Chapter 10-Genetics

second order equation

-dC/dt=kC^2. The rate depends on the concentration of both reactants -C1 and C2. Its rate is proportional to the product of the concentrations of both strands.

How do twisting forces affect DNa structure

A left handed twist ( underwinding) can either produce fewer turns or a negative supercoil. While a right handed twist ( overwinding) produces more turns or a positive supercoil. When a DNa structure has more or less than 10 bp per turn it is unstable.

Difference between prok and Euk for genome

Bacteria usually has a single circular chromosome while eukaryotes, the genome, refers to the complete set of chromosomes that resides in the cell nucleus. Euk. have a mitochondrial genome while plants also have a chloroplast genome.

equation for determining the concentration of the single stranded DNA changes from time zero to a later time.

C/C0=1/1+ k2C0t.

H1

Called the linker histone. it binds to the DNa in the linker region between nucleosomes and may help to compact adjacent nucleosomes. Less tightly bound to DNA than the core histones.

topoisomers

DNA conformations that differ with regard to supercoiling.

Steps in the chromosomal compaction in eukaryotics.

DNA double helix, wrapping of DNA around a histone octamer, ( nucleosomes, beads on a string), formation of a three dimensional zigzag pattern via histone H1 and other DNA binding proteins which creates a 30 nm fiber, and then anchoring of radial loops to the nuclear matrix creates radial loop domains and protein scaffold, and the formation of a sacffold from the nuclear matrix and further compaction of all radial loops creates a metaphase chromosome.

Besides for adding negative supercoils what else can DNA gyrase do

DNA gyrase in bacteria and topisomerase 2 in eukaryotes can untangle DNA molecules.

overview of DNA gyrase

DNA gyrase is composed of A and B subunits. The DNa binds to the lower jaws ( the A subuitys( and then the DNA wraps around the A subunits in a right handed direction. The upper jaws clamp onto DNA. Tehn the DNA held in the lower jaws is cut and the DNa in upper jaws is released and passes downward through the opening in the cut DNA. This process uses 2 ATP molecules. and the cut DNA is ligated back together and the DNa is released from the DNA gyrase.

How does bacterial DNA become negatively supercoiled

DNA gyrase, also known as topoisomerase 2, which contains four subunits ( two A and two B), introduces negative supercoils ( or relaxes positive supercoils) using energy from ATP. To alter supercoiling DNa gyrase has two sets of jaws that allow it to grab onto two regions of DNA. One of the DNA regions is grabbed onto by the lower jaws and then is wrapped in right handed direction around the two A subunits. The upper jaws then clamp onto another region of DNA. The DNa in the lower jaws is cut in both strands and the other region of DNA is then released fromthe upper jaws and passed through this double stranded break. The net result is that two negative super coils have been introduced into the DNa molecule.

chromatin

DNA-protein complex found within eukaryotic chromosomes. it can change its shape and composition during the life of a cell.

What is chromosome function influenced by

DNa supercoiling

Hypothesis for the nucleosome structure experiment created by Markus Noll

Dnase 1 should preferentially cut the DNA in the linker region thereby producing DNA pieces that are about 200 bp in length.

chromosome territory

Each chromosome in the cell nucleus is located in a discrete chromosome territory. These territories can be viewed when interphase cells are exposed to mutliple florescent molecules that recognize specific sequences on particular chromosomes.

Eukaryotic chromosomes

Eukarytoic species has one or more sets of chromosomes and each set is composed of several different linear chromosomes. Usually contains many more genes than bacteria does. The chromosomes are located within a separate cellular compartment known as nucleus. To fit the chromosomes need to be compacted.

Explain results of the equation

Ex. If you get .4 from the equation it means that after a certain period of time, 40 percent of DNA is still in the single stranded formation and 60 percent has renatured into the double stranded form.

Negative supercoiling consequences

Makes chromosomes more compact and therefore helps to decrease the size of the bacterial chromosome, creates tension in DNA strand that may be released by DNA strand separation. DNA strand separation enhances genetic activities such as replication and transcription that require the DNA strands to be separated.

How do telomeres prevent chromosome shortening

Telomeres protect chromosomes from digestion via enzyme called exonucleases that recognize the ends of DNA. Second and unusual form of DNa replication may occur at the telomere to ensure that eukaryotic chromosomes do not become shortened with each round of DNA replication.

repetitive sequences

These have been identified in many bacterial species. These sequences are found in multiple copies and are usually interspersed within the intergenic regions throughout the bacterial chromosome. Some of these sequences are transposable elements which move throughout the genome.

Arginines

They play a huge role in binding to the DNA. Arginines within the histone proteins form electrostatic and hydrogen bonding interactions with the phosphate groups along the DNA backbone.

eukaryotic chromosomes 2

Usually linear, a typical chromosome is 10s of millions to hundreds of millions of base pairs, occur in sets since many species are diploid which means that somatic cells contain 2 sets of chromosomes, genes are interspersed throughout the chromosome and contain between a few hundred/thousand genes, each chromosome contains many origins of replication, each chromosome contains a centromere that forms a recognition site for the kinetochore proteins, telomeres contain specialized sequences located at both ends of the linear chromosome, repetitive sequences are commonly found near centromeric and telomeric regions but they may also be interspered throughout the chromosome.

-dc

a change in concentration of a single strand.

origin of replication

a sequence that is a few hundred nucleotides in length. Bacterial chromosomes only have one of these. These nucleotide sequence functions as an initiation sire for the assembly of several proteins required for DNA replication.

cohesin

after s phase cohesin complexed bind along each chromatid thereby facilitating their attachment to each other. During the middle of prophase cohesin is released from the chromosome arms but some cohesin remains in the centromeric regions. At anaphase the remaining cohesin complexes are rapdily degraded by separase, which promotes siter chromatid separation.

moderately repetitive sequence

are found a few hundred to several thousand times in the genome. They may playa role in the regulation of gene transcription and translation. Ex. genes that encode rRNA, histone genes.

REsults form Nolls experiment

at high DNase 1 concentrations the entire sample of chromosomal DNA was digested into fragments of approx. 200 bp in length. this result is predicted by the beads on string model.

when H1 is not bound when treated with moderate salt concentrations.

beads on a string, but not as compact when there is H1 histones.

Where are genes located on chromosomes

between the centromeric and telomeric regions along the entire eukaryotic chromosome.

In which phase are chromosomes entirely heterochromatic

by the end of prophase, sister chromatids are entirely heterochromatic.

topoisomerase 1

can relax negative supercoils

constitutive heterochromatin

chromosomal regions that are always heterochromatic and permanently inactive with regard to transcription. Usually contains highly repetitive DNA sequences such as tandem repeats rather than gene sequences.

What are the two multiprotein complexes in cells

codensin and cohesin

kinetochore

composed of a group of cellular proteins that link the centromere to the spindle apparatus during mitosis and meiosis ensuring the proper segregation of the chromosomes to each daughter cell.

C

concentration of a single stranded DNa at a later time, t

What promotes the formation of metaphase chromosomes

condensin and cohesin

histone proteins

consists of globular domain and a flexible charged amino terminus called an amino terminal tail. They have a large number of positively charged lysine and arginine amino acids.

Nuclear matrix

consists of two parts, the nuclear lamina: a collection of fibers that line the inner nuclear membrane. These fibers are composed of intermediate filament proteins. And the internal nuclear matrix, which is connected to the nuclear lamina and fills the interior of the nucleus.

k

constant rate

What do viruses not contain

energy producing enzymes, ribosomes, and or cellular organisms.

During interphase chromosomal DNA is found in which compaction most commonly

euchromatin, in which the 30 nm fibers form radial loop domains that are attached to a protein scaffold.

Highly repetitive sequences

found tens of thousands or millions of times in the genome. Each copy of this sequence is relatively short. Ex. Alu family--> restriction enzyme.

What does the formation of chromosomal loops help make do?

helps make the bacterial chromosome more compact.

why did some fragments come out to 400 or 600 bp

if one linker region was not cut, a Dna piece would contain two nucleosomes and be 400 bp in length. If two consecutive linker regions were not cut a DNA piece would contain three nucleosomes containing 600 bp.

matrix attachment regions ( MARs)/ scaffold attachment regions ( SARs)

interspersed at regular intervals throughout the genome. The MARs bind to specific proteins in the nuclear matrix thus forming chromosomal loops.

loop domains

is a segment of chromosomal DNA folded into a structure that resembles a loop. DNA binding proteins anchor the base of the loops in place. and loop domains help aid compaction of bacterial chromosomes.

scaffold

is formed from nonhistone proteins of the nuclear matrix.

euchromatin

less condensed regions and reflect areas that are capable of gene transcription. the 30 nm fibers forms radial loops domains here.

Bacterial chromosome

most are circular however some are linear. Has a few million base pairs and has a few thousand genes.

bacterial chromosomes

most but not all contain circular chromosome DNA, a typical chromosome is a few million bp in length, most bacterial species contain a single type of chromosome but it may be present in multiple copies, several thousand different genes are interspersed throughout the chromosome, there is one origin of replication required to initiate DNA replication, and repetitive sequences may be interspersed throughout the chromosome.

introns

noncoding intervening sequences. They make structural genes longer.

structure of viruses

nucleic acid molecules ( RNA and DNA), surrounded by a capsid, or protein coat. Other viruses will also contain an envelope composed of a membrane and spike proteins.

H1 histones bound to linker region and therefore..

nucleosomes are more compact.

30 nm fiber

nucleosomes associate with each other for a form a more compact structure, 30 nm in diameter.

Structural genes

nucleotide sequences that encode proteins, and account for the majority of bacterial DNA.

What three types of regions are required for chromosomal replication and segregation

origins of replication, centromeres, and telomeres.

difference between point and regional centromeres

point: a defined DNA sequence that is about 125 bp in length. regional: centromeres found in more complex eukaryotes that are much larger and contain many copies of tandemly repeated DNA sequences.

SMC proteins

proteins that stand for structural maintenance of chromosomes. These proteins use energy from ATP to catalyze changes in chromosome structure. These proteins actively fold, tether, and manipulate DNA strands. They are dimers that have a V shaped structure.

which two things inhibit gyrase

quinolones and coumarins however they do not inhibit eukarytoic topoisomerase.

Genome

refers to a complete set of genetic material in a particular cellular compartment.

Facultative heterochromatin

refers to chromatin that can occasionally interconvert between heterochromatin and euchromatin. Ex. when in females one of the two X chromosomes is converted into a heterochromatic Barr body.

sequence complexity

refers to the number of times a particular base sequence appears throughout the genome.

Centromeres

regions that play a role in the proper segregation of chromosomes during mitosis and meiosis. They function as a site for the formation of kinetochores.

a high concentration of salt will..

remove both the linker and core histones and the high compaction of chromosomes is lost.

what is in DNA sequences and then the percentage of each one.

repetitive DNA> introns and other parts of genes such as enhancers> unique noncoding DNa >regions of genes that encode proteins ( exons).

In highly condensed chromosomes such as though found in metaphase the radial loops are highly compacted and remain anchored to...

scaffold

retroelement

seen in the Alu gene and its function is that it can be transcribed into RNA copied into DNA and inserted into the genome.

transposable elements

segments of DNA that have the ability to move within the genome.

Viruses

small infectious particles that contain nucleic acid as their genetic material, surrounded by a protein coat, or capsid.

what does negative supercoiling promote?

strand separation

host cells

the cells viruses infect for making new viruses

C0

the concentration of single stranded DNA at time zero.

viral genome

the genetic material that a virus contains. the genome can be DNA or RNA but never both, and it can either be single or double stranded DNA, and it can be linear or circular.

Distinctive feature of centromeres in eukaryotics

the histone H3 is replaced with CENP-A

Intergenic regions

the non transcribed regions of DNA located between adjacent genes.

nucleosome

the repeating structural unit within eukaryotic chromatin. a double stranded segment of DNA wrapped around an octamer of histone proteins. Each octamer contains eight histone subunits, two copies each of four different histone proteins.

k2

the second order rate constant for renaturation

Chromosomes

the structures within cells that contain the genetic material.

chromosomal sequences facilitate 4 important processes

the synthesis of RNA and cellular proteins, the replication of chromosomes, the proper segregation of chromosomes, and the compaction of chromosomes so they can fit within living cells.

DNA supercoiling

the two strands within DNA already coil around each other and the formation of additional coils are due to twisting forces.

telomeres

these are found at the end of linear chromosomes. Telomeres prevent chromosomal rearrangements such as translocations. They also prevent chromosome shortening in two ways.

what is the significance of highly repetitive sequences

they may be important in the proper segregation of chromosomes during meiosis 1.

what do condensin and cohesin do

they playa critical role in chromosomal condensation and sister chromatid alignment respectively. Therefore cohesin is released during prophase when you want the arms to separate

nucleoid

this is where a bacterial cell's chromosomes are found. The DNA in a nucleoid is in direct contact with the cytoplasm of the cell.

heterochromatin

tightly compacted regions of chromosomes. Usually transcriptionally inactive. In heterochromatin radial loops become even more condensed. It is most abundant in the centromeric regions of the chromosomes and to a lesser extent in the telomeric regions.

primary function of genetic material

to store the information needed to produce the characteristics of an organism,

why is the attachment of radial loops to the nuclear matrix important?

In addition to compaction the nuclear matrix serves to organize the chromosomes within the nucleus.

Function of the proteins of the nuclear matrix

Involved in compacting the DNA into radial loop domains, similar to those described for the bacterial chromosome.

What is the third level of compaction

It involves interactions between the 30 nm fibers and a filamentous network of proteins in the nucleus called the nuclear matrix.

structure of SMC proteins

It is a dimer that consists of a hinge, arm, and head regions. The head regions bind and hydrolyze ATP. Codensin and cohesin have additional protein subunits not shown here. N indicates the amino terminus C indicates the carboxyl terminus.

the rate of renaturation of complementary DNa strands provides what

A way to to distinguish between unique, moderately repetitive, and highly repetitive sequences.

how do we explain the difference in genome size?

Accumulation of repetitive DNA sequences present in many copies.

Rate of renaturation for moderately/highly repetitive sequences and unique DNA.

FAST-highly repetitive sequences Intermediate- moderately repetitive sequences SLOW- unique DNA.

What are the four different histone proteins

H2A, H2B, H3, and H4.

tandem array

Seen in moderately and highly repetitive sequences. It is a very short nucleotide sequence and is repeated many times ina row. They can be long and are seen in centromeric regions.

functions of noncapsid proteins

Some proteins, called scaffolding proteins catalyze the assembly process and are transiently associated with the capsid. When the virus is done being assembled the scaffolding proteins are expelled form the mature virus. There are also proteins that act as proteases which cleave viral capsid proteins.

What kind of sequences do eukaryotes contain

unique, moderately repetitive, and highly repetitive.

bacteriophages

viruses that infect bacteria. They may also contain a sheath, base plate, and tall fibers.

directed assembly

when virus assembly requires the participation of noncapsid proteins. These proteins direct the proper assembly of the virus.

C^2

which is also equal to -C1 times C2 but since -c1 is equal to C2 it is C^2.

dt

with respect to time