biochem final

Nucleic Acid

Biomolecules, including DNA and RNA, made up of nucleotide monomers containing a nitrogenous base, a sugar, and a phosphate group.

Deoxyribose

The sugar component of DNA, lacking a hydroxyl group on the 2' carbon.

Ribose

The sugar component of RNA, containing a hydroxyl group at the 2' carbon.

Polynucleotides

Long chains of nucleotides linked together by phosphodiester bonds.

Phosphodiester Bonds

Covalent bonds formed between the 3' hydroxyl and 5' phosphate groups of nucleotides.

Directionality

The orientation of a nucleic acid strand; the 5' end has a free phosphate group and the 3' end has a free hydroxyl group.

Purines

Nitrogenous bases that include adenine (A) and guanine (G).

Pyrimidines

Nitrogenous bases that include cytosine (C), thymine (T), and uracil (U).

Double Helix

The twisted ladder structure of DNA, formed by two antiparallel strands.

Antiparallel Strands

Strands of DNA that run in opposite directions, one from 5' to 3' and the other from 3' to 5'.

Secondary Structures

Complex shapes formed by RNA due to internal base pairing, such as stem-loops and hairpins.

Differential Gene Expression

The phenomenon where different cell types express different genes based on their function despite having the same DNA.

Gene

A sequence of DNA that codes for a functional product, either a protein or a functional RNA.

Operons

Groups of genes organized together in prokaryotes that can be transcribed as a single unit.

Polycistronic mRNA

A type of mRNA that codes for multiple proteins, characteristic of prokaryotic gene expression.

Monocistronic mRNA

An mRNA that codes for a single protein, typical in eukaryotic cells.

Introns

Non-coding regions of a gene that are removed during RNA processing.

Exons

Coding regions of a gene that remain in the mRNA after processing.

mRNA Processing

The modifications a pre-mRNA undergoes, including capping, splicing, and polyadenylation.

Semiconservative Replication

The method of DNA replication in which each new molecule consists of one parental strand and one new strand.

Origins of Replication

Specific sites on the DNA where replication begins.

Bidirectionally

Replication proceeds in two directions from the origin, forming two replication forks.

Leading Strand

The DNA strand synthesized continuously in the direction of the replication fork.

Lagging Strand

The DNA strand synthesized discontinuously, forming short fragments known as Okazaki fragments.

Okazaki Fragments

Short segments of DNA synthesized on the lagging strand during DNA replication.

DNA Ligase

Enzyme that joins Okazaki fragments together by sealing nicks in the DNA backbone.

Helicase

Enzyme that unwinds the DNA double helix during replication.

Topoisomerase

Enzyme that alleviates torsional strain ahead of the replication fork.

Primase

Enzyme that synthesizes RNA primers needed to initiate DNA synthesis.

DNA Polymerase III

The main enzyme that extends the new DNA strand from the RNA primer during replication.

DNA Polymerase I

Enzyme that replaces RNA primers with DNA during replication.

3' to 5' Exonuclease Activity

Proofreading function of DNA polymerases that helps reduce errors in DNA replication.

RNA Polymerase

The enzyme that synthesizes RNA from a DNA template during transcription.

Promoter

Sequence of DNA where RNA polymerase binds to initiate transcription.

σ Factor

Protein that assists RNA polymerase in binding to the promoter in prokaryotes.

RNA Pol I

RNA polymerase that synthesizes most ribosomal RNA (rRNA).

RNA Pol II

RNA polymerase that synthesizes messenger RNA (mRNA) and some small nuclear RNA (snRNA).

RNA Pol III

RNA polymerase that synthesizes transfer RNA (tRNA) and 5S ribosomal RNA.

General Transcription Factors (GTFs)

Proteins required for RNA polymerase II to initiate transcription at a core promoter.

Core Promoter

Region of DNA where the transcription machinery assembles, often containing a TATA box.

Pre-initiating Complex (PIC)

Complex formed during transcription initiation that includes RNA polymerase II and transcription factors.

Co-transcriptional Processing

Modifications made to mRNA simultaneously with transcription, including capping and splicing.

5’ Capping

The addition of a modified guanine nucleotide (7-methylguanosine) to the 5' end of mRNA.

Spliceosome

Molecular complex that removes introns from pre-mRNA during splicing.

3’ Polyadenylation

The addition of a poly-A tail to the 3' end of mRNA after transcription.

Translation

The process of synthesizing a protein from an mRNA template.

Ribosome

Cellular machinery made of rRNA and proteins that facilitates protein synthesis.

A Site (Aminoacyl)

The site on a ribosome where the incoming tRNA binds during translation.

P Site (Peptidyl)

The site on a ribosome where the growing peptide chain is held during translation.

E Site (Exit)

The site on a ribosome where tRNAs exit after donating their amino acids.

Initiation (Translation)

The phase where ribosomes assemble on mRNA and the first tRNA binds to the start codon.

Shine-Dalgarno Sequence

A ribosomal binding site in prokaryotic mRNA that helps initiate translation.

Kozak Sequence

Sequence surrounding the start codon in eukaryotic mRNA that aids in translation initiation.

Peptidyl Transferase

Enzymatic activity of the ribosome that forms peptide bonds between amino acids.

Translocation (Translation)

Process where the ribosome moves along the mRNA to the next codon during protein synthesis.

Stop Codon

Nucleotide triplet (UAA, UAG, UGA) that signals the termination of translation.

Release Factors

Proteins that bind to the A site and trigger the release of the completed polypeptide during termination.

Anticodon

Three-nucleotide sequence in tRNA that base-pairs with a complementary codon on mRNA.

Aminoacyl-tRNA Synthetase

Enzyme that attaches the correct amino acid to its corresponding tRNA.

Gene Regulation

The process by which cells control the expression of genes.

Constitutive Genes

Genes that are always expressed and do not change under different conditions.

Inducible Genes

Genes that are expressed only under specific conditions.

Transcription Initiation

The most common control point for gene regulation, where transcription begins.

Positive Regulation

Mechanism by which activator proteins enhance transcription by facilitating RNA polymerase binding.

Negative Regulation

Mechanism where repressor proteins inhibit transcription by binding to operators.

Lac Operon

A well-studied example of transcriptional regulation in prokaryotes responsible for lactose metabolism.

LacI Repressor

Protein that binds to the operator in the absence of lactose, blocking transcription of the lac operon.

cAMP (cyclic AMP)

A signaling molecule that promotes transcription in the absence of glucose by binding to CAP.

Dual Control

A regulatory mechanism ensuring an operon is active when certain conditions are met, such as lactose present and glucose absent.