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Biochem Exam 1
Terms in this set (108)
DNA is double helix; two strands one coding strand and one template strand. Genes can show up on either side. The two new strands must unzip to become templates, each new strand will have one old strand and a newly synthesized strand.
Explain the term semi-conservative replication
The oriC site represents the point at which DNA replication is initiated
Define the oriC site and discuss its importance.
The replisome is a combination of proteins used for separating and replicating the DNA
Define the replisome.
Methylation is important for distinguishing the coding strand from the template strand after DNA synthesis. The original template strand is methylated.
Explain the importance of DNA methylation.
-Helicase separates the helix
-Topoisomerase relieve supercoiling strain
-DNA binding proteins stabilize the open structure
-Primase puts down RNA primers, polymerase III synthesizes DNA
-Polymerase I removes RNA primers and puts down DNA instead
-polymerase II does proofreading for errors.
List the steps involved in DNA synthesis at the replication fork.
The direction of replication if 5' to 3' and it's bidirectional.
Polymerase III synthesizes DNA
Polymerase I removes RNA primers and puts down DNA instead
Polymerase II does proofreading. Proofreading is checking for errors in the newly synthesized DNA.
Explain the direction of replication and describe the first three prokaryotic DNA polymerase enzymes and what each one does. What is proof reading?
Termination starts at the OriC site and moves in two directions, clockwise, and counterclockwise.
Counterclockwise (TerA, B, D) clockwise (TerC, B, G, F)
Explain the process and list the requirements for termination.
The Ames test is a test used for DNA backed mutations which means DNA can mutate in a direction away from a normal DNA and also mutate spontaneously back to where it can't function. In Ames test there's a single point mutation, a single base pair that has been mutated and so bacteria can't synthesize its own histidine. If grown on histone-free plates it cannot multiply however if by random chance the DNA mutates at the exact point where it can correct the histidine mutation and it will back mutate and start growing. If you put a mutagenic compound on the plate this would increase amount of mutations that take place and increase the probability that back mutation that take place and therefore the bacteria can grow on a histidine free environment. There's a 90% correlation with compounds ability to cause back mutation and ability to cause cancer in humans
Explain and list out the steps for the Aims Test. What conclusions does this test let you draw?
During replication, the DNA that's replicating has methyl groups on it and the newly synthesized DNA does not. So if there is an error detected shortly after replication, the body would know which strand needs to be excised out and replaced. It's used for mismatched
What is Methyl directed mismatch repair and what is it used for?
Base excision repair is removing the damaged bases and it deals with chemical mutations
What is Base Excision repair and what is it used for?
Nucleotide excision is the same as base excision repair but used for larger chemical errors.
What is Nucleotide Excision repair and what is it used for?
Direct repair is very conservative but doesn't work as easily. Works by dedimerizing the thymine dimers.
What is Direct repair and what is it used for?
Recombination has a purpose to repair and enhance genetic diversity.
It takes place to overcome stalled replication forks due to DNA damage
Conjugation between bacterial cells (rare) example; exchange of antibiotic resistance between cells
Meiosis in eukaryotic cells
Describe Recombination and list the reasons it takes place.
On the DNA inside the nucleus of the cell.
Protein synthesis takes place on ribosome
Describe the locations of RNA synthesis.
Messenger RNA (mRNA), Ribosomal RNA (rRNA),
Transfer RNA (tRNA)
tRNA- used to translate which amino acid is going to be found for each codon on mRNA.
ribosomal RNA- used to make ribosomes.
List the 3 major types of RNA
Transcription bubble- uncoil the DNA and open up the double stranded double helix to a single stranded DNA. Rewinding and unwinding are required before and after the transcription bubble. Transcription bubble is where RNA is being synthesized
Describe the activity and components of the transcription bubble
The coding strand is not read and is sometimes called the non-template strand. The template strand is the complimentary strand to the coding strand that is read when making RNA transcript.
Compare and contrast the coding strand, the template strand and the RNA transcript.
Genes are in both side of double helix, so the direction that we read and the side that the gene is on is dependent on which gene it is. So, it's possible to have numerous overlapping genes going in opposite directions because of the double stranded helix. Genes can be any side of the double helix, as a consequence, they can overlap. There's no reason the genes can't overlap each other if they are on both sides of the double helix. The larger the genome the less likely it is to take place.
Describe the concept of overlapping genes.
The RNA polymerase consists of several subunits, two copies of an alpha subunit, a ß, a ß´, and a ω (omega) which are the major portion of RNA polymerase that make RNA. The subunit has a function to recognize specific recognition sites on the DNA and directs which genes are going to be transcribed. Once the genes are picked to be transcribed the subunit leaves the complex and the RNA polymerase makes the RNA.
Describe prokaryotic RNA polymerase
At about -10 base pairs there's a TATAAT and at about -35 there another consensus sequence and at some genes there's UP element. These consensus sequences are recognized by the subunit of the RNA polymerase. This is where the RNA polymerase binds to the gene and subunit directs which genes are going to be recognized and transcribed.
Describe and list the components of the "upstream" recognition and binding sites for RNA polymerase.
Looking for the -10. And -35 region and some case UP element we find those regions that are just upstream from the beginning of gene and which ones which we bind to is directed by the subunit of the RNA polymerase. Upon correct binding we open up the double helix of DNA and start transcription and then remove the which was only used to choose which gene to initiate
Explain the importance of the sigma factor.
We end transcription at the end of gene and come to a hairpin loop. This is called Rho-independent termination where at the end of gene the specific sequence creates complimentary base pair in the tail of RNA which forms a hairpin loop which destabilizes the RNA polymerase and the DNA complex causing the RNA polymerase to remove itself from the DNA and stop transcription.
Describe a "hairpin loop" in RNA and explain its importance.
In Eukaryotic DNA, upstream of about -30 base pairs from beginning of first codon there's a TATAA box, a consensus sequence right upstream from beginning of a gene, similar to the consensus of prokaryotic DNA.
Explain what the TATA box is.
Actinomycin D, Acridine.
Name 2 drugs that block RNA synthesis
Stretches of DNA in the gene that do not code for protein are called introns. These introns are transcribed right into RNA when it is synthesized. They must be removed before making proteins to make mRNA. The introns remove their selves by acting as their own enzymes.
Exons are parts of the gene that do code for protein.
To slow down degradation of our DNA a 5' cap is put on it. And poly A tail to protect the RNA on the 3´end
Explain the terms introns, exons, 5'-cap and poly A tail.
Primary transcript is a newly synthesized RNA molecule. Mature RNA is the molecule after cleavage of introns, polyadenylation, and splicing take place.
Contrast the terms primary transcript and mature RNA
In type 1 introns, the intron itself acts as a ribozyme and catalytically cleaves itself out. It does not use ATP to drive the reaction, it uses guanosine as nucleophile to attack the last base of the exon and split out the first base of the intron. Then catalytically direct the nucleophilic attack of the last base of exon onto the first base of the next exon splicing out the intron precisely
List the sequence of events for type 1 introns. Name the types of RNA that use this pathway.
Type 2 introns also cleave themselves out but not found in all DNA, usually found in mitochondria and chloroplast of fungi, algae, and plants. Adenosine within the intron itself acts as the first nucleophile to slice out the first base of intron. Then catalyzes the last base of the first exon to do nucleophilic attack on the first base of the next exon splicing out the type 2 intron.
List the sequence of events for type 2 introns. Name the types of RNA that use this pathway.
snRNP's are similar to type except they occur in the nuclear eukaryotic DNA. Adenosine as acts as the nucleophile in snRNP's just like in type 2 but require small ribonuclear proteins to catalyze the reaction.
Compare and contrast type 2 introns to snRNP's
In tRNA endonuclease is used to cleave the intron out of the RNA. As a result, a cyclic nucleotide is created on the 3´end of the leading exon. It is cleaved even further by cyclic nucleotide phosphodiesterase. On the 3´end of the latter exon it must be primed and energized by putting phosphate at expense of ATP and add another AMP on top of it at the expense of two more high energy phosphate bonds to form an AMP at beginning of next exon which is cleaved out when the two regions of the exons are ligated together
Describe enzymatic removal of introns.
On top of taking the introns out but also how we splice the RNA can allow for more than one protein product for any one gene. Depending on the cell and what splicing enzyme is in the cell, two different cells may splice the same gene differently and get different gene products.
Describe alternate splicing and the purpose it has.
Normally DNA can replicate itself, and DNA can be transcribed to RNA and translated to proteins. The central dogma had to be modified to add reverse transcription where RNA can be copied into DNA when retroviruses infect a cell. Also RNA can be replicated into RNA, there are certain RNA viruses that are able to use RNA instead of DNA and can replicate their RNA directly.
Explain how the central dogma of molecular biology had to be modified to take into account retro transcription.
If enough viruses inject enough reverse transcriptase into a cell, the RNA will be transcribed into a double stranded DNA, which can integrate into the host cell's DNA
List and describe the major enzymes that retroviruses must have so they can reproduce inside of a cell.
Transposons: "jumping genes" that tend to move within chromosomes. They are similar to virus genomic material. They are thought to might have arisen from viral infections where the genes have gone bad and these are no longer able to form virus particles, but they remained in our genes.
Retrotransposons: use an RNA intermediate, RNA does reverse transcription DNA.
Define Transposons and Retrotransposons.
During fertilization telomeres are added to new chromosomes by using RNA template to make DNA, and the telomeres are made by enzyme called telomerase which is a special type of naturally occurring reverse transcriptase.
Describe how telomeres are produced.
what is your name?
protein synthesis takes place in ribosomes
where in the cell does protein synthesis take place?
how many amino acids exist?
how many tRNA's?
Triplet code: t-RNA's bind to specific triplet codons
A sequence of three nucleotides
describe the triplet codon
Wobble position is not as specific as the other two.
Wobble position is position number 1 on the anticodon.
The codon and anticodon are antiparallel, so if the Wobble position is #1 in the anticodon, it will be #3 in the codon.
Position where the base is not important but the first two are important for binding
what is the wobble position?
Mutations: frameshift mutation
Insertion mutation: usually implies frameshift mutation
insertion causes framshift
single base --> a frameshift from that point forward
Insert 2 bases --> frameshift from that point forward
Insert 3 bases --> change amino acid will be put into protein adding amino acid or that point and forward we have normal protein being made
deletion mutation: single deletion
describe the different types of DNA mutations and how this affects RNA.
The codon is universal for almost all organisms except some variation in Mitochondria.
Describe how mitochondria are slightly different than cellular protein synthesis.
ApoB100 (in liver) and ApoB48 proteins are from the same gene.
ApoB48 uses the same gene but in the intestine the protein is truncated.
ApoB48 is half the size of ApoB100
ApoB48 has early stop codon
Describe the difference between ApoB48 and ApoB-100 and how & where this takes place.
Viruses are a bit sloppy
Permits overlapping genes on a small piece of RNA. The gag gene is expressed more frequently than the pol gene.
Describe how alternate reading of RNA increases the protein diversity of a cell or virus.
Ribosomes are about 65% ribosomal RNA, 35% proteins
Consist of a small and large subunit, 30S subunit, 50S subunit
Ribosome consist of mRNA that's being transcribed, 30S subunit first attaches itself then 50S subunit attaches itself after and gets things in place and last the tRNA comes in and does the protein synthesis.
Bacterial ribosomes are free floating, eukaryotic embedded in ER.
describe the ribosome
tRNA is not really a t shape, t stands for transfer.
Amino acid attached to 3' end of tRNA.
describe the 32 different tRNA's
Step 1: activation in the cytoplasm (Each tRNA molecule binds with a specific amino acid in the cytoplasm)
Step 2: The binding of an amino acid to the tRNA acceptor stem occurs
Step 3: The function of the ATP (phosphorylation) is to create a high energy bond that is transferred to the tRNA molecule
Describe the activation of a tRNA.
1. Proteins are synthesized starting at the N-terminal and grow towards the C-terminal.
Protein growth is in the amino terminus to carboxyl terminus direction
2. Initiation: mRNA will attach to 30S subunit, the first AUG will be found then process starts
3. Elongation into protein
List out and describe the steps involved in the peptide bond formations.
binds to the 30s ribosomal subunit in prokaryotic
interferes with the initiation
How many different codons are there?
3 prime end
the amino acid is attached to the
class 1 attaches amino acid to the second OH and class 2 attaches to the third OH
what is the difference between class 1 and 2?
is it critical that we attach the correct amino acid to the correct tRNA
N-terminus to C-terminus
direction of protein synthesis
recognition site on beginning of mRNA to attach to ribosome
what is shine-dalgamo sequence
binds the 30s subunit and blocks A site
second amino acid to bind
interferes with the transferase activity on the 50s subunit
binds 50s subunit
the a subunit catalyzes the ADP ribosylation on to eukaryotic EF2
how many stop codons
stop codons are
UAA, UAG, UGA
transcript RNA is converted into mature RNA
removing the first met
removing of signal sequence
modification of some amino acid
causes premature termination of the protein synthesis
blocks peptide transfer in bacteria, mitochondria and chloroplasts
blocks peptidyl transfer in eukaryotes.
used as an experimental tool and not marketed as drug
causes misreading of genetic code in bacteria
blocks the A site on the ribosome
adenine, thymine, guanine, cytosine
4 bases of DNA
uracil, adenine, guanine, cytosine
thymine has extra methyl than uracil
difference between Uracil and thymine
Adenine and Guanine
thymine and cytosine
Consists of the nitrogenous base adenine, the sugar ribose, and three phosphate groups.
consists of a nitrogenous base, a sugar, but without the phosphate group
T pairs with
Cytosine pairs with
distance between correctly paired bases
2 hydrogen bonds
How many hydrogen bonds are between adenine and thymine?
5 prime to 3 prime
The direction in which DNA and RNA are synthesized
template strand is read
normal form, right handed helix
left handed helix
right handed, only found in crystals
found at regulation points
single stranded and identical terminal nucleotides
complementary strand within a strand
happens on both strand at the same time
The removal of an amino group from amino acid.
a chemical reaction of purines
losing a purine
a type of drug used for cancer
all the genetic information in a cell
each segment of DNA molecule that codes for one gene product
How many chromosomes do humans have?
refers to the over and under winding of a DNA strand
enzymes that break the strand in order to relieve the strain, 2 different types
DNA to RNA to protein
percent of the dna codes for exons
material of which the chromosome is composed of
a sequence of three nucleotides that together form a unit of genetic code in a DNA or RNA molecule.
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