DNA, RNA, and Protein Lecture Notes

Flashcards covering the history of molecular biology, the structure and replication of DNA, the central dogma, and protein structure as presented in the lecture.

Friedrich Miescher

The scientist who discovered nuclein in pus in 1869.

Richard Altmann

The scientist who renamed nuclein to nucleic acid in 1889.

Phoebus Levene

Identified the components of nucleic acid (DNA and RNA) and named nucleotides in 1919.

Tetranucleotide hypothesis

The belief that DNA components existed in short chains that repeated in a fixed pattern.

Frederick Griffith

Discovered in 1928 that bacteria can transfer genetic information through a process called transformation.

Max Delbruck

Suggested in 1935 that chromosomes are very large molecules which change heritable characteristics if their shape is modified.

William Astbury

Determined in 1937 that DNA has a regular structure.

Oswald Avery

Repeated Griffith's experiments in 1943 and identified DNA as the 'transforming principle'.

Alfred Hershey and Martha Chase

Showed in 1953 that DNA is the genetic material in T2 phage.

James Watson and Francis Crick

Determined the double helix structure of DNA in 1953.

Central dogma of molecular biology

Proposed by Francis Crick in 1957, describing the flow of information from DNA to RNA to protein.

Meselson and Stahl

Conducted an experiment in 1958 using ${}^{15}N$ and ${}^{14}N$ to support the theory that DNA replicates semiconservatively.

DNA Nucleotide

The basic building block of DNA, consisting of a phosphate group, a deoxyribose sugar, and a nitrogenous base (A, G, C, or T).

Purines

Nitrogenous bases with a double-ring structure, specifically Adenine (A) and Guanine (G).

Pyrimidines

Nitrogenous bases with a single-ring structure, specifically Cytosine (C) and Thymine (T) in DNA.

Ribose

The five-carbon sugar found in RNA, containing a hydroxyl ($OH$) group on the $2'$ carbon.

Deoxyribose

The five-carbon sugar found in DNA, lacking an oxygen atom on the $2'$ carbon compared to ribose.

Semiconservative replication

The process of DNA duplication where each daughter molecule contains one old strand from the parent and one newly synthesized strand.

DNA Denaturation

The separation of the two strands of the DNA double helix into single strands using heat.

Melting temperature ($T_m$)

The specific temperature at which DNA strands are halfway separated during denaturation.

Hybridization

A process used to determine relatedness by heating DNA from two organisms to separate strands, then mixing and cooling them to see if they reanneal.

Telomere

The specialized structure found at the end of a linear chromosome arm.

Centromere

The region of a linear chromosome where the two arms are connected.

Transcription

The process of creating a single-stranded RNA molecule from a double-stranded DNA template.

Translation

The process where a ribosome links amino acids together into a protein based on the sequence in RNA.

70S Ribosome

The bacterial ribosome composed of a 30S subunit (containing 16S rRNA and 21 proteins) and a 50S subunit (containing 5S rRNA, 23S rRNA, and 32 proteins).

Genetic Code

The set of rules by which information encoded in genetic material is translated into proteins, featuring 64 possible codons.

Anticodon

A three-nucleotide sequence on a tRNA molecule that hydrogen bonds to a complementary codon on mRNA.

Peptide bond

The covalent bond formed between the amino group of one amino acid and the carboxyl group of another, eliminating water ($H_2O$).

N-terminus

The start of a polypeptide chain, marked by a free amino group ($H_2N$).

Carboxy terminus

The end of a polypeptide chain, marked by a free carboxyl group ($COOH$).

Primary Structure

The simple linear sequence of amino acids in a polypeptide chain.

Secondary Structure

Initial folding patterns in a protein, such as the $\alpha$-helix or $\beta$-sheet.

Tertiary Structure

The overall three-dimensional folding of a single polypeptide chain.

Quaternary Structure

The complex structure formed by the assembly of multiple polypeptide chains.

Active Site

A specific pocket or region formed after protein folding where residues interact with a substrate.

Regulatory Proteins

Proteins that control transcription by changing shape in response to signal molecules and binding to regulatory regions of DNA.

X-Ray Crystallography

A technique used to determine protein structure by analyzing the diffraction pattern of x-rays passing through a protein crystal.

Phosphodiester Bond / Ester Linkages

The covalent bonds that link nucleotides together in a nucleic acid chain via ester linkages between the 3' hydroxyl group of one sugar and the 5' phosphate group of the next.

Hydrogen Bonding in Base Pairing

Adenine pairs with Thymine via 2 hydrogen bonds, while Guanine pairs with Cytosine via 3 hydrogen bonds.

30S Subunit

The smaller bacterial ribosomal subunit containing 16S rRNA and 21 proteins.

50S Subunit

The larger bacterial ribosomal subunit containing 5S rRNA, 23S rRNA, and 32 proteins.

Stop Codons

Specific mRNA codons (UAA, UAG, UGA) that signal the termination of translation.

Start Codon

The primary mRNA codon (AUG, coding for Methionine) that signals the initiation of translation.

tRNA Acceptor Stem (CCA end)

The sequence located at the 3' end of a tRNA molecule where an amino acid attaches.

Prokaryotic vs. Eukaryotic Transcription Structure

Prokaryotes often translate polycistronic mRNA (multiple genes on one strand), while eukaryotes typical produce monocistronic mRNA (one gene per transcript).

Intergenic Regions

Non-coding DNA sequences located between genes on a chromosome

Transport Proteins

Membrane proteins (e.g., $Na^+$ pumps, channel proteins) that assist in the selective movement of molecules across biological membranes.

Replication Origins

Specific regions along a chromosome where DNA replication is initiated

Glycosidic Linkage (N-Glycosidic Bond)

The covalent bond connecting the 1’ carbon of the pentose sugar (ribose or deoxyribose) to the N9 position of a purine or N1 position of a pyrimidine.

Nucleoside vs. Nucleotide

A nucleoside consists only of a nitrogenous base attached to a 5 carbon sugar, a nucleotide is a nucleoside with one, two, or three phosphate groups attached (usually at the $5'$ position).

Phosphodiester Backbone Charge

The sugar phosphate backbone of nucleic acids carries a negative charge at physiological pH due to the ionized phosphate groups.

Charagaff's Rules

In double stranded DNA, the amount of Adenine equals Thymine ($\%A = \%T$) and Guanine equals Cytosine ($\%G = \%C$), meaning total purines ($A + G$) always equal total pyrimidines ($T + C$).

Z DNA Conformation

A left handed double helical structure formed by alternating purine-pyrimidine sequences (like GC repeats) under specific torsional stress, taking on a "zig-zag" backbone pattern.

Hyperchromic Effect

The dramatic increase in UV light absorption (at 260 nm) that occurs when double-stranded DNA denatures into single strands, caused by the unstacking of nitrogenous bases.

Absorbance Peak ($A_{260}$ vs. $A_{280}$)

Nucleic acids absorb UV light maximally at 260 nm (due to aromatic base rings), whereas proteins absorb maximally at 280 nm (due to aromatic amino acids like Tryptophan and Tyrosine).

Ribozyme

An RNA molecule capable of acting as an enzymatic catalyst for specific chemical reactions (e.g., self splicing introns or peptidyl transferase activity).

Zwitterion

An amino acid at neutral pH existing in a dipolar state, where the amino group is protonated and the carboxyl group is deprotonated, yielding a net neutral charge.

Isoelectric Point ($pI$)

The specific pH at which a molecule (such as an amino acid or protein) carries a net electrical charge of zero.

Disulfide Bonds (Cystine Links)

Strong covalent bonds formed by the oxidation of the sulfhydryl groups of two Cysteine residues, which stabilize tertiary and quaternary protein structures.

Fibrous vs. Globular Proteins

Fibrous proteins (like keratin and collagen) are elongated, water-insoluble structural proteins, whereas globular proteins (like enzymes and hemoglobin) are compactly folded and water-soluble.

Protein Native State

The fully folded, biologically active three dimensional conformation of a functional protein under normal physiological conditions