Exam one Flashcards
Whats a monoenoic acid
fatty acid with one double bond
Linear correlation of saturated fatty acids
melting temperature increases with size of FA
Whats an iso- branched FA
v
Whats an anteiso branched FA
isoleucine
How is the primer made in FA synthesis
Acetyl-CoA gets attached to ACP to make acetyl-ACP and then gets transferred to ketosynthase making acetyl-S-ketosynthase
How is the extender malonyl ACP made?
Acetyl-CoA gets carboxylated then the CoA is removed and malonyl is attached to ACP making malonyl-ACP
What are the steps in FA synthesis and what enzymes are involved?
The primer is in ketosynthase and is then extended with malonyl-ACP with ketosynthase. The double bond from the acetyl group is reduced with ketoreductase to a H and OH. The water is removed with a dehydrase making a double bond which is removed with enoylreductase. This molecule is still attached to an ACP with a thioester bond and becomes the primer for the next cycle.
What enzyme performs anaerobic desaturation and what is its FA substrate
beta-hydroxydecanoyl-ACP dehydrase (is not the dehydrase in FA synthesis) its substrate is the 10 carbon FA
How is anaerobic unsaturated FA synthesis performed
Water is removed via beta-hydroxydecanoyl-ACP forming a cis double bond in the alpha/beta carbon. This is isomerized to the cis configuration and the bond moved between the beta/gamma carbons. Then FA synthesis continues.
If the trans configuration between alpha and beta is accidently released from the enzyme it will be saturated and then regular FA synth continues
How does branched chain FA synthesis occur
This uses alpha-keto acids. Leucine is used in the iso-series and isoleucine is used in the anteiso-series. A transaminase makes a alpha-keto acid which acts as the primer then normal FA synth occurs using malonyl-ACP as a extender
What are polyketides
Family of molecules built from acyl-CoA and are usually secondary metabolites
What is a type III polyketide synthase
Has a single AS for each step in the assembly and has many modules.
What is the basic structure of an isoprenoid?
Is a five carbon unit that can have any sterochemistry.
Prenylated nucleotides are what and do what?
They are nucleotides that have an isoprenoid addition which improves the efficiency of tRNA translation and may have positive or negative impacts on translational fidelity (how accurate is the translations)
What is the MV pathway in isoprenoid synthesis
3 acetyl CoA are brought together to make mevalonate (uses HMGR cholesterol medication target) This is then converted to IPP and its isomer DMAPP (dimethylallyl diphosphate)
What is the MEP pathway in isoprenoid synthesis?
Puryvate + G3P are brough together and through subsequent steps make IPP (isopentenyl diphosphate) and DMAP (dimethylallyl diphosphate)
How does chain elongation in IPP synthesis occur?
DMAPP and IPP are brought together to make geranyl diphosphate then subsequent IPPs are added until desired length is achieved.
What is step 3 in isoprenoid synthesis
Following elongation there are various modifications that can be made: cyclization, condensation ect
General structure of phospholipids
a three carbon glycerol with a phosphate on the third carbon usually has FA attached at first and second carbons
what is a phosphatidic acid (PA)
has a hydrogen attached to the phosphate of glycerol-3-phosphate
what is a phosphatidyl serine? (PS)
A serine amino acid (R group=(OH-CH3) is attached to phosphate in G3P
What is phosphatidic acid synthesis?
Dihydroxyacetone Phosphate (DHAP) 3carbon molecule with double bonded oxygen at C2 is reduced to make an OH => glycerol-3-phosphate (G3P) and then FA acyls are added to the hydroxides on C1 and C2
What is the PlsB/PlsC pathway
Makes phosphatidic acid (PA) in E. coli
can happen one of two ways
1) a FA is imported, added to CoA (thioester) and it goes to PlsB which adds a FA to C1 making LPA it then goes to PlsC where another FA is added making PA. The PlsB can be skipped however.
2) FA synth –> acyl-ACP goes either to PlsB –> PlsC or just goes to PlsC.
Note: need energy from thioseter bond to add the acyl group
what is the PlsX/Y/C pathway?
Only happens with Acyl-ACP (end result of FA synthesis)
1) goes to PlsX where an acyl-phosphate is released from acyl-ACP via phosphorolysis. Acyl-phosphate goes to PlsY –> LPA then to PlsC –> PA
2) Acyl-phosphate skips PlsX and Y and goes straight to C where its added to at LPA (C2) making PA
Addition of head group to PA: Phosphatidyl ethanolamine synth.
start with CDP-DAG (cytosine diphosphate diacylglycerol). One phosphate is kicked off and replaced with a serine a.a., this is replated with ethanolamine making it.
addition of head group to PA: how is cardiolipin made
CDP-DAG, cytosine gets kicked off for G3P, the third phosphate is replaced with a OH making phosphatidyl glycerol and a second phosphatidyl glycerol is added.
How is membrane homeostasis maintained?
PssA is a regulatory enzyme that is used to maintain a molar ratio between zwitterionic FA (PtdEnt) and acidic FA the acidic form FA (PtdGro) are constitutively produced and the association of PssA is regulation by the mole fraction of the acidic form and the zwitterionic FA.
What is a zwitterion
When a charged molecules overall charge sums to zero because the charges “cancel”
Which stereoisomer is normally found in protein?
The L-form is usually found though there are some A.A. in proteins with the D-conformation as well
Where are D-amino acids found?
PPG, antibiotics and capsule of Bacillus anthracis
All amino acids come from what five intermediates of central metabolism?
OAA a-ketogluterate pyruvate G3P Phosphoribosyl pyrophosphate
Where do the alpha amino-groups of A.A. generally come from?
They come from the alpha amino group of glutamate via transamination –> the replacement of a double bonded oxygen with an amino group –> transaminases/aminotransferases.
Glutamine can also donate its side chain (R amino group)
What A.A. can be synthesized from aKGA?
Glutamate, glutamine, proline, and arginine.
What two ways is glutamate synthesis done?
1) glutamate synthase: transfers amino group from glutamines’ side chain to aKGA making glutamate.
2) direct transfer of ammonia to aKGA vis glutamate dehydrogenase (only at high [ammonia] due to high Km)
How is glutamine synthesized?
Uses glutamine synthase
-transfers ammonia to R-chain carboxyl of glutamate making glutamine. Uses ATP.
How is proline synthesized?
It is a member of the aKGA family. No transamination occurs 1) glutamate is phosphorylated. 2)this is then reduced with NADPH 3) the energy from the phosphate + NADPH ==> spontaneous cyclization
What are the members of the 3-Phosphoglycerate family?
Serine, cysteine and glycine
How is serine/glycine synthesized?
1) 3-phosphoglycerate is oxidized by NAD+ changing the C2 carbon to a double bonded oxygen
2) Transaminase rxn using glutamate. Changes double bonded oxygen to an amino group.
3) the phosphate is removed generating a OH attached to a carbon ==> serine
4) THF (tetrahydrofolate) removes a methyl group making a 2 carbon glycine and 5-10-methylenetetrahydrofolate
Glycine can be further broken down into an amino, CO2 and a methyl
How is cysteine synthesized?
1) serine can become glycine or it can become cysteine
2) a transacetylase (neg inhib by cysteine) attaches an acetyl group from CoA
3) the acetate group is replaced with a sulfhydryl via direct sulfhydration making cysteine.
PEP + erythrose 4-phosphate family
Phenylalanine, tyrosine, and tryptophan.
Aromatic A.A. synthesis
Uses shikimate pathway which makes a benzene ring using PEP and erythrose-4 phosphate ==> chorismate
1) uses bifunctional enzymes then branches into two paths
a) a dehydratase removes the OH on the bottom of the ring + removes the carboxyl group
- then glutamate transfers an amino group ==> phenylalanine
b) dehydrogenase, removes the carboxyl group leaving the OH on the bottom and then glutamate adds a amino group making tyrosine.
Pyruvate Family
Alanine, valine, leucine
How is alanine synthesized?
Pyruvate has a double bonded oxygen at C2 this is transaminated making Alanine
OAA family
Aspartate, lysine, threonine, isoleucine, methionine, and asparagine
Aspartate and asparagine synthesis
OAA is transaminated at C3 (alpha carbon) making aspartate then a second transamination at the R-carboxyl occurs making asparagine using glutamine R-chain amino group
-branches to make DAP, lysine, methionine, and threonine
synthesis of D amino acids
formed by racemases as free intermediates that are then incorporated into peptides could also be inversion after incorporation
What is a nucleotide
Has a nitrogenous base, a sugar, and one or more phosphate groups. The nitrogenous base is a purine or a pyrimidine
What is a purine?
Has two nitrogenous rings attached to each other: adenine and guanine
What is a pyrimidine?
It is a nitrogenous base with one benzene type ring: cytosine, uracil, thymine
Difference between ribose and deoxyribose?
Ribose is a 2’ OH group and deoxyribose is a 2’ H remember sugars counting starts from oxygen 1’ is where the base is attached 2’ can be either OH or H
Which is the first purine nucleotide formed?
Inosine monophosphate can become either AMP or GMP
Synthesis of pyrimidine nucleotides
Uses a carbamoyl phosphate and aspartate to form a 6 membered ring
Which is a the first pyrimidine formed
Uridine monophosphate using carbamoyl and aspartate
Nucleotide monophosphate ==> diphosphates
This conversion is done by specific nucleotide monophosphate kinases
triphosphates are made by a enzyme with broad specificity
UTP –> CTP
transamination of the pyrimidine double bonded oxygen
Determining L vs D configuration using Fischer projection
If the OH points to the right its D and this is determined by the chiral center farthest from the aldehyde or keytone
Sources of sugars
1) oxidation of polyols (small chain carbohydrates) glycerol oxidation leads to ring formation
2) gluconeogenesis energetically expensive
3) Sugar interconversion mostly at the monophosphate level unactivated sugars do not interconvert.
What is a glycosidic bond?
Bond between a sugar and an alcohol (OH) compound formed = glycoside
- bond is usually between anomeric carbons of sugars
- needs energy from phosphate bond
- this bond energy can be used to form other glycosidic bonds
What is trehalose and what role does it serve?
Trehalose is a disaccharide of glucose from an alpha 1,1 glycosidic linkage.
-used in both energy storage and protein/membrane protection
What is sucrose?
- The most abundant disaccharide in the environment.
- Eubacteria (G+ and G-) can metabolize sucrose
- made of glucose and fructofuranoside
What are the two ways sucrose is transported in bacteria?
1) Phosphotransferase system (PTS) transports sucrose in and simultaneously adds a phosphate ==> sucrose-6-P locking it in the cell.
- Broken into glucose and fructose ==> add P to fructose and both enter glycolysis.
2) Sucrose permease allows sucrose to enter without modification. This is broken into glucose and fructose and then each are modified (+P) and then enter glycolysis (fructokinase + phosphoglucomutase)
How is glycogen made?
An ADP-glucose is added to the the 4’ carbon of glycogen forming a 1-4 glycosidic linkage
-glycogen synthase
How are branches in glycogen made?
Branches are made at the 6’ carbon making a 1,6 glycosidic linkage then normal elongation can happen using glycogen synthase (1,4 lnkages)
How is glycogen degraded?
Phosphorylase (phosphorolysis) sequentially removed glycosyl residues but phosphorylase cannot remove branches
How glycogen are branches degraded?
Glycogen phosphorylase degrade glycosyl residues until four remain on each branch. Then a transferase transfers three residues from the branch down to the longer chain leaving the branch point residue. This is then degraded using 1,6 glucosidase. Then normal 1,4 degradation occurs.
Dextran and levan
Levan=polymer of fructose and dextran=polymer of glucose.
synthesized extracellularly both use sucrose but obviously only incorporate one half either glucose of fructose into growing chain.
