BIO 300 Summer Class 3.2 Study Guide

Transposition

Process in which a short segment of DNA is inserted into a new location in the genome.

Transposable Elements

DNA Segments that transpose themselves are known as transposable elements.

Main difference between Eukaryotic and Bacterial chromosomes

Eukaryotic Genome has multiple linear chromosomes

Bacterial Genome is a single circular chromosome

Key Features of Bacterial Chromosomes (5)

Typically, a few million base pairs,

contain a few thousand genes,

mostly protein-encoding,

have intergenic regions,
a single origin of replication.

What is the Origin of Replication and how many do bacterial chromosomes have?

Origin of replication is the point where replication begins, bacterial chromosomes only have one.

Repetitive Sequences

Sequences that repeat themselves multiple times, found interspersed in intergenic regions.

What is Nucleoid

Dense region of compacted bacterial chromosomes in Prokaryotes.

Basic Structural Arrangement of Bacterial Chromosomes?

Contains a central core and loops (Macrodomains and Microdomains),

compacted by NAPs and supercoiling.

NAPs

Nucleoid Associated Proteins

What do NAPs do?

Promote compacting and structural organization for domain formation

Significance of DNA Supercoiling

Allows for already coiled DNA to coil even further to make it more compact and stable.

Aids in processes like replication and transcription.

DNA Gyrase

Also known as Topoisomerase 2, it facilitates negative supercoils using ATP.

DNA Gyrase Mechanism

DNA is cut and another segment of DNA is passed through.

It is then resealed which causes an addition of supercoils.

Key features of Eukaryotic Chromosomes (4)

Long linear DNA with many origins of replication,

centromeres,

telomeres,

introns and exons.

Relationship between Genome Size and Organismal complexity

Genome size is not directly related to organismal complexity.

Difference between Unique and Repetitive sequences

Unique sequences occur once or a few times (~41% Human Genome).

Repetitive sequences occur many times. (10ks-million times)

What is the Alu family sequence and what group of species can it be found in?

Highly repeititves DNA Sequences

in primates 1 million copies, ~10% of human DNA

Tandem Arrays

Very short sequences that are repeated many times in a row, often in centromeres

Transposable Element

Segment of DNA that move to a new location to within the genome

Who identified TEs and what organism was first used?

Barbara McClintock identified TEs and used Corn.

What is Ds 'mutable locus' in McClintock's work and what alleles were involved?

Ds locus was a mutable site in chromosome 9. When transposed in the C allele, kernels were colorless; when it moved, red sectors appeared.

What is the distinction between simple transposition and retrotransposition?

Simple transposition uses cut an paste while Retro transposition uses an RNA intermediate copied into DNA and reinserted

What is the most basic TE?

The simplest TE is an insertion element (IS Element)

How do simple transposons differ from insertion elements?

Insertion elements contain only transposase and IRs, while simple transposons carry additional genes.

Which retrotransposons are evolutionarily related to retroviruses?

LTR retrotransposons are related to retroviruses

Which retrotransposons are not evolutionarily related to retroviruses?

Non-LTR retrotransposons are not related to retroviruses

What is the important distinction between LTR and non-LTR retrotransposons?

LTR retrotransposons have long terminal repeats, non-LTRs do not

What is the distinction between autonomous and nonautonomous elements?

Autonomos TEs encode enzymes needed for transposition;

Nonautonomous rely on other TEs

How does simple transposition increase the number of TEs?

Transposition can increase TE number when retrotransposons copy into new DNA

What are some consequences of transposition?

Consequences include mutations, altered gene expression, chromosomal rearrangements

What is the selfish DNA hypothesis explanation for TEs? How does it differ from adaptation hypothesis?

The Hypothesis states that TEs exist to replicate themselves;

Adaptation hypothesis: TEs may benefit host genome evolution

What is chromatin?

DNA + Histone Proteins that form chromosomes

What are nucleosomes and structure?

DNA Wrapped around histone proteins (Octamer), structural unit of chromatin.

What is a linker region of DNA?

Stretches of DNA between nucleosomes (Think of beads on a string)

What is the point of histones?

Package DNA,

Aid in compaction

Regulate gene expression.

What is the 30nm fiber and zig zag model?

Nucleosome feature organized in a zig zag pattern.

What is a loop domain?

Proteins organizing and compacting 30nm fiber

How do CTCF and SMC (Structural Maintenance of Chromosomes) proteins promote their formation?

They promote loops via binding sites, SMC proteins via cohesion