Genes Flashcards
Types of Blots
Sunny Day, No Rain, Why not Picnic
Southern Blot: DNA
Northern Blot: RNA
Western Blot : Protein
Start Codon
Stop Codons
Start: AUG
Stop: UAA, UAG, UGA
Central Dogma
DNA⇒RNA⇒Protein
DNA Nucleotide Bonding
Each nucleotide is bound to the next by a phosphodiester bond between the third carbon on one deoxyribose and the fifth carbon on the other creating the sugar-phosphate backbone of a single strand of DNA with a 5’→3’ directionality. The 3’ carbon is attached to the —OH group and the 5’ carbon end is attached to a phosphate group.
DNA Replication
- DNA helicase unwinds the DNA helix
- An RNA primer initiate
- DNA polymerase III builds new DNA by adding nucleotides to the primer and moves alone each DNA stran creating a new complemtary strand. DNA polymerase reads parental strand in the 3’→5’ and writes the new strand 5’→3’.
- DNA polymerase I removes the RNA primers.
- DNA ligase moves along the lagging strand and ties the Okazaki fragments together to complete the polymer.
- Telomerase lenghtens DNA by adding repetitive nucleotide sequences TTAGGG to the 3’ ends
RNA vs. DNA
- Carbon #2 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.
3 Types of RNA
- mRNA (messenger RNA is the largest) delivers the DNA code amino acids to the cytosol where the protiens are manufactured.
- rRNA (ribosomal RNA) combines with proteins to form ribosomes, the intracellular complexs that direct the synthesis of proteins. Prokaryotic ribosomal subunits are 30S and 50S in size with a combined 70S. Eukaryotic ribosomal subunits possess 40S and 60S combined 80S rRNA is synthesized in the nucleolus.
- tRNA (transfer RNA is the smallest and has a cloverleaf structure) collects amino acids in the cytosol, and transfers them to the ribosomes for incorporation into a protein.
- hnRNA is an RNA molecule that has not yet undergone post-transcriptional modification. Once modified, hnRNA becomes a mature mRNA.
Promoter vs Primer
Transcription requires a promoter, whereas replication requires a primer. A promoter is a spot on the DNA that tells RNA polymerase where to begin transcription. A primer is a short piece of RNA that jump starts replication.
Transcription
- Initiation, a group of proteins called initiation factors finds a promoter on the DNA strand, and assembles a *transcription initiation complex, *which includes RNA polymerase. After binding to the promoter, RNA polymerase unzips the DNA helix creating a transcription bubble.
- Elongation, RNA polymerase transscribes one strand of DNA into a complementary RNA sequence.
- Termination, a termination sequence and special proteins dissociate RNA polymerase from DNA.
Genetic Regulation
Most genetic regulation occurs at transcription. Activators and repressors bind to DNA close to the promoter, and either activate or repress the activity of RNA polymerase.
Lac Operon
An operon is a sequence of bacterial DNA containing an operator, a promoter and related genes. The operator act as an “on/off” switch.
Post-transcriptional Processing
Post-transcriptional modification only occurs in the nucleus.
- Introns are looped and spliced snRNPs, bringing together the exons to form mRNA.
- 5’ end is capped in a process using GTP
- 3’ end is polyadenyated with a poly A tail
Denatured DNA
To separate the two strands of DNA helix
- Heat
- Immersed in high concentration of salt solution
- high pH solution
Denatured DNA is less viscous, denser, and more able to absorb UV light.
Polymerase Chain Reaction (PCR)
- Target DNA is denatured and mixed with many complementary primers.
- Primers hybridize with DNA fragments
- Specialized polymerase replicates DNA fragments.
- Repeat
Blot “Recipe”
Southern and Northern
- Chop up some DNA
- Use an electric field 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.
Western
- Same as above, but uses antibodies to detect proteins
Translation
Translation begins on a free floating ribosome. A signal peptide at the beginning of the translated polypeptide may direct the ribisome to attach to the ER, in which case the polypeptide is injected into the lumen. It may then be secreted from the cell via the Golgi or may remain partially attached to the membrane.
Translation involves taking the message that’s in the messenger RNA and in a sense decoding the message from the language of nucleic acids to the language of proteins or polypeptides. it includes 3 distinct steps which are intialisation, elongation and termination.
- *Initiation**
1. Messenger RNA is bound to ribosome with the start codon (AUG) at the P site. A transfer RNA molecule with the amino acid methionine (M) and the anticodon UAC has bound to the exposed start codon. The codon UCA is exposed at the A site.
- A second transfer RNA molecule, with the anticodon AGU and the amino acid serine (S) has bound to the A site. The 2 amino acids are close enough to form a peptide bond between them.
- A peptide bond has formed between M and S and the peptide is bound to the A site. The methionine transfer RNA leaves, and the P site is exposed.
- The ribosome has moved along the messenger RNA one codon, bringing the peptide to the P site. This exposes the A site and the next transfer RNA, carrying alanine (A) is about to bind.
- *Elongation**
1. The ribosome then moves 1 codon down the mRNA in a 5’ to 3’ direction. This is achieved by a translocase enzyme. As the process of ribosome translocation continues, the “old” tRNA is released to bind another amino acid and go in search of a new codon. The binding of a new aminoacid is mediated by an enzyme called amino-acyl-tRNA synthase. - *Termination**
1. The process continues along the mRNA until a stop codon is reached. While there is no tRNA for a stop codon, there is an enzyme called release factor which cleaves the polypeptide chain resulting in a new protein.
- Finally, the entire complex is disrupted, the ribosome separates and the mRNA is released to be used again or degraded. Translation occurs at multiple sites along an mRNA so that many ribosomes can be seen by electron microscopy bound to a single mRNA strand with many polypeptide chains forming from each.
Point Mutation
Mutations
Cell Life Cycle
Mitosis
PMAT
Interphase
The cell is engaged in metabolic activity and performing its prepare for mitosis (the next four phases that lead up to and include nuclear division). Chromosomes are not clearly discerned in the nucleus, although a dark spot called the nucleolus may be visible. The cell may contain a pair of centrioles (or microtubule organizing centers in plants) both of which are organizational sites for microtubules.
Prophase
Chromatin in the nucleus begins to condense and becomes visible in the light microscope as chromosomes. The nucleolus disappears. Centrioles begin moving to opposite ends of the cell and fibers extend from the centromeres. Some fibers cross the cell to form the mitotic spindle.
Prometaphase
The nuclear membrane dissolves, marking the beginning of prometaphase. Proteins attach to the centromeres creating the kinetochores. Microtubules attach at the kinetochores and the chromosomes begin moving.
Metaphase
Spindle fibers align the chromosomes along the middle of the cell nucleus. This line is referred to as the metaphase plate. This organization helps to ensure that in the next phase, when the chromosomes are separated, each new nucleus will receive one copy of each chromosome.
Anaphase
The paired chromosomes separate at the kinetochores and move to opposite sides of the cell. Motion results from a combination of kinetochore movement along the spindle microtubules and through the physical interaction of polar microtubules.
Telophase
Chromatids arrive at opposite poles of cell, and new membranes form around the daughter nuclei. The chromosomes disperse and are no longer visible under the light microscope. The spindle fibers disperse, and cytokinesis or the partitioning of the cell may also begin during this stage.
Cytokinesis
In animal cells, cytokinesis results when a fiber ring composed of a protein called actin around the center of the cell contracts pinching the cell into two daughter cells, each with one nucleus. In plant cells, the rigid wall requires that a cell plate be synthesized between the two daughter cells.
Meiosis
A double nuclear division of germ cells which produces four haploid gametes.
Prophase 1
DNA coils into chromosomes, the nucleolus and nuclear envelope disappear, the mitotic spindle forms, and synapsis (crossing-over) occurs.
Metaphase 1
Tetrads line up randomly along the midline, spindle fibers attach to the centromere of each homologous chromosome.
Anaphase 1
Homologous chromosomes move to the opposite poles of the cell
Telophase 1
The chromosomes reach the opposite end of cell and cytokinesis begins
Prophase 2
Spindle fibers form and begin to move the chromosomes toward the midline of the dividing cell.
Metaphase 2
Chromosomes move to the midline of the dividing cell, facing opposite poles of the dividing cell
Anaphase 2
The chromatids seperate and move toward opposite poles of the cell.
Telophase 2
A nuclear membrane forms around the chromosomes in each of the 4 new cells.
Spermatogonium
Oogonium
- Replication takes place before birth, and the life cycle is arrestted at the primary oocyte stage until puberty.
- Just before ovulation, a primary oocyte undergoes the first meiotic dividison to become a secondary oocyte an then released.
- Penetration of a secondary oocyte by a sperm stimulates anaphase II of the second meiotic division in the oocyte.
