Chapter 10 Flashcards
What is a genome?
All of the chromosomes and DNA sequences that an organism or species can possess.
What four important processess does chromosomal sequences facilitate?
- Synthesis of RNA and Cellular Proteins
- Replication of Chromosomes.
- Segregation of chromosomes.
- Compaction of chromosomes
Bacteria usually contain a single type of what? But more than one what?
Chromosome
Copy
What are protein-encoding genes?
Genes that produce mRNA and encode polypeptides;
What is another name for protein-encoding genes?
Structural genes
What accounts for the majority of bacterial DNA?
Protein-encoding genes
What are intergenic regions?
A region of DNA in a chromosome that lies between two different genes.
What are the key features of bacteria?
- contain circular chromosomal DNA
- contain single type of chromosome, with multiple copies
- Has a few million base pairs
- Has intergenic regions
- One origin of replication is required to initiate DNA replication
- Repetitive sequences are interspersed throught the chromosome
What types of sequences constitue most of a bacterial genome?
Sequences of genes
Other sequences in chromosomal DNA influences what?
DNA replication
Gene transcription
Chromsome structure
What is the origin of replication?
A nucleotide sequences that functions as an initiation site for the assembly of several proteins required for DNA replication.
What are repetitive sequences?
DNA sequences that are present in many copies in the genome
The repetitive sequences are usually what throughout the chromosome?
Interspersed within the intergenic regions throughout bacterial chromosome
Repetitive sequences may play a role in what?
A variety of genetic processess including DNA folding
DNA replication
Gene regulation
Genetic recombination
A bacterial chromosome typically contains
a. a few thousand genes
b. one origin of replication
c. some repetitive sequences
d. all of the above.
d. all of the above.
What is a nucleoid?
A darkly staining region that contains the genetic material of mitochondria, chloroplasts or bacteria.
To fit within the bacterial cell, the chromosomal DNA must be compacted ________.
1000 fold
What are loop domains?
A segment of chromosomal DNA that is anchored by proteins, so it forms a loop.
Part of the compaction process involves the formation of what?
Loop domains
The number of loop domains vary according to what?
The size of the bacterial chromosome and the species.
E. coli chromosomes contain how many loop domains?
50-100 with 40,000-80,000 bp of DNA in each loop.
What holds the loop domain in place?
Proteins
What is DNA supercoiling?
The formation of additional coils in DNA due to twisting forces. Like twisting a rubber band
What happens with underwinding of DNA?
The underwinding motion can cause fewer turns
Cause a negative supercoil to form.
Overwinding DNA can cause what?
More turns
The formation of a positive supercoil.
What are topoisomers?
DNA conformations that differ with regard to supercoiling
In living bacteria what type of supercoil is usually seen?
Negative supercoil
Negative supercoil occurs at how many turns of the double helix?
40 turns
What are the consequences of negative supercoiling?
DNA is much more compact
Affects DNA function
How does negative supercoiling affect DNA function?
It creates tension on the DNA strand that may be released by DNA strand separation.
So, it may promote DNA strand separation in small regions.
This enhances replication and transcription
Why is strand separation beneficial?
It is needed for certain processes such as DNA replication and RNA transcription
What is DNA gyrase?
Tpopisomerase II
An enzymes that introduces negative supercoils into DNa using energy from TAP. Gyrase can also relax positive supercoils when they occur.
Who discovered DNA gyrase? When?
Martin Gellert
1976
How does DNA gyrase alter supercoiling?
It has two sets of jaws that allow it to grab onto two regions of DNA.
The lower jaw wraps in a right-handed direction around the two A subunits. The upper jaw 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 released from the upper jaw and it then passes through this double-stranded break.
The double-stranded break is ligated back together at the end.
What is the net result of DNA gyrase?
Two negative supercoils
What else can DNA gyrase do?
Untangle DNA molecules
Describe the steps that requires the use of ATP in recoiling of DNA?
ATP is needed so the DNA held in the upper jaws can pass through the break in the DNA and move to the region of the lower jaws
What is topoisomerase I?
An enzyes that alters the degree of supercoiling in DNA.
Topoisomerase I can do what?
Bind to a negatively supercoiled region and introduce a break in one of the DNA strands. After one DNA strand has been broken, the DNA molecule rotates to relieve the tension and relaxes supercoiling. the broken strand is then repaired.
What governs the overall supercoiling of the bacterial DNA?
The competing actions of DNA gyrase and topoisomerase I.
What is critical for bacterial survival?
The ability of gyrase to introduce negative supercoils into DNA
What inhibits DNA gyrase?
Quinolones
Coumarins
Mechanisms that make the bacterial chromosome more compact include
a. the formation of loop domains
b. DNA supercoiling
c. crossing over
d. both a and b.
d. both a and b.
Negative supercoiling may enhance activities like transcription and DNA replication because it
a. allows the binding of proteins to the major groove.
b. promotes DNa strand separation
c. makes the DNa more compact
d. causes all of the above.
b. promotes DNa strand separation
DNA gyrase
a. promotes negative supercoiling
b. relaxes positive supercoils
c. cuts DNA strands as part of its function.
d. Does all of the above.
d. Does all of the above.
What are the key features of Eukaryotic chromosomes?
- Usually linear
- Occur in sets usually diploid
- tens of millions to hundreds of millions of base pairs in length
- contains a few hundred and several thousand different genes
- Has many origins of replication dispersed every 100,000 base pairs.
- Has a centromere that forms a recognition site for the kinetochore proteins
- Telomeres contain specialized sequences located at both ends of chromosome
- Repetitive sequences found near centromeric and telomeric regions
What are some differences between the types of sequences found in eukaryotic chromosomes versus bacterial chromosomes?
Eukaryotes have centromeres and telomeres, which bacteria dont. Eukaryotes typically have much more repetitive sequences.
What are introns?
Intervening sequences that are found between exons. Introns are spliced out of the RNA prior to translation.
Protein-encoding genes tend to be much longer in eukaryotes, why?
The presence of introns
What are exons?
A segment of RNA that is contained within the RNA after splicing has occurred. IN mRNA, the coding sequence of a polypeptide is contained within the exon.
What is the range of introns?
100bp-10,000 bp
What are the three regions in eukaryotes chromosomes that are required fro chromosomal replication and segregation?
Origins of replication
Centromeres
Telomeres
What are centromeres?
A segment of eukaryotic chromosomal DNa that provides an attachment site for the kinetochore
What is the kinetochore?
A group of proteins that link the centromere to the spindle apparatus during mitosis and meiosis, ensuring the proper segregation of the chromosomes to each daughter cell.
What is a point centromere?
When centromeres have a defined DNA sequence.
What are regional centromeres?
Much larger centromeres that contain tandem arrays of short repetitive DNA sequences.
Is the repeated DNA sequences sufficient to form functional centromeres with a kinetochore?
No
What is a distinctive feature of all eukaryotic centromes?
Histone protein H3 is replaced with a histone variant called CENP-A
What are the important functions of telomeres?
Replication and stability of chromosome.
Telomeres prevent what?
Chromosome shortening
How do telomeres prevent chromosomes from shortening?
First they protect chromosomes from digestion via enzymes called exonucleases that recognize the ends of DNA.
Second, an unusual form of DNA replication occurs at the telomere to ensure that eukaryotic chromosomes do not become shortened with each round of DNa replication
The chromosomes of eukaryotes typically contain
a. a few hundred to several thousand different genes
b. multiple origins of replication
c. a centromere
d. telomeres at their ends
e. all of the above.
e. all of the above.
Is the size of the genome related to the complexity of the species?
No
If two different species have the same number og genes, but different genome sizes, what explains the difference in size?
It is due to the accumulation of repetitive DNa sequences present in many copies.
Do highly repetitive sequences encode proteins?
No
What are the two reasons for the wide variation in genome sizes among eukaryotic species?
The number of genes
The amount of repetitive sequences
What is sequence complexity?
The number of times a particular base sequence appears throughout the genome of a given species
What are unique or nonrepetitive sequences?
Sequences found once or a few times within the genome.
Protein-encoding genes are typically what?
Unique sequences of DNA
In humans, unique sequences make up roughly what percent of the genome?
41%
This includes 2% protein-encoding regions of genes
24% introns
15% unique regions that are not found within genes.
What are moderately repetitive sequences?
Sequences that are found a few hundred to several thousand times in the genome.
What is an example of moderately repetitive sequences?
rRNA