Exam 3

DNA Structure

The arrangement of nucleotide chains in a double-helix formation, consisting of a backbone made of sugars and phosphate groups with nitrogenous bases pairing in the middle.

Complementary Base Pairing

The specific pairing of nucleotides in DNA, where adenine pairs with thymine and guanine pairs with cytosine.

Semi-conservative Replication

The method of DNA replication where each daughter DNA molecule contains one original strand and one new strand.

DNA Polymerase

The enzyme responsible for adding nucleotides to a growing DNA strand during replication.

Euchromatin

A loosely packed form of chromatin that is transcriptionally active and accessible for gene expression.

Heterochromatin

A tightly packed form of chromatin that is generally transcriptionally inactive.

Nucleosome

The structural unit of chromatin, consisting of DNA wrapped around a core of histone proteins.

Chargaff’s Rule

The principle stating that in double-stranded DNA, the amount of adenine equals the amount of thymine, and the amount of guanine equals the amount of cytosine.

Polymerase Chain Reaction (PCR)

A technique used to amplify a specific segment of DNA, resulting in millions of copies of that target region.

RNA Primer

A short strand of RNA that provides a starting point for DNA synthesis by DNA polymerase.

Telomere

The repetitive nucleotide sequences at the ends of linear chromosomes that protect them from degradation.

Transcription

The process by which RNA is synthesized from a DNA template, producing messenger RNA (mRNA).

Capping

The addition of a 7-methylguanosine cap to the 5' end of an mRNA molecule, enhancing stability and translation.

Polyadenylation

The addition of a poly-A tail to the 3' end of mRNA, which protects the mRNA from degradation.

Splicing

The process of removing introns and joining exons in a pre-mRNA transcript to produce mature mRNA.

Rho Protein

A protein involved in the termination of transcription in prokaryotic cells through Rho-dependent mechanisms.

Sigma Factor

A protein that guides RNA polymerase to the promoter region of a gene during transcription initiation in bacteria.

Restriction Enzymes

Enzymes that cut DNA at specific recognition sites, often palindromic sequences.

Gel Electrophoresis

A method used to separate DNA fragments based on size, where smaller fragments migrate further in an electric field.

RNA Interference

A biological process where RNA molecules inhibit gene expression or translation by neutralizing targeted mRNA molecules.

Okazaki Fragments

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

Histones

Proteins that package and order DNA into structural units called nucleosomes.

Meselson & Stahl Experiment

An experiment that provided evidence for the semi-conservative model of DNA replication using isotopes of nitrogen.

Theta Replication

The process of DNA replication in prokaryotes that forms a replication bubble with two forks moving in opposite directions.

Linear Replication

The type of DNA replication that occurs in eukaryotes, involving multiple origins of replication along linear chromosomes.

RNA Polymerase II

The enzyme responsible for synthesizing mRNA in eukaryotic cells.

RNA Splicing Mechanism

A cellular process that removes introns from pre-mRNA and connects exons to form mature mRNA.

Transcription Factors

Proteins that assist RNA polymerase in binding to the promoter to initiate transcription in eukaryotes.

Facultative Heterochromatin

Chromatin that can exist in both condensed and relaxed states, influencing gene expression in different cell types.

DNA Ligase

An enzyme that joins Okazaki fragments on the lagging strand during DNA replication.

Reverse Transcription PCR (RT-PCR)

A technique used to convert RNA into complementary DNA (cDNA) followed by amplification.

Quantitative PCR (qPCR)

A technique used to quantify the amount of DNA or RNA in real-time during PCR amplification.

Mature mRNA

The final processed form of RNA that results after capping, polyadenylation, and splicing.

Spliceosome

A complex of proteins and RNA that facilitates the splicing of pre-mRNA to remove introns.

Operons

Genetic units in prokaryotes that consist of a group of genes regulated together.

Transcription Termination

The concluding phase of transcription where RNA polymerase detaches from RNA after synthesizing the complete mRNA.

Alternative Splicing

A regulatory mechanism that enables a single gene to produce multiple mRNA isoforms by varying the inclusion/exclusion of exons.

PCR Amplification Cycle

A cycle in PCR that includes denaturation, annealing, and extension, leading to the doubling of the target DNA.

B-DNA

The most common form of double-helix DNA structure, characterized as a right-handed helix.

Z-DNA

A left-handed helical form of DNA that is involved in gene regulation.

A-DNA

A more compact form of DNA that forms under dehydrated conditions.

Nucleotides

The building blocks of DNA and RNA, consisting of a sugar, phosphate group, and nitrogenous base.

Covalent Linkage in Nucleic Acids

Nucleotides are linked by phosphodiester bonds between the phosphate group of one nucleotide and the sugar of the next.

Gene Expression Regulation

The mechanisms controlling the rate and manner in which genes are expressed and produce their functional products.

DNA Extraction

The process of isolating DNA from cells, allowing it for further analysis or manipulation.

Transcription Units

Segments of DNA that are transcribed to produce RNA.

Transcription Initiation Complex

The assembly of RNA polymerase and transcription factors at the promoter to start transcription.

Ribonucleic Acid (RNA)

A single-stranded nucleic acid polymer involved in various roles including serving as a template for protein synthesis.

Cycling Conditions for PCR

The thermal conditions utilized during PCR to denature DNA, anneal primers, and extend new DNA strands.

DNA Nucleotide Composition

The relative amounts of adenine, thymine, cytosine, and guanine in a DNA molecule.

Protein Synthesis Direction

Both DNA replication and RNA transcription proceed in the 5' to 3' direction.

Intron Removal

The process during RNA processing where non-coding sequences are excised from pre-mRNA.

Transcription in Eukaryotes vs. Prokaryotes

Eukaryotic transcription involves multiple RNA polymerases and extensive processing, while prokaryotic transcription is simpler with one type of RNA polymerase.

Quantification of Gene Expression

The determination of how much a gene is being expressed in a sample, often using techniques like qPCR.

Transcriptional Regulation

The control of the level and timing of mRNA synthesis from a particular gene.

Histone Modification

Chemical changes to histones that affect chromatin structure and gene accessibility.

DNA Supercoiling

The over- or under-winding of DNA which affects replication and transcription.

RNA Processing Functions

The modifications made to precursor mRNA, including capping, polyadenylation, and splicing.

Nucleotide Composition in RNA

Consists of adenine, uracil, cytosine, and guanine; lacks thymine.

Telomere Function

Protects chromosome ends from degradation and prevents chromosome fusion.

RNA Sequencing

A method used to analyze the quantity and sequences of RNA in a sample.

Polymerase Enzymes

Enzymes that synthesize nucleic acids; includes DNA polymerases and RNA polymerases.

5’ and 3’ End Definition

Refers to the carbon numbers in the sugar backbone of nucleic acids that define directionality.

Template Strand

The DNA strand that serves as a template for RNA synthesis during transcription.

Non-template Strand

The strand of DNA that has the same sequence as the mRNA produced, except for thymine instead of uracil.

Heavy and Light DNA Bands

The bands observed in the Meselson & Stahl experiment, associated with different densities of DNA based on nitrogen isotopes.

DNA Replication Fork

The area where the two strands of DNA are separated to allow replication to occur.

Antiparallel Orientation

The opposite directionality of the two strands in a DNA double helix.

Experimental Evidence for DNA Models

Data collected from experiments, such as the Meselson & Stahl experiment, that support theories regarding DNA replication.

Protein Synthesis Types

The various forms of RNA involved in protein synthesis include mRNA, tRNA, and rRNA.

RNA Types in Gene Expression

Includes messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA).

Gene Regulation Mechanisms

Includes transcription factors, enhancers, silencers, and chromatin remodeling.

Eukaryotic Gene Expression Complexity

Involves multiple levels of regulation, intricate processing of RNA, and chromatin modifications.