Biological Molecules

Gly, G
Non-polar Hydrophobic

pK_R = N/A
alpha carbon is achiral

Ala, A
Non-polar Hydrophobic

pK_R=N/A

Val, V
Non-polar Hydrophobic

pK_R= N/A

Leu. L
Non-polar Hydrophobic

pK_R= N/A

Ile, I
Non-polar Hydrophobic

pK_R= N/A

Pro, P
Non-polar Hydrophobic

pK_R= N/A

Adds rigidity to polypeptide
Imino acid

Phe, F
Non-polar Hydrophobic

pK_R= N/A
Aromatic; shows up in UV-spec

Trp, W
Non-polar Hydrophobic

pK_R= N/A

Aromatic; shows up most intense in UV-spec
precursor to seratonin and melatonin

Tyr, Y
Polar Hydrophilic

pK_R= 10

Phosphorylation
Aromatic; shows up on UV-spec

Ser, S
Polar Hydrophilic

pK_R= 13 (not easily ionized or deprotonated)

Phosphorylation on its side chain

Thr, T
Polar Hydrophilic

pK_R= 13

Phosphorylation on its side chain

Tyr, Y
Polar Hydrophilic

pK_R= 8

Disulfide bonds (tertiary/quaternary structure)
(sometimes non-polar, somewhere in between)

Met, M
Non-polar Hydrophobic

pK_R= N/A (no acidic H so no disulfide bridges)

encoded by start codon AUG found in mRNA

Lys, K
Basic

pK_R= 10.5, pI= 9.5

Important role in histones; can be acetylated

Arg, R
Basic

pK_R= 12

His, H
Basic

pK_R= 6 (neutral at phys. pH)

Imidazole functional group

Asp, D
Acidic

pK_R= 4
deprotonated at phys. pH (Aspartate); net charge of -1

can form Ionic bonds, acceptor in H bonding

Glu, E
Acidic

pK_R= 4
deprotonated at phys. pH (Glutamate); net charge of -1

can form Ionic bonds, acceptor in H bonding

Asn, N
Polar Hydrophilic

pK_R= N/A

Gln, Q
Polar Hydrophilic

pK_R= N/A

C6H12O6

C6H12O6

C12H22O11 (reducing sugar)

C12H22O11 (non-reducing sugar)

C12H22O11

C24H42O21

(C6H10O5)n

6 Carbons, glycolysis start

Glycolysis Step 1 -one way reaction, traps glucose in cell, 6 CARBONS
adds first phosphate

enzyme: Hexokinase

uses 1 ATP -> ADP

Glycolysis Step 2 -requires open/linear form intermediate to isomerase, 6 CARBONS
convert to fructose

enzyme: Phosphoglucoisomerase

Glycolysis Step 3 -one way reaction, rate limiting step, 6 CARBONS
adds second phosphate

enzyme: Phosphofructokinase

uses 1 ATP -> ADP

Glycolysis Step 4 -F16BP <-> G3P and DHAP, G3P: 3 CARBONS
breaks open/linear form of fructose in half (one phosphate to each)

enzyme: Aldolase

Glycolysis Step 5 - this step produces a second G3P for phase 2 of glycolysis, DHAP: 3 CARBONS
reason why 1 glucose makes 2 pyruvate

enzyme: Triose Phosphate Isomerase (TPI)

Glycolysis Step 6 -redox reaction (first release of high energy electrons); oxodative phosphorylation (ADP + Pi), 1-3BPG: 3 CARBONS
adds a phosphate to each G3P

enzyme: Glyceraldehyde-3 Phosphate Dehydrogenase

makes 2 NADH + 2 H+ (cuz 2 G3Ps)

Glycolysis Step 7 -substrate level phosphorylation (ADP + molecule), 3PG: 3 CARBONS
extracts first phosphate to make ATP (from each 1-3BPG)

enzyme: Phosphoglycerate Kinase

makes 2 ATP (cuz 2 1-3BPGs)

Glycolysis Step 8 -mutate phosphate to middle C, 3 CARBONS
2-3 BPG: stable intermediate; signals HGB to bring O2

enzyme: Phosphoglycerate Mutase

Glycolysis Step 9 - convert to enol, 3 CARBONS

enzyme: Enolase

produces 2 H2O (cuz 2 2PGs)

Glycolysis Step 10 - one way reaction (big energy release), substrate level phosphorylation (ADP + molecule), 3 CARBONS
extract second phosphate to make ATP (from each PEP)

enzyme: Pyruvate Kinase

makes 2 ATP and 2 pyruvate (cuz 2 PEPs)

pyruvate -> lactate from fermentation

3 CARBONS

Pyruvate -> Acetyl CoA during pyruvate dehydrogenase complex (PDC)
(produces NADH and CO2) (x2 since 2 pyruvate from glycolysis)

start of citric acid cycle

2 CARBONS (for ONE pyruvate)

added to oxaloacetate at start (2 + 4)

Step 1 Citric Acid Cycle

Acetyl CoA + Oxaloacetate -> Citrate
hydrolysis/ breaking of CoA-SH from C powers reaction

enzyme: Citrate Synthase

6 CARBONS
acetyl coA added to oxaloacetate at start (2 + 4)

Step 2 Citric Acid Cycle

Citrate -> Isocitrate
rearrangement - dehydration and hydration reaction with intermediate (Cis-Aconitase) in between

enzyme: Aconitase

6 CARBONS

Step 3 Citric Acid Cycle

Isocitrate -> alpha-ketoglutarate
oxidative decarboxylation (middle carboxyl leaves), produces NADH + CO2

enzyme: Isocitrate dehydrogenase

5 CARBONS

Step 4 Citric Acid Cycle

alpha-ketoglutarate -> Succinyl-CoA
oxidative decarboxylation (bottom carboxyl leaves, adds S-CoA in its place), produces NADH + CO2

enzyme: alpha-ketoglutarate dehydrogenase

4 CARBONS

Step 5 Citric Acid Cycle

Succinyl-CoA -> Succinate
breaking SH-CoA and C bond drives phosphorylation of GDP, produces GTP

enzyme: Succinyl-CoA synthetase

4 CARBONS

Step 6 Citric Acid Cycle

Succinate -> Fumarate
dehydrogenation, an H leaves from EACH of the two middle CH2s, produces FADH2

enzyme: Succinate Dehydrogenase

4 CARBONS

Step 7 Citric Acid Cycle

Fumarate -> Malate
hydration reaction, adds H2O (lower CH gets an H and the top CH gets an OH)

enzyme: Fumarase

4 CARBONS

Step 8 Citric Acid Cycle

Malate -> Oxaloacetate
dehydrogenase reaction, produces NADH

enzyme: Malate Dehydrogenase

4 CARBONS
acetyl coA added to oxaloacetate at start (2 + 4)

nicotinamide adenine dinucleotide

Flavin adenine dinucleotide

adenosine tri phosphate (nucleoside naming in order to know the exact number of phosphates attached)

cyclic adenosine mono phosphate

end product of oxidative phase of pentose phosphate pathway (PPP) - 5 CARBONS

start of non-oxidative phase of pentose phosphate pathway (PPP) - 5 CARBONS

regulates fatty acid synthesis (rate determining itntermediate) and oxidation (allosteric inhibitor)

2 Acetyl CoA combined (ketogenesis), precursor to ketones (BHB and acetone)

ketone produced by liver in ketogenesis, used in brain to regenerate acetyl-CoA

BHB, ketone produced by liver in ketogenesis, used in brain to regenerate acetyl-CoA

reduced form of quinone, precursor of coenzyme Q

AKA: coenzyme Q, part of the ETC; reduced by NADH to its hydroquinone form, Ubiquinol.

quinone; easily reversed oxidized form of hydroquinone, precursor of coenzyme Q

picture is ethyl acetate

"benzyl is bigger"

O/N are opposite from the name

O/N are opposite from the name

acetic acid

H3PO4

H3PO3