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Genetics Chapter 12

Terms in this set (47)

DNA from the phage T2
The DNA is 52 μm long and is normally packed
into the head of the phage shown in the center of
the photo
Bacterial DNA
-Double stranded DNA molecule, linear or circular. Some bacteria have more than one chromosome
-Typically compacted to form nucleoid

-E. coli has a circular chromosomes associated with proteins
-The E. coli genome contains 4,640,000 bp (4.6 Mb) and approximately 4400 genes
Supercoiled DNA
-a particularly characteristic of closed-circular molecules
-a DNA configuration in which the helix is coiled upon itself
-supercoils can exist in stable forms only when the ends of the DNA are not free, as in a covalently closed circular DNA molecule
DNA of Human Mitochondria
-Circular molecule - 16,000bp

-5-10 copies per mitochondria

-Encodes genetic information for energy production:
--13 proteins
--22 tRNA molecules
--2 rRNAs
Disorders of Mitochondria
-Mitochondria are maternally inherited
-Mutations in mitochondrial DNA cause malfunction in energy transduction:
--Myoclonic epilepsy
--Leber's neuropathy
--Kearns-Sayre syndrome

-Mostly affect organs with high energy demands such as nervous system, muscles
Polytene Chromosome
-Literally, a many stranded chromosome; one that has undergone numerous rounds of DNA replication w/o separation of the replicated strands, which remain in exact parallel register

-the result is a giant chromosome w/ aligned chromomeres displaying a characteristic banding pattern, often studied in Drosphilia larval salivary gland cells
Chromomeres
-individual bands of a polytene chromosome
-a more generalized term describing lateral condensations of material along the axis of a chromosome
Puff
-each uncoiling event in a polytene chromosome is represented by a ________
-visible manifestations of a high level of gene activity (transcription that produces RNA) is evidenced by their high rate of incorporation of radioactively labeled RNA precursors
Organization of Eukaryotic Chromosomes
How is DNA packed into chromosomes?
--1o coiling of DNA double helix (Fig10.14) --Nucleosome structure (Fig12.9a)
---2o coiling of DNA around histone core, histone octamer: 2 X(H2A, H2B, H3, H4) + linker DNA (histone H1 )
---3o coiling of core + linker forms "Solenoid"

-Chromatin structure (Fig12.9b)
--4o coiling of DNA + histone protein +
non-histone protein
Chromatin
-4o coiling of DNA + histone protein +non-histone protein

-the complex of DNA, RNA, histones, and nonhistone proteins that make up uncoiled chromosomes, characteristic of the eukaryotic interphase nucleus

-while in interphase it is dispersed throughout the nucleus

-chromatin structure is based on the assumption that chromatin fibers, composed of DNA and protein, undergo extensive coiling and folding as they are condensed within the nucleus

-produces regularly spaced diffraction rings, suggesting that repeating structural units occur along the chromatin axis

-consists of some type of repeating unit, each of which protects the DNA from enzymatic cleavage except where any two units are joined

-contain nucleosomes
Histones
-one of the proteins associated with chromosomal DNA in all phases of the cell cycle
-positively charged proteins complexed w/ DNA in the nucleus
-they are rich in the basic amino acids arginine and lysine, and function in coiling DNA to form nucleosomes
--this makes it possible for them to bond electrostatically to the negatively charged phosphate groups of nucleotides

-play a part in chromatin structure
--if chemically removed, it disrupts chromatins diffraction pattern

-play an important role in packaging DNA into the nucleosomes that make up chromatin
Nucleosomes
-MAIN DEFINITION: octomeric structures of two molecules of each histone (H2A, H2B, H3, and H4) except H1. B/w nucleosomes and complexed with linker DNA is histone H1. A 146-base-pair sequence of DNA wraps around the ________


-2o coiling of DNA around histone core histone octamer: 2 X(H2A, H2B, H3, H4) + linker DNA (histone H1 )
-3o coiling of core + linker forms "Solenoid"

-in eukaryotes, a complex consisting of four pairs of histone molecules wrapped by two turns of a DNA molecule
-it is the major structure associated with the organization of chromatin in the nucleus

-linear arrays of spherical particles
--regularly occur along the axis of a chromatin strand and resemble beads on a string
--suggest the existence of repeating units
Nucleosome core particle
-when nuclease digestion time is extended, some of the 200 base pairs of DNA are removed from the nucleosome, creating what is called a ___________ consisting of 147 base pairs
Linker DNA
-the DNA lost in the prolonged digestion is responsible for linking nucleosomes together
-associated with the fifth histone, H1
Solenoid
-MAIN DEFINITION: As chromosome condensation occurs, a 300 A fiber is formed. It appears to be composed of five or six nucleosomes coiled together. These fibers form a series of loops that further condense into the chromatin fiber, which are then coiled into chromosome arms making up each chromatid

-in the nucleus, the chromatin fiber seldom exists in the extended form
-instead, the 11nm diameter fiber is packed into a thicker, 30 nm structure called a _______
-it is dependent on the presence of histone H1, consists of numerous nucleosomes coiled around and stack upon one another, creating a second level of packing
Chromatin Remodeling
-a process in which the structure of chromatin is altered by a protein complex, resulting in changes in the transcriptional state of genes in the altered region

-this is done b/c when present in several levels of compaction within the the chromatin fiber, DNA is inaccessible to interaction w/ other important DNA-binding proteins
--to accomadate these protein-DNA interaction, chromatin must change its structure

-to allow replication and gene expression, chromatin must relax its compact structure and expose regions of DNA to these proteins, and there must also be a mechanism for reversing the process during period of inactivity
Histone tails
-unstructured that are not packed into the folded histone domains within the core of the nucleosomes but instead protrude from it
--happens during remodeling

-they provide potential targets along the chromatin fiber for a variety of chemical modifications that may be linked to genetic functions, including chromatin remodeling and the possible regulation of gene expression
Acetylation
-a histone modification
-by the action of the enzyme histone acetyltransferase (HAT)
-the addition of an acetyl group present on the side chain of the amino acid lysine changes the net charge of the protein by neutralizing the positive charge
--lysine is abundant in histones

-linked to gene activation

-high levels of _________ open up, or remodel, the chromatin fiber, an effect that increases in regions of active genes and decreases in inactive regions

-adding acetyl group usually increases transcription of those genes
--making chromatin more active on those genes
--regulataory mechanism to turn genes on and off
Methylation
-Enzymatic transfer of methyl groups from S-adenosymethionine to biological molecules, including phospholipids, proteins, RNA, and DNA
-_________ of DNA is associated with the regulation of gene expression and with epigenetic phenomena such as imprinting

-can be added to arginine and lysine residues in histones

-positive or negative impact on gene activity

--can add methyl group to cytosine to turn genes off to decrease expression
--methylating DNA turns genes off or makes chromatin more heterochromatic (tightly coiled)
Phosphorylation
-phosphate groups can be added to the hydroxyl groups of the amino acids serine and histidine, introducing a negative charge on the protein

-increased _________ of histone H3 is believed to be related to the cycle of chromatin unfolding and condensation that occurs during and after DNA replication
Heterochromatin
-MAIN DEFINITION: chromosomal material that stains deeply and remains condensed when other parts of chromosomes, such as euchromatin, are otherwise pale and uncondensed. Relatively inactive b/c there are few genes present, or if they are present, they are repressed
--Telomeres and that areas adjacent to centromeres are composed of heterochromatin

-the heavily staining, late-replicating regions of chromosomes that are prematurely condensed in interphase

-condensed chromatin
--DNA Methylation (5 methyl cytosine)
--CPG Islands have high amount of methyl group of cytosine

-genetically inactive b/c they lack genes or contain genes that are repressed

-replicates later during the S phase of cell cycle than euchromatin

-presence is unique to and characteristic of the genetic material of eukaryotes

-when certain heterochromatic areas from one chromosome are translocated to a new site on the same or another nonhomologous chromosome, genetically active areas sometimes become genetically intert if they now lie adjacent to the translocated heterochromatin
5-methyl cytosine
-a histone
-methalylation of the nitrogenous base cytosine within polynucleotide chains of DNA, forming ______, is usually negatively correlated with gene activity
CpG island
-methylation of cytosine occurs most often when the nucleotide cytidylic acid is next to the nucleotide guanlytic acid, form a _______

-have high amount of methyl group of cytosine
--Controls whether genes are on or off
--They methylate the promoter
--DNA methylated at most of genome
Position Effect
-position of a gene or group of genes relative to all other genetic material may affect their expression
Chromosome Banding Patterns
-cytological procedures that made possible differential staining along the longitudinal axis of mitotic chromosomes
-the staiing patterns resemble bands of polytene chromosomes
C-Banding
-if chromosome preparations from mice were heat denatured and then treated with Giesma stain, a unique banding pattern emerged: only the centromeric regions of mitotic chromosomes took up the stain

-this cytological technique identifies a specific area of the chromosome composed of heterochromatin
G-Banding
-produces a staining pattern differentially along the length of each chromosome
-involves digestion of the mitotic chromosomes with the proteolytic enzyme trypsin, followed by Giesma staining

-differential staining reactions reflect the heterogeneity and complexity of the chromosome along its length
Repetitive DNA
-included functional sequences and sequences with no known function
-a DNA sequence present in many copies in the haploid genome
Functional Sequences
-includes families of coding genes (and related pseudogenes)
-includes noncoding funcional sequences
Sequences with no known function
-includes repeats in centromeric heterochromatin
-includes variable number tandem repeats
-transposed sequences
families of coding genes (and related pseudogenes)
-dispered gene families and tandem gene families
Transposed sequences
-transposons
-retro-transposons
Satellite DNA
-a repetitive DNA
-DNA that forms a minor band when genomic DNA is centrifuged in a cesium salt gradient
-this DNA usually consists of short sequences repeated many times in the genome

-variable [G+C] content
--tandem / dispersed repeats

-varies slightly in density from normal DNA
-highly repetitive DNA, consisting of short sequences of repeats

-it is a peak on the main band of DNA that differs in density

-differs from the main band of DNA in its molecular composition

-it is found in the heterochromatic centromeric regions of chromosomes
Repetitive DNA
-may account for >50% of human genome
Alphoid Family (of satellite DNA)
-found mainly in the centromere regions
--centromeric heterochromatin, --170bp x ~103 copies

-about 170bp in length
-are present in tandem arrays of up to 1 million base pairs
-such repetitive DNA in eukaryotes is transcribed and that the RNA that is produced is ultimately involved in kinetochore function
Middle (or moderately) repetitive DNA
-a repetitive DNA
-most prominent in this category or either noncoding tandemly repeated sequences or noncoding interspersed sequences
-no function has been ascribed to these components of the genome

-includes tandem repeats and intersperesed retrotransposons
Variable number tandem repeats
-a repetitive DNA
-a middle repetitive sequence
-repeating DNA sequences may be up to 15 to 100 bp long and are found within and b/w genes
-much such clusters are dispersed throughout the genome, and they are referred to as minisatellites

-b/c the number of repeat at each locus is variable, the loci are known as _________
-used in the preparation of DNA fingerprints and DNA profiles
Minisatellites
-a repetitive DNA
-series of short tandem repeats sequences (STRS) 10-100 nucleotides in length that occur frequently throughout the genome of eukaryotes
-b/c the number of repeat at each locus is variable, the loci are known as _________
-used in the preparation of DNA fingerprints and DNA profiles
Short tandem repeats (STRS or microsatellites)
-a repetitive DNA
-a middle repetitive sequence
-dispersed throughout the genome and vary among individuals in the number of repeats present at any site

-short tandem repeats 2-9 base pairs long found within minisatellites
-these sequences are used to prepare DNA in forensics
Transposable sequences
-mobile and can potentially move to different locations within the genome
SINES (Short Interspersed Nuclear Elements)
-a repetitive DNA
-repetitive transposed sequences
-Alu family - 200 ~ 300 bp x 105 copies per genome
-Alphoid family - centromeric heterochromatin 170bp

-repetitive sequences found in the genomes of higher organisms
-are less than 500 base pairs long and may be present 1,500,000 or more in the genome

-constitute 13% of human genome
Alu (family)
-a repetitive DNA
-repetitive transposed sequences
-200 ~ 300 bp x 105 copies
-dispersed rather uniformly throughout genome, both b/w and within genes

-in humans, this family encompasses more than 5% of the entire genome
-some members are transcribed into RNA, although the specific role of RNA is not certain
-the consequence of ________ sequences is their potential for transposition within the genome, which is related to chromosome rearrangements during evolution
-though to have arisen from an RNA element whose DNA complement as a result of the activity of reverse transcriptase
Long interspersed elements (LINEs)
-another category of reptitive transposable sequences
-about 6 kb in length and in the human genome are present approximately 850,000 times
-most prominent example in humans is the L1 family

-referred to as retrotransposons
-constitute 21% of human genome
NORs (nucleolus organizer regions )
-18S & 28S rDNA gene clusters
L1 family (of retrotransposon)
-are apart of LINEs
-__________ are ~6kb long
-Dispersed on all chromosomes
-500,000 copies in the human genome
-Make up 17% of the genome

-5' end highly variable and role within the genome has yet to be identified
-this DNA sequence is first transcribed into an RNA molecule
--the RNA then serves as the template for synthesis of the DNA complement using the enzyme reverse transcriptase
---this enzyme is encoded by a portion of the __________
----the new __________ then integrates into the DNA of the chromosome at the new site
Retrotransposons
-mobile genetic elements that are major components of many eukaryotic genomes, which are copied by means of an RNA intermediate and inserted at a distant chromosomal site
Pseudogenes
-look like genes but can't make proteins
-a nonfuncitonal gene with sequence homology to a known structural gene present elsewhere in the genome
-it differs from the functional version by insertions or deletions and by the presence of flanking direct-repeart sequences of 10-20 nucleotides

-MAIN DEFINITION: DNA sequences representing evolutionary vestiges of duplicated copies of genes that have undergone significant mutational alteration
--as a result, although they show some homology to their parent gene, they are usually not transcribed b/c of insertions and deletions throughout their structure
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