Simple sugars / sugar phosphates:

Glucose

Glucose-6-phosphate

3-Phosphoglycerate

Ribose-5-phosphate

Metabolic intermediates

Pyruvate

Acetyl-CoA

α-Ketoglutarate

Oxaloacetate

Amino acids:

Glutamate

Glutamine

Cysteine

Methionine

ATP

GTP

CTP

UTP

Shikimate pathway

Nitrogenous bases (A, U, G, C)

Ribose sugar

Phosphate groups

Nucleotides

dATP

dTTP

dGTP

Codons

nucleic acids

TTAGGG

Histones

Polypeptide chain

Proteins:

Cytochrome c

RuBisCO

p53

Caspases

Cyclins

BDNF

GPCRs

Rhodopsin

Antibodies (Immunoglobulins)

ATP Synthase

DNA Polymerase

RNA Polymerase

Ribosome Complex

Mitochondrial DNA

Ribonucleotides

Ribonucleotide Diphosphates (NDPs)

NTPs

dNTPs

Pentose phosphate pathway

D-Loop

Origin of Heavy-strand replication

LSP (Light-strand promoter)

7S DNA

Ribosomal RNA Genes

12S rRNA

16S rRNA

POLG

TWINKLE helicase

mtSSB

POLRMT

TFAM

TFB2M

HSP

ND1

ND2

ND3

ND4

ND4L

ND5

ND6

CYB (cytochrome b)

COX I

COX II

COX III

ATP6

ATP8

Complex I (NADH dehydrogenase)

Complex III

Complex IV

Complex V (ATP synthase)

Chromosomes

Atomic / Chemical Components

Central Atom

Phosphorus (P)

Oxygen Atoms

Phosphoryl oxygen

Hydroxyl oxygens

Phosphate Group (PO₄³⁻) Parts

Nitrogenous bases

Purines

Pyrimidines

β-alanine

β-aminoisobutyrate

Deoxyribose sugar

Phosphate groups

Molecular Units / Precursors

Base + Ribose → Nucleoside

Nucleoside + Phosphate → Nucleotide

Nucleotides

dNTPs

NTPs

PRPP → IMP → AMP/GMP

PRPP + carbamoyl phosphate → UMP → CMP/TMP

Metabolic conversion

DNA / RNA Building Blocks

Phosphodiester bond

Nucleotide (Basic Unit)

Conversion into nucleotides

DNA Structural Features

DNA structures

Double helix

Deoxyribose sugar

Phosphate group

Major groove

Minor groove

Antiparallel Strands

DNA Sequence and Coding Units

DNA sequences

Codons

Genes

Promoter

Start Codon

ATG

Exons

Introns

Stop Codon

TAA, TAG, or TGA

Enhancers

Silencers

Operators

Telomeres

TTAGGG

G-rich strand

Complementary C-rich strand (AATCCC)

Double-Stranded Telomeric Region

3′ Single-Stranded Overhang

T-Loop Structure

Shelterin Complex (Protein Cap)

TRF1

TRF2

POT1

TIN2

TPP1

RAP1

Telomerase

TERT

TERC

Centromeres

Centromeric DNA

Alpha-satellite DNA

CENP-A Nucleosomes

Cohesin complexes

Chromosomal Passenger Complex

Pericentromeric Region

Heterochromatin

Origins of replication

Origin Recognition Complex (ORC)

AT-Rich Region

Cdc6

Cdt1

MCM helicase complex

Replication Bubble

Histone Proteins

H2A

H2B

H3

H4

H1

Histone Octamer

Linker DNA

Nucleosomes

Histone Tails

Acetylation

Methylation

Phosphorylation

Ubiquitination

Chromatin Fiber

Euchromatin

Heterochromatin

Higher-Order Chromatin Structures

Chromatin fiber (30 nm fiber)

Folding Arrangement

Solenoid Model

Zig-Zag Model

Looped domains

Loop Base (Anchor Points)

Scaffold / Matrix Attachment Regions (SARs/MARs)

Cohesin complex

CTCF (CCCTC-binding factor)

Topologically Associating Domains (TADs)

CTCF (Architectural Protein)

Chromosome Scaffold

Condensed metaphase chromosome

Topoisomerase II (relieves supercoiling)

Metaphase Chromosome Shape

Sister chromatids

Centromere

Telomere

Kinetochore

CENP-A nucleosomes

CENP-C, CENP-T

KMN Network: Knl1 complex, Mis12 complex, Ndc80 complex

Fibrous Corona

MAD1, MAD2, BUB1, BUBR1

Aurora B kinase

PLK1

Dracae Tree DNA

Individual mitochondrial genes (protein-coding)

cox1, cox2, cox3

cob – cytochrome b

atp1, atp4, atp6, atp8, atp9

nad1, nad2, nad3, nad4, nad4L, nad5, nad6, nad7, nad9

Individual rRNA genes

5S rRNA

18S rRNA

26S rRNA

Nuclear DNA

Chloroplast DNA

Photosynthesis genes (protein-coding)

Photosystem II (PSII) subunits:

psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT

Photosystem I (PSI) subunits:

psaA, psaB, psaC, psaI, psaJ

Cytochrome b6f complex subunits:

petA, petB, petD, petG, petL, petN

ATP synthase subunits:

atpA, atpB, atpE, atpF, atpH, atpI

Multi-subunit protein complexes

Photosystem II (PSII) – large light-harvesting complex.

Photosystem I (PSI) – large light-harvesting complex.

Cytochrome b6f complex – multi-subunit electron transport complex.

ATP synthase – multi-subunit enzyme complex for ATP production.

Neurotransmitters

Glucose

3-Phosphoglycerate

α-Ketoglutarate

Succinyl-CoA

Acetyl-CoA

Glutamate

Glutamine

GABA

Glycine

Serine

Cysteine

δ-Aminolevulinic acid (ALA)

Nucleotides / Energy Carriers

ATP

ADP + Pi

AMP + PPi

AMP

cAMP

Adenine

Ribose-5-Phosphate

Adenosine

β-N-glycosidic bond

Triphosphate

Enzymes / Catalytic Proteins

Glutamate dehydrogenase (GDH)

Glutamine synthetase / Glutaminase

Endopeptidases (e.g., neprilysin)

Aminopeptidases

Carboxypeptidases

Phospholipase C

Amino Acid Precursors to Neurotransmitters

Phenylalanine

Tyrosine

L-DOPA (Levodopa)

Dopamine

Norepinephrine

Adrenaline

Tryptophan

5-Hydroxytryptophan

Serotonin (5-HT)

N-Acetylserotonin

Melatonin

Histidine

Histamine

Choline

Acetylcholine

Antioxidants / Cofactors

Glutathione (GSH)

Antioxidant

NMDA co-agonist

Peptide Hormones / Neuropeptides — Precursors

TAC1 gene → preprotachykinin A mRNA → Preprotachykinin A (PPT-A) → Sequence: Arg–Pro–Lys–Pro–Gln–Gln–Phe–Phe–Gly–Leu–Met–NH₂ → TAC1 mRNA → Substance P

POMC (precursor of endorphins)

Proenkephalin / PENK / PDYN → Enkephalins (Tyr–Gly–Gly–Phe–Met / Tyr–Gly–Gly–Phe–Leu) → μ-opioid / δ-opioid

NPY gene → Prepro-NPY → Neuropeptide Y (NPY) → GPCRs: Y1, Y2, Y4, Y5, Y6

Peptide Hormones — Oxytocin & Vasopressin

OXT gene → Prepro-oxytocin → Oxytocin sequence (Cys–Tyr–Ile–Gln–Asn–Cys–Pro–Leu–Gly) → OXTR → MAPK pathways

AVP gene → Vasopressin sequence (Cys–Tyr–Phe–Gln–Asn–Cys–Pro–Arg–Gly) → V1 Receptor / V2 Receptor / V1b/V3 Receptor → MAPK pathways

Structural Hierarchy (Small → Large / Simple → Complex)

Rhodopsin

Small Molecules / Atomic-Level Components

Lys296

11-cis-retinal

all-trans-retinal

Schiff base

Post-Translational Modifications

Glycosylation (N-terminal)

Palmitoylation (C-terminal tail)

Phosphorylation

Protein Domains / Structural Units

Opsin Protein (Apoprotein)

Seven transmembrane α-helices / Transmembrane Helices (TM1–TM7)

Extracellular N-terminus

Cytoplasmic C-terminus / Cytoplasmic C-Terminus

Extracellular loops

Cytoplasmic loops

Scaffold / Membrane Organization

GPCR scaffold

Photoreceptor membrane

Protein Interactions / Signaling Partners

Arrestin

Rhodopsin kinase

Transducin (G-protein)

Phosphodiesterase (PDE)

Functional Complexes / Processes

Rhodopsin–transducin complex

Downstream phototransduction

cGMP hydrolysis

RuBisCO

Atomic / Chemical Components

Lysine

Aspartate, Glutamate, Histidine

Phosphate Groups

Hydroxyl Groups (-OH)

C2 carbonyl group

Phosphate oxygens

Magnesium ion (Mg²⁺)

Molecular Modifications / Reactive Forms

Carbamate (from Lys201)

Carbamylation of Lys201

Enolization

Small Molecules / Substrates

Ribulose-1,5-bisphosphate (RuBP)

5-carbon ketopentose (ribulose)

Positions C1 and C5 phosphates

3-phosphoglycerate (3-PGA)

Protein Secondary Structures / Motifs

β/α Barrel (TIM Barrel) Structure / β/α barrel (TIM barrel)

8 α-helices and 8 β-strands

β-Sheet Core

Four-stranded β-sheets

α-Helices

Protein Domains / Subunit Features

N-Terminus

Cytoplasmic-facing region

Transit peptide sequences

C-Terminus

Small subunits (RbcS) / Small Subunit (SSU / RbcS)

Chloroplast transit peptide

Chloroplast stroma

Subunit Interfaces / Binding Sites

Cofactor binding site (Mg²⁺, carbamate)

Active site residues: Lys201, Asp203, Glu204, His294

LSU–LSU interfaces

LSU–SSU interfaces

LSU–SSU interactions

Oligomers / Quaternary Structures

Large Subunit (LSU / RbcL) / RbcL

L2 Dimer

Lx Oligomers

L8S8 holoenzyme

Quaternary structure

RuBisCO activase

CO₂ + RuBP → 2 × 3-phosphoglycerate (3-PGA) reaction

Receptors - Common Anatomy

α-helices

β-sheets and loops

Disulfide bonds

Ligand recognition residues

Ligand-binding pocket

Phosphorylation sites

Protein interaction motifs

G-protein coupling regions

Trafficking signals

Regulatory phosphorylation sites

Anchoring/scaffolding interaction sites

7 α-helices

Transmembrane Domains

Extracellular Loops

ECL1

ECL3

Extracellular / Ligand-Binding Domain (LBD)

Intracellular Loops / Cytoplasmic Domains

Cytoplasmic C-Terminus

G-proteins (GPCRs)

Kinases

Phosphatases

Scaffolding proteins

Intracellular signaling molecules

Ion flux (ionotropic receptors)

Intracellular signaling

Adrenaline Receptors

Catechol hydroxyl (-OH) group

Catechol ring

Catecholamines

Serine residues in TM5

Negatively charged aspartate residue in TM3 (Asp³·³²)

Catecholamine-Specific Binding Pocket

Extracellular Loop 2 (ECL2)

PKA phosphorylation sites

GRK phosphorylation clusters

Subtype-Specific Intracellular Loop 3 (ICL3)

β-Adrenergic Receptor Regulatory Tail

α₁ → couples to Gq

α₂ → couples to Gi

β receptors → couple to Gs

β-adrenergic receptors

Phosphorylation pattern

β-arrestin binding

Desensitization

Internalization

Resensitization

Low-affinity state (inactive)

High-affinity state (G-protein coupled)

Dopamine Receptors

Catechol ring

Aspartate residue in TM3 (Asp³·³²)

Serine residues in TM5

29–amino acid insertion in intracellular loop 3

GRK phosphorylation motifs

β-arrestin recruitment domains

Desensitization control regions

Affinity

Limbic localization

Unique intracellular loop 3 (ICL3) length

Long Intracellular Loop 3

Distinct C-terminal tail structure

Dopamine Binding Pocket (Catecholamine-Specific)

Different G-protein coupling signatures

β-arrestin signaling pathways

Excitatory pathways (Gs coupling)

Inhibitory pathways (Gi coupling)

D2S (short)

D2L (long)

D1

D2

D3

D4

D3/D4 receptors

D1 receptors

D2 receptors

D1-like family

D2-like family

DRD Subtype Variations (D1-like vs D2-like)

GABA Receptors

M2 transmembrane helices

β–α Interface

β and α subunit interaction

Coiled-coil interaction

Cl⁻ influx → hyperpolarization

GABA_B1

GABA_B2

4 transmembrane segments (M1–M4)

Central ion-conducting pore

GABA Binding Site (β–α Interface)

Benzodiazepine Allosteric Site (α–γ Interface)

Coiled-Coil C-Terminal Dimerization Domain

Gi/o Protein Coupling

Chloride Ion Channel (Cl⁻ Pore)

Venus Flytrap Extracellular Domain

Pentameric Cys-Loop

Subunits: 2α, 2β, 1γ

Obligatory Heterodimer

Diversity Layers:

α (1–6), β (1–3), γ (1–3), δ, ε, θ, π, ρ

Pentameric Structure

Conformational twist of extracellular domain

GABAA receptor (Ionotropic)

GABAB receptor (Metabotropic)

Glutamate Receptors

M3 helices

Activation gate

M3 Helix Gate

Voltage-dependent Mg²⁺ block

Cation-Selective Pore

Venus Flytrap Domain

Tetrameric Structure

Obligatory Dimer (Class C GPCR)

AMPA receptor

Kainate receptor

NMDA receptor

Metabotropic glutamate receptor

Glycine Receptors

Loop A

Loop B

Loop C

Aromatic Residue Cage

π–π and cation–π interactions

Loop A, Loop B, Loop C (Principal Face)

Complementary Face Loops (D, E, F)

Loop D

Loop E

Loop F

Strychnine High-Affinity Binding Site

Gephyrin-Specific Anchoring (β Subunit)

Dimerization Interface (within E-Domain)

Gephyrin

Trimerization Interface

Threefold symmetric unit

GlyR α subunits

Homopentamers

Postsynaptic scaffold lattice