Genes Flashcards
Genome
The entire DNA sequence of an organism is called the genome. There are between 20K and 25K genes in the human genome. Only a little over 1% of the human genome actually codes for protein.
There is little variation of the nucleotide sequence among humans. Human DNA differs between individuals at approximately one nucleotide out of every 1200 or about 0.08%. A small variation in the genome can make a big difference.
Gene
A gene is a sequence of DNA nucleotides that codes for rRNA, tRNA, or a single polypeptide via a mRNA intermediate. It is the gene, or DNA sequence, and not the trait, that is inherited.
Eukaryotes have more than one copy of some genes. Prokaryotes have only one copy of each gene.
Genes are often referred to as unique sequence DNA. Regions of non-coding DNA, which is found only in eukaryotes, are called repetitive sequence DNA. Eukaryotes have more unique sequence DNA.
Eukaryotic genes being actively transcribed by a cell are associated with regions of DNA called euchromatin. Genes not being actively transcribed are associated with tightly packed regions of DNA called heterochromatin.
In general: one gene, one polypeptide.
Central dogma
The central dogma of gene expression is that DNA is transcribed to RNA, which is translated to amino acids, which are the building blocks of proteins. All living organisms use this method to express their genes.
DNA
Deoxyribonucleic acid is a polymer of nucleotides.
Each nucleotide is made up of three parts- the phosphate group, the five carbon sugar, and the nitrogenous bases. DNA nucleotides differ from each other only in their nitrogenous base. The four nitrogenous bases in DNA are adenine, guanine, cytosine, & thymine.
Each nucleotide is bound to the next by a phosphodiester bond between the third carbon of one deoxyribose and the fifth carbon of the other, creating the sugar-phosphate backbone of a single strand of DNA, with 5’ -> 3’ directionality.
In a living organism, two DNA strands are anti-parallel, and held together by hydrogen bonds between nitrogenous bases, forming a double-stranded structure. In order for two strands to bind together, their bases must match up in the correct order. When complementary strands bind together, they curl into a double helix.
DNA is confined to the nucleus and mitochondrial matrix.
Purines
Adenine and guanine are two ring structures called purines
Pyrimidines
Cytosine and thymine are single ring structures called pyrimidines. Uracil is also a pyrimidine.
Phosphodiester Bond
Each nucleotide is bound to the next with a phosphodiester bond between the third carbon of one deoxyribose and the fifth carbon of the other. This creates the sugar phosphate backbone of a single strand of DNA, and has 5’ to 3’ directionality.
5’ to 3’ directionality
The 5’ and 3’ indicate the carbon numbers on the sugar. The end 3’ carbon is attached to an -OH group, and the end 5’ carbon is attached to a phosphate group. In a living organism, two DNA strands life side-by-side in opposite 3’ to 5’ directions.
Anti-parallel orientation
In a living organism, two DNA strands of my side-by-side in opposite 3’ to 5’ directions. This is called anti-parallel orientation. These two DNA strands are bound together with hydrogen bonds, forming a double-stranded structure.
Double-stranded structure
Hydrogen bonding between nitrogenous bases forms a double-stranded structure. This hydrogen bonding is commonly referred to as base pairing.
Base pairing
The hydrogen bonding between nitrogenous bases, which forms a double-stranded structure, is called base pairing. The length of a DNA strand is measured in base pairs (bp).
Complementary strands
Under normal circumstances, the hydrogen bonds form only between specific purine-pyrimidine pairs. Adenine forms 2 hydrogen bonds with thymine. Guanine forms three hydrogen bonds with cytosine. (This means that GC bonds require more energy to separate.)
In order for two strands to bind together, their bases must match up in the correct order. Two strands that match like this are called complementary strands.
Double helix
When complementary strands bind together, they curl into a double helix. The double helix contains two distinct groups called the major groove and the minor groove. Each groove spirals once around the double helix for every 10 base pairs. The diameter of the double helix is about 13 times the diameter of a carbon atom, or 2 nm.
DNA replication
One time in each life cycle, a cell replicates it’s DNA.
The process of DNA replication is governed by the replisome. Replication begins at the middle of a chromosome at a site called the origin of replication. A single eukaryotic chromosome contains multiple origins on each chromosome, while replication in prokaryotes usually takes place from a single origin on the circular chromosome.
From the origin, two replisomes proceed in opposite directions along the chromosome making replication a bidirectional process. The place where the replisome attaches to the chromosome is called the replication fork. Each chromosome of eukaryotic DNA is replicated in many discrete segments.
DNA replication has five steps:
- Helicase unzips the double helix
- RNA polymerase builds a primer
- DNA polymerase assembles the leading and lagging strands
- The primers are removed
- Okazaki fragments are joined with ligase
DNA replication is fast and accurate. replication in a human cell requires about eight hours.
Although there are some differences, replication in eukaryotes and prokaryotes is very similar.
DNA polymerase
The enzyme that builds the new DNA strand. It can only add nucleotides to existing strands, and thus adds deoxynucleotides to the primer and moves along each DNA strand creating a new complementary strand. DNA polymerase reads the parental strand in the 3’ to 5’ direction, and creates the new complementary strand in the 5’ to 3’ direction. By convention, the nucleotide sequence in DNA is written 5’ to 3’ as well.
One of the subunits in DNA polymerase is also an exonuclease. It removes nucleotides from the strand. This enzyme automatically proofreads each new strand, and makes repairs when it discovers any mismatch nucleotides. DNA replication in eukaryotes is extremely accurate.
RNA primer
Because DNA polymerase can only add nucleotides to existing strands, primase, an RNA polymerase, creates an RNA primer approximately 10 ribonucleotides long to initiate the strand.
Lagging strand
The polymerization of the new strand is continuously interrupted and restarted with the new RNA primer. This interrupted strand is called the lagging strand. It is made from a series of disconnected strands called Okazaki fragments. Okazaki fragments are about 100 to 200 nucleotides long and eukaryotes and about 1000 to 2000 nucleotides long in prokaryotes.
Leading strand
The continuous new strand created by DNA polymerase is called the leading strand.
DNA ligase
Moves along the lagging strand and ties the Okazaki fragments together to complete the polymer.
Semidiscontinuous
Since the formation of one strand in DNA replication is continuous and the other fragmented. The process of replication is said to be semi-discontinuous.
Telomeres
The ends of eukaryotic chromosomes on DNA possess telomeres. Telomeres are repeated six nucleotide units from 100 to 1000 units long that protect the chromosomes from being eroded through repeated rounds of replication. Telomerase catalyzes the lengthening of telomeres.
RNA
Ribonucleic acid is identical to DNA in structure except that:
- Carbon number two on the pentose is not deoxygenated, it has a hydroxyl group attached
- RNA is single-stranded
- RNA contains the pyrimidine uracil instead of thymine
Unlike DNA, RNA can move through the nuclear pores and is not confined to the nucleus.
mRNA
Messenger RNA. Delivers the DNA code for amino acids to the cytosol where the proteins are manufactured. Almost all mRNA is directly translated to protein. mRNA is the template which carries the genetic code from the nucleus to the cytosol in the form of codons.
rRNA
Ribosomal RNA. Combines with proteins to form ribosomes, the intracellular complexes that directs the synthesis of proteins. rRNA is synthesized in the nucleolus.
tRNA
Transfer RNA. Collect amino acids in the cytosol, and transfers them to the ribosomes for incorporation into a protein.
Transcription
All RNA is manufactured from a DNA template in a process called transcription. Eukaryotic transcription takes place in the nucleus and mitochondrial matrix, since DNA cannot leave those two spots. Transcription starts with initiation.
Only the template strand of the DNA double helix is transcribed. The sequence of the coding strand resembles the sequence of the newly synthesized mRNA.
Initiation
The beginning of transcription is called initiation. A group of proteins find a promoter on the DNA strand and assemble a transcription initiation complex, which includes RNA polymerase. Prokaryotes have one type of RNA polymerase. Eukaryotes, except plants, have three: one each for mRNA and snRNA, tRNA, and rRNA.
Promoter
A promoter is a sequence of DNA nucleotides that designates a beginning point for transcription. The promoter and prokaryotes is located at the beginning of the gene, “upstream”. The transcription start point is part of the promoter. The first base pair at the transcription start point is designated +1, base pairs located before the +1 transcription site are designated by negative numbers.
Elongation
After binding to the promoter, RNA polymerase unzips the DNA double helix creating a transcription bubble. Next the complex switches to to elongation mode. In elongation, RNA polymerase transcribes only one strand of DNA nucleotide sequence into a complementary RNA nucleotide sequence.
Only one strand in a molecule of double-stranded DNA is transcribed, the template strand. The other strand, coding strand, protects its partner against degradation.
RNA polymerase
RNA polymerase is included in the transcription initiation complex. After binding to the promoter, it unzips the DNA double helix, creating a transcription bubble. Like DNA polymerase, RNA polymerase moves along the DNA strand in the 3’ to 5’ direction, building the new RNA strand in the 5’ to 3’ direction.
Note that RNA polymerase does not have a proofreading mechanism, so the rate of errors for transcription is higher than for replication.
Termination
The end of transcription is called termination. This requires a special termination sequence and special proteins to dissociate RNA polymerase from DNA.
Activators and repressors
Replication makes no distinction between genes. Instead, genes are activated or deactivated at the level of transcription. Most regulation occurs via proteins called activators and repressors. These bind to DNA close to the promoter, and activate or repress the activity of RNA polymerase. They are allosterically regulated by small molecules like cAMP.
The amount of a given type of protein within a cell is likely to be related to how much of it’s mRNA is transcribed.
Operon
An operon is a sequence of bacterial DNA containing an operator, a promoter, and related genes. The genes of an operon are transcribed on one mRNA. Genes outside the operon may code for activators and repressors.
The lac operon codes for enzymes that allow E. coli to import and metabolize lactose when glucose is not present in sufficient quantities. Low glucose levels lead to high cAMP levels. cAMP binds to and activates CAP. Activated CAP to a CAP site, activating the promoter, allowing the formation of an initiation complex and the subsequent transcription and translation of three proteins. The operator, located adjacent and downstream of the promoter, provides a binding site for a repressor protein. The repressor protein is inactivated by the presence of lactose in the cell. It will bind to the operator unless lactose binds to the repressor protein.
The binding of the lac repressor to the operator in the absence of lactose prevents the transcription of the lac genes. Lactose can induce the transcription of the operon only when glucose is not present.
Post transcriptional processing
The addition of the 5’ cap to eukaryotic mRNA, which serves as an attachment site in protein synthesis and as a protection against degradation by exonucleases.
The polyadenylation of the 3’ end of mRNA with a poly-A tail, also protecting it from exonucleases.
The splicing of introns from the primary transcript.
Primary transcript
The initial mRNA nucleotide sequence arrived at through transcription is called the primary transcript. The primary transcript is processed in three ways: by the addition of nucleotides, deletion of nucleotides, and modification of nitrogenous bases.
Introns and exons
The primary transcript is much longer than the mRNA that will be translated into a protein. Before leaving the nucleus, the primary transcript is cleaved into introns and exons. Enzyme-RNA complexes called small nuclear ribonucleoproteins (snRNPs) recognize nucleotide sequences at the end of the introns. Several snRNPs associate with proteins to form the spliceosome. Inside the spliceosome, the introns are looped bringing the exons together. The introns are then excised by the splicesome and the exons are spliced together to form the single mRNA strand that ultimately codes for a polypeptide. Intron’s do not code for protein and integrated within the nucleus. Although there are only an estimated 20 to 25,000 protein coding genes in the human genome, there are about 120,000 proteins made possible by differential splicing of exons. Introns represent about 24% of the genome. Exons represent about 1.1%.
Denaturing
When heated or immersed in high concentrations salt solution or high pH solution, the hydrogen bonds connecting the two strands in a double-stranded DNA molecule are disrupted and the strands separate. The temperature needed to separate the DNA strands is called the melting temperature. DNA with more GC base pairs has a greater melting temperature, since guanine and cytosine make three hydrogen bonds. Heating two 95°C is generally sufficient to denature any DNA sequence.
Denatured DNA is less viscous, denser, and more able to absorb UV light. Separated strands will spontaneously associate with their original partner or any other complementary nucleotide sequence.
Nucleic acid hybridization
Separated strands will spontaneously associate with their original partner or any other complementary nucleotide sequence. Thus different double-stranded combinations can be formed through hybridization- DNA and DNA, DNA and RNA, and RNA and RNA. Hybridization techniques allows scientists to identify nucleotide sequences by binding unknown sequence with an unknown sequence.
Restriction enzymes
One method bacteria use to defend themselves from viruses is to cut the viral DNA into fragments with restriction enzymes. These bacteria protect their own DNA from enzymes by methylation. Methylation is usually associated with inactivated genes. Also called restriction endonucleases, these digest, or cut, nucleic acids only at certain nucleotide sequences along the chain called restriction sites.
Most restriction enzymes cleave the DNA strand unevenly, leaving complementary single-stranded ends which can reconnect through hybridization called sticky ends.
Once paired, the phosphodiester bonds of the fragments can be joined by DNA ligase. There are hundreds of restriction endonucleases known, each attacking a different restriction site. Two DNA fragments cleaved by the same endonuclease can be joined together regardless of the origin of the DNA.
Recombinant DNA
To DNA fragments cleaved by the same endonuclease can be joined regardless of the origin of the DNA. When DNA is artificially recombined like this, it is called recombinant DNA.
Vector
Recombinant DNA can be made long enough for bacteria to replicate and then placed within the bacteria using a vector, typically a plasmid or a virus. The bacteria can then be grown in large quantity.
Clone
When recombinant DNA is placed within bacteria, and then grown in large quantity, it forms a clone of cells containing the factor with the recombinant DNA fragment. These clones can be saved separately producing a clone library.
Clone library
To make a DNA library, take a DNA fragment, use a vector to insert it into a bacterium, and reproduce that bacterium like crazy. Now you have clones of bacteria with your DNA fragment.
Because the cloning process isn’t perfect, some bacteria in a library don’t have the vector and some vectors don’t have the DNA fragment. To screen out these undesirable elements, include the gene of interest and an antibiotic resistant gene when you prepare your clone. Also when preparing your clone, use an endonuclease that will insert your DNA fragment into the middle of the gene of interest and inactivate it.
Probe
The radioactively labeled complementary sequence of the desired DNA fragment, which is used to search the library.
Complementary DNA
cDNA. This is DNA reverse transcribed from mRNA. It lacks the introns that would normally be found in eukaryotic DNA. This is used because bacteria have no mechanism for removing introns, so it is useful to clone DNA with no introns.
PCR
Polymerase chain reaction is a much faster method of cloning, which uses a specialized polymerase enzyme found in a series of bacterium adapted to life in nearly boiling waters. In PCR, the double-stranded DNA to be cloned (amplified) is placed in a mixture with many copies of two DNA primers, one for each strand.
The mixture is heated to 95°C to denature the DNA. The mixture is then cool to 60°C, where the primers hybridize, or ANNEAL, to their complementary ends of the DNA strands. Next, the heat resistant polymerase is added with a supply of nucleotides, and the mixture is heated to 72°C to activate the polymerase. The polymerase amplifies the complementary strands, doubling the amount of DNA. This procedure can be repeated many times without adding more polymerase because it is heat resistance. The result is an exponential increase in the amount of DNA. Starting with the single fragment, 20 cycles produces over 1 million copies.
Southern blotting, Northern blot
Southern blotting is used to identify target fragments of known DNA sequence in a large population of DNA. It can be used to map the structure of particular genes.
Chop up DNA, use electrophoresis to spread out pieces according to size. Blot it onto a membrane. Add a radioactive probe made from DNA or RNA. Visualize with radiographic film.
A northern blot uses the same techniques to identify specific sequences of RNA.
Western blot
A Western blot can detect a particular protein in a mixture of proteins. It detects a protein using anti-bodies. The reaction catalyzed by the enzyme attached to the anti-body produces a reaction product which can be visualized with x-ray film.
RFLP
Identifies individuals, as opposed to identifying specific genes. The DNA of different individuals possesses different restriction sites and varying distances between restriction sites. The population of humans is polymorphic for restriction sites. RFLP’s are the DNA fingerprints used to identify criminals in court cases. They fragment the DNA sample with endonucleases, and reveal a band pattern unique to an individual on radiographic film, via southern blotting techniques.
Genetic code
mRNA nucleotides are strung together to form a genetic code which translates the DNA nucleotide sequence into an amino acid sequence and ultimately into a protein.
There are four different nucleotides in RNA that together must form an unambiguous code for the 20 common amino acids. The code is a combination of three nucleotides.
Because more than one series of three nucleotides may code for any amino acid, the code is degenerative. But any single series of three nucleotides will code for one and only one amino acid, thus, the code is unambiguous. In addition, the code is almost universal, nearly every living organism uses the same code.
The start codon is AUG (codes for methionine). The stop codons are UAA, caps UAG, and UGA.
To figure out how many possible codons exist, take the number of possible nucleotides and raise it to the number of positions.
Codon
Three consecutive nucleotides on the strand of mRNA represent a codon. All but three possible codons code for amino acids. The remaining codons are stop codons.
Stop codons
Stop codons are also called termination codons. Stop codons signal an end to protein synthesis. The stop codons are UAA, UGA, and UAG.
Translation
Translation is the process of protein synthesis directed by mRNA.
Each of the three major types of RNA plays a unique role in translation. mRNA carries the genetic code from the nucleus to the cytosol in the form of codons. tRNA contains a set of nucleotides that is complementary to the codon, called the anti-codon. tRNA sequesters the amino acid that corresponds to its anticodon. rRNA with protein makes up the ribosome, which provides the site for translation to take place.
Translation may take place on a free-floating ribosomes in the cytosol, producing proteins that function in the cytosol. Otherwise, a ribosome may attach itself to the rough ER during translation and inject proteins into the ER lumen. Proteins injected into the ER lumen are destined to become membrane bound to proteins of the nuclear envelope, ER, Golgi, lysosomes, plasma membrane, or bound for secretion.
Small and large subunits
The ribosome is composed of a small subunit and a large subunit made from rRNA and many separate proteins. The ribosome and its subunits are measured in sedimentation coefficients given in Svedberg units. The sedimentation coefficient gives the speed of a particle in a centrifuge, and is proportional to mass and related to shape and density. Prokaryotic ribosomes are smaller than eukaryotic ribosomes. The ribosome is assembled in the nucleolus, and the small and large subunits are exported separately to the cytoplasm.
Nucleolus
The complex structure of ribosomes requires a special organelle called the nucleolus in which to manufacture them. Prokaryotes do not possess a nucleosis, but synthesis of prokaryotic ribosomes is similar to eukaryotic ribosomes. Although the ribosome is assembled in the nucleosis, the small and large subunits are exported separately to the cytoplasm.
Initiation
After post transcriptional processing in a eukaryote, mRNA leaves the nucleus through the nuclear pores and enters the cytosol. With the help of protein initiation factors, the 5’ end and attaches to the small subunit of a ribosome. A tRNA possessing the 5’-CAU-3’ anticodon sequesters the amino acid methionine and settles in at the P site, peptidyl site. This is the signal for the large subunit to join and form the initiation complex. This process is termed initiation.
Elongation
After initiation, elongation of the polypeptide begins. A tRNA with its corresponding amino acid attaches to the A site (aminoacyl site) at the expense of two GTP’s. The C terminus of the methionine attaches to the N terminus of the amino acid at the A site in a dehydration reaction. In an elongation step called translocation, the ribosome shifts three nucleotides along the mRNA toward the 3’ end. The tRNA that carried methionine moves to the E site where it can set the ribosome. The tRNA carrying the nascent dipeptide moves to the P site, clearing the a site for the next tRNA. Translocation requires the expenditure of another GTP. The location process continues and repeats until a stop codon reaches the P site.
Translocation
Translocation is the shifting of the ribosome three nucleotides along the mRNA toward the 3’ end. It requires the expenditure of a molecule of GTP.
Termination
Translation ends when a stop codon is reached in a step called termination. When a stop or nonsense codon reaches the A site, proteins known as release factors bind to the A site allowing a water molecule to end the polypeptide chain. The polypeptide is freed from the tRNA and ribosome, and the ribosome breaks up into its subunits to be used again for another round of protein synthesis later.
Post translational modifications
Even as the polypeptide is being translated, it begins folding. The amino acid sequence determines the folding confirmation and the folding process is assisted by proteins called chaperones. Post translational modifications include the addition of sugars, lipids, or phosphate groups two amino acids. The polypeptide may be cleaved in one or more places. Separate polypeptides may join to form the quaternary structure of a protein.
Signal peptide
Translation begins on a free-floating ribosome. A signal peptide at the beginning of the translated polypeptide may direct the ribosome to attach to the ER, in which case the polypeptide is injected into the ER lumen. Polypeptides injected into the lumen maybe secreted from the cell via the Golgi or may remain partially attached to the membrane. The signal peptide is recognized by protein-RNA signal recognition particle that carries the entire ribosome complex to receptor protein on the ER.
Mutation
Any alteration in the genome that is not genetic recombination is called a mutation. Mutations may occur at the chromosome level or on the nucleotide level. In multicellular organisms, a mutation and a somatic cell is called a somatic mutation. A somatic mutation of a single cell may have very little effect on an organism with millions of cells. A mutation in a germ cell, from which all other cells arise, can be very serious for the offspring. Only about one of every million gametes will carry mutation for a given gene. Mutations can be spontaneous or induced. Induced mutations are due to physical or chemical agents called mutagens.
Mutagens that cause cancer are called carcinogens.
Gene mutation
A gene mutation is the alteration in the sequence of DNA nucleotides in a single gene.
Chromosomal mutation
A chromosomal mutation occurs when the structure of a chromosome is changed.
Mutagen
Mutagens are the physical or chemical agents which cause induced mutations. They increase the frequency of mutation above the frequency of spontaneous mutations.
Point mutation
If the mutation changes a single base pair of nucleotides in a double strand of DNA, that mutation is called a point mutation.
Base pair substitution mutation
A type of point mutation in which one base pair is replaced by another. When one purine is exchanged for the other (A for G), or one pyrimidine is exchanged for the other (C for T), it is called the transition mutation. Changing a purine for a pyrimidine is called a transversion mutation.
Missense mutation
A base pair mutation that occurs in the amino acid coding sequence of the gene. May or may not alter the amino acid sequence of the protein. The alteration of a single amino acid may or may not have serious effects on the function of the protein. If there is no change in protein function, the mutation is called a neutral mutation. If the amino acid is not changed, it is called the silent mutation. Even a silent mutation may be significant because it may change the rate of transcription.
Insertions and deletions
And insertion or deletion of a base pair may result in a frameshift mutation. This results when the deletions or insertions occur in multiples other than three. Frameshift mutations often result in a completely nonfunctional protein, whereas non-frameshift mutations may still result in a partially or even completely active protein. If a base pair substitution or insertion or deletion mutation creates a stop codon, a nonsense mutation results. Nonsense mutations are usually very serious because they prevent the translation of a functional protein.
Chromosomal deletions and duplications
Structural changes may occur to a chromosome in the form of deletions, duplications, translocations, and inversions. Chromosomal deletions occur when a portion of the chromosome breaks off, or is lost during homologous recombination and/or crossing over. Duplications occur when a DNA fragment breaks free of one chromosome and incorporates into a homologous chromosome. Deletion or duplication can occur with entire chromosomes, aneuploidy, or even entire sets of chromosomes, polyploidy.
Translocations and inversions
When a segment of DNA from one chromosome is exchanged for a segment of DNA on another chromosome, the resulting mutation is called a reciprocal translocation. In inversion, the orientation of the section of DNA is reversed on chromosome. Translocation and inversion can be caused by transposition. Trends position takes place in both prokaryotic and eukaryotic cells. The DNA segments called transposable elements or transposons can excise themselves from a chromosome and reinsert themselves at another location. when moving, the transposon may excise itself from the chromosome and move, copy itself and move, or copy itself and stay, moving the copy. Transfer position as one mechanism by which a somatic cell of a multicellular organism can alter its genetic makeup without meiosis.
Forward and backward mutations
A mutation can be forward or backward. The mutation in the forward direction changes the organism even more from its original state. The mutation in the backward direction reverts the organism back to its original state, called the wild type.
Oncogenes
Certain genes that simulate normal growth in humans are called proto-oncogenes. Proto-oncogenes can be converted to oncogenes, genes that cause cancer, by mutations such as UV radiation, chemicals, or random mutations. Mutations that cause cancer called carcinogens.
Chromatin
Since the nucleus is much smaller than the 5 feet of unwrapped DNA it contains, the sections of DNA that are not in use are wrapped tightly around globular proteins called histones. Eight histones wrapped in DNA form y a nucleosome. Nucleosomes wrap into coils called solenoids, which wrap into supercoils. The entire DNA/protein is called chromatin. Chromatin is one third DNA, two thirds protein, and a small amount of RNA.
Chromatin received its name because it absorbs basic dyes due to the large basic amino acid content and histones. The basicity of histones gives them a net positive charge at the normal pH of the cell.
Chromatin condensed in the manner above is called heterochromatin. Some chromatin is permanently coiled. When transcribed, chromatin must be uncoiled. Chromatin that can be uncoiled then transcribed is called euchromatin. Euchromatin is only coiled during nuclear division.
Chromosome
Inside the nucleus of the human somatic cell, there are 46 double-stranded DNA molecules. The chromatin associated with each one of these molecules is called the chromosome. Each chromosome contains hundreds or thousands of genes.
In human cells, each chromosome possesses a partner that codes for the same traits as itself. Two such chromosomes are called homologues. Humans possess 23 homologous pairs of chromosomes.
Although the traits of the same, the actual genes might be different. Different forms of the same gene are called alleles. Any cell containing Homologous pairs is said to be diploid. Any cell that does not contain homologs is said to be haploid.
Interphase
G1, S, and G2 collectively are called interphase
G1
In G1, the cell has just split, and begins to grow in size producing new organelles and proteins. Regions of heterochromatin have been on wound and decondensed into euchromatin. RNA synthesis and protein synthesis are very active. The cell must reach a certain size, and synthesize sufficient protein in order to continue to the next stage. So growth is assessed at the G1 checkpoint near the end of G1. If conditions are favorable for division the cell enters S-phase, otherwise the cell enters G0 phase. The main factor in triggering the beginning of S is cell size based on the ratio of cytoplasm to DNA. G1 is normally the longest stage.
G0
A non-growing state distinct from interface. Allows for the differences in length of the cell cycle. In humans, enterocytes of the intestine divide more than twice per day, while liver cells spend a great deal of time and G0 dividing less than once per year. Mature neutrons and muscle cells remain in G0 permanently.
G2
The cell prepares to divide. Cellular organelles continue to duplicate. RNA and protein are actively synthesized. G2 occupies about 10 to 20% of the cell lifecycle. Need the end is the G2 checkpoint. This checks for mitosis promoting factor, when MPF is high enough, mitosis is triggered.
S
The cell devotes most of its energy to replicating DNA. Organelles and proteins are produced more slowly. Each chromosome is exactly duplicated, but the cell is still considered to have the same number of chromosomes, only now each chromosome is made of two identical sister chromatids. This is a convention.
Mitosis
Nuclear division without the genetic change. Four stages: prophase, metaphase, anaphase, telophase PMAT). Mitosis results in genetically identical daughter cells.
Prophase
Characterized by the condensation of chromatin into chromosomes. Centrioles located in the centrosomes move to opposite ends of the cell. First the nucleolus and then the nucleus disappear. The spindle apparatus begins to form consisting of aster, (microtubules radiating from the centrioles), kinetochore microtubules growing from the centromeres, and spindle microtubules connecting the two centrioles.
Centromeres
A group of proteins located toward the center of the chromosome, part of the spindle apparatus.
Spindle microtubules
Connect the two centrioles in prophase
Kinetochore
A structure of protein and DNA located at the centromere of the joined chromatids of each chromosome
Metaphase
Chromosomes align along the equator of the cell
Anaphase
Begins when sister chromatids split at their attaching centromeres, and move to an opposite ends of the cell. The split is termed disjunction. Cytokinesis, the actual separation of the cellular cytoplasm due to construction of microfilaments about the center of the cell, make amends to the end of this phase.
Telophase
The nuclear membrane reforms, followed by the reformation of the nucleolus. Chromosomes deco dense and become difficult to see under the light microscope. cytokinesis continues.
Meiosis
A double nuclear division which produces four haploid gametes, also called germ cells. In humans, only the spermatogonium and the oogonium undergo meiosis. All other cells are somatic cells and undergo mitosis only.
Meiosis is like mitosis except that in meiosis, there are two rounds, the daughter cells are haploid, and genetic recombination occurs. Recognize that, under the light microscope, metaphase in mitosis would appear like metaphase II in meiosis and not like metaphase I.
Meiosis I is reduction division.
Meiosis II creates four haploid gametes, each with 23 chromosomes.
Primary spermatocyte
After replication occurs NES phase of interphase, the cell is called the primary spermatocyte or primary oocyte. In the human female, replication takes place before birth, and the lifecycle of all germ cells are rested at the primary oocyte stage until puberty. Just before ovulation, a primary oocyte undergoes the first meiotic division to become a secondary oocyte. The secondary to say is released upon ovulation, and the penetration of the secondary oocyte by the sperm stimulates anaphase II the second meiotic division in the oocyte.
Prophase I
Homologous chromosomes line up alongside each other, matching up genes exactly. At this time, they may exchange sequences of DNA nucleotides in a process called crossing over. Genetic recombination in eukaryotes occurs during crossing over. Since each duplicated chromosome in prophase I appears as an x, the side-by-side homologs exhibit a total of four chromatids, and are called tetrads. If crossing over does occur, the two chromosomes are zipped along each other where nucleotides are exchanged. This forms a complex which, under the light microscope, appears as a single point where the two chromosomes are attached, creating an x shape called a chiasma. Genes located close together on a chromosome are more likely to cross over together, and are said to be linked.
Metaphase I
The homologues remain attached, and move to the metaphase plate. Rather than single chromosomes aligned along the plate as in mitosis, tetrads align in meiosis.
Telophase I
A nuclear membrane may or may not form. Cytokinesis may or may not occur. In humans both of these events occur. The new cells are haploid with 23 replicated chromosomes, and are called secondary spermatocytes or secondary oocytes.
In the case of the female, one of the oocytes, called the first polar body, is much smaller and degenerates. This occurs in order to conserve cytoplasm, which is contributed only by the ovum. The first polar body may or may not go through meiosis II, producing two polar bodies.
Meiosis II
The final products are haploid gametes each with 23 chromosomes. In the case of the spermatocyte, four sperm cells are formed. In the case of the oocyte, a single ovum is formed. In the female, telophase II produces one gamete and a second polar body.
Non-disjunction
If during anaphase I or II the centromere of any chromosome does not split.
In the case of primary nondisjunction, one of the cells will have to extra chromatids, a complete extra chromosome. The other will be missing a chromosome. The extra chromosome will typically lined up along the metaphase plate and behave normally in meiosis II.
Nondisjunction in anaphase II will result in one cell having one extra chromatid and one cell lacking one chromatid.
Nondisjunction can also occur in mitosis, but the ramifications are less severe since the genetic information in the new cells is not passed on to every cell in the body. Destruction of chromosome 21 causes Down’s syndrome. An abnormal gamete with two chromosome 21s may combine with a normal gamete, and the resulting zygote will have three copies of chromosome 21. This is sometimes referred to as trisomy 21.
