions:: C is configuration A cis double bond puts a kink in the long-chain hydrocarbon tail, whereas the shape of a trans fatty acid is like that of a saturated fatty acid in its fully extended conformation E ss ential nutrients: They should be obtained from the diet, and couldn t be synthesised in the human body. Non-essential nutrients :
They do not have to be taken in with the diet, but can be synthesized by the human body from other compounds. Glycolipid The prefix -glyco- means sugar, sugars are exposed to the outside of the cell, this is why it is a phospholipid that is found in the outer leaflet of the bilayer, and it is involved in cell recognition. Imino acid Amino acids containing a secondary amine group. Phosphatidylinositol, A phospholipid that is found in the inner leaflet of the lipid bilayer, this is why it is involved in signaling. Not Included Further Explanation about how it is involved in signalling: one example is, Phosphatidylinositol 4,5- bisphosphate (PIP 2), the hydrolytic cleavage of PIP2 by phospholipase C. The products of this cleavage, is IP3 and DAG, mediating the mobilization of intracellular calcium and activation of protein and the activation of protein kinase C, which evoke specific cellular responses. S ignal transmission across the membrane is thus accomplished. Steroids Are a group of lipids with a characteristic molecular structure containing four rings of carbon atoms (three six-membered and one five-membered). Zwitterion ion: a molecule or ion having separate positively and negatively charged groups.