Gene to Protein: Macromolecules, DNA Replication, Transcription, and Translation

Vocabulary flashcards covering the structure and types of biological macromolecules, DNA structure and replication, transcription, RNA processing, and translation.

Organic Molecule

A molecule that contains carbon.

Carbon (in Biological Chemistry)

An abundant element that serves as the foundation of living chemistry because it can easily form up to four covalent bonds with other common elements ($H$, $O$, $N$), and its reactions to create large, complex molecules occur readily in water.

Polymer

A large molecule composed of a repeating chain of smaller units called monomers.

Monomer

A small repeating unit that serves as a building block for polymers.

Four Macromolecules and Their Subunits

Carbohydrates (monomers: sugars), proteins (monomers: amino acids), nucleic acids (monomers: nucleotides), and lipids (subunits: fatty acids and glycerol).

Hydrolysis

Hydrolysis is a chemical reaction where a water molecule is added to break the bonds of a larger molecule, splitting it into smaller pieces

What the Word Means

• Hydro means water.

• Lysis means to break or unbind.

• Literally: "breaking apart with water.

Dehydration Synthesis

Dehydration synthesis is a chemical reaction that joins smaller molecules (monomers) together to build a larger molecule (polymer) by removing a molecule of water.

Monosaccharide

A single sugar molecule with a ring structure, such as glucose, galactose, or fructose.

Disaccharide

A carbohydrate composed of two linked sugar units, such as lactose, maltose, or sucrose.

Cellulose and Starch

Plant carbohydrates; cellulose provides structural support, while starch (amylose, amylopectin) serves as an energy storage molecule.

Glycogen

A carbohydrate used by animals for energy storage.

Chitin

A structural carbohydrate found in fungi and animals.

Lipids

A diverse class of biological molecules that are all insoluble in water; includes triglycerides, phospholipids, steroids, and waxes.

Triglyceride

A lipid composed of one glycerol molecule bonded to three fatty acids; used primarily for energy storage and insulation.

Saturated Fatty Acid

A fatty acid that contains the maximum possible number of bonded hydrogen atoms, giving it a straight shape that packs densely and behaves like a solid at room temperature.

Unsaturated Fatty Acid

A fatty acid with one or more missing hydrogen atoms where double bonds form, causing kinks/bends that prevent dense packing and cause it to behave like a liquid.

Phospholipids

The primary class of lipids that forms cell membranes.

Steroids

Lipids that often function as cholesterol-based hormones enabling intercellular communication throughout the body.

Waxes

Lipids with diverse structures whose common functional purpose is to form protective coatings.

Polypeptide vs. Protein

Both refer to a polymer of amino acids; 'polypeptide' refers to the linear, unfolded amino acid polymer, while 'protein' refers to the molecule in its final folded functional form (including secondary, tertiary, and quaternary structures).

Primary Structure

The linear sequence of amino acids in a polypeptide chain.

Secondary Structure

Local folding patterns within a polypeptide chain formed by hydrogen bonds, creating structures such as alpha helices and beta sheets.

Tertiary Structure

The overall three-dimensional folding structure of an entire single polypeptide chain resulting from interactions among its secondary structures.

Quaternary Structure

The structural arrangement that forms when multiple distinct polypeptide chains (subunits) assemble together (e.g., hemoglobin).

Chargaff's Rule

Erwin Chargaff's principle stating that in DNA, the amount of adenine ($A$) always equals thymine ($T$), and the amount of cytosine ($C$) always equals guanine ($G$) because they specifically pair together.

Rosalind Franklin's Contribution

Deduction from X-ray diffraction images that DNA has a helical, double-stranded structure.

Watson and Crick

Scientists who first published the modern model of DNA structure as an antiparallel, double-stranded helix governed by Chargaff's base-pairing rules.

DNA Molecule Structure (Diagram)

1. Deoxyribose; 2. Nitrogenous base; 3. Nucleotide; 4. Base pairs; 5. Hydrogen bonds; 6. Phosphate group.

Purines vs. Pyrimidines

Purines are nitrogenous bases containing a double-ring structure (adenine, guanine); pyrimidines are nitrogenous bases containing a single-ring structure (thymine, cytosine, uracil).

Complementary Strands

The property of DNA strands whereby the sequence of one strand strictly dictates the opposite strand because adenine always bonds to thymine and cytosine always bonds to guanine.

Antiparallel

The parallel orientation of the two strands in a DNA double helix running in opposite directions ($5'$ to $3'$ and $3'$ to $5'$).

$5'$ and $3'$ Directionality

Terms used to track strand orientation and enzymatic movement along nucleic acids based on carbon numbering, where the oxygen of deoxyribose points toward the $5'$ end.

Semi-Conservative Replication

The mechanism of DNA duplication where each new double-stranded DNA molecule consists of one original parent strand and one newly synthesized strand.

Replisome

The multi-protein complex that works collectively to carry out DNA replication; composed of DNA helicase, single-strand binding proteins (SSBs), primase, DNA polymerase, and ligase.

DNA Helicase

The replisome enzyme that initiates replication at the origin of replication, moving from $5'$ to $3'$ along a strand to unwind DNA and break hydrogen bonds between bases.

Single-Strand Binding Proteins (SSBs)

Proteins that bind to exposed single-stranded DNA during replication to prevent strands from twisting, re-annealing, or forming secondary bonds with themselves.

Primase

An enzyme that binds to single-stranded DNA and synthesizes a short complementary RNA primer to serve as a starting point for DNA polymerase.

DNA Polymerase

The enzyme that reads a template DNA strand in the $3'$ to $5'$ direction and synthesizes a new complementary strand by adding nucleotides from the $3'$ end of an RNA primer toward the $5'$ end.

Leading Strand

The DNA strand that is synthesized continuously toward the replication fork.

Lagging Strand

The DNA strand that is synthesized discontinuously away from the replication fork, requiring repeated primer placement.

Okazaki Fragments

Short stretches of newly synthesized DNA formed discontinuously on the lagging strand.

DNA Ligase

An enzyme that scans synthesized strands, removes RNA primers, and seals breaks (nicks) in the sugar-phosphate backbone by joining adjacent DNA fragments.

DNA Proofreading

A built-in error-correction function of DNA polymerase that detects structural distortions caused by mispaired bases, halts synthesis, excises the mismatch, and replaces it with the correct nucleotide.

DNA Replication Fork (Diagram)

a. Single-strand binding proteins (SSBs); b. DNA helicase; c. DNA polymerase; d. Leading strand; e. Lagging strand; f. DNA ligase; g. Okazaki fragment; h. Primer; i. Primase; j. Replication fork; k. $3'$; l. $5'$.

Central Dogma of Biology

The principle stating that genetic information flows unidirectionally from DNA to RNA via transcription, and from RNA to protein via translation; a cell cannot reverse-engineer DNA from a protein.

Structural Differences: DNA vs. RNA

DNA is double-stranded, uses the sugar deoxyribose, and contains thymine; RNA is single-stranded, uses the sugar ribose, and contains uracil.

Messenger RNA (mRNA)

The RNA transcript that carries genetic instructions from DNA inside the nucleus out through nuclear pores to ribosomes in the cytoplasm.

Ribosomal RNA (rRNA)

The RNA component that combines with proteins to construct the structure and active sites of ribosomes.

Transfer RNA (tRNA)

Specialized RNA molecules that carry specific amino acids to the ribosome, matching their anticodon to the corresponding mRNA codon.

Promoter

A regulatory DNA sequence upstream of a gene that signals RNA polymerase where to bind and initiate transcription.

TATA Box

A specific consensus sequence located within the promoter region where RNA polymerase binds to separate DNA strands.

Spliceosome

A large protein-RNA complex that edits pre-mRNA by removing non-coding introns and joining coding exons into a mature mRNA strand.

Introns and Exons

Introns are non-coding sequences spliced out of pre-mRNA; exons are coding sequences that are retained and spliced together to form the mature mRNA coding for a protein.

Ribosome Active Sites (A, P, E)

The three catalytic regions of a ribosome: the A site receives incoming aminoacyl-tRNAs; the P site holds the tRNA carrying the growing polypeptide chain; the E site allows discharged tRNAs to exit.

Codon

A triplet sequence of nucleotides on an mRNA transcript that corresponds to a specific amino acid or stop signal.

Anticodon

A three-nucleotide sequence on a tRNA molecule complementary to a specific mRNA codon, ensuring fidelity during amino acid incorporation.

Start Codon (AUG)

The universal mRNA initiation codon recognized by the ribosome to begin translation; codes for the amino acid methionine.

Stop Codon

One of three specific triplet codons that terminate translation; they bind tRNAs lacking amino acids, prompting hydrolysis and release of the finished polypeptide.

Chaperonins

Specialized helper proteins that assist nascent polypeptide chains in correctly folding into their functional tertiary three-dimensional structures.