Biochemistry Fundamentals: Biomolecules, Molecular Biology, Techniques, and Acid-Base Chemistry

Vocabulary practice flashcards covering biomolecules, properties of water, nucleic acid structure, central dogma processes (replication, transcription, translation), molecular biotechniques, acid-base chemistry, and amino acid classifications.

Proteins

Polymers of amino acids linked by peptide bonds that serve as the workhorses of the cell and carry out cellular functions.

Nucleic acids

Polymers of nucleotides that manage genetic information; DNA stores genetic information, while RNA makes that information accessible.

Lipids

Hydrophobic biomolecules whose primary roles include energy storage and the structural formation of cell membranes.

Carbohydrates

Sugars that can link together to function as a cellular fuel source and participate in cell identification and communication.

Central dogma of biology

The principle describing the flow of genetic information within a cell from DNA to RNA via transcription, and from RNA to protein via translation.

Replication

The biological process in which an existing DNA molecule is copied to produce DNA.

Transcription

The biological process in which DNA is utilized as a template to synthesize RNA.

Translation

The cellular process in which information encoded within mRNA is used to synthesize a protein.

Polarity of water

An uneven distribution of electric charge where oxygen is more electronegative than hydrogen, giving oxygen a partial negative charge ($\delta^-$) and hydrogen a partial positive charge ($\delta^+$).

Hydrogen bond

A noncovalent interaction formed between a hydrogen atom bonded to an electronegative atom (such as O, N, S, or F) and another electronegative atom, involving a donor and an acceptor.

Electrostatic interactions

Noncovalent interactions (also referred to as ionic interactions or salt bridges) that occur between electrical charges of opposite signs to stabilize charged molecules.

Van der Waals interactions

Very weak noncovalent attractions (also called London dispersion forces) between atoms that arise from temporary asymmetric distributions of electrons as atoms approach one another.

Hydrophobic interactions

The tendency of nonpolar, hydrophobic molecules to aggregate in an aqueous environment, thermodynamically driven by an increase in the entropy of the surrounding water system.

Nucleoside

A nucleic acid building block composed solely of a five-carbon sugar attached to a nitrogenous base, lacking a phosphate group.

Nucleotide

The basic monomer of nucleic acids composed of three distinct components: a five-carbon sugar, a nitrogenous base, and one or more phosphate groups.

Purines

Double-ring nitrogenous bases found in nucleic acids, specifically adenine (A) and guanine (G).

Pyrimidines

Single-ring nitrogenous bases found in nucleic acids, specifically cytosine (C), thymine (T), and uracil (U).

Phosphodiester bond

A covalent linkage connecting the $3'$ position of one sugar to the $5'$ position of the adjacent sugar, establishing the sugar-phosphate backbone of DNA and RNA.

Promoter sequence

A regulatory DNA sequence (such as the eukaryotic TATA box or bacterial $-10$ Pribnow box) that positions the transcription machinery and influences transcription levels.

mRNA

Messenger RNA; the class of RNA that carries transcribed genetic information used as a template to synthesize proteins.

tRNA

Transfer RNA; an adaptor RNA molecule that delivers specific amino acids to the ribosome and pairs with mRNA codons through its anticodon.

rRNA

Ribosomal RNA; the RNA species that forms a core structural constituent of the ribosome and catalyzes peptide bond formation.

Ribosomal A site

The aminoacyl site of the ribosome where incoming aminoacyl-tRNA molecules enter during translation elongation.

Ribosomal P site

The peptidyl site of the ribosome that holds the tRNA carrying the growing polypeptide chain, and where the initiator tRNA carrying fMet initially binds.

Ribosomal E site

The exit site of the ribosome through which deacylated, empty tRNA molecules leave during translation elongation.

EF-G

An elongation factor that hydrolyzes GTP to power the translocation of the ribosome along mRNA during protein translation.

Restriction endonucleases

Enzymes that cleave double-stranded DNA molecules at specific target nucleotide sequences.

Probes

Nucleic acid fragments employed to recognize and bind complementary DNA or RNA sequences.

DNA cloning

A recombinant DNA method that produces identical copies of a target DNA sequence by inserting it into a cloning vector and propagating it within a host cell.

Polymerase Chain Reaction (PCR)

A method used to amplify a specific DNA sequence through recurring temperature cycles of denaturation (heat separation), annealing (primer binding), and extension by Taq DNA polymerase.

RT-PCR

Reverse transcription PCR; a technique in which extracted RNA is converted into cDNA using reverse transcriptase and subsequently amplified by PCR to evaluate gene expression.

cDNA microarray

A technique where cDNA samples labeled with distinct fluorescent tags are hybridized to immobilized DNA sequences to compare the expression profiles of many genes simultaneously.

SDS-PAGE

Sodium dodecyl sulfate polyacrylamide gel electrophoresis; a technique that separates denatured proteins based on size through a gel mesh to assess purity and molecular weight.

Sodium dodecyl sulfate (SDS)

A detergent that denatures proteins by removing their 3D structure and coats them with negative charges, providing an identical charge-to-mass ratio so migration depends primarily on size.

Western blot

An analytical method in which proteins separated by SDS-PAGE are transferred onto a membrane and detected using specific primary and secondary antibodies to determine the size and presence of a specific protein.

ELISA

Enzyme-linked immunosorbent assay; an antibody-based assay using an enzyme-linked secondary antibody to detect the presence and quantify the amount of a target protein via measurable color change.

Acid

A chemical substance that acts as a proton donor by releasing $H^+$ into solution.

Base

A chemical substance that acts as a proton acceptor by binding $H^+$ from solution.

pH

A logarithmic measurement of hydrogen ion concentration in solution, defined by the relationship $\text{pH} = -\log_{10}[H^+]$.

pKa

The characteristic pH value at which a titratable, ionizable chemical group is exactly $50\%$ protonated and $50\%$ deprotonated.

Buffer

An aqueous solution that resists changes in pH when small amounts of acid or base are introduced, operating most effectively within approximately $\text{p}K_a \pm 1$ pH unit.

Zwitterion

A dipolar molecule carrying both positive and negative charges at separate functional groups while bearing an overall net electrical charge of zero.

Isoelectric point (pI)

The specific pH at which an amino acid or protein possesses an average net electrical charge of zero.

Amino acid

A monomeric unit consisting of a central $\alpha$-carbon bonded to an amino group, a carboxyl group, a hydrogen atom, and a variable side chain (R group) that defines its chemical properties.

Glycine

The smallest nonpolar amino acid, possessing a single hydrogen atom ($-H$) as its side chain, which confers high structural flexibility to the peptide backbone.

Proline

A nonpolar amino acid with a rigid cyclic side chain covalently bonded back to the amino nitrogen, restricting conformational movement of the polypeptide backbone.

Cysteine

A polar uncharged amino acid containing a sulfhydryl (thiol) side group capable of forming covalent disulfide bonds with other cysteine residues.

Histidine

A basic amino acid whose imidazole ring side chain has a $\text{p}K_a$ near physiological pH, allowing it to readily gain or lose a proton ($H^+$).