Survey of Biochemical Principles: The Biochemistry of Nucleic Acids

Comprehensive vocabulary flashcards covering metabolic pathways, functional groups, protein basics, nucleotide structure, DNA replication enzymes, RNA varieties, transcription, and translation based on the Survey of Biochemical Principles lecture and exam review.

Glycogenesis

The metabolic process involving the formation of glycogen from glucose.

Glycogenolysis

The metabolic breakdown of glycogen into glucose.

Gluconeogenesis

The metabolic pathway resulting in the creation of glucose from non-carbohydrates.

Glycolysis

The catabolic breakdown pathway of glucose.

NADH and FADH2

Coenzymes whose primary function is to carry electrons from one biochemical reaction to another.

Amino Acids

The molecular subunits that serve as the building blocks of proteins, consisting of an amine, a carboxylic acid, an "R" group, and an $\alpha$-hydrogen.

Glycine

The only standard amino acid that is unique because it lacks a chiral center and does not have stereoisomers.

Peptide Bond Linkage

The covalent bond that links amino acids together, formed specifically between the amino group of one amino acid and the carboxylic acid group of another.

Zwitterion

The dipolar ionic state in which amino acids naturally exist at physiological pH.

Essential Amino Acids

Amino acids that cannot be synthesized by human cells and therefore must be supplied through the diet.

Nucleotide

The monomer subunit of nucleic acids, composed of three chemical groups: a nitrogenous base, a pentose sugar, and a phosphate group.

Nitrogenous Base

A heterocyclic, nitrogen-containing amine base (also called a nucleobase) categorized into purines and pyrimidines.

Purines

The larger, two-ring nitrogenous bases utilized in nucleic acids; includes adenine and guanine.

Pyrimidines

The smaller, single-ring nitrogenous bases utilized in nucleic acids; includes cytosine, thymine (DNA only), and uracil (RNA only).

Nucleoside

A biochemical molecule formed by bonding a nitrogenous base to a pentose sugar (ribose or deoxyribose), without a phosphate group.

Ribose

A five-carbon pentose sugar incorporated into ribonucleotides used for the synthesis of RNA.

Deoxyribose

A five-carbon pentose sugar lacking an oxygen atom compared to ribose, incorporated into deoxyribonucleotides for DNA synthesis.

Phosphate Group

A chemical unit consisting of a phosphorus ($\text{P}$) atom bonded to 4 oxygen ($\text{O}$) atoms, carrying a $-3$ charge.

Cyclic Adenosine Monophosphate (cAMP)

A regulatory nucleotide second messenger synthesized from ATP by adenylate cyclase that regulates cellular glycogen, monosaccharide, and lipid metabolism via G-protein coupled receptors.

Chromatin

The highly compacted nucleoprotein mass formed by cellular DNA wound around histone proteins.

Nucleosome

A ball-like structural unit formed when the DNA double helix wraps around a bundle of histone proteins.

Euchromatin

The active, less compacted form of chromatin in the nucleus that is regularly accessed and transcribed.

Heterochromatin

Densely compacted nuclear chromatin containing conserved genetic code that is almost never accessed for transcription.

Origin of Replication

The specific chromosomal site where the replication of DNA initiates.

DNA Gyrase

A topoisomerase enzyme that relieves supercoiling by uncoiling and stabilizing the DNA superstructure ahead of the replication fork.

Helicase

The enzyme that "unzips" the DNA double helix by breaking the hydrogen bonds holding complementary base pairs together.

Single-Strand Binding Proteins

Proteins that bind to separated single strands of parent DNA to stabilize them and prevent recoiling or re-zipping during replication.

Primase

The enzyme responsible for synthesizing short RNA primers/templates required for DNA polymerases to initiate synthesis.

DNA Polymerase III

The primary enzyme that synthesizes most DNA in a $5' \rightarrow 3'$ direction at a rate of approximately $1{,}000$ nucleotides per second.

DNA Polymerase I

The enzyme that replaces RNA primers with DNA and proofreads parent-daughter pairings with an error frequency of $10^{-7}$.

Okazaki Fragments

Short pieces of DNA synthesized discontinuously along the lagging strand during replication.

DNA Ligase

The enzyme that joins Okazaki fragments together into a continuous daughter strand on the lagging strand.

Ribozymes

RNA molecules that possess enzymatic and catalytic activity, such as performing the intranuclear splicing of mRNA.

Ribosomal RNA (rRNA)

The predominant type of cellular RNA that comprises approximately $60\%$ of a ribosome's structure alongside $40\%$ protein.

Messenger RNA (mRNA)

A single-stranded nucleic acid transcribed from DNA that acts as an informational blueprint carrying genetic codons from the nucleus to ribosomes for protein synthesis.

Codon

A three-nucleotide sequence in mRNA that specifies a particular amino acid or signals a STOP to translation.

Transfer RNA (tRNA)

A folded, single-stranded RNA molecule that attaches to a specific amino acid and delivers it to the ribosome during protein synthesis.

Anticodon

The three-base segment on a tRNA molecule that base-pairs complementarily with an mRNA codon.

Sequence Hypothesis

Francis Crick's 1958 hypothesis stating that the specificity of a nucleic acid is expressed solely by its base sequence, which directly encodes the amino acid sequence of a protein.

Central Dogma of Molecular Biology

The foundational principle stating that sequential genetic information transfers from nucleic acid to nucleic acid or nucleic acid to protein, but cannot transfer from protein back to protein or nucleic acid.

Transcription

The process of synthesizing a complementary RNA strand from an antisense DNA template using the enzyme RNA polymerase.

Introns

Non-coding RNA sequences within newly synthesized pre-mRNA that are excised and removed inside the nucleus by ribozymes.

Exons

The coding sequences of an mRNA transcript that are retained and spliced together to produce mature mRNA for translation.

Translation

The cytoplasmic process in which ribosomes read mRNA codons and assemble matching amino acids brought by tRNAs into a growing polypeptide chain.

Chaperonins

Cellular protein structures that receive nascent polypeptides escorted by chaperone proteins and assist them in folding into their correct active conformation.