MT 1 Flashcards
(140 cards)
1
Q
what is BCAT and what does it do
A
branched chain amino acid transaminase
uses alpha ketoglutarate to make BCAAs from keto acids (specifically makes isoleucine, valine, and leucine)
2
Q
what amino acids are formed directly from alpha ketoglutarate
A
glutmate; glutamate can then be made into glutamine, proline, and arginine
3
Q
describe glutamate biosynthesis
A
made from alphaketoglutarate by a transaminase (aspartante, alanine, or BCAA transaminase) when making an AA from a keto acid; or by glutamate dehydrogenase when interconverting NADP+ and NADPH
4
Q
describe glutamine biosynthesis (enzyme, substrates etc)
A
done by glutamine synthase using glutamate
glutamate activated w/ ATP to an acyl-phosphate intermediate (add phosphate to end of the carboxylic acid group, making it an ester); add an NH3 and release a phosphate to make glutamine
5
Q
describe proline biosynthesis
A
Glu –> Pro with 2 NADPH
Glutamate kinase: activate glutamate with ATP, making glutamyl-t-phosphate
Glutamate-5-semialdehyde dehydrogenase: consume NADPH converting it to NADP+ to make glutamate semialdehyde
glutamate semialdehyde spontaneously forms a rin via reversible dehydration, making 5PC
5PC reductase: uses NADPH to make proline from 5PC
6
Q
what AAs are made from oxaloacetate
A
aspartate, which can be used to make asparagine, or lysine/methionine/threonine
7
Q
describe aspartate biosynthesis
A
done by a transaminase reaction
Aspartate transaminase converts oxaloacetate to aspartate, turning glutamate into alpha ketoglutarate in the process
8
Q
describe asparagine biosynthesis
A
done by a Gln amidotransferase reaction
asparagine synthetase turns ATP to AMP+PPi (2 ATP equivalent) and glutamine into glutamate (taking amide) to run aspartate into asparagine
2 step reaction; use ATP to make adenylate, an AMP activated intermediate
then use glutamine and water to release AMP and glutamate, get asparagine
9
Q
describe serine biosynthesis
A
3 step reaction
1) 3-phosphoglycerate is oxidized/NAD+ reduced to NADH by 3-phosphoglycerate dehydrogenase to get 3-hydroxypyruvate
2) transaminase reaction; PLP uses glutamate to release alphaketoglutarate and 3-phosphoserine
3) removal of phosphate via hydrolysis; 3-phosphoserine hydrolyzed by 3-phosphoserine phosphatase to serine
10
Q
describe glycine biosynthesis
A
uses serine and THF
PLP is used to donate a methylene from Ser to THF, getting glycine and 5,10-methylenete-trahydrofolate (N5,N10 methylene THF) and releasing water
highly active pathway in cancer cells
11
Q
describe cysteine biosynthesis
A
methionine converted to SAM, which is converted to cysteine (uses 2 ATP)
12
Q
what AAs are synthesized by phenylalanine
A
aromatic AAs like tyrosine (we lack the enzymes to produce them)
13
Q
describe tyrosine biosynthesis
A
phenylalanine from diet converted to tyr by phenylalanine hydroxylase (a monooxygenase)
using THBP (tetrahydrobiopterin), leaving DHBP (dihydrobipterin); DHBP regenerated to THBP using NADH via dihydropteridine reductase
14
Q
what is phenulketonuria (PKU)
A
deficiency in phenylalanine hydroxylase, which is needed to make tyrosine from diet acquired phenylalanine
15
Q
what is the GS-GOGAT cycle
A
done in plants
GS: glutamine synthase; GOGAT: glutamate synthase
GS uses NH4 and 1 ATP to turn glutamate to glutamine
GOGAT uses alphaketoglutarate and oxidizes NADPH to make 2 glutamate from 1 glutamine
overall consume 1 ATP per NH4 used; attain one net glutamate
16
Q
how do plants make aromatic AAs
A
use 1 ATP equivalent to convert PEP (phosphoenylpyruvate) + E4P (erythrose 4-phosphate) to chorismite
chorismite is used to make phenylalanine and tyrosine (transaminase rxns involved in both paths) as well as tryptophan
17
Q
how do plants make lysine, thronine, and methionine
A
start with aspartate; get aspartate beta semialdehyde
can be converted to lysine through an 8 step pathway
or to threonine and methionine
18
Q
how do plants make BCAAs
A
start with tyrosine; get alpha-ketobutyrate and 2 pyruvate
alphaketobutyrate and pyruvate can make alpha-keto-beta-methylvalerate, which is converted to isoleucine
2 pyruvate can make alpha ketoisovalerate, which can make leucine or valine
19
Q
what is anaplerosis
A
reactions that add net carbon to the TCA cycle (more added than removed by TCA cycle turning; eg adding acetyl CoA isn’t net addition cause you use 2 C to use it)
20
Q
what amino acids can be converted to pyruvate
A
Ala, Cys, Gly, Ser, Thr, Trp
glucogenic (by converting to pyruvate they enter the TCA cycle)
21
Q
describe glycine/serine catabolism
A
THF/5,10-methylene THF used by serine hydroxymethyl transferase to interconvert Gly and Ser
PLP used by serine dehydratase to catabolize serine; release NH4 and get pyruvate
22
Q
describe threonine catabolism
A
2 pathways; make pyruvate and acetyl CoA
23
Q
describe cysteine catabolism
A
transaminase to remove amino from cysteine (uses PLP), then remove thiol via desulfurylation to get pyruvate
24
Q
describe tryptophan catabolism
A
aromatic ring broken by dioxygenase (uses 2 O atoms from O2), later use a monooxygenase (use 1 O atom from O2)
makes acetyl CoA, also generates alanine which will later be converted to pyruvate
25
what amino acids are converted to alpha ketoglutarate
Arg, Glu, Gln, His, Pro
26
describe glutamate/glutamine catabolism
glutamine has amine removed by glutaminase to get glutamate
glutamate converted to alpha ketoglutarate by either aspartate transaminase (AST) or glutamate dehydrogenase
27
describe proline/arginine catabolism
involves urea cycle enzymes like arginase
make glutamate and then alpha ketoglutarate
28
describe histidine catabolism
amino group removed, ring breaks by hydrolysis, then THF takes the formimidoyl group; generates glutamate and then alpha ketoglutarate
29
what amino acids are converted to oxaloacetate
Asn, Asp
30
describe aspartate and asparagine catabolism
asparagine hydrolyzed by asparaginase, releasing NH4 and aspartate
aspartate converted to oxaloacetate by aspartate aminotransferase
31
what AAs are converted to succinyl-CoA
Ile, Met, Thr, Val
32
describe methionine catabolism
similar to cysteine synthesis; make SAM, and then homocysteine as intermediates
branched chain alpha-ketoacid dehydrogenase rxn uses PLP to convert serine to cysteine, also makes succinyl CoA
33
what AAs are converted to acetyl CoA and acetoacetyl CoA
Ile, Leu, Thr, Trp --> acetyl CoA
Leu, Lys, Phe, Trp, Tyr --> acetoacetyl CoA
34
describe phenylalanine and tyrosine catabolism
use phenylalanine hydroxylase to turn Phe to Tyr (without this you get PKU); makes fumarate as well as acetoacetate, which is converted to acetyl CoA
fumarate here is not transported to mitochondria so not glucogenic
35
describe lysine catabolism
pathway not done in humans
alpha ketoglutarate combines with Lys, C from alphaketoglutarate converted to Glu and leave
later use another alpha ketoglutarate to make another glutamate and 2 acetyl-CoA (2 Glu, 2 acetyl-CoA)
36
describe BCAA catabolism
occurs in extrahepatic tissue (muscle, adipose, etc, BCAA transaminase isn't in liver); similar to pyruvate dehydrogenase complex
use BCAA transaminase, decarboxylation (BC alphaketoacid dehydrogenase), and dehydrogenation (acyl-CoA dehydrogenase) to make acetyl-CoA, acetoacetate, and succinyl CoA
37
what is vitamin b3 used for (aka niacin)
precursor of NAD+, NADH, NADP+, NADPH, all of which facilitate redox rxns
38
describe vitamin b5 (pantothenic acid)
precursor of CoA, considered nature's leaving group and an acyl carrier (acetyl CoA, succinyl CoA)
39
describe vitamin b6 (pridoxine)
precursor of PLP (pyridoxal phosphate), which facilitates many reactions including transaminase rxns
40
describe vitamin b7 (biotin)
cofactor in metabolic enzymes; facilitates carboxylation eg acetyl CoA carboxylase in lipid metabolism, pyruvate carboxylase
41
describe vitamin b9 (folic acid)
precursor of THF (tetrahydrofolate) which facilitates transfer of carbon groups like formyl
42
what do you get from targeted metabolomics
targeted analyses generate discrete lists of known compounds/their amounts
43
what do you get from untargeted metabolomics
analyze all known and unknown metabolites in a sample
untargeted analyses use statistics to understand data, good for comparing differences in metabolite profiles between control and test groups/healthy and diseased groups
44
what are the main methods for metabolomics
1) enzyme assays
2) NMR spectroscopy (1D NMR, 2D NMR)
3) Mass spectrometry (LC-MS, GC-MS)
45
46
what are the pros and cons of NMR based assays for metabolomics
pros: quantitatively robust, unambiguous chemical identification, detects H and/or C containing molecules
cons: poor sensitivity, difficult to do
47
what are the pros and cons of mass spectrometry for metabolomics
GC-MS: pros are simple, sensitive, cheap, and easy ID, but cons are it's limited and not as sensitive as LC-MS and frequently requires derivization
LC-MS: pros are very sensitive and flexible with simpler sample prep, cons is it's complex and expensive with complex ID
48
describe the steps of LC-MS
1) LC; uses a mobile phase (solvent) and stationary phase (column); separate metabolite (change solvent type) over time via chemical differences
2) ionization (ESI); after separation, passed through opening connected to positive part of power supply (electrons go to power supply and to mass spectrometer); droplets shot to mass spectrometer; droplets evaporate; ionized molecules ejected into gas phase towards MS
3) mass analyzer; measures m/z ratio, signal intensity; can be calibrated to measure concentration, can see tiny mass differences
49
what causes nitrogen waste
amino acid degradation (eg deamination); AA metabolic rxns make toxic free ammonium (NH4+) ions; the liver processes this into urea
50
what reactions change whether glutamate has its amino group (eg deamination) and what is the result of this
transaminase: amino group transferred to alpha ketoglutarate to form glutamate
glutamate dehydrogenase: glutamate deaminated, leaving ammonium
51
name the steps of the urea cycle
0: CPS-1 (carboamoyl phosphate synthetase 1)
1: ornithine transcarbamylase
2: argininosuccinate synthetase
3: argininosuccinase
4: arginase
52
describe the initial step of the urea cycle (step 0)
CPS 1 step
enzyme CPS1 is in the mitochondrial matrix; binds free ammonium to bicarbonate; produces carbonyl phosphate, which then enters the urea cycle
multistep rxn in its specific pockets
1) activate bicarbonate with Pi via ATP to get labile intermediate carboxyphosphate
2) amino attack on carbonyl to get carbamic acid (another intermediate)
3) activate again w/ ATP to make carbamoyl phosphate, which enters the urea cycle
53
what is the role of CPS-1 in the urea cycle
primary regulation point for the cycle (step 0); allosterically activated by NAG (N-acetyl-glutamate), which is produced when glutamate is abundant during fasting/high protein diets
(NAG synthase uses acetyl-CoA to form NAG from glutamate, releases CoA-SH)
54
what is step 1 of the urea cycle
ornithine transcarbamoylase
combines ornithine (lysine but one CH2 shorter) and carbamoyl phosphate, forming citrulline and releasing Pi
55
what is step 2 of the urea cycle
argininosuccinate synthetase
uses ATP to add AMP to citrulline (2 ATP equivalent, release 2 phosphate)
aspartate from Asp transaminase used to remove AMP from citrullyl-AMP intermediate, forming argininosuccinate
citrulline + ATP + aspartate -> argininosuccinate + PPi + AMP
56
what is step 3 of the urea cycle
argininosuccinase (only reversible reaction in the cycle)
breaks argininosuccinate into arginine, as well as fumarate, which enters mitochondria for use in the TCA cycle
57
what is step 4 of the urea cycle
arginase
hydrolyzes arginine into ornithine and urea, which diffuses into blood for excretion by kidneys
restores ornithine so it can re-enter cycle in mitochondria
58
describe the net energetics of the urea cycle
CO2 + NH4 + 3 ATP + aspartate + 2 H2O -> urea + 2 ADP + 2 Pi + AMP + PPi + fumarate
consume 4 ATP, but produce 1 NADH from fumarate entering TCA which will produce 2.5 ATP
net 1.5 ATP consumed
59
what is a G6P dehydrogenase deficiency, what does it cause, and how is it treated
deficiency of enzyme Glucose 6-phosphate dehydrogenase, enzyme involved in the first committed step in the pentose phosphate pathway
this rxn makes NADPH, so this deficiency results in a lack of NAPH
this causes increased sensitivity to oxidative stress, but protects against malaria for nebulous reasons
treated by blood transfusion if anemic
60
what is GSD
Glycogen Storage Disease
different types caused by deficiencies of different enzymes involved in glycogen metabolism, disrupting glycogen breakdown or storage
61
what are the symptoms of GSD
glycogen storage disease can result in diff symptoms depending on the type; eg hypoglycemia
62
how is GSD treated
glycogen storage disease treated by managing blood glucose levels
63
how does lactose intolerance work
low levels of enzyme lactase (necessary to mobilize sugar for humans, suppressed in most mammals after infancy)
lactose consumed later in life is catabolized by microbes in large intestine, which release gas and acids, causing diarrhea
64
describe hereditary fructose intolerance
inability to break down fructose due to absence of the enzyme fructose 1-phosphate aldolase
causes low weight, hypoglycemia, vomiting
65
describe galactosemia
failure to break down galactose due to lack of certain enzymes (3 types; type 1 lacks galactose-1-phosphate uridyl transferase, type 2 lacks galactokinase, type 3 lacks UDP galactose 4-epimerase)
results in buildup of galactose/galactitol, symptoms vary by type
66
describe pyruvate dehydrogenase complex deficency
mitochondrial issue
mutation in any enzyme in PDH complex blocks the bridge reaction (pyruvate can't be converted to acetyl CoA to enter TCA cycle)
results in toxic buildup of lactic acid
causes neurological damage, low muscle tone, ataxia, microcephaly etc
treated with ketogenic diet
67
describe citrullinemia
citrulline unable to be converted to argininosuccinate
2 types, blocking either argininosuccinate synthetase (makes it from citrulline or aspartate) or citrin (Asp transporter that gets Asp out of mitochondria to make argininosuccinate in cytosol)
causes citrulline and ammonia buildup in blood and urine
symptoms vary by type; treated by low protein diet
68
describe PKU
stands for phenylketonuria
mutation in Phe hydroxylase or in cofactor THBP
causes buildup of Phe and phenylpyruvate
results in intellectual disabilities/behavioural issues
treated with low Phe diet, avoiding aspartame
69
describe maple syrup urine disease
inability to break down BCAAs due to mutation in branched-chain alpha-ketoacid dehydrogenase complex
results in BCAA/keto acid buildup in blood/urine
causes lack of energy and poor feeding
treated by monitoring ketones in urine and BCAAs in blood; low protein diet, vit B1 supplement, liver transplant
70
what is the precursor of melanin
tyrosine; converted via many rxn steps, 1st two using tyrosinase
lack of tyrosinase can cause albinism
71
how is epinephrine synthesized and what does it do
aka adrenaline; a neurotransmitter that mediates fight/flight response
synthesized from Tyr
72
how is norepinephrine synthesized and what does it do
aka noradrenaline; a neurotransmitter that mediates fight/flight response
synthesized from Tyr
73
how is dopamine synthesized and what does it do
neurotransmitter that stimulates pleasure feeling
synthesized from Tyr
74
what does histamine do and how is it made
involved in immune response by increasing permeability of capillaries, allowing white blood cells and fluid to come through
made from His via histidine carboxylase removing the carboxyl group at its end
75
what is GABA and how is it made
neurotransmitter involved in suppression signals in the brain (inhibitor)
made from Glu via GAD (glutamic acid decarboxylase); this is a part of the GABA shunt that converts alpha ketoglutarate into succinate for use in the TCA cycle
disruptions in GABA linked to anxiety/mood disorders, schizophrenia, autism, depression, epilepsy
76
how is serotonin synthesized
synthesized from Trp
77
how is melatonin synthesized
synthesized from serotonin, which is synthesized from Trp
78
what is the difference between purines and pyrimidines
purines are double ringed bases, pyrimidines are single ring
79
what bases are purines
adenine and guanine
80
what are is the precursor of purines
inosine
81
what is the end product of purine catabolism
uric acid
82
what is gout and what causes it
excess uric acid in blood (hyperuricemia) causing uric acid crystals to form in joints and inflame them
83
describe the purine catabolic pathway
start with ribonucleotides (AMP, IMP, XMP, GMP) and use nucleotidase to get the nucleosides (adenosine, inosine, xanthosine, guanosine;)
adenosine made into inosine by adenosine deaminase
then PNP (purine nucleside phosphorylase) used to get hypoxanthine from inosine, xanthine from xanthosine, and guanine from guanosine
hypoxanthine becomes xanthine via xanthine oxidase
guanine becomes xanthine via guanine deaminase
xanthine becomes uric acid by xanthine oxidase; excreted
84
what is SCID
severe combined immunodeficiency
adenosine deaminase deficiency from mutation causes buildup of deoxyadenosine in immature lymphocytes, killing them and hampering immune system
'bubble babies'
85
where does purine biosynthesis occur
cytosol
86
succintly describe the de novo pathway of purine synthesis
building purine ring directly from its building blocks (eg activated ribose PRPP + AA, ATP, CO2 etc)
87
succinctly describe the salvage pathway of purine synthesis
building nucleotide from existing parts (eg activated ribose PRPP + base)
88
what are the sources of the atoms of the purine ring in purine biosynthesis
aspartate (provides N), formate (provides 2 Cs), CO2 (provides 1 C), glycine (provides 2 Cs and 1 N), amide N of glutamine (provides 2 Ns)
Ns come from Gly, Gln, Asp
88
describe de novo purine nucleotide biosynthesis
10 step rxn
precursor is R5P (ribose 5-phosphate from PPP)
involves conversion of two N10-formyl-THF to THF
7 ATP equivalent for each IMP formed (will be converted to adenine or guanine)
89
describe AMP and GMP biosynthesis and why it works how it does
both made from IMP
GTP is used to synthesize ATP, and ATP used to make GMP
balances purine biosynthesis (don't use up ATP to make ATP)
90
describe the purine salvage pathway
recycle free purines from degraded nucleic acids, skipping most energy-intensive steps in de novo pathway
uses PRPP (phosphoribosyl diphosphate) to add ribose and make the monophosphate form, releasing PPi
for adenine -> AMP use adenine phosphoribosyl transferase
for hypoxanthine -> IMP and guanine -> GMP both use HGPRT (hypoxanthine-guanine phosphoribosyl transferase)
91
how is purine biosynthesis regulated
de novo synthesis regulated by negative feedback
low energy state (high GDP and ADP) shuts down biosynthesis (not enough energy to do it)
each nucleotide monophosphate inhibits the first step of its own synthesis
high amounts of purines inhibits 1st committed step of purine synthesis
92
what is the catabolic product of cytosine
beta-alanine
93
what is the catabolic product of cytosine
beta-alanine
94
what is the catabolic product of thymine
3-aminoisobutyric acid
95
describe how pyrimidines are degraded
start at nucleotides and break down to nucleosides with nucleotidase
turn cytidine to uridine with cytidine deaminase
turn uridine, deoxyuridine, and deoxythymine to uracil/thymine with uridine phosphorylase
96
what is the precursor of pyrimidines
orotate
97
succinctly describe pyrimidine anabolism
6 steps from bicarbonate to UMP
bicarbonate and NH3 use 2 ATP to become carbamoyl phosphate
carbamoyl phosphate gives 2 atoms (N and C) for pyrimidine ring, aspartate gives the other 4 (3C and 1N)
PRPP (a ribose phosphate) then is used to make UTP from it
98
describe the enzymes in de novo pyrimidine nucleotide biosynthesis of ribonucleotides
CAD protein involved in steps 1, 2, 3; domains are CPSII, ATCase (asp transcarbamoylase), and dihydroorotase
UMP synthase in steps 5, 6; orotate phosphoribosyltransferase, OMP decarboxylase
99
how is pyrimidine biosynthesis regulated
CPSII is the main regulatory enzyme in mammals (ATP and PRPP activate, UDP and UTP inhibit)
ATCase is the main regulatory enzyme in bacteria (ATP activates, UTP inhibits for most, CTP inhibits for E coli)
100
how are deoxyribonucleotides made
start with NDP (ADP, GDP, CDP), use ribonucleotide reductase to get dNDPs, further processed to dNTPs
101
describe RNR
enzyme that makes dNTPs from ribonucleotides
regulated allosterically by nucleotides (ATP, dATP, dTTP, dGTP etc)
102
what is the Warburg effect and why is it done
cancer cells have an increased rate of glucose uptake and use of fermentation to make lactate even when oxygen is plentiful
despite anaerobic metabolism being less efficient (only 4ATO per glucose rather than 36) it's much faster; used because the cells want to grow and divide as fast as possible
103
what are three large metabolic changes in cancer cells
Warburg effect; higher glucose uptake and use of fermentation regardless of oxygen conditions
glutamine metabolism: upregulated in cancer cells; used when sugar is exhausted; source of N for biosynthesis, C for TCA cycle, and precursor of glutathione, nucleotides, and lipids; upregulated in distal sites
albumin metabolism; take up and consume albumin from blood to get AAs
104
what happens when glutamine is depleted in cancer cells
autophagy to get nutrients
105
what are IDH mutants and how do they work
IDH mutants are enzymes in tumours that make 2-hydroxyglutarate from alpha-ketoglutarate
this promotes cancer progression via 2-HG competing with aKG, affecting processes like DNA demethylation, disrupting genetic regulation
2HG also helps inhibit Tet dioxygenases, also resulting in increased DNA methylation
106
what are clofarabine and fludarabine; how do they work
cancer medications; purine analogues that inhibit ribonucleotide reductase and inhibit DNA synthesis (when you make nucleic acids with it the chain becomes nonfunctioning and growing cell dies)
treats acute leukemia
107
what is 5-fluorouracil and how does it work
a pyrimidine analogue that treats several types of cancer
inhibits thymidylate synthase by binding to active site, which inhibits DNA replication since you can't make molecules needed to make deoxyribonucleotides
108
describe methotrexate and what it does
folate analogues for cancer treatment
competitively inhibits dihydrofolate reductase (DHFR); cell can't regenerate Me-THF, which is needed for the redox rxns used to make deoxyribonucleotides; inhibits DNA replication
109
describe Taxol/paclitaxel and what it does
isolate of pacific yew tree, Taxus brevifolia
treats several cancer types
stabilizes microtubules by preventing individual units from coming apart, preventing cells from rapidly dividing and also killing them
actual mechanism still being investigated
110
where do light rxns in photosynthesis take place
thylakoid membrane
111
what are dark rxns in plant cells and where do they take place
(calvin cycle); use light rxn products (reducing power and ATP) to reduce CO2 into glucose
happens in stroma
112
how do light reactions in plants work and what is the net reaction
photosystems 1 and 2
PS2 (PSII) oxidizes water and transfers electrons through cytochrome b6f; H go to ATP synthase to help make ATP
cytochrome b6f pumps H+ ions into thylakoid lumen
PS1 reduces NADP+ to NADPH
2 NADP+ + 3 ADP + 3 Pi + H+ --> O2 + 2 NADPH + 3 ATP + H2O
113
describe the calvin cycle
net 3 ATP + 2 NADPH --> 1 CO2, then 6CO2--> 1 hexose
1) carbon fixation via rubisco (rate limiting, slow); take up inorganic carbon
2) reduction; convert 2,3-phosphoglycerate to hexose phosphate, ultimately getting sucrose, starch, and cellulose
3) regeneration; regenerate rubulose 1,5-bisphosphate for more rubisco rxns
114
what is the difference between C3 and C4 plants
C4 plants eg sugarcane/corn are 50% more efficient, better for hot, high light environments; use Hatch-Slack pathway to convert CO2 to malate to transfer it to bundle-sheath cell from mesophyll; accelerates carboxylase rxn over photorespiration
115
what is CAM
crassulacean acid metabolism
done by certain C4 plants; separates CO2 accumulation and utilization by time, not spatially like other C4 plants
CO2 fixed to malate at night
in the day, malate decarboxylated to make CO2 for calvin cycle
grow slower (malate storage is limited)
116
what are plant secondary metabolites
help plants survive in their specific environments
3 major classes
1) terpenoids
2) phenolics
3) nitrogen & sulphur-containing compounds
117
describe terpenes
class of plant secondary metabolites
contain repeating 5C isoprene units
attract pollinators, defend from herbivores, resist disease, regulate growth, communicate w/ other plants
118
describe phenolics
class of plant secondary metabolites
contain at least one phenol
protect from oxidative stress, structural polymer, attract pollinators, protect from UV, pigmentation, signalling, resist disease, defend from herbivores
119
give an example of a nitrogen containing compound
capsaicin; defense from mammals and fungi
120
what is the kinetic isotope effect
higher activation energy for heavier isotopes, thus they will react slower
14C has a half life of 5730 years, so amount of 14C will show how old something is
121
describe the nitrogen cycle
nitrogen fixation: N2-->NH3
nitrification: NH4-->NO2-->NO3
denitrification: NO3-->N2
122
describe the nitrogenase complex
2 protein complex; reductase (Fe protein) and nitrogenase (MoFe protein)
transfer electrons from Fe to MoFe via ATP hydrolysis so MoFe can reduce N2 to NH3
hydrolyze 2 ATP per electron transferred; 8 e transferred so 16 ATP consumed per N2
net:
N2 + 8e + 8H + 16ATP + 16H2O ⇌ 2NH3 + H2 + 16 ADP + 16Pi
123
what is the glyoxylate shunt
pathway in plants, bacteria, and fungi to convert FAs/acetate to carbs
1) isocitrate lyase: isocitrate --> succinate + glyoxylate
2) malate synthase: glyoxylate + acetyl-CoA --> malate
124
what are ketone bodies used for
energy under starvation (acetone, acetoacetate, beta-hydroxybutyrate)
made from fatty acids (after beta oxidation) and ketogenic amino acids
transported to other cells via bloodstream
then in extrahepatic tissues, converted to acetyl-CoA to fuel TCA instead of glucose (downregulate glycolysis)
125
describe the hexokinase reaction
first reaction in the preparatory step of glycolysis
addition/elimination reaction; uses ATP to turn glucose to glucose 6-phosphate (G6P)
addition: OH on C6 of glucose attacks phosphate, pushing electron from the bond with the rest of ATP to a proton
elimination; ADP as leaving group
126
describe the phosphoglucose isomerase reaction
second reaction in the preparatory step of glycolysis;
isomerize G6P to make fructose 6-phosphate
ring opening: base extraction of H on the hydroxyl of C1; double bond forms on O, breaking the ring to form a carbonyl
move carbonyl from C1 to 2 with two base extractions, first on C2 and then on the OH on C2
OH on C5 attacks carbonyl on C2, foming 5 membered ring of fructose
127
describe the phosphofructokinase reaction
third reaction in the preparatory step of glycolysis
use ATP to add phosphate to C1 of fructose 6-phosphate to make fructose 1,6-bisphosphate
OH on C1 attacks phosphoryl on ATP, causing ADP to leave
128
describe the aldolase reaction
fourth reaction in the preparatory step of glycolysis
from fructose 1,6-bisphosphate, get GAP and DHAP
open ring, nucleophilic attack of lysine in the enzyme; form Schiff base intermediate and form GAP; reform schiff base and detach enzyme to get DHAP
129
describe the triose phosphate isomerase reaction
fifth reaction in the preparatory step of glycolysis
convert DHAP from previous reaction to GAP so you have two for the payoff/oxidation step; overall moves carbonyl from C2 to C1
convert keto to enol: base extraction of proton, electron pushed to make an alkene, double bond with O grabs a proton to make enol
convert enol to keto; base extraction to form carbonyl on first carbon, eliminate alkene to make GAP
130
describe the glyceraldehyde dehydrogenase reaction
first reaction in the payoff step of glycolysis after the preparatory step
use 1 NAD+ to oxidize GAP, forming 1,3-bisphosphoglycerate
1) sulfur on thiol from Cys of the enzyme attacks aldehyde group, forming intermediate
2) hydrogen donated to NAD+; base extraction to reform carbonyl, pushes electrons from H onto NAD+ to make NADH
3) inorganic phosphate attacks carbonyl, causing enzyme to leave and replacing it, forming 1,3-bisphosphoglycerate
131
describe the phosphoglycerate kinase
second reaction in the payoff step of glycolysis after the preparatory step
substrate-level phosphorylation; use 1,3-bisphosphoglycerate and ADP to make ATP and 3-phosphoglycerate
phosphate group of ADP acts as nucleophile, attacking phosphate on 1,3-bisphosphoglycerate to form ATP
132
describe the phosphoglycerate mutase reaction
third reaction in the payoff step of glycolysis after the preparatory step
overall moves phosphate on 3-phosphoglycertae to C2 using a phosphorylated histidine, making 2-phosphoglycerate
1) OH on C2 attacks phosphoryl on phosphorylated His, forming His and intermediate
2) His attacks phosphoryl on C3, so C3 phosphoryl goes to His, leaving 2-phosphoglycerate
133
describe the enolase reaction
fourth reaction in the payoff step of glycolysis after the preparatory step
overall form an alkene, leaving phosphoenolpyruvate
base extraction of H, forming alkene; electrons pushed from double bond of carbonyl onto O to form an intermediate; intermediate stabilized by Mg2+ ions in the enzyme
alkene moves, causing OH to grab proton and leave as water
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describe pyruvate kinase reaction
fifth reaction in the payoff step of glycolysis after the preparatory step
substrate level phosphorylation of ADP, leaving behind pyruvate
ADP attacks remaining phosphoryl from substrate; electrons from the bond being broken move to create carbonyl, alkene becomes alkane single bond
135
describe the lactate dehydrogenase reaction
performs lactic acid fermentation after getting pyruvate from glycolysis
overall reduce pyruvate to lactate and oxidize 1 NADH to NAD+
hydride attack on NADH by carbonyl; lone pair on N of NADH forms double bond, shifting alkene causing H to attack pyruvate's carbonyl, leaving NAD+
carbonyl O grabs proton, forming lactate
136
describe gluconeogenesis
reverse of glycolysis, mainly in liver and in cytoplasm of cells
2 pyruvate --> glucose
however steps 1, 3, and 10 in glycolysis are irreversible so diff enzymes are used for the reverse in gluconeogenesis
consumes more energy than glycolysis produces (4 ATP, 2 GTP, 2 NADH vs 2 ATP, 2 NADH)
137
why do animals use glycogen rather than storing glucose directly or storing starch/cellulose
glucose is water soluble, so water follows glucose when it enters cell, which raises osmotic pressure to a dangerous degree
glycogen has heavy branching, giving it more non reducing ends than starch (eg amylose has only one reducing end, amylopectin has a few) and cellulose; means glucose can be broken off one by one
138
what is glycogenin
primer enzyme in catalyzing first few glucose to form glycogen before other enzymes can elongate it
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