Biochemistry of Metabolism

Index of Key-words

A,  B,  C,  D,  E,  F,  G,  H,  I,  J,  K,  L,  M,  N,  O,  P,  Q,  R,  S,  T,  U,  V,  W,  X,  Y,  Z

14-3-3
A

AAA ATPase - of dynein motor domain

alpha, beta barrel (TIM barrel)
acceptor stem  - of tRNA
acetaminophen

acetoacetate (ketone body)
acetyl-coenzyme A (acetyl-CoA)
acetyl-CoA carboxylase - role in synthesis of malonyl-CoA
acetylglutamate - activator of carbamoyl phosphate synthase
N-acetylglucosamine
N-acetylglucosamine as O-linked glycosylation
N-acetylneuraminate
actin
actin cytoskeleton - regulation
actin-related proteins
a-actinin

active transport
acute hepatic porphyria
acyl carrier protein domain - in fatty acid synthase
acyl-CoA dehydrogenase
acyl-CoA synthase (fatty acid activation)
adenine

adenine nucleotide translocase (ADP/ATP antiporter)
adenosine triphosphate (ATP)
S-adenosylmethionine (SAM)

adenylate cyclase

adenylate kinase

ADP ribosylation of G_a
AGS (Activator of G-protein Signaling) protein

AKAP (A kinase anchoring protein)

Akt (protein kinase B)
ALA (d-aminolevulinate)

alanine
alanine transaminase
albumin (serum)

aldolase

aldose vs ketose

alpha helix
ameboid movement

amino acids
amino acid metabolism - amino N
amino acid metabolism - carbon skeletons
aminoacyl tRNA synthetases
d-aminolevulinate (ALA)
aminotransferase (transaminase)
AMP-activated protein kinase: regulation of fatty acid catabolism
AMP-activated protein kinase: regulation of fatty acid synthesis

AMPPNP (ATP analog)

amylopectin
angiogenesis - promotion by COX-2

anomer

antiport
apolipoprotein A-I (of HDL): structure
apoptosome (activator of apoptosis)
arachidonate - precursor for prostaglandin synthesis
arginase

arginine
argininosuccinase
argininosuccinate synthase
Arp1
Arp2/3
asparaginase

asparagine

aspartate
aspartate proteases
aspartate transaminase
aspirin
atherosclerosis

ATP (adenosine triphosphate)

ATP analog

ATP Synthase (F₁F_o)
autophagy

avidin
axoneme

B

base pairs - between complementary nucleotide bases (e.g., G-C)
bases - in RNA
beta oxidation pathway: mitochondrial fatty acid catabolism
beta oxidation pathway: peroxisomal pathway
beta propeller (in G_b)

beta pleated sheet
bilayer (lipid membrane)
bile acid (bile salt)
BimC

binuclear center of cytochrome oxidase

bioenergetics

biotin - in pyruvate carboxylase
biotin - in acetyl-CoA carboxylase

1,3-bisphosphoglycerate

C

C₃ vs C₄ plants
Ca⁺⁺-ATPase of ER membranes (SERCA)

Ca⁺⁺-binding proteins

Ca⁺⁺ release channel, IP₃-activated

Ca⁺⁺ release channel, ryanodine receptor

Ca⁺⁺ signals

calmodulin
calpain
calpain - regulation of actin cytoskeleton
Calvin cycle (photosynthetic dark reaction)
Calvin cycle - regulation

cAMP (cyclic AMP)

cAMP signal cascade in regulation of glycogen metabolism

cAMP-dependent protein kinase (protein kinase A)

cAMP signals
capZ
carbamate (in RuBisCO)
carbamoyl phosphate synthase

carbohydrate
carboxyarabinitol-1,5-bisphosphate (CABP)
carnitine acyl transferase (fatty acid transport)
carnitine palmitoyl transferase

carrier
caspase
cathepsin

caveolae
caveolin
Cdc42

cellulose
centriole
centrosome (microtubule organizing center)

ceramide

channel (ion channel)

channel gating

channel - K⁺

chemiosmotic theory
chloroplast

cholera toxin

cholesterol (structure)

cholesterol (synthesis)
cholesteryl ester
ChREBP (carbohydrate responsive element binding protein)
chylomicron
chymotrypsin
cilia & flagella

citric acid cycle (Krebs cycle)
CO₂ fixation by RuBP Carboxylase

coenzyme A (CoA)
coenzyme B₁₂ (vitamin B₁₂)

coenzyme Q (CoQ)

coenzyme Q - role in Q cycle
cofilin
colchicine

complex I (NADH dehydrogenase)

complex II (succinate dehydrogenase)
complex III (bc₁ complex)

complex IV (cytochrome oxidase)

Cori cycle
COX-1 & COX-2 (cyclooxygenases 1 & 2)
COX-3

creatine kinase

cyclic AMP (cAMP)

cyclic AMP signal cascade (regulation of glycogen metabolism)

cyclic AMP-dependent protein kinase (protein kinase A)

cyclic AMP & cell signaling
cyclooxygenase (PGH₂ Synthase)
cystatin

cysteine
cysteine proteases
cytochalasin

cytochrome

cytochrome oxidase (complex IV)
cytochrome P₄₅₀ - role in synthesis of cholesterol
cytochrome P₄₅₀ epoxygenase
cytosine

D

dark reaction - Calvin cycle
DCCD (dicyclohexylcarbodiimide, ATP synthase inhibitor)

debranching enzyme (glycogen debranching)

diacylglycerol

dicyclohexylcarbodiimide (DCCD, ATP synthase inhibitor)

dihydroxyacetone phosphate
dimethylallyl pyrophosphate

2,4-dinitrophenol
dipyrromethane

disaccharide
dolichol pyrophosphate
dynactin
dynamic instability of microtubules
dynamitin
dynein

F

F₁ subunit composition

F₁ crystal structure

F_o subunit composition

F₁F_o (ATP Synthase)
F-actin
Fab fragments - use in crystallizing K⁺ channel

FAD (flavin adenine dinucleotide)
FAK (focal adhesion kinase)
familial hypercholesterolemia
farnesyl pyrophosphate - synthesis
farnesyl pyrophosphate - precursor for synthesis of isoprenoids

fatty acid
fatty acid activation (acyl-CoA synthase)
fatty acid binding protein

fatty acid catabolism (b-oxidation pathway)
fatty acid elongation & desaturation
fatty acid oxidation: summary & stoichiometry
fatty acid synthase
fatty acid transport (carnitine acyl transferase)

fermentation
ferrochelatase
ferroportin

Fe-S (iron-sulfur center)
filamin
filopodia
flagella
FLAP (5-lipoxygenase-activating protein)

flavin mononucleotide (FMN)

flip flop

fluidity (membrane fluidity)

FMN (flavin mononucleotide)
focal adhesion
focal adhesion kinase (FAK)
formin

fructose

fructose-1,6-bisphosphatase

fructose-1,6-bisphosphate

fructose-2,6-bisphosphate

fructose-6-phosphate
FtsZ

G

G_abg

G_a structure

G_b structure
G-actin

GAP (GTPase activating protein)

gating (channel gating)

GEF (guanine nucleotide exchange factor)
gelsolin
genetic code
geranyl pyrophosphate
GlcNAc (N-acetylglucosamine)

GlcNAc as O-linked glycosylation
glucogenic amino acids

glucokinase

gluconeogenesis

gluconeogenesis summary
glucosamine

glucose

glucose-1-phosphate

glucose-6-phosphatase

glucose-6-phosphate

glucose-6-phosphate dehydrogenase
glucose-6-phosphate dehydrogenase - regulation
glued

glutamate
glutamate dehydrogenase

glutamine
glutathione
glyceraldehyde-3-phosphate - formation in Calvin cycle

glyceraldehyde-3-phosphate dehydrogenase
glycerol catabolism

glycerophospholipid

glycine

glycogen

glycogen debranching

glycogen metabolism

glycogen metabolism regulation

glycogen phosphorylase

glycogen phosphorylase structure

glycogen storage diseases

glycogen synthesis

glycogenin

glycolysis

glycolysis - pathway summary

glycolysis - regulation of pathway

glycoprotein

glycosaminoglycan

glycosidic bond

G-protein signal cascades

G-protein coupled receptor (GPCR)

gramicidin

GTPase activating protein (GAP)

GTP-binding proteins (small GTP-binding proteins)

GTPgS
guanine

guanine nucleotide exchange factor (GEF )

H

H⁺ transport linked to respiration

H⁺ transport linked to ATP synthesis
HDL (high density lipoprotein)
helicase (role in translation)

a-helix

a-helix, transmembrane

heme

heme a

heme c
heme synthesis
hemochromatosis
heparan sulfate
heparin
hepcidin

heterotrimeric G-protein

hexokinase

hexose monophosphate shunt
high density lipoprotein (HDL)

"high energy" bonds

histidine
histidine catabolism
homocysteine
HMG-CoA (hydroxymethylglutaryl-coenzyme A)
HMG-CoA Reductase
HMG-CoA Reductase - regulation
5-HPETE
hyaluronate

hydropathy plot

hydropathy plot: studio exercise
hydroxyacyl-CoA dehydrogenase
b-hydroxybutyrate (ketone body)
b-hydroxybutyrate dehydrogenase
hydroxylation - role of cytochrome P₄₅₀
hydroxymethylbilane
hydroxymethylglutaryl-coenzyme A (HMG-CoA)
hyperammonemia
hypercholesterolemia

I

ibuprofen
I-CLiPs
inactivation - K⁺ channel
initiation factors (initiation of protein synthesis)

integral protein
integrin
integrin-linked kinase

ion channel

ionophore

inositol-1,4,5-trisphosphate (IP₃)
Insig
intraflagellar transport

IP₃-activated Ca⁺⁺ release channel

IP₃ (inositol-1,4,5-trisphosphate)
IRES (internal ribosome entry site)

iron-sulfur center (Fe-S)

isoleucine
isomerase
isopentenyl pyrophosphate
isoprene

L

lactate dehydrogenase
lactose permease
lamellipodia
lanosterol - formation
lanosterol - conversion to cholesterol

lateral mobility
LDL (low density lipoprotein)
LDL receptor

lectin

leucine
leukotriene

lipid
lipid anchor
lipid digestion & transport

lipid rafts

lipid rafts & signal complexes

lipoamide
lipoprotein
lipoxygenase
liquid crystal state of lipid membranes
LIS1
low density lipoprotein (LDL)

lysine
lysophospholipid
lysosome

M

malonyl-CoA: precursor for fatty acid synthesis
malonyl-CoA: role in regulation of fatty acid oxidation
mannan-binding lectin
MAPs (microtubule associated proteins)
matrix metalloprotease (MMP)
membrane fluidity

membrane proteins
metalloprotease

methionine
methionine metabolism
methylated bases in RNA (e.g., methylguanine)
methylmalonyl-CoA mutase
mevalonate
microtubule
microtubule associated proteins (MAPs)
microtubule organizing center (centrosome)
microtubules - dynamic instability

mid-point potential (E^o')
miRNAs

mitochondrial compartments
mixed function oxidation: cytochrome P₄₅₀
mixed function oxidation: fatty acid desaturase

monosaccharide

micelle
myosin
myosin I
myosin II
myosin II reaction cycle
myosin V
myosin VI
myosin light chain kinase

N

NAD⁺

NADP⁺
NADH dehydrogenase (complex I)
Nedd8
nexin
Nitric oxide synthase (NOS)

N-linked oligosaccharide
nocodazole
norepinephrine (methylation)
NOS (nitric oxide synthase)
NSAID (non-steroidal anti-inflammatory drug)
nucleic acid
nucleotide

O

oligomycin (ATP synthase inhibitor)

ornithine/citrulline transporter
ornithine transcarbamylase
OSCP (oligomycin sensitivity conferral protein)

oxidative phosphorylation

P

~P

P₄₅₀ - role in synthesis of cholesterol
paddles - K⁺ channel voltage sensors
patch clamp

patch clamp studio exercise
PBG (porphobilinogen)

P-class ion pump

pentose phosphate pathway

pentose phosphate pathway - alternative metabolic scenarios

pentose phosphate pathway - regulation

PEP carboxykinase
PEP carboxylase - role in C₄ plants

peptide bond
peptide bond synthesis (transpeptidation)
peroxisomes: role in fatty acid oxidation

pertussis toxin
PGH₂ (prostaglandin H₂)
PGH₂ Synthase (cyclooxygenase)

phalloidin
phenylalanine
phenylalanine hydroxylase
phenylketonuria

phosphate carrier (mitochondrial)
phosphate esters: free energy of hydrolysis

phosphatidate

phosphatidylcholine

phosphatidylinositol

phosphatidylinositol-4,5-bisphosphate (PIP₂)

phosphatidylinositol-3-phosphate

phosphatidylinositol signal cascades
phosphoanhydride linkages: free energy of hydrolysis

phosphocreatine

phosphodiesterase

phosphoenolpyruvate formation

phosphoenolpyruvate (PEP) as phosphate donor

phosphofructokinase

phosphofructokinase 2/fructose bisphosphatase 2 (PFK2/FBPase2)

phosphoglucomutase
6-phosphogluconate
phosphogluconate dehydrogenase

phosphogluconate pathway
6-phosphogluconolactone

phosphogluconolactonase

phosphoglucose isomerase

3-phosphoglycerate

phosphoglycerate kinase
phosphoglycolate
phospholipase A₂ - role in arachidonate release
phospholipase A₂ - formation of lysophospholipid

phospholipase C
phosphopantetheine - in fatty acid synthase acyl carrier protein domain

phosphorylase

phosphorylase kinase - regulation by Ca⁺⁺

phosphorylase structure
photorespiration
photosynthetic dark reaction (Calvin cycle)
photosynthetic dark reaction - regulation
PI-3 Kinase

PIP₂ (phosphatidylinositol-4,5-bisphosphate)

b-pleated sheet

pleckstrin homology domain

PLP (pyridoxal phosphate) - in glycogen phosphorylase
PLP - in transaminase
PMP (pyridoxamine phosphate) - in transaminase

polyamines
polyphosphate

polysaccharide

porin
porphobilinogen (PBG)
porphobilinogen deaminase
porphobilinogen synthase
porphyria
prenyl transferase
prenylation of proteins

primary structure of proteins
processive movement - of myosin V
profilin

proline
propionyl-CoA metabolism
prostaglandins
proteases
protease inhibitors
proteasome
protein degradation

protein kinase

protein kinase A (cAMP-dependent protein kinase)

protein kinase B (Akt)

protein kinase C

protein phosphatase

protein primary structure

protein quaternary structure

protein secondary structure
protein synthesis

protein structure

protein tertiary structure

proteoglycan
protofilament - in microtubule structure

proton transport linked to respiration

proton wire
protoporphyrin IX
pseudouracil
putrescine

pyridoxal phosphate (PLP) - in glycogen phosphorylase
pyridoxal phosphate (PLP) - in transaminase
pyridoxamine phosphate (PMP) - in transaminase
pyrrole

pyruvate carboxylase

pyruvate carboxylase animation

pyruvate dehydrogenase

pyruvate dehydrogenase - regulation

pyruvate kinase

Q

Q cycle

quaternary structure of proteins

Rac
rafts (lipid rafts)
Ras
release factors

respiratory chain

respiratory control
Rho
Rho - signaling in ameboid movement

rhodopsin
Rho kinase
ribose-5-phosphate - synthesis
ribosome - structure
ribosome recycling factor (RRF)
ribulose-1,5-bisphosphate - role in Calvin cycle
ribulose-1,5-bisphosphate carboxylase (RuBisCO)
ribulose bisphosphate carboxylase activase
ribulose-5-phosphate - role in pentose phosphate pathway
ribulose-5-phosphate epimerase
ribulose-5-phosphate isomerase
Rieske iron-sulfur center (Fe-S)
RNA structure
ROCK (Rho kinase)

rotation in F₁F_o

rotor & stator in F₁F_o
RRF (ribosome recycling factor)

RuBisCO (RuBP Carboxylase/Oxygenase)
RuBisCO - subunit composition

RuBP carboxylase
RuBP carboxylase activase
ryanodine receptor (Ca⁺⁺ release channel)

S

SAM (S-adenosylmethionine)
scanning (during eukaryotic translation initiation)

SCAP (SREBP cleavage activating protein)
Scar (WAVE)
secondary structure of proteins
sedoheptulose-7-phosphate - role in pentose phosphate pathway
selectin

selectivity of K⁺ channel
selenocysteine tRNA

SERCA (Ca⁺⁺-ATPase)

serine
serine dehydratase
serine proteases
serpins

b-sheet
sialic acid

signal transduction cascades

SMP (submitochondrial particle)
spectrin
spermidine

sphingolipid

sphingomyelin

sphingosine
squalene
SREBP (sterol response element binding protein) - activation

SREBP - role in regulation of cholesterol synthesis
SREBP - role in regulation of fatty acid synthesis
stathmin
statin drugs
stress fiber

submitochondrial particle (SMP)

succinate dehydrogenase (complex II)

sugar
Sulfs

symport

T

taxol
termination of protein synthesis
tertiary structure of proteins
tetrahydrobiopterin
tetrahydrofolate (THF)
tetratrico peptide repeats (TPRs) - of kinesin light chains

thermogenin (uncoupling protein)

thiamine pyrophosphate (TPP)

thioester
thiokinase (acyl-CoA synthase)
thioredoxin

threonine
thymosin

TIM barrel (ab barrel)
+TIPs

TPP (thiamine pyrophosphate)
TPP - role in transketolase
tRNA - structure
transaldolase
transaminase (aminotransferase)
transferrin
transketolase
translation (protein synthesis)
translation in eukaryotes
transpeptidation (peptide bond synthesis)
treadmilling in actin filaments

triosephosphate isomerase (TIM)
trypsin

tryptophan
tubulin - a,b heterodimer
g-tubulin ring complex
twinfilin

tyrosine

W
WASP/Scar
WAVE

zinc proteases

A,  B,  C,  D,  E,  F,  G,  H,  I,  J,  K,  L,  M,  N,  O,  P,  Q,  R,  S,  T,  U,  V,  W,  X,  Y,  Z