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Lecture 13
Nucleosome
Nucleosomes form the fundamental repeating units of eukaryotic chromatin which is used to pack the large eukaryotic genomes into the nucleus
In mammalian cells approximately 2 m of linear DNA have to be packed into a nucleus of roughly 10 µm diameter
Nucleosomes are folded through a series of successively higher order structures to eventually form a chromosome
This both compacts DNA and creates an added layer of regulatory control which ensures correct gene
expression.
Nucleosome
Nucleosomes are thought to carry epigenetically inherited information in the form of covalent modifications of their core histones
The nucleosome core particle consists of approximately 147 base pairs of DNA wrapped in 1.67 left-handed superhelical turns around a histone octamer consisting of 2 copies each of the core histones H2A, H2B, H3, and H4
Linker histones such as H1 and its isoforms are involved in
chromatin compaction and sit at the base of the nucleosome near the DNA entry and exit binding to the linker region of the DNA
Bacterial Chromosome Structure
Prokaryotic cells (bacteria) contain their chromosome as
circular DNA. Usually the entire genome is a single circle, but often there are extra circles called plasmids. The DNA is packaged by DNA-binding proteins
The bacterial DNA is packaged in loops back and forth.
The bundled DNA is called the nucleoid. It concentrates the DNA in part of the cell, but it is not separated by a nuclear membrane (as in eukaryotes.)
The DNA does form loops back and forth to a protein core, attached to the cell wall
The DNA is accessible to enzymes that make RNA and protein.
In the bacterial cell, the DNA gets transcribed to RNA, and the RNA gets translated to protein before it is even completed
Plasmid
A plasmid is an extra chromosomal DNA molecule separate from the chromosomal DNA which is capable of replicating independently from the chromosomal DNA, it is circular and double-stranded
Plasmids are considered transferable genetic elements, or
"replicons", capable of autonomous replication within a suitable host
Similar to viruses, plasmids are not considered a form of "life" as it is currently defined.
Unlike viruses, plasmids are "naked" DNA and do not encode
genes necessary to encase the genetic material for transfer to a new host.
The number of plasmids in a cell generally remains constant from generation to generation.
Plasmid types
There are five main classes:
1. Fertility-F-plasmids, which contain tra-genes. They are capable of conjugation (transfer of genetic material between bacteria which are touching).
2. Resistance-(R)plasmids, which contain genes that can build a
resistance against antibiotics or poisons and help bacteria produce pili.
3. Col-plasmids, which contain genes that code for (determine the production of) bacteriocins, proteins that can kill other bacteria.
4. Degradative plasmids, which enable the digestion of unusual substances, e.g., toluene or salicylic acid
5. Virulence plasmids, which turn the bacterium into a pathogen (one that causes disease
).
Episome
Episome , unit of genetic material composed of a series of genes that sometimes has an independent existence in a host cell and at other times is integrated into a chromosome of the cell, replicating itself along with the chromosome.
Episomes have been studied in bacteria. One group of episomes are actually viruses that infect bacteria.
As autonomous units they destroy host cells, and as segments integrated into a chromosome they multiply in cell division and are transferred to daughter cells.
Episomes called sex factors determine whether chromosome material will be transferred from one bacterium to another.
Other episomes carry genes that make bacteria resistant to the inhibitory action of antibiotics
Viruses genome
The genome; either DNA or RNA The genes are few in number (3 - 100 depending on the species). They encode those proteins needed for viral reproduction that the host cell will not supply. Often, one or more proteins (enzymes) needed to start the process of
reproduction within the host cell.
Either DNA or RNA, never both.
DNA viruses can be further divided into
those that have their genes on a double-stranded DNA molecule (dsDNA). Example: smallpox
those that have their genes on a molecule of single-stranded DNA (ssDNA). Example: Adeno-Associated Virus (AAV)
Viruses genome
RNA viruses occur in four distinct groups:
1. Those with a genome that consists of single-stranded antisense RNA; that is, RNA that is the complement of the message sense.
This is also called negative-stranded RNA. Examples: measles, Ebola
2. Those with a genome that consists of single-stranded sense RNA;
that is, the RNA has message sense (can act as a messenger RNA - mRNA). This is also called positive-stranded RNA. Examples:
poliovirus
3. Those with a genome made of several pieces of double-stranded RNA. Example: reovirus.
4. Retroviruses. Their RNA (also single-stranded) is copied by reverse transcriptase into a DNA genome within the host cell.
Example: HIV-1
Ribosome
Ribosomes are the components of cells that make proteins from amino acids.
One of the central tenets of biology is that DNA makes RNA, which then makes protein.
The DNA sequence in genes is copied into a messenger RNA (mRNA).
Ribosomes then read the information in this RNA and use it to produce proteins.
Ribosomes do this by binding to a messenger RNA and using it as a template for the correct sequence of amino acids in a particular protein
The amino acids are attached to transfer RNA (tRNA) molecules, which enter one part of the ribosome and bind to the messenger RNA sequence.
Ribosome
The attached amino acids are then joined together by another part of the ribosome.
The ribosome moves along the mRNA, "reading" its sequence and producing a chain of amino acids
Ribosomes are made from complexes of RNA and protein
Ribosomes are divided into two subunits, one larger than the other.
The smaller subunit binds to the mRNA, while the larger subunit binds to the tRNA and the amino acids
When a ribosome finishes reading a mRNA these two subunits split apart.
Ribosomes have been classified as ribozymes, since the ribosomal RNA seems to be most important for the peptidyl transferase
activity that links together amino acids.
Ribosome
Ribosomes read the sequence of messenger RNAs and
assemble proteins out of amino acids bound to transfer
RNAs. Large (red) and small (blue) subunit fit together
Ribosome
Ribosomes are about 20 nm (200 ångströms) in diameter and are composed of 65% ribosomal RNA and 35% ribosomal proteins
(known as a ribonucleoprotein or RNP).
They translate messenger RNA (mRNA) to build polypeptide chains (e.g., proteins) using amino acids delivered by transfer RNA (tRNA).
Their active sites are made of RNA, so ribosomes are now classified as "ribozymes
Ribosomes build proteins from the genetic instructions held within messenger RNA
Free ribosomes are suspended in the cytosol; others are bound to the rough endoplasmic reticulum or to the nuclear envelope
Ribosomes are sometimes referred to as organelles
The structure and function of the ribosomes and associated molecules, known as the translational apparatus
