Cellular and Molecular Biology Study Guide: DNA Replication, Transcription, mRNA Processing, Translation, and Mutations (copy)

Central Dogma of Molecular Biology

The concept that biological information flows unidirectionally from DNA to RNA to protein.

Transcription

The process of synthesizing a complementary RNA transcript from a DNA template catalyzed by RNA polymerase.

Translation

The decoding of the nucleotide sequence of an mRNA transcript into a specific amino acid sequence to construct a protein.

RNA Intermediate

RNA serves as a transient intermediate between DNA and protein, allowing for signal regulation and flexibility.

Signal Amplification

The ability for one genomic DNA sequence to be transcribed into multiple mRNA transcripts which can be translated into many proteins.

Differential Gene Regulation

The independent regulation of specific genes allowing them to be transcribed at varying rates.

Prokaryotic Gene Expression

In bacteria, transcription and translation occur simultaneously in the cytoplasm.

Eukaryotic Gene Expression

In eukaryotes, transcription occurs in the nucleus and mRNA processing occurs before translation in the cytoplasm.

Ribose vs. Deoxyribose

RNA contains ribose sugar while DNA contains 2'-deoxyribose sugar.

Uracil and Thymine

RNA uses uracil (U) instead of thymine (T), which pairs with adenine (A) during base pairing.

Strandness in DNA and RNA

DNA is double-stranded while RNA is typically single-stranded.

RNA Structural Flexibility

RNA can fold into various 3D structures, allowing it to have diverse functions.

Coding RNA

mRNA that serves as a template for protein synthesis.

tRNA (Transfer RNA)

Small RNA molecules that deliver specific amino acids to ribosomes during translation.

rRNA (Ribosomal RNA)

The type of RNA that makes up the structure and function of ribosomes and catalyzes peptide bond formation.

miRNA (MicroRNA)

Short non-coding RNAs that regulate gene expression by binding to target mRNAs.

snRNA (Small Nuclear RNA)

RNA that plays a role in the splicing of pre-mRNA.

snoRNA (Small Nucleolar RNA)

RNA that directs chemical modifications of rRNAs within the nucleolus.

siRNA (Small Interfering RNA)

Double-stranded RNA involved in RNA interference to silence gene expression.

LncRNA (Long Non-Coding RNA)

Long RNA molecules that regulate gene expression at various levels.

DNA Replication

The process by which DNA is copied to produce identical replicas.

Semiconservative Replication

Each new DNA helix contains one old and one new strand.

DNA Helicase

Enzyme that unwinds double-stranded DNA during replication.

DNA Primase

Enzyme that synthesizes short RNA primers needed for DNA synthesis.

Leading Strand

The DNA strand that is synthesized continuously in the same direction as the replication fork.

Lagging Strand

The DNA strand synthesized in short pieces (Okazaki fragments) in the opposite direction to the replication fork.

DNA Polymerase

The main enzyme responsible for synthesizing new DNA strands.

Proofreading Activity

The ability of DNA polymerases to correct errors during DNA replication.

Eukaryotic Pre-mRNA Processing

Modifications of pre-mRNA including capping, polyadenylation, and splicing.

5' Cap

A modified guanine nucleotide added to the 5' end of mRNA for protection and ribosome recognition.

Poly-A Tail

A stretch of adenine nucleotides added to the 3' end of mRNA, enhancing stability and transport.

Splicing

The process of removing introns and joining exons in pre-mRNA to form mature mRNA.

Proteasome

A protein complex that degrades unneeded or damaged proteins tagged with ubiquitin.

Silent Mutation

A change in DNA that does not alter the amino acid sequence of a protein.

Missense Mutation

A change in DNA that results in the substitution of one amino acid for another in a protein.

Nonsense Mutation

A change in DNA that creates a premature stop codon in a protein.

Frameshift Mutation

An insertion or deletion of nucleotides that alters the reading frame of the genetic message.

Splice Site Mutation

A mutation affecting the boundaries of exons and introns, potentially disrupting splicing.

Promoter

A specific DNA sequence where RNA polymerase and transcription factors bind to initiate transcription.

Transcription Factors

Regulatory proteins that bind to specific DNA sequences to control the rate of transcription.

DNA Ligase

An enzyme that joins Okazaki fragments on the lagging strand by forming phosphodiester bonds.

Topoisomerase

An enzyme that relieves strain and prevents supercoiling ahead of the DNA replication fork.

Single-Stranded Binding Proteins (SSBs)

Proteins that bind to and stabilize unwound single-stranded DNA during replication.

Telomeres and Telomerase

Repetitive DNA sequences at chromosome ends and the specialized enzyme that maintains them to prevent truncation.

Codon

A sequence of three mRNA nucleotides that specifies a specific amino acid or stop signal.

Anticodon

A triplet nucleotide sequence on tRNA that base-pairs with a complementary mRNA codon.

Degeneracy of the Genetic Code

The phenomenon where multiple distinct codons can encode the same amino acid.

Ribosomal A, P, and E Sites

The three functional tRNA binding sites on a ribosome responsible for aminoacyl entry, peptidyl transfer, and exit.

Operon

A functioning unit of genomic DNA containing a cluster of genes under the control of a single promoter in prokaryotes.

Enhancers and Silencers

Non-coding DNA sequences that increase or decrease transcription levels when bound by specific regulatory proteins.

DNA Methylation

An epigenetic mechanism involving the addition of methyl groups to DNA bases, usually inhibiting gene transcription.

Histone Acetylation

An epigenetic modification that adds acetyl groups to histones, relaxing chromatin structure and activating transcription.

Mismatch Repair (MMR)

A DNA repair pathway that identifies and fixes mismatched bases that escaped polymerase proofreading.

Wobble Hypothesis

The flexibility in base-pairing rules at the third nucleotide position of a codon, allowing a single tRNA to pair with multiple codons.

Alternative Splicing

A molecular mechanism in eukaryotes where different combinations of exons are joined, producing multiple distinct protein isoforms from a single gene.

Nucleotide Excision Repair (NER)

A DNA repair pathway that recognizes and removes bulky lesion damage, such as UV-induced pyrimidine dimers.

TATA Box

A conserved DNA sequence found in promoter regions of eukaryotes that guides the positioning of transcription factors and RNA polymerase II.

Reverse Transcriptase

An enzyme that synthesizes complementary DNA (cDNA) from an RNA template, reversing the standard direction of information flow.

Post-Translational Modifications (PTMs)

Covalent modifications to proteins after synthesis, such as phosphorylation or glycosylation, which alter protein function, localization, or stability.

Nuclear Envelope Barrier

The eukaryotic cellular structure that physically separates nuclear transcription from cytoplasmic translation, preventing them from occurring simultaneously.

Evolutionary Advantage of Genetic Code Degeneracy

It provides a buffer against mutations, allowing many single nucleotide substitutions to result in the same amino acid without disrupting protein function.

Directionality of Nucleic Acid Synthesis

Nucleic acids are always synthesized in the 5' to 3' direction because polymerases require a free 3'-OH group to attach incoming nucleotides.

Epigenetic Modifications vs. Genetic Mutations

Epigenetic modifications are heritable changes that do not alter the DNA sequence itself, while genetic mutations are permanent alterations in the DNA sequence that can affect gene function.

Promoter (Molecular Analogy)

Compares to a bright neon directional sign, marking the location on DNA where RNA polymerase and transcription factors must dock to start transcription.

Ribosome (Molecular Analogy)

Compares to an automated factory 3D printer, reading instruction strips (mRNA) and assembling precise component sequences (amino acids into proteins).

tRNA (Molecular Analogy)

Compares to a specialized delivery truck with a specific key adapter, bringing matching cargo (amino acids) to specific delivery slots (mRNA codons).

DNA Helicase (Molecular Analogy)

Compares to a zipper slider, opening and separating the double strands of DNA so template sequences can be read.

Spliceosome (Molecular Analogy)

Compares to a movie editor, removing unwanted filler clips (introns) and joining crucial story scenes (exons) into a continuous final cut.

Base Excision Repair (BER)

A DNA repair mechanism that removes single damaged bases (such as oxidized or deaminated bases) using specific DNA glycosylases.

Shine-Dalgarno Sequence

A conserved ribosomal binding site in prokaryotic mRNA located upstream of the start codon that correctly aligns the ribosome for translation initiation.

Molecular Chaperones

Helper proteins that bind to newly synthesized polypeptide chains to assist in their correct three-dimensional folding and prevent aggregation.They play a crucial role in protein folding, ensuring proper functionality and stability of proteins.

RNA polymerase

An enzyme that synthesizes RNA from a DNA template during the process of transcription, facilitating the formation of messenger RNA (mRNA) and other types of RNA.

role of RNA in replication

RNA serves as a primer for DNA synthesis during replication, providing the necessary 3'-OH group for DNA polymerase to elongate the new DNA strand.

role of DNA in replication

DNA serves as the template for synthesizing a new complementary strand during replication, ensuring accurate copying of genetic information.

steps of translation

initiation, where the ribosome assembles around the mRNA; elongation, where amino acids are added to the growing polypeptide chain; and termination, when the ribosome reaches a stop codon, leading to the release of the completed protein.

steps of transcription

initiation, where RNA polymerase binds to the promoter region of the DNA; elongation, where RNA polymerase synthesizes the RNA strand complementary to the DNA template; and termination, when RNA polymerase reaches a termination signal, releasing the newly formed RNA molecule.

steps of replication

initiation, where DNA strands are unwound; elongation, during which new nucleotide strands are synthesized; and termination, where replication ends and two identical DNA molecules are formed.

all main enzymes involved and their functions

The main enzymes involved in DNA replication include helicase, which unwinds the DNA double helix; DNA polymerase, which synthesizes new DNA strands by adding nucleotides; primase, which lays down an RNA primer to start synthesis; and ligase, which connects Okazaki fragments on the lagging strand.

septa and mini-cells

Septa are structures that divide cells or compartments in bacteria, while mini-cells are small, often non-replicating cells that lack genetic material, typically formed during cell division. Both are important in understanding bacterial cell structure and growth.

what proteins form Z-ring

The Z-ring is primarily formed by the protein FtsZ, which is a tubulin-like protein that polymerizes to create a filamentous structure. This structure plays a crucial role in bacterial cell division by aiding in the constriction of the cell membrane during cytokinesis.

what are ORIs

Origins of replication, specific sites on DNA where replication begins, marked by specific sequences to initiate the process.

what are ORCs

Origin Recognition Complexes, multi-protein complexes that bind to origins of replication to initiate DNA replication.

role of methylation

Methylation is a biochemical process that involves the addition of a methyl group to DNA, typically at cytosine bases, which can regulate gene expression by altering DNA accessibility and influencing chromatin structure.

what is the replication fork and ALL the elements

The replication fork is the Y-shaped structure formed during DNA replication where the DNA double helix is unwound, separating into two strands. Essential elements at the replication fork include helicase, which unwinds the DNA, DNA polymerase, which synthesizes new DNA strands, and single-strand binding proteins, which stabilize the unwound single strands.

what are plasmids

Small, circular DNA molecules found in bacteria that replicate independently of chromosomal DNA, often carrying genes for antibiotic resistance or other traits.

what is the replisome

The replisome is a complex of proteins responsible for DNA replication, including DNA polymerases, helicases, and various accessory factors that work together to synthesize new DNA strands at the replication fork.

what is the role of topiosomes

Topoisomerases are enzymes that alleviate the torsional strain generated ahead of the replication fork by creating temporary breaks in the DNA strands, allowing them to unwind and prevent supercoiling during DNA replication.

control of replication in prokaryotes

The control of replication in prokaryotes involves several mechanisms that regulate the timing and initiation of DNA synthesis, primarily through the binding of specific proteins to the origin of replication, ensuring that replication occurs only once per cell cycle.

replication “Correcting” proofreading

is a process where DNA polymerases detect and correct errors during DNA synthesis to ensure high fidelity of the newly synthesized strands.

what are the fragments of okazaki

Okazaki fragments are short segments of DNA synthesized discontinuously on the lagging strand during DNA replication. They are later joined together by DNA ligase to form a continuous strand.

explain flow of information from gene to protein and why RNA exists as an intermediate

The flow of information from a gene to a protein involves transcription of the gene into messenger RNA (mRNA), which is then translated into a protein by ribosomes. RNA exists as an intermediate because it provides a temporary, stable, and versatile carrier of genetic information that can be edited and regulated before the final translation into protein.

how are codons ambiguous and degenerate

Codons are considered ambiguous and degenerate because multiple codons can code for the same amino acid, resulting in redundancy in the genetic code. This means that changes in the DNA sequence may not always lead to changes in the protein produced.

how many amino acids, tRNA, codons are there

There are 20 standard amino acids encoded by 64 possible codons in the genetic code. Each tRNA molecule is specific to one amino acid and recognizes one or more corresponding codons during translation.

parts of tRNA

tRNA consists of three main parts: an anticodon region that pairs with the corresponding codon on mRNA, an amino acid attachment site for binding a specific amino acid, and a cloverleaf structure that facilitates its function during translation.

3 parts of mRNA processing

The three main parts of mRNA processing are capping, polyadenylation, and splicing. Capping adds a modified guanine nucleotide to the 5' end, polyadenylation adds a poly(A) tail to the 3' end, and splicing removes introns while joining exons together.