Biochem Exam II (except ch. 31)

A complete set of vocabulary flashcards covering key terms, definitions, molecular structures, and enzymatic mechanisms across DNA/RNA structure, biotechnology techniques, bioinformatics, replication/repair, and transcription/processing.

Nucleoside

A compound composed of a purine or pyrimidine base linked to a pentose sugar (ribose or deoxyribose) at the $\text{C-1'}$ position via a $\beta\text{-glycosidic linkage}$.

Nucleotide

A nucleoside that has one or more phosphoryl groups attached to its sugar moiety.

$$\beta\text{-Glycosidic Linkage}$$

The covalent bond connecting the $\text{C-1'}$ carbon atom of the sugar to the $\text{N-9}$ atom of a purine base or the $\text{N-1}$ atom of a pyrimidine base.

Purines

A class of nitrogenous bases with a double-ring structure, which includes Adenine and Guanine.

Pyrimidines

A class of nitrogenous bases with a single-ring structure, which includes Cytosine, Thymine (in DNA), and Uracil (in RNA).

3'-to-5' Phosphodiester Linkage

The covalent linkage connecting adjacent nucleotides in nucleic acids, formed between the 3'-hydroxyl group of one sugar and the 5'-phosphoryl group of the next sugar.

A-DNA

A right-handed DNA double helix that forms under less hydrated conditions, featuring a diameter of $\sim 26\,\text{\AA}$, 11 base pairs per turn, a pitch of $25.3\,\text{\AA}$, a base pair tilt of $19^\circ$ from perpendicular, and sugar puckering in the $\text{C-3'-endo}$ conformation.

B-DNA

The standard right-handed double-helical structure of hydrated DNA in cells, featuring a diameter of $\sim 20\,\text{\AA}$, 10.4 base pairs per turn, a rise of $3.4\,\text{\AA}$ per base pair, a pitch of $35.4\,\text{\AA}$, a base pair tilt of $1^\circ$, and sugar puckering in the $\text{C-2'-endo}$ conformation.

Z-DNA

A left-handed DNA double helix with a zigzagged phosphate backbone, featuring a diameter of $\sim 18\,\text{\AA}$, 12 base pairs per turn, a pitch of $45.6\,\text{\AA}$, a base pair tilt of $9^\circ$, and alternating anti and syn glycosidic bond conformations.

Melting Temperature ($T_m$)

The temperature at which half of the helical DNA molecules in a solution are denatured into single strands.

Restriction Enzymes

Bacterial endonucleases that recognize specific palindromic cleavage sites of 4 to 8 nucleotides in length and cleave double-stranded DNA in a highly specific manner.

Southern Blotting

A molecular technique where DNA fragments separated by gel electrophoresis are transferred to a sheet of nitrocellulose paper and hybridized with a complementary, radioactively labeled DNA probe to identify specific sequences.

Northern Blotting

A blotting technique in which RNA sequences separated by gel electrophoresis are identified using complementary DNA probes.

Western Blotting

A technique where proteins separated by SDS-PAGE are transferred to a polymer sheet and detected using a primary antibody specific for the target protein, followed by a tagged secondary antibody.

Edman Degradation

A chemical method for sequencing proteins by sequentially removing and identifying N-terminal amino acid residues, with a operational limit of 50 amino acids.

Sanger Dideoxy Method

A enzymatic DNA sequencing technique that incorporates $\text{2', 3'-dideoxy}$ nucleoside triphosphate analogs to terminate strand elongation, capable of sequencing sequences up to $\sim 1000\,\text{bp}$.

Solid-Phase Peptide Synthesis

A method for synthesizing peptides by sequentially coupling t-Boc-protected amino acids to a growing chain anchored on an insoluble reactive resin support.

Phosphite Triester Method

A solid-phase chemical synthesis method for DNA chains up to $\sim 100$ nucleotides long, using activated deoxyribonucleoside $3'\text{-phosphoramidite}$ monomers blocked with DMT and $\beta\text{CE}$ groups.

Homologs

Two or more biological molecules that are derived from a common ancestral gene or sequence.

Orthologs

Homologous molecules present in different species that perform similar biological functions.

Paralogs

Homologous molecules present within a single species that have evolved to perform different functions.

BLAST

Basic Local Alignment Search Tool; an alignment program that compares query nucleotide or protein sequences to databases to calculate statistical significance and identify homologous sequences.

Sequence Identity Homology Rule

A sequence comparison guideline for proteins longer than 100 amino acids stating that identities greater than $25\%$ indicate probable homology, whereas identities below $15\%$ indicate an absence of homology.

Protein Data Bank (PDB)

An international archive that curates and annotates three-dimensional structural data for biological macromolecules determined by methods like X-ray diffraction and neutron diffraction.

DNA Polymerase Active Site Structure

A catalytic domain shaped like a right hand, in which palm, fingers, and thumb subdomains position the DNA substrate and incoming dNTPs.

Two-Divalent-Cation Mechanism

The catalytic mechanism of DNA polymerase requiring two bound $\text{Mg}^{2+}$ ions; one orients the incoming dNTP relative to the primer's 3'-OH, and the other stabilizes the negative charges of the pyrophosphate product.

Primase

A specialized RNA polymerase that synthesizes a short RNA primer ($\approx 5$ nucleotides) complementary to the DNA template strand to initiate DNA synthesis.

Leading Strand

The DNA strand at the replication fork that is synthesized continuously in the 5'-to-3' direction toward the replication fork movement.

Lagging Strand

The DNA strand at the replication fork that is synthesized discontinuously in the 5'-to-3' direction as short Okazaki fragments away from the replication fork.

DNA Ligase

An enzyme that joins DNA strands by catalyzing the formation of a phosphodiester bond between a free 3'-hydroxyl group and a 5'-phosphoryl group, using ATP (or $\text{NAD}^+$ in bacteria).

Helicase

An ATP-driven hexameric protein ring that unwinds double-stranded DNA ahead of the replication fork by acting as a wedge.

Topoisomerases

Enzymes that regulate DNA supercoiling; Type I topoisomerases relax supercoils without ATP, while Type II topoisomerases (such as DNA gyrase) introduce negative supercoils at the expense of ATP hydrolysis.

Processivity

The ability of an enzyme, such as DNA polymerase III, to catalyze multiple consecutive additions of nucleotides without releasing the DNA template, enabled by the sliding clamp ($\beta_2$ subunit).

oriC locus

The unique 245 base-pair origin of replication site in E. coli where DnaA protein hexamers bind to initiate unwinding and assembly of the replication complex.

Polymerase Switching

The process in eukaryotic DNA replication where initiator DNA polymerase $\alpha$ (which synthesizes an RNA primer plus $\approx 20$ dNTPs) is replaced by the highly processive DNA polymerase $\delta$.

Telomeres

Repetitive single-stranded and double-stranded DNA structures containing tandem 6-nucleotide G-rich sequence repeats at the ends of linear chromosomes that protect them from degradation.

Telomerase

A specialized reverse transcriptase ribonucleoprotein enzyme that uses an intrinsic RNA template to elongate the single-stranded G-rich overhang of telomeres.

8-Oxoguanine

An oxidized derivative of guanine caused by hydroxyl radicals that mispairs with adenine instead of cytosine during replication.

Hypoxanthine

A deaminated derivative of adenine that base-pairs with cytosine instead of thymine, leading to mutagenic transitions.

Mismatch Repair System

A DNA repair mechanism in E. coli utilizing MutS to recognize mismatches and MutL/MutH to recruit an endonuclease, removing errors escaping proofreading.

UvrABC Excinuclease

An enzyme complex involved in nucleotide excision repair that cleaves DNA on both sides of structural distortions, such as pyrimidine dimers, to excise a 12-nucleotide fragment.

Uracil DNA Glycosylase

A base excision repair enzyme that hydrolyzes uracil formed by spontaneous cytosine deamination in DNA, leaving an AP site for subsequent repair.

Ames Test

A biological assay developed by Bruce Ames that uses histidine-requiring mutant strains of Salmonella to screen chemicals for mutagenic activity.

RNA Polymerase Holoenzyme (Prokaryotic)

The complete E. coli transcription complex comprising the core enzyme ($\alpha_2\beta\beta'\omega$) and a $\sigma$ subunit required for specific promoter recognition.

Core Promoter (Prokaryotic)

The region of DNA containing the $-10$ sequence (TATAAT) and $-35$ sequence (TTGACA) recognized by the RNA polymerase $sigma$ subunit to direct transcription initiation.

Rho ($\rho$) Protein

An ATP-hydrolyzing hexameric protein that binds specific sequences on nascent RNA and tracks along the transcript to dissociate the transcription bubble from RNA polymerase.

Eukaryotic RNA Polymerases

Three nuclear enzymes with distinct functions: RNA Polymerase I (nucleolus; 18S, 5.8S, 28S rRNA; $\alpha\text{-amanitin}$ insensitive), RNA Polymerase II (nucleoplasm; mRNA precursors and snRNA; strongly inhibited by $\alpha\text{-amanitin}$), and RNA Polymerase III (nucleoplasm; tRNA and 5S rRNA; inhibited by high $\alpha\text{-amanitin}$ concentrations).

5' Cap

A post-transcriptional modification at the 5' end of eukaryotic pre-mRNA consisting of a 7-methylguanosine attached via an unusual 5'-to-5' triphosphate linkage, protecting mRNA from nucleases and enhancing translation.

Poly(A) Tail

A tract of approximately 250 adenylate residues added to the 3' end of cleaved eukaryotic pre-mRNA by poly(A) polymerase to increase mRNA stability and translation efficiency.

MicroRNAs (miRNAs)

Small non-coding RNA molecules ($\approx 20\text{--}23$ nucleotides) cleaved from precursor transcripts that bind Argonaute proteins to regulate eukaryotic gene expression.

RNA Editing

The post-transcriptional alteration of an mRNA sequence (such as deamination of cytidine to uridine in apolipoprotein B mRNA) that changes coding information without RNA splicing.

Spliceosome

A large nuclear ribonucleoprotein complex composed of pre-mRNA, splicing factors, and five snRNPs (U1, U2, U4, U5, U6) that catalyzes the removal of introns and joining of exons.

Lariat Intermediate

A looped intron structure generated during nuclear mRNA splicing when the 2'-OH group of an adenylate residue at the branch site attacks the 5' splice site via transesterification.

Group I Self-Splicing Introns

Self-splicing RNA introns that require a guanosine nucleoside or nucleotide cofactor whose 3'-OH group initiates the first nucleophilic transesterification attack on the 5' splice site.

Carboxyl-Terminal Domain (CTD)

The flexible tail of eukaryotic RNA polymerase II whose phosphorylation coordinates transcription with 5' capping, splicing factor recruitment, and 3' polyadenylation cleavage.

Alternative Splicing

A gene regulatory mechanism in eukaryotes where pre-mRNA exon combinations are selectively included or excluded, producing multiple protein isoforms from a single gene.

Ribozyme

A catalytic RNA molecule capable of accelerating specific chemical reactions, such as RNase P, snRNAs in the spliceosome, and rRNAs in the ribosome.