Unit 11 Flashcards
Define chromatin
The complex of DNA and protein
What are some characteristics of euchromatin form heterochromatin?
- Less condensed
- On chromosome arms
- Comprised of unique sequences
- Many genes
- Crossing over is common
- Transcription occurs often
- Replicated throughout S phase
What part of the chromosome is highly heterochromatic?
Centromeres and telomeres
What causing supercoiling of DNA?
When energy is used to add or remove any turns and strain is places on the molecule
Define Positive supercoiling
Over rotating
Define Negative Supercoiling
underrotating
What is a nucleoid?
Bacterial DNA confined to a definite region of the cytoplasm
What is a nucleosome and what are its components?
-The fundamental repeating unit of chromosome
Comprised of
- Eight histone proteins
-associated with about 200 bp of DNA
What is the role of histone protein H1?
H1 binds to 20-22 bp of DNA where the DNA joins and leaves the histone octamer and helps lock DNA into place, acting as a clamp around the nucleosome.
What comprises the “beads-on-a-string” model of chromatin?
-linker (spacer) DNA
-H1
-Nucleosome core
What is a telomere?
The natural ends of a chromosome, serving as caps that stabilize the ends of the chromosome.
Describe the DNA sequence of a human telomere.
5’ - TTAGGG - 3’ - Telomere
3’ - AATCCC - 5’ Telomerase
What is meant by the C-value paradox?
The absence of a relation between C-value (genome sizes) of eukaryotes and organismal complexity
What is a gene family?
Set of genes that are similar in sequence and that arose through duplication events; often encode different protein products
Give an example of a gene family:
-The genes that encode beta-like globins
-The genes that encode immunoglobulin proteins in vertebrates
Give an example of moderately repetitive DNA that is functional:
Multiple copies of the genes for ribosomal RNAs and transfer RNAs.
What is the non-transcribed DNA between adjacent genes termed?
Intergenic regions
What are structural genes?
Protein-encoding genes
Describe bacterial DNA:
Circular, double-stranded DNA compacted into nucleoid (non-membrane bound structures) and associated with ”histone-like” proteins
What are microdomains?
looped domains emanating from the core – can compact further forming macrodomains
What are NAPs in prokaryotes?
nucleoid-associated proteins that
facilitate compaction and organization
What are H-NS proteins in prokaryotes?
histone-like nucleoid proteins
(note: prokaryotes do not have histones)
What are two main classes of drugs that inhibit eukaryotic topoisomerases?
- Quinolones
- Coumarins
Explain the experiment performed by Kavenoff and Zimm?
They wound DNA around paddles and then released it to measure the Viscoelastic (VE) Recoil and they found a proportional relationship between size of the chromosome molecule and VE Recoil. This was evidence that there was 1 DNA molecule in a chromosome.
What do the different types of histone proteins have in common?
- They are positively charges proteins associated with chromosomal DNA in eukaryotes
- Contain large amounts of lysine and arginine
-They make electrostatic bonding to negatively charged phosphate possible
What are the five main types of histones and which ones are there two of?
- H1
- H2A X 2
- H2B X2
- H3 X2
- H4 X 2
What is the experimental evidence for the beads on a string model?
- 3 test tubes were each filed with a solution containing different concentrations of DNase 1 (1 was low, 2 was medium, and 3 was high) and DNA and then heated to 37 degrees Celsius.
- They were then treated with detergent and phenol was added.
- Agarose Gel Electrophoresis was then done to determine the size of the DNA fragments in each of the tube.
- The tube that had the highest concentration of DNase1 had the largest and brightest marking at the 200 bp point.
What is the first level of compaction of the chromosome?
Level I: DNA double helix
What is the second level of compaction of the chromosome?
Level II: Beads-on-a-string
What evidence did Roger Kornberg base his model of nucleosome structure in 1974 on?
- X-ray diffraction studies
- Electron microscopy images
What structure for the nucleosome did Roger Kornberg propose in 1974?
Beads-on-a-string
What is the third level of chromosome compaction?
Level III: Solenoid
What is a solenoid?
It is dependent on H1 histone consisting of several nucleosomes coiled around and stacked upon one another (Internalization of 6 H1 Histones
What is the fourth level of compaction of chromosomes?
Level IV: Looped Domains
Explain looped domains:
It is the formation of scaffold (non-histone chromosome proteins)
-DNA attaches based on sequence:
-SARs = scaffold attachment regions
-MARs = matrix attachment regions
What is level V compaction of the chromosome?
Level V: Metaphase chromosome
What percentage of the human genome is protein encoding?
about 2%
Describe euchromatin:
It is relatively uncoiled and active
Describe heterochromatins:
They are condensed areas and are inactive because they either lack genes or contain genes that are repressed.
Replicate later in S phase
What are three roles of constitutive heterochromatin:
- Telomere maintains chromosome integrity
- The centromere is involved in chromosome movement
- Most of the mammalian Y chromosome is heterochromatice
What is a good example of facultative heterochromatin?
The inactivated X chromosome (barr body) in a female’s cell mediated via the Xist gene.
What is satellite DNA and where is it found?
It is highly repetitive and consists of short, repeated sequences that makes up variable proportion of total DNA profile of main-band versus satellite DNA (different GC richness)
Found in the heterochromatic centromeric regions of chromosomes in eukaryotes and not prokaryotes
What are telomeric DNA sequences?
They are terminal heterochromatic caps that consist of short tandem repeats that contribute to the stability and integrity of linear chromosomes
What is the telomeric DNA sequence in Humans?
TTAGGG-TTAGGG-TTAGGGsa
What are VNTRs?
Variable number tandem repeats are 15-100 bp repeating segments found between genes and often referred to as minisatellites.
What are STRs?
Short tandem repeats are 2-5 bp repeats that are dispersed throughout the genome and are a good DNA profiling tool.
Also know as microsatellites
What are retrotransposons?
Transposable elements generated via RNA intermediates (LINEs)
What are three qualities of short and long interspersed elements?
(SINEs and LINEs)
- Transposable sequences that are mobile and can relocate within the genome
- They are dispersed throughout the genome instead of tandemly repeated (so not back to back to back)
- Constitute 1/3 of the human genome
What is the primary SINE in humans and when was it identified?
Primary human SINE – Alu.
About 300 bp
Non-autonomous
Over 1 million copies in human genome
Mobility identified in 1991 in NF1 gene
What’s a nickname of SINEs and LINEs?
Jumping genes
What are middle repetitive genes?
Middle repetitive DNA includes functional genes present in multiple copies.
For example, many copies exist of the genes encoding ribosomal RNA (rRNA).
Do human have middle repetitive genes?
Yes, multiple copies on p arm of acrocentric chromosomes 13,14,15,21, and 22
