Final Biochem Summary

⚠️ EXAM TRAPS & COMMON MISTAKES

#	Trap
1	Galactose is an ALDOHEXOSE (not aldopentose) — epimer of glucose at C4
2	α-Amylase hydrolyzes STARCH (α bonds), NOT cellulose (β bonds)
3	Sucrose is NON-reducing (both anomeric carbons in glycosidic bond)
4	Amino acids in protein synthesis are ALPHA (α) type, L configuration
5	Competitive inhibitor → ↑Km, Vmax unchanged | Non-competitive → ↓Vmax, Km unchanged
6	Km corresponds to [S] at ½ Vmax — NOT to reach Vmax
7	Allosteric enzymes do NOT follow Michaelis-Menten kinetics (sigmoidal curve)
8	BPG binds β-subunit interface of Hb in T state ONLY (not myoglobin)
9	Fetal Hb (HbF) = α2γ2 — higher O2 affinity than adult (cannot bind BPG)
10	Scurvy = Vit C deficiency → no hydroxyproline in collagen → weak connective tissue
11	Sickle cell: Glu→Val at position 6 of β-globin (HbS)
12	DNA replication: Leading strand = continuous | Lagging = discontinuous (Okazaki fragments)
13	Primase synthesizes RNA primers; side products = pyrophosphate
14	Eukaryote: Pol I→rRNA, Pol II→mRNA, Pol III→tRNA
15	Shine-Dalgarno pairs with 3’ end of 16S rRNA (30S subunit)
16	Stop codons: UAA, UAG, UGA | Start: AUG (Met/fMet)
17	Waxes are NOT polar lipids (glycerophospholipids and sphingolipids ARE polar)
18	LDL = highest cholesterol content | HDL = highest density, reverse transport
19	HMG-CoA reductase = rate-limiting step in cholesterol synthesis | statins inhibit it
20	Peptide bond: partial double bond character → PLANAR and RIGID → trans configuration

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01 · Carbohydrates

Classification

Concept	Details
Monosaccharides	Single sugar unit (glucose, fructose, galactose, ribose, deoxyribose)
Disaccharides	2 units via glycosidic bond (maltose, lactose, sucrose)
Polysaccharides	>10 units (starch, glycogen, cellulose)

Monosaccharide Essentials

Concept	Details
Aldose vs Ketose	Aldose = aldehyde at C1 (glucose, galactose, ribose) | Ketose = ketone at C2 (fructose)
D vs L sugar	D = –OH on bottom chiral C points RIGHT in Fischer projection (biological sugars are D)
Chiral centers	Glucose (aldohexose): 4 chiral carbons → 2⁴ = 16 stereoisomers
Epimers	Differ at ONE chiral C only | Glucose & Mannose (C2) | Glucose & Galactose (C4)
Anomers	α = –OH axial (below ring) | β = –OH equatorial (above ring) | Created at anomeric carbon on cyclization
Mutarotation	Interconversion of α⇌β through open-chain form in solution
Pyranose/Furanose	6-membered ring = pyranose | 5-membered ring = furanose
Reducing sugar	Has FREE hemiacetal/hemiketal → can donate electrons | Glucose, fructose, maltose, lactose are reducing | SUCROSE is NOT (both anomeric C involved in bond)

Key Disaccharides

Sugar	Details
Maltose	α-D-Glc–α(1→4)–D-Glc | Reducing | From starch hydrolysis | Hydrolyzed by maltase
Lactose	β-D-Gal–β(1→4)–D-Glc | Reducing | Milk sugar | Hydrolyzed by lactase (β-galactosidase)
Sucrose	α-D-Glc(1↔2)β-D-Fru | NON-reducing | Both anomeric C involved | Plant transport sugar

Polysaccharides Comparison

Polysaccharide	Details
Amylose	Linear α(1→4) | ~20% of starch | Helical | Iodine = blue-black
Amylopectin	α(1→4) + α(1→6) branch every 24–30 units | ~70–90% of starch | Plants
Glycogen	α(1→4) + α(1→6) branch every 8–12 units | MORE branched than amylopectin | Animals (liver + muscle) | Contains glycogenin core protein
Cellulose	β(1→4) linear | Structural in plants | Humans lack cellulase → dietary fiber

ABO Blood Groups

Type	Details
Nature of antigens	CARBOHYDRATES on glycolipids/glycoproteins on RBC surface
Type A	N-acetyl-D-galactosamine (GalNAc) | Anti-B antibodies
Type B	D-galactose | Anti-A antibodies
Type AB	Both antigens | No antibodies | Universal recipient
Type O	No specific antigen | Both anti-A and anti-B | Universal donor

Enzymes for Digestion

Enzyme	Details
α-Amylase	Cleaves α(1→4) bonds RANDOMLY (saliva + pancreas) → dextrins
β-Amylase	Cleaves from reducing end → maltose (plants/bacteria)
Maltase	Maltose → 2 glucose
Lactase	Lactose → glucose + galactose
α-Amylase ≠ cellulase	Hydrolyzes α bonds (starch/glycogen), NOT β bonds (cellulose)

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02 · Lipids

Fatty Acid Nomenclature

Fatty Acid	Details
Palmitic	C16:0 | Hexadecanoic | Saturated | MP 63°C
Stearic	C18:0 | Octadecanoic | Saturated | MP 70°C
Oleic	C18:1 Δ9 | cis | ω-9 | MP 16°C | Monounsaturated
Linoleic (EFA)	C18:2 Δ9,12 | ω-6 | MP −5°C | Essential
α-Linolenic (EFA)	C18:3 Δ9,12,15 | ω-3 | MP −11°C | Essential
Arachidonic	C20:4 Δ5,8,11,14 | ω-6 | MP −50°C (lowest) | From linoleic acid
Palmitoleic	C16:1 Δ9 | Monounsaturated

Melting Point Rules

Rule	Details
More double bonds → lower MP	More kinks = less packing = easier to melt
Longer chain → higher MP	More van der Waals contacts
cis > trans for fluidity	cis kink prevents packing | trans stays straight like saturated
Lowest MP among common FA	α-Linolenic (C18:3) has 3 double bonds → lowest MP of 18-C FA | Arachidonic (C20:4) is lowest overall
Oleic → trans (elaidic)	MP increases (trans packs better like saturated)

Essential Fatty Acids & Eicosanoids

Concept	Details
EFAs	Linoleic (ω-6) and α-Linolenic (ω-3) — cannot be made by humans
Arachidonic acid (ω-6)	→ Prostaglandins, Thromboxanes, Leukotrienes (via COX and lipoxygenase)
Aspirin	Irreversibly inhibits COX → blocks prostaglandin/TXA2 synthesis → anti-inflammatory, antiplatelet
ω-3 vs ω-6 eicosanoids	ω-3 → anti-inflammatory | ω-6 → pro-inflammatory

Glycerides & Phospholipids

Lipid	Details
Triglyceride	Glycerol + 3 fatty acids (ester bonds) | Main energy storage in adipocytes | ~9 kcal/g
Phospholipids	Amphipathic | Hydrophilic phosphate head + 2 hydrophobic FA tails → form bilayer
Glycerophospholipids	Backbone = glycerol | PC, PE, PS, PI, cardiolipin
Sphingolipids	Backbone = sphingosine (18C amino alcohol) | Ceramide = sphingosine + FA (amide bond)
Sphingomyelin	Ceramide + phosphocholine | Only sphingolipid that is also a phospholipid | Abundant in myelin sheath
Waxes	FA + long-chain alcohol (NOT glycerol) | NOT polar lipids | Waterproofing
Polar lipids	Glycerophospholipids + sphingolipids | WAXES are NOT polar lipids

Cholesterol & Lipoproteins

Concept	Details
Cholesterol	Steroid nucleus (3×6-ring + 1×5-ring) | –OH at C3 | Regulates membrane fluidity
Cholesterol functions	Membrane component | Precursor of bile acids, sex hormones, corticosteroids, Vitamin D
HMG-CoA reductase	Rate-limiting enzyme in cholesterol synthesis | INHIBITED BY STATINS
Chylomicrons	Lowest density | Largest | 80–90% dietary TG | From intestine
VLDL	Liver → endogenous TG to tissues | Low density
LDL	Medium density | ~50% cholesterol | ‘Bad’ — deposits in arteries | ApoB-100
HDL	Highest density | Smallest | Reverse cholesterol transport | ‘Good’ — cardioprotective | ApoA-I
Lipoprotein lipase (LPL)	Enzyme on capillary walls | Hydrolyzes TG in chylomicrons and VLDL

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03 · Amino Acids & Peptides

General Structure

Concept	Details
α-Amino acids	NH3+ and COO- both on α-carbon | All L-stereoisomers in proteins (except Gly)
Glycine	Only non-chiral AA | R = H
Zwitterion	At physiological pH 7.4: NH3+ + COO- | Net charge depends on R group
pI formula	Simple AA: (pKa1 + pKa2)/2 | Acidic: (pKa1 + pKaR)/2 | Basic: (pKa2 + pKaR)/2
Peptide bond	Amide bond | Partial double bond character | PLANAR and RIGID | Trans >99.95%
Φ (phi)	Rotation around N–Cα bond | FREE to rotate
Ψ (psi)	Rotation around Cα–C bond | FREE to rotate

Classification of 20 AAs

Group	Amino Acids
Nonpolar aliphatic	Gly, Ala, Val, Leu, Ile, Met, Pro
Nonpolar aromatic	Phe, Trp (Tyr is POLAR)
Polar uncharged	Ser, Thr, Cys, Asn, Gln, Tyr
Negatively charged (acidic)	Asp, Glu | pI very low (~2.9, 3.2) | net – at pH 7
Positively charged (basic)	Lys (pKaR 10.5) | Arg (pKaR 12.5 — most basic) | His (pKaR 6.0 — near physiological pH)
Proline special	Imino acid | Rigid ring | Breaks α-helix | ~6% cis peptide bonds
Cysteine special	–SH thiol | Two Cys → disulfide bond (–S–S–) via oxidation
His special	pI 7.58 | Can act as acid/base at physiological pH → key in enzyme catalysis

Essential Amino Acids (9)

Concept	Details
Mnemonic: PVT TIM HaLL	Phe, Val, Thr, Trp, Ile, Met, His, Leu, Lys
Non-essential	Ala, Asn, Asp, Glu
Conditional	Arg, Cys, Gln, Gly, Pro, Ser, Tyr

Key Side Chain Polarity (Exam Traps)

Amino Acid	Polarity
Proline	NON POLAR
Alanine	NON POLAR
Valine	NON POLAR
Cysteine	POLAR NOT CHARGED
Serine/Threonine	POLAR NOT CHARGED
Aspartate/Glutamate	POLAR CHARGED (–)
Lysine/Arginine	POLAR CHARGED (+)

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04 · Proteins

4 Levels of Structure

Level	Details
PRIMARY	Amino acid sequence | Held by peptide bonds (covalent)
SECONDARY	Local folding: α-helix, β-sheet, β-turn | Held by HYDROGEN BONDS
TERTIARY	Full 3D fold of one polypeptide | Hydrophobic effect, H-bonds, ionic, disulfide bonds, vdW
QUATERNARY	2+ polypeptide chains (subunits) | Same forces as tertiary ± disulfide bonds

Secondary Structures

Structure	Details
α-Helix	Right-handed | 3.6 residues/turn | Pitch 5.4Å | i→i+4 H-bond | R-groups point outward | Proline BREAKS it| Ala promotes it
β-sheet	β-strands aligned side by side | H-bonds BETWEEN strands | Antiparallel (more stable) or Parallel | R-groups alternate above/below
β-turn	4 residues | 180° direction change | Gly + Pro favored | Connects antiparallel β-strands
Random coil	No regular pattern | Loops, linkers | 4–20 residues

Fibrous Proteins

Protein	Details
α-Keratin	Almost entirely α-helical | Coiled-coil | Hair, nails, skin | Hard (nails) = more disulfide bonds | Permanent wave = break then reform S-S bonds
Collagen	Most abundant protein (~25–35%) | Left-handed collagen helix | 3 chains → right-handed triple helix (tropocollagen) | Gly-X-Y repeat | Gly at every 3rd position | Pro + Hyp | Requires Vitamin C for hydroxylation | SCURVY = Vit C deficiency → weak collagen
Silk fibroin	Highest β-sheet content | Gly-Ala-Gly-Ala sequence

Globular vs Fibrous

Type	Details
Fibrous	One secondary structure type | Insoluble | Structural function | Keratin, collagen
Globular	Multiple secondary structures | Water-soluble | Functional (enzymes, transport, hormones) | Myoglobin, hemoglobin, antibodies

Stabilizing Forces & Clinical Links

Concept	Details
Hydrophobic effect	MAJOR driving force for folding | Buries nonpolar residues in core | Releases ordered water → ↑ entropy
Disulfide bonds	Covalent | Oxidizing environment needed | NOT in cytoplasm (reducing environment)
Denaturation	Disrupts 2°/3°/4° — NOT primary structure | Heat, extreme pH, urea, detergents
Anfinsen	Primary sequence contains ALL folding information | Ribonuclease A refolds spontaneously
Scurvy (clinical)	Vit C deficiency → Proline NOT hydroxylated → unstable collagen triple helix
Sickle cell (clinical)	Glu6Val mutation in β-globin → hydrophobic patch → HbS polymerizes when deoxygenated

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05 · Myoglobin & Hemoglobin

Myoglobin vs Hemoglobin

Property	Myoglobin	Hemoglobin
Structure	Monomer	Tetramer α2β2
Heme groups	1	4
Location	Muscle	Blood (erythrocytes)
Function	O2 STORAGE	O2 TRANSPORT
O2 binding curve	Hyperbolic	Sigmoidal
P50	2.8 mmHg (HIGH affinity)	26 mmHg
Cooperativity	None	Yes

Concept	Details
Heme group	Fe2+ porphyrin ring | Proximal His (F8/His93) = 5th coordination | Distal His (E7/His64) = H-bonds with O2
Deoxyheme	Fe2+ out of porphyrin plane | On O2 binding, Fe2+ pulls into plane → moves F-helix → T→R transition

Cooperative Binding

Concept	Details
T state (tense)	Deoxy | Low affinity | Many salt bridges | BPG binds in central cavity
R state (relaxed)	Oxy | High affinity | Fewer salt bridges | BPG expelled
Sigmoidal curve	Hallmark of cooperativity | Hill coefficient n ≈ 2.8 (1 = no cooperativity, 4 = perfect)
MWC model	Concerted: all subunits switch T→R simultaneously
Sequential model	Each O2 binding induces local change → influences neighbors

Allosteric Regulators

Regulator	Details
Bohr Effect	↑H+ (↓pH) → ↓O2 affinity → shifts curve RIGHT → more O2 released to tissues | His146 β-chain key
CO2 transport	~70% → carbonic anhydrase → HCO3- + H+ | ~15–20% → carbamate (binds N-terminus of globin, stabilizes T state)
BPG	Binds central cavity between β-subunits | ONLY in T state | 5 negative charges | Stabilizes T → ↓affinity | ↑ at high altitude
Temperature	↑ temp → shifts curve RIGHT → less affinity → more O2 released (exercising muscle)
Fetal Hb (HbF)	α2γ2 | γ-subunit cannot bind BPG → HIGHER affinity than HbA | Transfers O2 from mother to fetus at placenta

Sickle Cell Anemia

Concept	Details
Mutation	Glu6Val in β-chain (HbS) | GAG → GTG in gene
Mechanism	Val is hydrophobic → sticky patch on deoxy-HbS → polymerization → sickle shape → blocks capillaries
Genetics	Autosomal recessive | Homozygous = severe disease | Heterozygous = malaria protection
Treatment	Hydroxyurea (↑HbF), voxelotor, stem cell transplant (only cure)
Why Mb can’t transport O2	Hyperbolic curve + P50 = 2.8 mmHg → would NOT release O2 at physiological tissue pO2

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06 · Enzymes

Enzyme Basics

Concept	Details
Catalyst properties	↓ activation energy (ΔG‡) | Does NOT change ΔG or Keq | Not consumed | Specific
Active site	Complementary to TRANSITION STATE (not substrate) | Induced fit model (Koshland 1958)
Lock & Key (Fischer 1894)	Rigid complementarity | Insufficient — doesn’t explain transition state stabilization
Induced Fit	Active site changes shape on substrate binding | Hexokinase example
Cofactors	Metal ions (Fe2+, Mg2+, Zn2+, Cu2+) | Coenzymes (NAD+, FAD, CoA)
Ribozymes	Catalytic RNA — not all enzymes are proteins

Michaelis-Menten Kinetics

Concept	Details
Equation	V0 = Vmax[S] / (Km + [S])
Km	[S] at which V0 = ½ Vmax | LOWER Km = HIGHER affinity
Vmax	Max velocity at enzyme saturation | All active sites occupied
When [S] << Km	V0 ≈ (Vmax/Km)×[S] → linear
When [S] >> Km	V0 ≈ Vmax → constant (zero-order kinetics)
Hexokinase Km	D-Glucose 0.05 mM (highest affinity) | ATP 0.4 mM | D-Fructose 1.5 mM (lowest)
Allosteric enzymes	SIGMOIDAL curve | NOT Michaelis-Menten kinetics

Inhibition Summary

Type	Km	Vmax	Overcome by ↑[S]?
Competitive	↑ increased	unchanged	Yes
Non-competitive	unchanged	↓ decreased	No
Uncompetitive	↓ decreased	↓ decreased	No
Irreversible	—	—	No (covalent)

Inhibitor	Details
Suicide inhibitors	Penicillin (transpeptidase) | Clavulanic acid (β-lactamase) | Enzyme activates inhibitor → inhibits itself
Allopurinol	Competitive inhibitor of xanthine oxidase | Used for gout
Aspirin	Irreversible inhibitor of COX | Blocks prostaglandin/TXA2

Regulation

Mechanism	Details
Feedback inhibition	End product inhibits early enzyme in pathway
Phosphorylation	Most common reversible covalent modification | Kinase (adds Pi) / Phosphatase (removes Pi)
Zymogens	Inactive precursors | Trypsinogen → Trypsin (by enteropeptidase) | Prothrombin → Thrombin
pH effect	Pepsin optimal pH = 2 | NO activity at pH 7.4

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07 · DNA & RNA

Nucleotide Structure

Concept	Details
Components	Nitrogenous base + Pentose sugar + Phosphate group(s)
Nucleoside	Base + Sugar (no phosphate) | N-β-glycosidic bond
Purines	Adenine (A), Guanine (G) | Bicyclic | In both DNA and RNA
Pyrimidines	Cytosine (C) in both | Thymine (T) in DNA only | Uracil (U) in RNA only
DNA sugar	2’-deoxyribose | No OH at C2 → chemically stable
RNA sugar	Ribose | OH at C2 → susceptible to alkaline hydrolysis
Linkage in strand	3’,5’-phosphodiester bonds | 5’→3’ direction

DNA Double Helix

Concept	Details
Chargaff’s rules	A=T and G=C | A-T = 2 H-bonds | G-C = 3 H-bonds
B-form DNA	Most stable physiologically | Right-handed | 10.5 bp/turn | Major + minor grooves
A-form	Right-handed | Shorter, wider | RNA:DNA hybrids
Z-form	Left-handed | Longer, thinner | High GC content
Denaturation	↑ temp or extreme pH breaks H-bonds | ↑ GC content → ↑ Tm
DNA Methylation	5-methylcytosine (5mC) | Epigenetic regulation

RNA Types

RNA	Details
mRNA	Protein-coding message | ~2% of RNA by mass | 5’ cap + 3’ poly-A tail (eukaryotes)
rRNA	80–90% of total RNA | Structural + catalytic in ribosome | Prokaryote: 16S, 23S, 5S | Eukaryote: 18S, 28S, 5.8S, 5S
tRNA	Most numerous by molecule | Cloverleaf structure | 3’ end CCA (amino acid attachment) | Anticodon loop
snRNA	Small nuclear RNA | Part of spliceosome (removes introns)

DNA Organization

Concept	Details
Nucleosome	DNA wrapped around histone octamer (H2A, H2B, H3, H4 ×2) | ~146 bp | ‘Beads on a string’
Chromatin	Nucleosome → 30nm fiber → loops → chromosomes
Topoisomerase I	Cuts ONE strand | Relaxes supercoils | No ATP
Topoisomerase II	Cuts BOTH strands | Uses ATP | Target of antibiotics (quinolones) and anticancer drugs

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08 · DNA Replication

Key Features

Concept	Details
Semiconservative	Each daughter: 1 parental + 1 new strand | Proven by Meselson-Stahl (1957) with 15N/14N
Direction	ALWAYS 5’→3’ synthesis | Antiparallel template read 3’→5’
Primer needed	DNA polymerase cannot start de novo | Requires RNA primer (made by PRIMASE)
Origin	Specific sequences (oriC in E. coli) | Eukaryotes: multiple origins
Replication fork	Y-shaped structure | Bidirectional

Key Proteins (E. coli)

Protein	Function
Helicase (DnaB)	Unwinds double helix at replication fork
SSB proteins	Stabilize single-stranded DNA
Topoisomerase II (Gyrase)	Relieves positive supercoiling ahead of fork
Primase (DnaG)	Synthesizes short RNA primers | Side products = PYROPHOSPHATE
DNA Pol III	Main replicative polymerase | 5’→3’ synthesis + 3’→5’ proofreading exonuclease
DNA Pol I	Nick translation | Removes RNA primers (5’→3’ exonuclease) + fills gap
DNA Ligase	Seals nicks | Joins Okazaki fragments
Sliding clamp (β-clamp)	Processivity factor | Keeps Pol III on template

Leading vs Lagging Strand

Strand	Details
Leading strand	Synthesized CONTINUOUSLY 5’→3’ | ONE primer
Lagging strand	Synthesized DISCONTINUOUSLY | Multiple Okazaki fragments | Each needs primer
Okazaki fragments	~1–2 kb (prokaryote) | ~150 nt (eukaryote) | RNA primer + DNA | Joined by ligase after primer removal

Accuracy & Eukaryotes

Concept	Details
Raw error rate	1 per 10³–10⁴ bases
+ Proofreading	1 per 10⁶–10⁷ bases
+ Mismatch repair	1 per 10⁹–10¹⁰ bases (final)
Eukaryote Pol α	Has primase activity | Synthesizes RNA-DNA primer
Eukaryote Pol δ/ε	Main replicative polymerases (analogous to Pol III)
Telomeres	TTAGGG repeats at chromosome ends | Protect from shortening
Telomerase	Reverse transcriptase with RNA template | Extends telomeres | High in cancer cells

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09 · Transcription

RNA Polymerases

Polymerase	Details
Prokaryote RNAP	5 subunits: α2ββ’ω = core | + σ (sigma) = holoenzyme | σ recognizes promoter
Eukaryote Pol I	Transcribes large pre-rRNA → 18S, 5.8S, 28S rRNA
Eukaryote Pol II	Transcribes pre-mRNA + snRNA + miRNA | Most regulated
Eukaryote Pol III	Transcribes tRNA + 5S rRNA
Key difference	All RNA types in prokaryotes: ONE RNAP | Rifamycin targets prokaryotic RNAP

Transcription Mechanism

Concept	Details
Reaction	(NMP)n + NTP → (NMP)n+1 + PPi | PPi hydrolysis drives reaction forward
Direction	5’→3’ | Template strand read 3’→5’
No primer needed	Unlike DNA replication — RNAP can initiate de novo
Side products	PYROPHOSPHATE (PPi)
Prokaryote promoters	–10 box (TATAAT) + –35 box (TTGACA) | σ factor recognizes these
Termination	Rho-independent (hairpin + poly-U) | Rho-dependent (Rho helicase)

mRNA Maturation (Eukaryotes Only) ← EXAM QUESTION

Step	Details
1. 5’ Capping	7-methylguanosine (m7G) cap added co-transcriptionally | Protects mRNA + helps ribosome binding
2. 3’ Polyadenylation	Poly-A tail (~200 A residues) | AAUAAA signal | Protects from degradation
3. Splicing	Introns removed by SPLICEOSOME (snRNPs) | Exons joined | Alternative splicing → protein diversity
Overall order	Capping → transcription → polyadenylation → splicing → export from nucleus

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10 · Translation

Genetic Code

Concept	Details
Codon	3 nucleotides (triplet) = 1 amino acid | 64 codons total
Start codon	AUG = Methionine (eukaryotes) | fMet (prokaryotes)
Stop codons	UAA, UAG, UGA — no tRNA (recognized by release factors)
Degeneracy	64 codons for 20 AAs → multiple codons per AA (synonymous codons)
Code features	Universal | Non-overlapping | No punctuation | Unambiguous
Wobble hypothesis	3rd codon position allows non-Watson-Crick pairing → one tRNA reads multiple codons

Ribosomes

Concept	Details
Prokaryotic	70S = 30S (16S rRNA + proteins) + 50S (23S + 5S rRNA + proteins)
Eukaryotic	80S = 40S (18S rRNA) + 60S (28S, 5.8S, 5S rRNA)
Ribosome sites	A site (aminoacyl, incoming) | P site (peptidyl, growing chain) | E site (exit)
Shine-Dalgarno	Prokaryotic mRNA sequence | Pairs with 3’ end of 16S rRNA (30S subunit)
Kozak sequence	Eukaryotic ribosome recognition sequence around AUG

Translation Stages

Stage	Details
Initiation (prok.)	30S binds mRNA via Shine-Dalgarno | fMet-tRNA enters P site | 50S joins | IFs
Initiation (euk.)	40S + eIF4 cap recognition | Scans for AUG | 60S joins
Elongation cycle	1. Aminoacyl-tRNA enters A site (EF-Tu + GTP) | 2. Peptide bond by peptidyl transferase (23S rRNA!) | 3. Translocation (EF-G + GTP) | mRNA advances 3 nt
Energy cost	2 GTP/AA (EF-Tu + EF-G) + 2 ATP for tRNA charging = 4 high-energy bonds per AA
Termination	Stop codon in A site | Release factors (RF) | Ribosome disassembles | Polypeptide released

Post-Translational Events

Modification	Details
Glycosylation	N-linked (Asn) in ER | O-linked (Ser/Thr) in Golgi
Phosphorylation	Ser, Thr, Tyr | Kinases/phosphatases
Proteolytic cleavage	Signal peptide removal | Proinsulin → insulin
Disulfide bonds	Cys-Cys oxidation in ER (oxidizing environment)
Protein targeting	Signal peptide (N-terminal) → ER → secretory pathway | Nuclear localization signal → nucleus

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Built from lecture notes · UniBO · Biochemistry Module 1 & 2