Chapter 4: DNA, Chromosomes and Genomes

Flashcards covering key vocabulary from the lecture on DNA, Chromosomes, and Genomes, including the central dogma, DNA structure, replication, transcription, and translation.

Central Dogma of Biology

The fundamental principle that genetic information flows from DNA to RNA to protein.

Replication

The process by which DNA is copied, performed by DNA Polymerases.

Transcription

The process by which DNA is used as a template to synthesize RNA, performed by RNA Polymerases.

Translation

The process by which RNA directs the synthesis of protein, performed by Ribosomes.

DNA (Deoxyribonucleic Acid)

A double-stranded, right-handed helix that carries genetic information.

Base Pairs

The units of DNA consisting of two nucleobases bound together by hydrogen bonds (A:T and G:C) that have essentially the same shape.

Hydrogen Bonds

Bonds that hold complementary base pairs together in the DNA double helix.

Base Stacking

Interactions between adjacent base pairs in the DNA double helix, contributing to its stability due to van der Waals forces and hydrophobic effect.

Minor Groove

A narrower indentation on the surface of the DNA double helix.

Major Groove

A wider indentation on the surface of the DNA double helix.

E. coli Genome

One circular chromosome consisting of 4.6 million base pairs.

Non-coding DNA

Regions of DNA that do not code for proteins and constitute the majority of DNA in human cells.

Indels (Insertion/Deletion)

Small insertions or deletions of base pairs in the DNA sequence that contribute to individual differences (~1.2%).

CNVs (Copy Number Variants)

Variations in the number of copies of specific DNA sections that contribute to individual differences.

SNPs (Single Nucleotide Polymorphisms)

Variations at a single base pair position in the DNA sequence that contribute to individual differences (~0.1%).

Chromosomes

Packaged structures of DNA within the nucleus that exist in pairs (diploid) in human cells.

Diploid

Having two sets of chromosomes, one from each parent.

Chromatin

The complex of DNA and proteins (histones and non-histone proteins) that forms chromosomes; its mass is 1/3 DNA and 2/3 proteins.

Gene Expression

The process where chromosomes decondense to allow the use of genetic information.

Heterochromatin

Highly condensed DNA regions within chromosomes that are inaccessible for transcription, resulting in no gene expression.

Euchromatin

Less condensed DNA regions within chromosomes that are accessible for transcription, allowing gene expression.

Exon

A protein-coding region of a gene that is retained in the mature mRNA.

Intron

A non-coding sequence within a gene that is removed during RNA splicing.

Regulatory DNA Sequences

DNA sequences that control gene activity, as shown by the example of regulatory DNA associated with a gene.

Nucleosome

The basic compaction unit of DNA, consisting of 146 base pairs of DNA wrapped in 1.6 negative turns around a protein core.

Histones

Positively charged proteins (containing lots of lysine and arginine) that form the protein core of a nucleosome and interact with negatively charged DNA.

Histone Core

Composed of 8 histone proteins (2 each of H2A, H2B, H3, H4) around which DNA is wrapped.

Histone Tails

Extensions of histone proteins whose side chains can be modified to regulate DNA packaging and thereby transcription.

Reader Proteins

Proteins that bind to eu- or heterochromatin based on post-translational modifications, helping to maintain chromatin structure.

Writer Proteins

Proteins that change post-translational modifications on histones, helping to maintain chromatin structure.

DNA Replication

The process where DNA is duplicated, preceding cell division, and involves the displacement of parental chromatin components.

Interphase

A phase of the cell cycle characterized by chromosome duplication and gene expression, generally when chromosomes are not condensed.

M Phase

The mitotic phase of the cell cycle where duplicated chromosomes are ready for division, showing a condensed mitotic chromosome.

Replication Origin

Specific sites on a chromosome where DNA replication begins.

Centromere

A constricted region on a chromosome essential for proper segregation during cell division, attached to the kinetochore.

Telomere

Protective ends of chromosomes that prevent degradation and ensure complete replication.

Kinetochore

A protein structure on the centromere that attaches to the mitotic spindle during cell division.

DNA Polymerases

Enzymes that synthesize DNA, working directionally from 5' to 3'.

Pol III

A DNA polymerase that contains both a polymerase unit and a 3' → 5' exonuclease unit for DNA proofreading and correction.

Proofreading

The activity of DNA polymerases (e.g., via 3' → 5' exonuclease) to remove incorrect nucleotides during replication, ensuring high precision.

Template-Primer Duplex

The structure formed by a DNA template and a short primer, which provides the 3' OH for DNA polymerases to extend.

Multiple Origins of Replication

Numerous active starting points (30,000 – 50,000 per cell cycle) along eukaryotic DNA where replication begins simultaneously, allowing DNA polymerase to run in both directions.

RNA Polymerase

An enzyme that copies one strand of DNA into RNA during transcription, less precise than DNA polymerase as it lacks exonuclease activity.

Uracil (U)

A nitrogenous base found in RNA that replaces Thymine (T) found in DNA.

Messenger RNA (mRNA)

A single-stranded RNA polymer transcribed from DNA that carries genetic information to ribosomes for protein synthesis.

Promoter

A DNA sequence located in front of a gene where RNA polymerase binds to initiate transcription.

Termination in Transcription

Often signaled by intrinsic stop signals or, in eukaryotes, a polyadenylation signal.

Transcription Factor

Proteins (like activators) that bind to specific DNA sequences (e.g., enhancer side, TATA box) to regulate the assembly of RNA polymerase and initiate transcription.

TATA Box

A DNA recognition sequence involved in the assembly of transcription factors and RNA polymerase recruitment.

RNA Processing

A series of modifications RNA needs before export from the nucleus, including 5' capping, splicing, and adding a poly-A tail.

5' Capping

An alteration to the 5' side of RNA to avoid degradation.

Splicing

The process of removing introns from protein-coding exons in pre-mRNA.

Poly-A Tail

A sequence added to the 3' side of RNA for enhanced stability and export from the nucleus.

RNA-splicing

The process by which introns are removed from pre-mRNA and exons are joined, resulting in mature mRNA.

Isoforms

Multiple different proteins that can arise from a single gene due to RNA-splicing, different translation starting sites, or gene duplications.

Transfer RNA (tRNA)

RNA molecules that act as a key between amino acids and codons, carrying specific amino acids to the ribosome during translation.

Ribosomal RNA (rRNA)

Makes up 85% of RNA and is a building block of ribosomes.

Micro RNA (miRNA)

Non-coding RNA involved in gene regulation.

Eukaryotic RNA Processing Features

Includes nuclear import/export, complex transcriptional regulation (eu vs heterochromatin), and RNA processing (splicing), which are not present in bacteria.

Codon

A sequence of 3 nucleotides in mRNA that codes for 1 amino acid or a stop signal.

Amino Acid

The building blocks of proteins, with 20 different types specified by up to 6 different codons.

STOP Codons

Three specific codons that serve as a termination site for protein synthesis.

Start Codon

The codon AUG, which initiates translation and codes for methionine.

Wobble Base

The phenomenon where the third position of a codon is more flexible in its base pairing with tRNA.

Ribosomes

Structures made from rRNA that mediate interactions between mRNA and tRNA and catalyze protein synthesis.

Elongation Factors

Mediating proteins involved in the various processes of protein synthesis.

DNA Compaction

The process by which histone proteins bind to DNA to form nucleosomes, making the DNA become shorter.

Histone Variants

Different forms of histones that can determine which parts of the DNA are 'turned off'.

Junk DNA

A colloquial term for non-coding DNA, referring to the fact that most of our DNA is never used.