Ch. 15, 16 & 21

Molecular Biology II


II. Connections


1. Lysogenic & Binary Fission: When viruses attack host cells, the cells can divide and multiply in two different pathways.  A lysogenic pathway when a latent period extends the duration of the cycle because the virus does not kill the host right away.  Instead, a viral enzyme cleaves the host's chromosomal DNA, and integrates the viral genes into its base sequence.  This happens before prokaryotic fission, which is the cell reproduction mechanism for prokaryotic cells only.  Prokayotic fission can sometimes be confused with binary fission, but binary fission refers to the asexual reproductive mode among some animals where the body splits spontaneously, then both parts grow what is missing.


2. Conjugation & Bacterial Transformation: Conjugation is a mode of gene transfer that is possible when one of the cells has an F, or fertility, plasmid.  A plasmid is a small, self-replicating circle of DNA with a few genes.  Plasmids are only found in prokaryotic cells.  Bacteria are examples of prokaryotic cells.  Conjuction involves the transferring of replicated DNA from one prokaryotic cell to another.  The recipient cell receiving the replicated DNA can sometimes receive transferred DNA that has been transformed into infectious DNA.  This transformation is bacterial transformation.


3. Plasmid & Retrovirus: Plasmid is a small, self-replicating circle of DNA with a few genes.  Plasmids are used during cell reproduction in prokaryotic cells.  A virus cannnot reproduce on its own, which means it can only reproduce when its genetic material enters the host cell and becomes replicated.  Common animal viruses, such as retroviruses, have double or single stranded DNA or RNA that has been replicated with the virus gene in it.  HIV is a retrovirus, that leads to AIDS.  A virus that weakens the immune system by destroying white blood cells can cause the inability to fight infections such as HIV that may not otherwise be life threatening.


4. Operator & Hydrolysis: An operator is a binding site for a type of regulatory protein know as repressor, which stops transcription.  Operators can be found at the end of E. coli DNA, after three genes that code for lactose-metabolizing enzymes.  E. coli likes to consume glucose, but can settle for lactose when glucose is not present.  Lactose is a carbohydrate, and can be broken down with hydrolysis.  Hydrolysis is a cleavage reaction that uses enzymes to split molecules at specific groups.


5. Okazaki Fragments & Restriction Enzymes: Restriction enzymes cut double-stranded DNA at a specific base sequence between for and eight base pairs in length.  It makes staggered cuts that produce a sticky end on the DNA fragments.  The tail can base pair with a tail from another fragment cut by the same enzyme.  Restriction enzymes can cut base pairs form Okazaki fragments, which are the fragments of new DNA copied along with the parent strands.  Just like for the Okazaki fragments, DNA ligases seal the nicks of the base pairing between the cut fragments.


III. Few Essentials 


1. Promoters are short stretches of base sequences in DNA where regulatory proteins gather and control transcription of specific genes, often in response to hormonal signal.  Enhancers are binding sites where such proteins increase transcription rates.  Before transcription, acetylation can make histones loosen their grip so that the polymerases can access genes.  Some gene sequences can be rearranged or multiplied.  During transcript processing, exons for genes can be put together in different combinations in different types of cells.  Proteins attached to a nuclear envelope can move the transcript to the region where its supposed to be translated or stored.  Unfertilized eggs that stockpile maternal messages keep them silent with the help of controls called Y-box.  During translation, how long an mRNA lasts depends on the proteins that are attached to it and the length of its poly-A tail.  If translation is blocked, mRNA cannot attach to a ribosome when proteins bind to it, and initiation factors can be inactivated.  After translation, a new protein may be inactivated or activated.  Control of enzymes and other proteins influences many cell activities. 


2. look on notecard


3. DNA fragments can be separated by gel electrophoresis, a technique that sorts fragments as they move through a semisolid slab of polyacrylamide in response to an electric field.  DNA fingerprinting reveals differences in the tandem repeats among individuals.  Fragments are cut; the sizes of the fragments are unique to an individual.  The fragments can be subjected to gel electrophoresis to form distinct bands according to their length.  The banding patter of the fragments is the DNA fingerprint of the individual.


4. A prokaryotic cell nearly doubles in size, then divides in two.  Each daughter cell inherits a single bacterial chromosome, a circularized, double-stranded DNA molecule that has a few proteins associated with it.  This is different from  a eukaryotic cells genome because it is smaller, only having one chromosome where eukaryotic cells have 23 chromosomes.  DNA replication is simpler in prokaryotic cells.  After the DNA replicates, the parent molecule and the cope are both anchored to the plasma membrane at adjacent sites while the cell is growing.  The growing cell moves the molecules of DNA apart.  The cytoplasm splits in two, and the result is two genetically identical daughter cells.


5. In the lytic cycle, a virus particle injects genetic material into a suitable host cell after binding to its wall.  The viral DNA directs host cell to make viral proteins and replicate viral DNA.  The viral proteins are assembled into coats around viral DNA.  The coats get tail fibers.  Lysis of the host cell is induced and infectious particles escape.  The lysogenic cycle is different because the virus does not kill the host right away.  Instead, a viral enzyme cleaves the host's chromosomal DNA, then integrates the viral genes into its base sequence.  The viral DNA is excised from the chromosome.

Ch. 13 & 14

Molecular Biology 1


II. Connections


1. 5' & Electronegativity: The 5' carbon on a nucleotide is the highest carbon on the sugar component.  This carbon attaches to a phosphate group on the end.  A free nucleotide has a tail of three phosphate groups dangling from the 5' carbon.  A DNA polymerase detaches two of the phosphates.  The last phosphate is driven towards the -OH group dangling off from the 3' carbon, the carbon on the bottom of the sugar component, of another nucleotide.  Since the electronegativities of the phosphate group and the -OH are different, their energies connect and form a bond, linking two nucleotides together.


2. Start Codon & Incomplete Dominance: A codon is a base triplet of three nucleotides in mRNA.  There are 64 different codons, making up the genetic code for an organism.  One of these codons is called a start codon, that specifically codes as a start signal for translating three bases at a time.  The typical start codon is AUG, but one change in the nucleotide can alter the purpose of the codon.  This variation of codons cause genetic mutations in the codes for proteins.  Some of the mutations cause genetic variations of traits, including incomplete dominance, when a heterozygous gene codes for a new trait than a homozygous gene.


3. Semiconservative & Barr Body: Semiconservative replication is a mechanism by which a DNA molecule is duplicated.  For this to occur, the double helix unzips along its length, exposing the bases. The bases are used as a template, and a new strand is assembled.  The two stands are wound back up into a double helix.  Semiconservative replication can only occur if the chromosome decondenses into its chromatin form, so that the strands of DMA can be read and copied.  This form of replication cannot occur then in a Barr Body, a chromosome that does not decondense into its chromatin form, but stays condensed.


4. RNA Polymerase & Nucleolus: RNA polymerase is an enzyme that adds ribonucleotides one at a time to the end of a growing strand of RNA.  The enzyme is primarily used in transcription of RNA, resulting in mRNA.  To ensure the mRNA has no mistakes on it, the transcripts are modified of their mistakes before leaving the nucleolus, where the transcription is occuring.


5. DNA Polymerase & Glycosidic Linkage: DNA polymerase is an enzyme that catalyze the formation of two brand-new strands of DNA from free nucleotides.  These enzymes also catalyze the hydrogen bonding of each  new strand to the unwound region of one of the two parent DNA strands.  The nitrogen bases connect to each other based on pairing, A with T and C with G, by a glycosidic linkage.


6. Helicase & G2 Karyotype: DNA replication occurs during interphase in a cell's life cycle. Interphase starts with the G1 stage, when the DNA is unwinding and preparing to be replicated.  S phase is the phase of replication.  G2 stage is the when the replicated DNA is checked for mistakes in the replication.  To start this replication process, the DNA needs to be unwound into its chromatin form.  An enzyme called helicase unzips the DNA and breaks the hydrogen bonds between the nucleotides.  Helicases are primarily found in the S phase of a cell's life because that is when the replication occurs.  In G2, the DNA is already replicated, which is why in the karyotype, there will be twice as much DNA as before.


III. Few Essentials


1. For DNA replication, the DNA polymerases can only assemble new strands in a 5'-3' direction.  DNA in a double helix are formed by two strands of nucleotides that are anti-parallel, meaning they line up in different directions.  One strand in a 5'-3' direction is opposite of a strand in a 3'-5' direction.  Since DNA polymerases can only assemble in one direction, the nucleotides are assembled in short stretches.  DNA ligases are in charge of sealing the short stretches together into a continuous strand, so that it is complementary with the 3'-5' direction strand.


2. 3 structural differences between RNA and DNA:

1. RNA has 3 classes of molecules for protein synthesis, while DNA only has one.  mRNA is the outcome of of transcription, where the protein-building codes are carried.  rRNA becomes a component of ribosomes.  tRNA delivers amino acids one by one to ribosomes in the orders specified by mRNA.
2. RNA molecules have four kinda of ribonucleotides, like DNA.  Adenine, guanine, and cytosine are the same.  But, instead of thymine, RNA has uracil, a new nitrogen base. Uracil can bind with adenine.
3. Transcription results in one free RNA strand, not a hydrogen-bonded double helix like DNA. 

3. RNA has 3 classes of molecules for protein synthesis, while DNA only has one.  mRNA is the outcome of of transcription, where the protein-building codes are carried.  rRNA becomes a component of ribosomes.  tRNA delivers amino acids one by one to ribosomes in the orders specified by mRNA.

4. Protein Synthesis

    a. Transcription

        - 1st step in protein synthesis

        - sequence of nucleotide bases is exposed in an unwound region of DNA strand

        - sequence: template strand RNA is assembled from

        - RNA uses adenine, cytosine, guanine, and uracil

        - RNA polymerase adds nucleotides one at a time to end of growing strand of RNA

        - promoter: start signal that RNA polymerase binds to so it start adding nucleotides

        - when RNA polymerase reaches sequence that marks "the end": it stops

    b. RNA Splicing

        - occurs in the nucleus before being released

        - pre-mRNA is modified with a cap at the beginning and a poly-A tail at the end

        - all introns, noncoding sequences, are snipped from pre-mRNA strand

        - exons, protein-coding base sequences, are all kept

        - can be combined together to form a mature mRNA

    c. Translation

        - initiation stage: small ribosomal subunit and an initiator tRNA arrive at an mRNA transcript's start codon

        - large ribosomal subunit binds to them

        - anticodon and codon meet up here

        - elongation stage: tRNAs deliver amino acids to a ribosome in the order said by the sequence of mRNA codons

        - polypeptide chain lengthens as peptide bonds form between the amino acids

        - termination stage: stop codon triggers events that cause polypeptide chain and the mRNA to detach from ribosome