Term
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Definition
Amino group.
Acid (carboxylate) group.
Side chain, denoted here as "R". This is the part that varies from one amino acid to another.
All of these are attached to the alpha carbon atom.
The alpha carbon is chiral, with S-absolute configuration, making it an L-amino acid (except when R = H). |
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Term
| Which part of amino acid is what?(Basic, acidic ect)? |
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Definition
| Note that the amino group is basic, and the carboxylate group is acidic. This means that they can exist in either neutral or ionic (charged) forms. |
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Term
| At PH of 7 what will net charge be? |
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Definition
| at neutral pH (7.0) or body pH (7.3-7.4), a free amino acid will have a protonated amino group and an ionized carboxylate group, so the net charge (ignoring the sidechain for now) will be zero. |
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Term
| Which amino acids are iconic/ charged? |
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Definition
| Ionic/charged (Asp, Glu, His, Lys, Arg) |
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Term
| Which amino acids are polar but not charged? |
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Definition
| Polar but not charged (Ser, Thr, Cys, Asn, Gln) |
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Term
| Which amino acids are large with neutral side chains? |
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Definition
| Hydrophobic, with large neutral sidechain (Trp, Phe, Tyr, Leu, Ile, Val, Met, Pro) |
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Term
| Which amino acids have small neutral side chains? |
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Definition
| Small neutral sidechain (Gly, Ala) |
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Term
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Definition
| Tyrosine has a hydrophobic aromatic ring, but it also has a polar -OH group, so some texts put it in the "polar" category. And the -OH group can ionize (perhaps 1% at neutral pH. |
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Term
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Definition
| Tryptophan has two fused aromatic rings (very hydrophobic), but it has a polar NH group that can donate a hydrogen bond. This nitrogen is not basic, though--it cannot carry a positive charge. |
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Term
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Definition
| In cysteine, the -SH hydrogen is not as polar as the corresponding -OH of serine. But it is slightly acidic. |
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Term
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Definition
| Histidine is weakly basic, with a pKa close to physiological pH. The actual pKa of a given histidine in a protein depends a great deal on its environment. |
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Term
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Definition
Aspartic acid (Asp) and glutamic acid (Glu)
Asp= COOH
Glu=COO- |
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Term
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Definition
Lysine (Lys) and arginine (Arg)
These are usually positively charged at neutral pH, with pKa well above 10. |
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Term
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Definition
| This makes histidine a very useful amino acid when proteins need to transfer an H+ from one molecule to another. But it makes it difficult to write simple exam questions, unless the pKa is specified. |
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Term
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Definition
| Serine and threonine have a polar -OH group; the oxygen atom has a partial negative charge, and the hydrogen atom has a partial positive charge. This allows serine and threonine to be both hydrogen bond donors and hydrogen bond acceptors. |
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Term
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Definition
| Asparagine (Asn) and glutamine (Gln) are the amide derivatives of aspartic acid and glutamic acid, respectively. Again, the oxygen atom has a partial negative charge, and the NH hydrogens have partial positive charge, so they can be both hydrogen bond donors and acceptors. |
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Term
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Definition
Cysteine (Cys) is another special case. Its -SH (sulfhydryl) group is polar, but not as polar as serine, since sulfur isn't as electronegative as oxygen. So it's not as good at making hydrogen bonds.
Cys structure
But the -SH group is a little bit acidic, with a pKa around 8.3, so at neutral pH it may be in the ionic form to the extent of a few percent. |
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Term
| Hydrophobic Amino Acids--Aromatics |
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Definition
There are three amino acids with aromatic hydrophobic side chains: Tryptophan (Trp), phenylalanine (Phe), and tyrosine (Tyr).
Tryptophan has an indole ring on its side chain. Remember that the -NH group on tryptophan can serve as a hydrogen bond donor (but it is not a basic nitrogen). The -OH group on tyrosine can serve as both a hydrogen bond donor and an acceptor. It is also weakly acidic, with a pKa near 11. |
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Term
| Hydrophobic Amino Acids--Aliphatics(part 1) |
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Definition
| There are three amino acids with branched aliphatic side chains: Leucine (Leu), isoleucine (Ile), and valine (Val). Leucine and isoleucine have 4 carbons in the side chain, and valine has 3. |
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Term
| Hydrophobic Amino Acids--Aliphatics(part 2) |
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Definition
| Proline (Pro) also has an aliphatic side chain composed of 3 carbons. It is unique among all of the amino acids because its side chain cyclizes to the amine nitrogen. This means that, when a peptide bond forms to this nitrogen, there will be no polar -NH group. |
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Term
| Hydrophobic Amino Acids--Aliphatics(part 3) |
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Definition
| One more hydrophobic side chain: Methionine (Met) has an aliphatic side chain with a methyl-thioether at the end. The sulfur is not particularly polar, so the methionine side chain is very hydrophobic. |
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Term
| Small Neutral Amino Acids |
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Definition
Our last two amino acids are small in size and neutral. Alanine (Ala) has a single methyl group as its side chain, so it is a little hydrophobic in character. Glycine (Gly) has only a hydrogen atom, the smallest possible "side chain". Note that glycine is no longer asymmetrically substituted on the alpha-carbon, so it is technically not an L-amino acid.
Ala & Gly structures
The absence of a side chain means that glycine introduces more conformational freedom into the backbone of the protein. |
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Term
| How are peptide bonds formed? |
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Definition
| The peptide bond (or amide bond) is formed by combining the carboxylate group of one amino acid with the amino group of a second amino acid. Formally, water (H2O) is removed. |
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Term
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Definition
| The fatty acids are important as metabolic fuel, and as building blocks for other lipids. They are composed of a hydrocarbon chain with a carboxylate at one end. |
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Term
What is the difference between saturday and unsaturated fatty acids?
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Definition
Saturated fatty acid chains and trans-unsaturated fatty acid chains can readily pack together and form solids at body temperature; cis-double bonds induce a kink in the chain, which prevents packing and keeps the lipid in a more fluid state.
The hydrocarbon chain of the fatty acid may be saturated (no double bonds, nowhere to add more hydrogens) or unsaturated (one or more double bonds, to which hydrogens could be added). |
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Term
What are fatty acids that contain more then one double bond called?
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Definition
| Fatty acids that contain more than one double bond are called polyunsaturated. These double bonds typically are separated by a single methylene (-CH2-) group, so that they are not conjugated. |
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Term
| What are the two polyunsaturated fatty acids that are considered essential? |
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Definition
| There are two polyunsaturated fatty acids that are considered essential. These arelinoleic acid and linolenic acid. Humans need these, but cannot make them. |
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Term
| A particularly important polyunsaturated fatty acid is arachidonic acid, composed of 20 carbons. It is systematically named as an eicosatetraenoic acid (20 carbons, 4 double bonds). It is all-cis, Δ5,Δ8,Δ11,Δ14. |
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Definition
Arachidonic acid is synthesized from the essential fatty acid linoleic acid, and it is the precursor for prostaglandin, leukotriene, and thromboxane synthesis
**know difference between three |
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Term
| Differences between prostaglandins, thromboxanes, and leukotrienes? |
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Definition
Prostaglandins are characterized by a 5-membered all-carbon ring.
Thromboxanes have a 6-membered ring that includes an oxygen atom.
Leukotrienes are linear, not cyclic. They typically have four double bonds, but the "triene" name is based on the three conjugated double bonds. |
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Term
| What is three fatty acids together? |
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Definition
| When 3 fatty acids are attached, the product is a triglyceride (also calledtriacylglycerol). This is a common storage form for fats. |
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Term
| What is diphosphatidyl glycerol? |
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Definition
| Mitochondrial inner membranes contain a unique glycerophospholipid: diphosphatidyl glycerol. It is also called cardiolipin, because it was first discovered in heart tissue. It consists of two phosphatidic acids (diacylglycerol phosphate), linked to a third glycerol. |
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Term
| How do ether phospholipids and glyverophospholipids differ? |
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Definition
| The ether phospholipids differ from other glycerophospholipids in the nature of the attachment of the hydrocarbon chain to C1 of the glycerol. While the C2 still has anester, C1 has an ether linkage. |
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Term
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Definition
| Plasmalogens are important components of myelin membranes. Phosphatidal choline (corresponds in structure to phosphatidyl choline) has an α,β-unsaturated hydrocarbon chain ether-linked to C1 of the glycerol. |
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Term
| How are Sphingolipids construcuted?(non glycerol base lipids) |
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Definition
| The sphingolipids are constructed using a long-chain amino-alcohol calledsphingosine. Sphingosine is converted to ceramide by addition of a long chain fatty acid. So ceramide has two long hydrocarbon tails, plus a polar head group. |
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Term
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Definition
Ceramide is an intermediate that can be further modified to make the importantsphingolipids.
If phosphocholine is added to the terminal -OH group, the product is sphingomyelin, which is an important component of the myelin sheath surrounding nerve fibers. |
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Term
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Definition
| If glucose (shown) or galactose is added to the terminal -OH group, the products are glycosphingolipids called cerebrosides which are important components of nerve and muscle cell membranes. |
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Term
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Definition
| Gangliosides are glycosphingolipids in which more complex oligosaccharides are attached to ceramide. These usually contain one or more sialic acid (N-acetyl-neuraminic acid, NANA) residues. The gangliosides tend to concentrate in lipid rafts. Don't worry about the exact structure of NANA, but do note the negative charge. You will learn later that it's important for the function of gangliosides. |
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Term
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Definition
Cholesterol is an important component of many membranes. It is also a precursor for the biosynthesis of steroid hormones, bile acids, and vitamin D. The structure of cholesterol is shown below. It is amphipathic, with a hydrophobic hydrocarbon making up most of the structure, and a hydrophilic hydroxyl group at the 3-position.
The numbering of the carbon skeleton is shown. The following carbons should be known, in order to discuss steroid hormones: C-11, C-17, C-18, C-19, and C-21. |
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Term
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Definition
| Terpenes are built using the branched 5-carbon building block isopentenyl pyrophosphate. These compounds are also sometimes called isoprenoids because of their relationship to the structure of isoprene. You must be able to recognize the terpenes that follow. |
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Term
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Definition
| Cholesterol and other sterols are derived from a 30-carbon compound, squalene. |
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Term
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Definition
| Dolichol is another terpene built using 5-carbon isoprenoid blocks |
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Term
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Definition
| Retinol (Vitamin A) is another terpene built using 5-carbon isoprenoid blocks |
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