Lecture 3 Flashcards
What is unique about viral and bacterial chromosomes?
- single nucleic acid molecule
- largely devoid of associated proteins
- much smaller than eukaryotic chromosomes
- contains less genetic information
What is unique specifically about viral chromosomes?
- nucleic acid, either DNA or RNA, single or double stranded
- circular or linear molecules
- viral genetic material is inert until released into host cell
- able to package long DNA into a small volume just like bacteria and eukaryotic cells
- viruses are not considered to be alive
Bacterial chromosomes
- circukar, double-stranded DNA compacted into nucleoid
- their DNA is associated with HU and histone-like nucleoid structuring
- unlike viral chromosomes, bacterial chromosomes are readily replicated and transcribed
What is supercoiling?
- supercoiling is the compaction of DNA
- closed circular molecules
- more compact and sediment more rapidly than linear forms
What changes in a super coiled piece of DNA?
2 turns of the helix are removed to hinder the stability of the strand, this promotes the formation of DNA super coils that are very stable again
ex) if the strand started with 20 turns it would end up with 18
Topoisomerases
- enzyme that cut one or both strands of DNA
- winds or unwinds helix before resealing ends
In what type of cells is supercoiled DNA and topoisomerases found?
Eukaryotic
What is common between Prokaryote and eukaryote DNA when it comes to supercoiling?
Replication and transcription create supercoils downstream as double helix unwinds
Chromatin
- not visible during cell cycle
- at interphase, eukaryotic chromosomes uncoil and decondense into a form called chromatin
- during interphase, chromatin is dispersed throughout the nucleus
- during cell division, chromatin coils and condenses back into visible chromosomes
Histones
- positively charge proteins associated with chromosomal DNA in eukaryotes
- contain large amounts of lysine and arginine
- makes electrostatic bonding to negatively charged phosphate possible
What are the five main types of histones
H1, H2A, H2B, H3, H3
- when two combine they form an octomer histone complex
nucelosomes
- electron microscopic observations of chromatin revealed fibers composed of linear array of these spherical particles
- resemble bead on a string
- are condensed several times to form intact chromatids
- resemble beads on a string
- are condensed several times to form intact chromatids
Chromatin remodeling
- to accommodate DNA-protein interactions, chromatin structure must change
What happens to chromatins to facilitate replication and gene expression?
- relax compact structure
- expose regions of DNA to regulatory proteins
- have a reversal mechanism for inactivity
Superhelix
- twists and turns of DNA superhelix encircle histones
- principal packaging unit of DNA in eukaryotic nucleus
Histone tails
unstructured histone tails are not packed into folded histone domains within nucleosome
- tails that hare devoid of secondary structure protrude through minor groove
Chemical modifications
are important to genetic function
Acetylation
- enzyme histone acetyltransferase
- addition of acetyl group to positively charged amino group on side chain (lysine)
- changes net charge of protein by neutralizing positive charge
How are targets for chemical modification made along chromatin
By histone tails
Methylation
- enzyme methyltransferase
- adds methyl groups to arginine and lysine residues in histones
- positive correlation with gene activity
Phosphorylation
- enzyme kinase
- adds phosphate groups to hydroxyl groups of amino acids serine and histidine
Methylation of the nitrogenous base cytosine within polynucleotide chains of DNA
- forms 5-methyl cytosine
- usually negatively correlated with gene activity
CpG island
- long repeats of cytosine and guanine
- region of DNA where many cytosine guanine dinucleotides are present
Euchromatin
- uncoiled and active
- appears unstained during interphase
Heterochromatin
- condensed areas are mostly inactive appears stained during interphase
- genetically inactive: lacks genes or contains repressed genes
- replicated later in S phase than euchromatin
- telomere maintains chromosome integrity
- centromere involved in chromosome movement
Chromosome-banding techniques
- differential staining along longitudinal axis of mitotic chromosome
- staining patterns resemble polytene chromosome
C-banding
- mitotic chromosomes have a characteristic banding pattern
- only centromeres (heterochromatin) take up stain
G-banding
- differential staining along length of each chromosome
- digestion of mitotic chromosome by enzyme
- introduce trypsin to DNA
Nomenclature for human chromosome banding
- based on G-banding
- nomenclature applied to X chromosome
- regions of X chromosome are distinguished but its banding pattern
Repetitive DNA sequences
- are repeated many times within eukaryotic chromosomes
- several categories of repetitive DNA
Satellite DNA
- highly repetitive and consists of short repeated sequences
- makes up variable proportion of total DNA
- found in heterochromatic centromeric regions of chromosomes
- not found in prokaryotes
Centromeres
- separation of homologs during mitosis and meiosis depends on centromeres
- are the primary constrictions along eukaryotic chromosomes
Kinetochore proteins
region that binds to spindle fiber microtubules during cell division
Moderately repetitive DNA includes…
- variable number tandem repeats (VNTRs)
- minisatellites
- microsatellites (short tandem repeats, STRs)
VNTRs
Variable number tandem repeats
- repeating DNA sequences 15-100 bp long
- found within and between genes
Microsatellites or STRs
short tandem repeats
- tandemly repeated sequences
- dispersed throughout genome
- consist of di-, tri-, tetra-, and pentanucleotides
SINES and LINES
Short interspersed elements and long interspersed elements
- 850k LINES in human genome
- transposable sequences that are mobile and can relocate within genome
- dispersed throughout genome rather than tandemly repeated
- constitute 1/3 of human genome
Retrotransposons
- transposable elements generated bia RNA intermediate (LINEs)
What portion of eukaryotic genome constitutes protein-encoding genes
2-10%
Pseudogenes
- large number of single-copy noncoding regions
DNA sequences representing evolutionary vestiges - have undergone significant mutational alterations (insertions and deletions)
- are not transcribed
