unit 3 biology test Flashcards
CHAPTER 5 KEY THINGS TO KNOW
→ scientists last name → major contribution to genetics
→ dna replication → all enzymes involved and leading vs lagging strands
PROCESS OF DNA REPLICATION:
→ scientists last name → major contribution to genetics
Miescher discovered the DNA molecule
Griffith experiments with strep help to establish dna as the material of heredity
Griffith injected mice with s strain and r strain. Mice LIVED THRU R STRAIN AND DIED thru s strain. Mice lived thru heated s strain and died thru mix of heat s strain and regular r strain.
Avery, macleod, and mccarty built off Griffith’s experiments using three enzymes: one that destroys proteins, dna, and rna. They also concluded that dna is the hereditary material.
Hershey and Chase ruled out that protein was, until their experiment of sulfur and phosphorus isotopes proved otherwise. 25s was for proteins and 32p was for dna. They concluded viral DNA had the genetic info for viruses to reproduce.
Levene isolated two types of nucleic acids, dna and rna and each was made up of a sugar, phosphate, and 4 nitrogen bases.
Chargaff discovered that a=t and g=c
Pauling discovered many proteins have helix shaped structures and watson and crick used this discovery to deduct dna structure
Franklin woman used x ray diffraction and math theory to discover the dna shape and that nitrogen was on insane and sugar phosphate backbone was outside
Watson and Crick discovered the DNA structure that had a double helix. They also discovered that a is with t and g is with c.
Matthew and meelson stahl discovered that they could use diff isotopes to differentiate between parent and daughter strands of dna. They used light N and Heavy N. Nitrogen
→ dna replication → all enzymes involved and leading vs lagging strands
DNA REPLICATION INVOLVES:
HELICASE: unwinds the parent dna apart and breaks hydrogen bonds
SSB PROTEINS: helps keep the strands apart
GYRASE: Helps relieve any tension
RNA PRIMASE: synthesizes an rna primer needed to begin the new strand (provides a 3’ end)
DNA polymerase III adds nucleotides to the 3’ end of the growing chain
DNA Polymerase I removes the rna primer, replaces it with dna and can also proofread newly synthesized dna.
DNA polymerase II proofreads newly synthesized dna.
DNA ligase joins the okazaki fragments in the lagging strand.
PROCESS OF DNA REPLICATION
PROCESS OF DNA REPLICATION:
INITIATION: helicase unwinds dna and breaks h bonds between the strands. Ssb proteins keep the strands apart and gyrase helps relieve any tension. Initiation creates a replication bubble with two y shaped regions at each end of the unwound area. This is called a replication fork.
ELONGATION: rna primase synthesizes an rna primer and dna polymerase iii adds nucleotides to the 3’ end that rna primer provides. It can only work in the 5’ to 3’ direction but adds to the 3’ end.
In the LEADING STRAND, rna polymerase adds 10 rna nucleotides to the 3’ end as it moves along the same direction as the replication fork. Then, dna polymerase I comes in and removes the primer to attach new dna molecules.
In the LAGGING STRAND, it must also be built in the 5’ to 3’ direction and dna
polymerase iii must move in the opposite direction of the replication fork. This results in the lagging strand to occur in short segments and in a discontinuous matter. These short fragments are called okazaki fragments.
primase then adds several small rna primers
The primers are elongated by dna polymerase 3 to provide okazaki fragments
Dna polymerase 1 removes the primer and replaces it with dna nucleotides
Dna ligase joins in and binds the okazaki fragments together by using phosphodiester bonds.
TERMINATION:
Termination occurs when the synthesis of new strands occur
The two dna molecules separate from each other and the replication machine is dismantled.
Dna polymerase i and ii have proofreading abilities. Dna polymerase iii does not. These two enzymes recognize and correct errors of newly synthesized strands of dna. This method repairs 99 percent of mismatch errors that occur during replication.
Another method for correcting mismatch errors is called mismatch pairs.
This is when a group of proteins recognize a mispaired nucleotide on the newly synthesized strands of dna and replace it with a correctly paired nucleotide
Errors that stay after the dna polymerase has done proofreading or mismatched paired is called a mutation once cell division occurs.
CHAPTER 6: KEY THINGS TO KNOW
→ how to read genetic code
→ transcription vs translation
→ mutation: types and how amino acid sequence is affected
→ trp and lac operons
→ transcription vs translation
TRANSCRIPTION: the purpose of transcription is to produce an mRNA from a dna template. There are three stages of transcription. Initiation, elongation, and termination, just like dna replication, same for mRNA replication.
INITIATION: In initiation, rna polymerase binds to the dna promoter region aka the tata box upstream of the gene and unwinds double helix, beginning to copy mrna on the antisense strand.
ELONGATION: the rna polymerase complex then moves from the 5’ to 3’ direction to synthesize an mrna molecule that is complementary to the antisense strand. T is replaced with U and hundreds of mrna molecules can be synthesized as long as the rna polymerase complex has moved from the promoter region, allowing another rna polymerase complex to bind.
TERMINATION: rna polymerase reaches the termination sequence downstream of the gene and mrna is released, then dna forms the double helix again!
5’ CAP is added to 5’ end to protect it from digestion
Poly a tail is added to 3’ end to protect it from degradation by nucleus
Mrna is still chopped up but the poly tail gives it more time.
Spliceosomes cut out introns to join the remaining exons together.
TRANSLATION: this is translating the nucleic code of mrna into an amino acid of a protein and occurs in the cytoplasm. Once the mrna is synthesized in the nucleus, it goes to translation and interacts to a free ribosome or one attached to a rough er. It interacts with a trna molecule there.
INITIATION: each codon is an amino acid. This is how mRNA can be translated to a protein. During initiation, we have a ribosome composed of two subunits. The small and large. In the large subunit, there are 3 active sites. The E, P AND A. tRNA has the methionine amino acid attached to it and the start codon AUG, so in the small subunit, AUC is there. tRNA enters through the p site where the peptide bonds are formed.
ELONGATION: another tRNA molecule enters the A site. A covalent bond will form between the two amino acids (from P to A site). The tRNA molecule in the P site will move to the E site, and will lose an amino acid. This will result in a growing chain of amino acids that will extend out of the ribosome. The tRNA molecules enter A site, and exit out the E site, in the process the amino acids are joined together and the polypeptide chain will grow, creating a protein!
TERMINATION: begins when a stop codon is read. Stop codons do not code for any specific tRNA molecule. The protein leaves and enters the golgi body and undergo folding where they create a specific shape to perform a specific function.
→ mutation: types and how amino acid sequence is affected
Mutation: a mutation is a permenant change in the nucleotide sequence of a cells dna.
Single gene mutaiton: a single gene mutation is a mutation that involves the change in the nucleotide sequence of one gene.
Point mutation: a point mutation is involving a single base substitution, intersession or deletion,
Frame shift mutation: a frameshift mutation is a mutation caused by the addition or deletion of a number of nucletoidies not divisible by three, resulting in a change in the reading frame.
Silent mutation: a silent mutation is a mutation that does not change the amino acid sequence of a protein.
Missense mutation: a missense mutation is a mutation that changes the amino acid sequence of a protein.
Nonsense mutation: a nonsense mutation is a mutation that shortens the protein by introducing a stop codon.
Chromosome mutation: a chromosome mutation is a mutation that involves changes in chromosomes and may involve many genes.
Deletion
Duplication
Inversion
Reciprocal translocation
Cause of mutations:
Transpons: transpons are a short segment of dna capable of moving within the genome of an organism also called a jumping gene.
Mutagen: a mutagen is an event or substance that increase the rate of changes to the dna sequence of an organisms genome.
Mutations that affect amino acid sequences are missense mutations. They can be harmful. For example, in alcaptonuria, there is an accumulation of homogentisic acid is due to a missense mutation in the gene coding for the enzyme that breaks down this compound. The most common mutation reusltsi n one amino acid change in the enzyme ,which affects the activity in the enzyme. Missense mutations can also develop new proteins that can help an organism survive. They play a good role in producing the great variety of antibodies the human body uses to fight new infections.
Nonsense mutations also are harmful and shorten a protein by introducing a stop codon.
→ trp and lac operons
Trp operon: the trp operon is always on unless a repressor turns it off. The similarities the trp and lac operon share is they both have a regulatory region. When tryptophan levels are low, it must be synthesized and therefore the repressor is not bound to the operator and transcription occurs. When tryptophan levels are high, the tryptophan binds to the repressor which then binds to the operator to reduce transcription activity.
Lac operon: Rna polymerase is a builder enzyme. It’s needed in order to start transcription. Rna polymerase needs a promoter region but an operator is also needed. A repressor can bind to an operator and can block rna polymerase therefore no mrna can be made = no proteins. In a lac operon, there is a regulatory region which contains the promoter region, the operator region and 3 genes that code for enzymes that help in the process of breaking down lactose. The repressor is there so there’s no waste made. If lactose is not present, then the repressor binds to the operator so mrna cannot be made. If lactose is around, the allolactose binds to the repressor and breaks it down. The repressor can no longer bind to the operator and then the rna polymerase can continue transcribing to make the mrna of the genes on the operon. The mrna will then make enzymes to break down the lactose.
CHAPTER 7 BIG IDEAS
→ restriction enzymes and how they work
→ purpose, steps and materials of pcr
→ concepts of gel electrophoresis
→ dna fingerprinting (STP and RFLP)
→dna sequencing manuel method
→ restriction enzymes and how they work
Recombining dna is a molecule of DNA composed of genetic material from different sources. This was made possible by RESTRICTION ENZYMES. (enzymes in bacteria that cleave/cut apart viral dna to prevent infection)
Restriction endonuclease is a restriction enzyme. Endonuclease recongnize a specific sequence of nucletodies called a target sequence within dna molecule. The enzymes then cut phosphodiester bonds of the dna at a specific point called the restriction site with the target sequence.
BLUNT ENDS are amde when ends of DNA are fully base paired
STICKY ends are made when ends of dna are single stranded.
→ purpose, steps and materials of pcr
Pcr does not require a host system or recombinant dna construction
Kakry mullis invented it and pcr is an automated process that amplifies specific regions of dna form small quanittes of template DNA.
Billions of copies of dna can be made in a few hours.
PCR is carried out in special machines called thermocyclers. These machines are automated and programmed to change temperatures quick and accurately. The machine is set to perform 30 cycles when performing pcr.
Materials required are:
Dna target sequence, dna primers, dna nucleotides and taq polymerase. (dna polymerase taken from the heat loving bacterial thermos aquaticus) (this synthesizes strands by adding nucletodies via complementary base paring and can withstand high temperatures without denaturing.
The steps are:
Place material in thermocycler
The dna sample is heated to 95 celsius to separate the dna strands
The dna s cooled to 55 celsius to allow primers to anneal
Dna is heated to 72 celsius which is optimal temp for taq polymerase to extend primers
The dna is taken thru several cycles to produce multiple copies
The purpose can be used for
medical applciations, dna from one cell of a young embryo can be amplified to screen for genetic defects
Criminal investigations where small quantities of dna found at crime scenes are amplified so that further analysis can be done to identify both victim and criminal
Evolutionary applications which are able to compare dna extracted from mummies and from animal fossils millions of years old
→ concepts of gel electrophoresis
For gel electrophoresis, we need to know that it separates DNA according to size/fragments(its purpose). DNA is negative and moves towards the positive terminal. Smaller fragments travel faster and longer fragments are closer to top. Put chemicals in it to make it visible.
→dna sequencing manuel method
Dna sequencing refers to detemring, base by base, the nucleotide sequence of a dna fragment.
The two main methods include:
Manual method & automated method
During the manuel method, its referred to as the dideoxy chain terminating method or dideoxy sequencing and was developed by frederick sanger in 1977
It relies on the principles of dna replication
It requires: a primer, dna polymerase, regular nucletodies & dideoxynucleotides.
Dideoxynucleotides are similar to regular nucleotides but sugar lacks an OH group at carbon 3. This difference prevents the addition of another nucleotide and the reaction stops.
The steps are four separate reactions are prepared that each include
Multiple copies of single stranded DNA that needs sequencing. This is called the template strand.
Multiple copies of a 5’ primer that will bond with the 3’ end of the template strand
Dna polymerase and all four regular nucleotides
One of the dideoxynucleotides in each reaction
2. All 4 dna synthesis reactions are allowed to proceed
3. Fragments of diff lengths will be produced for each reaction because of the ddnucleotides.
4. The dna in each of the four reactions is separated using gel electrophoresis
5. A radioactive tag attached to the dideoxynucleotides is used to see the dna.
The gel is read and the short fragments is the 5’ end of the new dna strand and is complementary to the 3’ end of the template strand
7. The dna strnad that requires the sequencing (template strand) is the complement to the sequence on the gel.
