Genetics - Molecular Structure of Chromosomes (Chapter 10)

Define genome.

The totality of all genetic material in a given organism.

Eukaryotic genome

1. Linear chromosomes
2. higher organisms with membrane-bound organelles
3. Linear chromosomes found in the nucleus
4. Chromosomes packaged into chromatin

prokarytoic genome

1. Circular chromosomes
2. Found in bacteria
3. Chromosomes found in the nucleoid
4. Packaged through supercoiling

What's similar about eukaryotic genome and prokaryotic genome?

You can find circular genomes in eukaryotes in mitochondria and chloroplasts.

What are four important processes chromosomes facilitate?

1. synthesis of RNA and cellular proteins
2. replication of chromosomes
3. proper segregation of chromosomes
4. compaction of chromosomes to fit in living cells

What are intergenic regions?

nontranscribed DNA between adjacent genes

What is the function of the origin of replication?

An initiation site for assembling proteins to begin the process of DNA replication.

How many origin of replications do bacteria chromosomes have?

one

how many origin of replication do eukaryotes have

multiple

What are the two steps of chromosomes condensation for bacteria?

1. microdomains
2. macrodomains

Microdomains

Loops of bacterial chromosomal DNA, tythat emanate from a central core

Macrodomains

Large contiguous regions on chromosomes that appear to act as independent units. Organize and further condense.

What is supercoiling?

Formation of additional coils within DNA due to twisting forces from already coiled DNA. Allows for strand separation.

What are nucleoid-associated proteins?

A set of DNA-binding proteins that form microdomains and marcodomains.

How does supercoiling promote strand separation? Why is that beneficial?

It increases the compaction of the chromosome. It allows for strand separation, which is important for replication and transcription to access the DNA sequence.

DNA gyrase (topoisomerase II)

introduces negative supercoils; underwinding; relax positive supercoils

Topoisomerase I

relaxes negative supercoils; overwinding

Do eukaryotes or prokaryotes have more spaces in between genes?

Eukaryotes

introns

Noncoding segments of nucleic acid that lie between coding sequences.

exons

Coding segments of eukaryotic DNA.

Are exons and introns found in eukaryotes or prokaryotes?

Eukaryotes

Centromeres

areas that play a role in the proper segregation of chromosomes during mitosis and meiosis. One per chromosome. Eukaryotic structure.

Telomeres

Found at the end of chromosomes. Functions in replication and stability. Eukaryotic structure.

True or false. Scientists do not understand the exact purpose of repetitive DNA.

True

Unique sequences

sequences found once or a few times within a genome

moderately repetitive sequences

found a few hundred to several thousand times in the genome

highly repetitive sequences:

sequences that are found tens of thousands or even millions of times throughout the genome

Tandem array

a short nucleotide sequence that is repeated many times in a row

chromatin

Substance found in eukaryotic chromosomes that consists of DNA tightly coiled around histones

what makes up a nucleosome?

histone octet w/ DNA wrapped 1.65 times around it

what proteins are found in a nucleosome?

histones

What are the components of a single nucleosome?

A. About 147 bp of DNA and four core histone proteins
B. About 147 bp of DNA and eight core histone proteins
C. About 200 bp of DNA and four core histone proteins
D. About 200 bp of DNA and eight core histone proteins

B. About 147 bp of DNA and eight core histone proteins

Why are the bands in Noll's agarose gel so large?

There are bands in 400 and 600 because incomplete digestion of DNA is why we get larger sizes of DNA
Extra base pairs are the linker regions themselves

Why is it important that histone proteins contain a lot of arginines and lysines?

They form electrostatic and hydrogen-bonding interactions with the phosphate groups alone the DNA backbone.

H1 histone

By binding to DNA in the linker region between nucleosomes, it helps organize adjacent nucleosomes.

DNase

a protein that cuts a part naked DNA;DNA backbone

Noll's experiment

determine the size of the DNA complex

Noll tested Kornberg's model of nucleosomes

digested chromatin with the enzyme DNase I, which cuts the DNA backbone → accurately measured the molecular mass of the resulting DNA fragments by gel electrophoresis

hypothesis for Noll's experiment

hypothesis for Noll's experiment

results of Noll's experiment

Low concentration of DNase I- some linker regions remained uncut, produced fragments unequal in lengthHigher concentrations of DNase I- mostly cut DNA into fragments of 200bp, consistent with the beads on a string model

What evidence proves histone H1 helps package the nucleosomes more compactly?

Without H1, the nucleosomes are classic beads-on-a-string, but with H1, it its more compacted together.

Mechanisms that compact eukaryotic DNA:

1. wrapping DNA within nucleosomes
2. arrangement of nucleosomes to form a 30-nm fiber
3. formation of loops

loop domains

a segment of chromatin that is organized into a loop; the 30-nm fiber folded into loops

CTCF

binds to 3 regularly spaced repeats; promoting the formation of a loop domain

SMC

forms a dimer that can wrap itself around two segments of DNA to create a loop.

True or false. chromosomes are distributed randomly around the nucleus.

False.

heterochromatin

Eukaryotic chromatin that remains highly compacted during interphase and is generally not transcribed.

euchromatin

The less condensed form of eukaryotic chromatin that is available for transcription.

when are chromosomes most highly condensed?

metaphase

condensin

proteins that cause greater compaction of the loop domains starting at M phase

cohesion

protein that sticks the sister chromatids together starting at the end of S phase

Condensin I can only bind to chromatin after the nuclear envelope breaks apart. What part of the cell cycle does it play a role in?

Metaphase