Molecular Biology: Nucleic Acids & Proteins

Nucleotide

The basic building block of nucleic acids, consisting of a phosphate group, a 5-carbon sugar, and a nitrogenous base.

Deoxyribose

The 5-carbon sugar found in DNA; lacks one oxygen atom (has an H at the 2' carbon) compared to ribose.

Ribose

The 5-carbon sugar found in RNA; contains an OH group at the 2' carbon.

Purines

Nitrogenous bases with a double-ring structure; includes adenine (A) and guanine (G).

Pyrimidines

Nitrogenous bases with a single-ring structure; includes cytosine (C), thymine (T), and uracil (U).

Purine Mnemonic

Pure As Gold (Purines = Adenine and Guanine).

Pyrimidine Mnemonic

CUT the PY (Cytosine, Uracil, Thymine are pyrimidines).

Adenine (A)

A purine that pairs with thymine (T) in DNA and uracil (U) in RNA via 2 hydrogen bonds.

Guanine (G)

A purine that pairs with cytosine (C) via 3 hydrogen bonds.

Cytosine (C)

A pyrimidine that pairs with guanine (G).

Thymine (T)

A pyrimidine found only in DNA; pairs with adenine (A).

Uracil (U)

A pyrimidine found only in RNA; replaces thymine and pairs with adenine (A).

Phosphodiester Bond

The covalent bond linking nucleotides between the 3' OH of one sugar and the 5' phosphate of the next.

Sugar-Phosphate Backbone

The repeating chain of alternating sugars and phosphates that forms the structural framework of DNA and RNA.

Antiparallel

The two DNA strands run in opposite directions: one 5' to 3', the other 3' to 5'.

Complementary Base Pairing

Specific base pairing (A-T and G-C) based on hydrogen bonding that allows accurate DNA replication.

Chromatin

DNA wrapped around histone proteins, forming a compact structure that organizes and regulates gene expression.

Semiconservative Replication

DNA replication where each new DNA molecule contains one original (parental) strand and one newly synthesized strand.

Central Dogma of Molecular Biology

The flow of genetic information: DNA to RNA to Protein.

DNA Replication Direction

New DNA is synthesized in the 5' to 3' direction because DNA polymerase adds nucleotides to the 3' OH end.

DNA Charge

Negatively charged due to the phosphate groups in the sugar-phosphate backbone.

DNA Width Consistency

Maintained because a two-ring purine always pairs with a single-ring pyrimidine.

Major and Minor Grooves

Structural grooves in the DNA double helix where proteins interact to regulate gene expression and replication.

Amino Acid Composition

Polymers made of tens of thousands of amino acid monomers; 20 common amino acids are found in organism proteins.

Central Alpha Carbon

The central carbon atom in an amino acid bonded to an amino group, a carboxyl group, a hydrogen atom, and a variable R-group.

Universal Functional Groups of Amino Acids

Every amino acid contains an amino group (-NH2) and a carboxyl group (-COOH).

Zwitterion

The ionized form of an amino acid at physiological pH where the carboxyl group loses a proton (-COO-) and the amino group gains one (-NH3+).

R-Group

The side chain that determines the chemical identity, properties, and classification of an amino acid.

Acidic Amino Acids

R-groups that are negatively charged and hydrophilic at physiological pH (e.g., Aspartate, Glutamate).

Basic Amino Acids

R-groups that are positively charged and hydrophilic at physiological pH (e.g., Lysine, Arginine, Histidine).

Peptide Bond

A covalent C-N bond formed between the carboxyl group of one amino acid and the amino group of another via a condensation reaction.

Polypeptide Directionality

Chains run from the N-terminus (free amino group) to the C-terminus (free carboxyl group).

Protein Backbone

The repeating N-Cα-C structural framework of a polypeptide chain with R-groups extending outward.

Primary Protein Structure (1°)

The specific linear sequence of amino acids in a polypeptide, held together by peptide bonds.

Secondary Protein Structure (2°)

Local folding of the polypeptide backbone into alpha-helices and beta-pleated sheets, stabilized by backbone hydrogen bonds.

Tertiary Protein Structure (3°)

The overall 3D shape of a single polypeptide chain driven by R-group interactions (hydrophobic interactions, H-bonds, ionic bonds, disulfide bonds).

Disulfide Bond

A strong covalent bond formed between two cysteine sulfhydryl (-SH) groups, stabilizing tertiary structure.

Quaternary Protein Structure (4°)

The assembly of two or more separate polypeptide chains (subunits) into a functional protein complex.

Structure Determines Function

A core biological principle stating that a protein must maintain its correct 3D shape to perform its proper job.

Sickle Cell Disease

A condition caused by a single amino acid change (glutamate to valine) in hemoglobin, altering protein structure and cell behavior.

Molecular Chaperones

Proteins that assist other proteins to fold correctly and avoid inappropriate interactions.

Prions

Abnormal infectious proteins that share the same primary sequence as normal proteins but possess a misfolded 3D structure that causes disease.

Genetic Code

The set of rules defining how nucleotide triplets in mRNA are translated into specific amino acids during protein synthesis.

Reading Frame

The specific division of a continuous nucleotide sequence into consecutive, non-overlapping triplets during translation.

Codon

A three-nucleotide sequence in mRNA that specifies a particular amino acid or a termination signal.

Anticodon

A three-nucleotide sequence on a tRNA molecule that base-pairs with a complementary mRNA codon.

Aminoacyl tRNA

A charged tRNA molecule that is covalently bound to its corresponding amino acid.

Aminoacyl-tRNA Synthetase

An enzyme that catalyzes the specific attachment of an amino acid to its matching tRNA molecule.

EPA Sites

The three functional ribosomal slots for tRNA: Aminoacyl site (A), Peptidyl site (P), and Exit site (E).

Start Codon

The specific mRNA triplet ($AUG$) that signals the initiation of translation and codes for methionine.

Stop Codons

The three mRNA triplets ($UAA$, $UAG$, $UGA$) that signal the termination of polypeptide synthesis.

Free Ribosome Protein Destinations

Cytosol, nucleus, mitochondria, and peroxisomes.

ER-Associated Ribosome Protein Destinations

Secreted proteins, integral membrane proteins, and endomembrane system residents (e.g., lysosomes).

Initial Site of Translation

Free ribosomes in the cytosol for all nuclear-encoded proteins prior to organelle targeting.

Signal Sequence

A short amino acid sequence acting as a molecular address label to direct a newly synthesized protein to its targeted cellular destination.

Signal Hypothesis

The model proposing that an amino-terminal peptide tag directs the ribosome-polypeptide complex to the ER membrane during synthesis.

Signal Recognition Particle (SRP)

A cytosolic complex that binds an ER signal sequence, pauses translation, and targets the ribosome to an ER receptor.

Translocon

A membrane-bound protein channel in the ER through which a nascent polypeptide chain enters the lumen or integrates into the membrane.

Signal Peptidase

An ER enzyme that cleaves the N-terminal signal sequence from a polypeptide after translocation into the lumen.

Nuclear Localization Signal (NLS)

An amino acid sequence on a protein that facilitates its transport into the nucleus through nuclear pore complexes.

Secretory Pathway Sequence

Free ribosome $\rightarrow$ rough ER $\rightarrow$ transport vesicle $\rightarrow$ Golgi apparatus $\rightarrow$ secretory vesicle $\rightarrow$ plasma membrane.

Cis Face vs. Trans Face of the Golgi Apparatus

The receiving entry side facing the ER versus the shipping exit side facing the plasma membrane.

Membrane Protein Topology Preservation

The structural rule where the polypeptide domain facing the ER lumen eventually faces the extracellular space upon exocytosis.

Phagosome

A membrane-bound vesicle formed around an engulfed particle during phagocytosis prior to lysosomal fusion.

Kinesin

A motor protein powered by ATP that walks toward the plus end of microtubules (toward the cell periphery).

Dynein

A motor protein powered by ATP that walks toward the minus end of microtubules (toward the cell center).

Myosin

A motor protein powered by ATP that moves along actin microfilaments.

Phenotypic Effect of Defective Signal Sequences

Mislocalization of proteins to the cytosol, causing loss of essential pathway functions and modified traits.