Amino Acids, Carbohydrates, Lipids; structure and trivia Flashcards

Terms Definitions
What are the nine essential amino acids?
Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan, Valine
Glycine, Gly
not optically active; 33% of collagen
Alanine, Ala
Major AA in blood; precursor to glucose; transports ammonia; hydrophobic
Valine, Val
Essential; hydrophobic
Leucine, Leu
Essential; hydrophobic
Isoleucine, Ile
Essential; hydrophobic
Proline, Pro
Comprises 15% of collagen (in a hydroxylated form); disrupts alpha helices
Phenylalanine, Phe
Aromatic; accumulates in patients with PKU
Tyrosine, Tyr
Aromatic; has hydroxyl group that is frequently de/phosphorylated to regulate proteins; precursor to thyroid hormones, catecholamines, DOPA and melanin
Tryptophan, Trp
Precursor to serotonin; does NOT cause sleepiness
Serine, Ser
Reversibly phosphorylated to regulate proteins
Threonine, Thr
Reversibly phosphorylated to regulate proteins
Cysteine, Cys
Oxidized post-translationally to form disulfide bridges (thus 2ndry structure)
Methionine, Met
1st AA in translation; methyl donor in activated form s-adenosyl methionine
Aspartate, Aspartic Acid, Asp
Negatively charged (acidic); produced by intermediates in the TCA cycle
Asparagine, Asn
Uncharged; carrier of ammonia
Glutamate, Glutamic Acid, Glu
Negatively charged (acidic); produced by intermediates in the TCA cycle; precursor of GABA
Glutamine, Gln
Uncharged; carrier of ammonia
Lysine, Lys
Positively charged; basic; E-amino group can be acetyl/methylated to neutralize (-) charged histones
Arginine, Arg
Precursor to urea and NO
Histidine, His
Buffers pH; precursor to histamine
Hydroxyproline
15% of collagen
How does glutathione function as an antioxidant?
It eliminates H2O2: two molecules of Glutathione (GSH) are oxidized to Glutathione disulfide (GSSG) with the help of glutathione reductase.
What might a hydrophobicity plot predict?
Transmembrane domains or interior/exterior protein surfaces
What is glutathione and what role does it have in determining protein structure?
Glutathione reduces disulfide bonds to cyteines, thus regulating the appropriate number of such bonds
Between which parts of how many AAs are the hydrogen bonds forming an alpha helix?
Between the CO group of an AA and the NH group of the AA four (4) residues ahead of it; the helix is right-handed
What is the major difference in hydrogen bonding between parallel and anti-parallel beta sheets?
In parallel, each AA is bonded to two separate AAs in the same adjacent strand; in antiparallel, the AAs may be bonded to two AAs, but in strands to either side.
What are two variably defined 3rnary structural elements?
Omega loop: larger? Beta turn: smaller?
What are three forces responsible for tertiary (and, for that matter, quaternary) structure?
1. (most important) sequence of AAs
2. Water; hydrophobic/hydrophilic regions
3. Thermodynamic stability
4. Bonds (hydrogen, ionic, disulfide VdW forces)
What is cooperative binding?
The binding of substrate at one place (subunit) on a protein encourages binding of at another place (subunit). Ex. Once one subunit of Hemoglobin has bound O2, the others change from T to R and binding affinity is increased.
How is insulin created from proinsulin?
Proinsulin is a single polypeptide strand; the two future subunits are stabilized with S-S linkages. The C peptide is removed by a proteolytic enzyme
What is protein denaturation? What are some classes of denaturing agents?
Destruction of the quaternary and tertiary structure; some agents include high heat, acids, urea, detergents, oxidizing agents.
What is PAGE?
Polyacrylamide gel electrophoresis. Denatured proteins (subunits separated; 3ry structure unfolded); SDS is added and evenly coats the polypeptides (it is (-) charged); voltage is applied and proteins migrate according to their molecular weight (the smallest move the farthest).
What is Western blotting?
Using Ab specific to the protein of interest to identify it on a PAGE gel.
Glyceraldehyde, Glc
Where can sugars be added to proteins and what are the classes of this action called?
In N-glycosylation, sugars are added to the -NH2 group of Asparagine; in O-glycosylation, sugars are added to the -OH group of threonine, serine, or tyrosine.
Where can lipids be added to proteins?
These are called prenyl groups and they are added to the -SH of cysteine or the NH group of an N-terminal Gly
What does "ul" in the name of a sugar indicate?
This indicates the sugar is a ketose
About which carbon is galactose an epimer of glucose?
Carbon 4 is the difference
About which carbon is mannose an epimer of glucose?
Carbon 2 is the difference
Amylopectin
Amylose
Cellulose
Dihydroxyacetone
Mannose
Fructose
Fructose
Galactose
Galactose
GlcNac
Glucose
Glucosamine
Glucose
Glucose
Glyceraldehyde
Glycogen
Isomaltose
Lactose
Maltose
Sucrose
Sucralose
Which common sugar is not reducing and why?
Sucrose, because both of the monomer's anomeric carbons are involved in the glycosidic linkage.
What is lactulose and what is it used for?
It is a synthetic saccharide used to make you poop. It is not digested and increases water in the gut
What is used in Fehling's or Benedict's reaction, and what information is gleaned from the results?
Cu++; if the copper is reduced to Cu+ there is a reducing sugar present
What conditions might cause the presence of galactose and fructose in the urine, respectively?
Galactosemia and fructose intolerance
What does the HbA1c measure and what is a normal value?
Glycation of hemoglobin due to elevated average blood sugar; normal is %5 or below.
What two things are on the same side to identify a Beta anomer?
The anomeric carbon and the -CH2OH group on the ring are on the same side
When the anomeric carbon and the -CH2OH group are on opposite sides of the ring, what do you have?
An alpha anomer
What is the linkage in maltose?
Alpha 1->4 linkage, Glc-Glc
What is the linkage in isomaltose?
Alpha 1->6, Glc-Glc
What is the linkage in sucrose?
Alpha 1->2, Glc-Fru
What is the linkage in lactose?
Beta 1->4, Gal-Glc
What two polysaccharides make up starch?
Amlyose and amylopectin
What is the linkage in amylose?
Alpha 1->4, (Glc)n, helical
What is the linkage in amylopectin?
Both alpha 1->4 (Glc)n and alpha 1->6 (Glc)n, 20 residues between branches
What is the linkage in glycogen?
Both alpha 1->4 (Glc)n and alpha 1->6 (Glc)n, 10 residues between branches
What breaks down glycogen into glucose units?
Phosphorylase
What is the linkage in cellulose?
Beta 1->4 (Glc)n
To what purpose and where is lysine often acetylated/methylated?
In histones; this removes the positive charge on lysine and causes negatively charged DNA to associate more loosely with the histone
Where is the fatty acid attached in palmitolation?
To an -SH of an internal cysteine
Where is the fatty acid attached in myristolation?
To the -NH group of an N-terminal Gly
Where does a prenyl group attach?
To the -SH group of a cysteine.
What does cer stand for?
Ceramide, which is sphingosine linked to a fatty acide via an amide bond
What is the abbreviation for glucose?
Glc
What does NANA stand for?
N-acetylneuraminate (sialate)
What does GalNAc stand for?
N-acetylgalactosamine
What does GlcNAc stand for?
N-acetylglucosamine
What is a glycosphingolipid?
A ceramide linked to sugar(s)
What are the two kinds of glycosphingolipids?
Neutral (sugar + ceramide) and acidic, also called gangliosides (NANA + sugar + ceramide)
Give three examples of glycosphingolipid antigenicity.
ABO blood groups, haemmagluttinin (gangliosides), cholera toxin action in the body (GM1), tetanus toxin action (gangliosides in the CNS)
What is characteristic of EFAD?
Lack of essential fatty acids, particularly linoleic acid (18:2w6) and the abnormal presence of 20:3w9
How does the steroid nucleus numbering system progress?
It begins with 1 at the top left of a lower case omega, and then proceeds through the omega, and then starts up again at the hop squiggle of an inverted, sideways funky lower case delta.
What modifications are made to the steroid nucleus to yield cholesterol?
-OH at position 3; double bond between 5 & ^; methyl at position 10; methyl at position 13; heptane with a methyl at the 2nd from R c, attached to position 17 to the 2nd from L c.
What is arachidonic acid?
20:4w6; it is often at position 2 in membrane lipids. derivatives are called eicosanoids and are inflammatory
What is the arachidonic acid cascade?
Arachindonic acid is freed from membrane lipis by phospholipase A2, byproduct lysophosphotidylX. Cox1&2 produce prostaglandins and thromboxanes from AA; leukotrienes are made by a different enzyme
What are Cox 1 and 2?
Cyclooxygenases 1 and 2 have two components: a cyclooxygenase and a peroxidase.
When acted upon by Cox2, what produces anti-inflammatory molecules, including docosanoates?
Long chain unsaturated fatty acids; when DHA is the substrate, docosanoates are the result
How does aspirin "thin the blood"?
It irreversibly binds to the cyclooxygenase portion of Cox1/2 and prevents binding of arachidonic acid, preventing the formation of TXA2 (thromboxane A2), which in platelets participates in clotting. It may increase leukotrienes.
What is palmitoleic acid?
16:1w7
What is oleic acid?
18:1w9
What is linoleic acid?
18:2w6; it is essential
What is linolenic acid?
18:3w3; it is essential
What is sphingomyelin made up of?
Ceramide + phosphotidylcholine
Describe the structure of sphingosine.
CH3-(CH2)12-CH=CH-CH(OHup)-CH(NH2down)-CH2OH
Describe the structure of inositol
A six membered ring, with each member substituted with -OH. Three in a row are up, then 1 down, 1 up, 1 down.
Describe the structure of phosphatidic acid
Glycerol backbone: two fatty acids at position 1 & 2, linked by ester bonds; at position 3, a phosphoric acid (CH2-O-P(=Oup)(OHdown)OH
Describe the structure of ethanolamine.
H3N+CH2CH2OH
Describe the structure of choline
H3CN+(CH3up)(CH3down)CH2CH2OH
Describe the structure of serine
-OC(=O)CH(NH2)CH2OH
Describe the structure of sphingomyelin
CH3(CH2)12CH=CHCH(OH)CH(NHC=Ofattyacid)CH2phosphocholine
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