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69 Cards in this Set

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What is a gene and its purpose?
Genes code for proteins, and proteins are made of amino acid. So, a gene contains the nucleotides that specify the amino acids of a protein.
What is the general shape of genes?
Genes and proteins are colinear, there is a direct correspondence between the nucleotide sequence of DNA and the amino acid sequence of a protein.
What is the relationship between the nucleotides in a gene and amino acids?
The number of nucleotides in a gene in proportional to the number of amino acids in the protein that the gene codes for.
What is the weird thing with DNA-RNA hybrids?
DNA is clearly much longer than RNA, because DNA loops out from the hybridized molecules.
What are the two important regions in most eukaryotic genes?
Many eukaryotic genes have coding regions called exons, and noncoding regions called “intervening sequences”, or introns.
What are introns?
Introns are common in eukaryotic genes and rare in bacterial genes. They are present in mitochondrial, chloroplast, and nuclear genes. The size and number of introns is directly related to the complexity of an organism. Introns do not usually encode proteins.
What are the four major types of introns?
There are four major types of introns: Group I, Group II, Nuclear mRNA introns, and Transfer RNA introns.
Describe Group I introns.
Group I introns are found in some rRNA genes, they are self-splicing, they can catalyze their own removal.
Describe Group II introns.
Group II introns are found in some protein-coding genes of mitochondria, chloroplasts, and a few eubacteria. They self-splice but do it differently than group I introns.
Describe Nuclear mRNA introns.
Nuclear mRNA introns are found in the protein-coding genes of the eukaryotic nucleus. They don't self-splice, so they need snRNAs and proteins to be removed (spliceosomal).
Describe Transfer RNA introns.
Transfer RNA introns are found in tRNA genes. They are spliced with enzymes to cut and reseal the RNA (enzymatic).
What is Messenger RNA (mRNA)?
Messenger RNA is a template for making proteins. It carries genetic information from DNA to a ribosome and helps assemble the amino acids in their correct order.
How is messenger RNA (mRNA) transcribed in bacteria?
In bacteria, mRNA is transcribed directly from DNA.
How is messenger RNA (mRNA) transcribed in eukaryotes?
In eukaryotes, there is a pre-mRNA (the primary transcript) that is transcribed first from the DNA and then processed to get the mature mRNA.
Describe mature mRNA and its three primary regions.
In mature mRNA, each amino acid in a protein is specified by a set of three nucleotides, the codon. Prokaryotic and eukaryotic mRNAs have three primary regions: the 5’ untranslated region (5’ UTR, or the “leader”), the protein-coding region, and the 3’ untranslated region (3’ UTR, or the “trailer”).
Describe and give the function of the 5' untranslated region of mature mRNA.
The 5’ untranslated region is a sequence of nucleotides at the 5’ mRNA end, doesn’t encode any amino acids for the protein.
Describe and give the function of the protein coding region of mature mRNA.
The protein-coding region is the codons that specify the amino acid sequence of the protein. It begins with a start codon and ends with a stop codon.
Describe and give the function of the 3' untranslated region of mature mRNA.
The 3’ untranslated region is a sequence of nucleotides that is at the 3’ end of the mRNA. It is not made into a protein. It affects the stability of the mRNA and the translation of the protein-coding sequence.
What is the difference between the 5' untranslated regions of bacterial and eukaryotic mRNA?
In bacterial mRNA, there is a Shine-Dalgarno sequence, which is a ribosome binding site during translation. It is found seven nucleotides upstream from the first codon to be made into an amino acid (the start codon).
When do transcription and translation happen in bacterial cells?
In bacterial cells, transcription and translation take place at the same time. While the 3’ end is doing transcription, ribosomes attach to the Shine-Dalgarno sequence by the 5’ end and start translation. There isn’t much time for the mRNA to be modified before protein synthesis (translation).
When do transcription and translation happen in a eukaryotic cell?
In eukaryotic cells, transcription and translation take place at different times and in different spaces. Transcription is in the nucleus, translation is in the cytoplasm; this way, RNA is modified before it is translated.
What are the three main modifications to RNA before translation?
Adding the 5' cap, adding the poly(A) tail, and RNA splicing.
Describe the 5' cap.
The 5' cap is an extra nucleotide added to the 5’ end of the pre-mRNA, and methylation by adding a methyl group (CH3) to the base of the new nucleotide and to the 2’-OH group of either the sugar, or 1+ nucleotides at the 5’ end.
When is the 5' cap added, and what does it do the the RNA?
It is added after transcription, and it helps initiate translation and increases the mRNA stability, and helps remove the introns. Cap-binding proteins recognize and attach to it, and a ribosome binds to the proteins and moves downstream along the mRNA until it gets to a start codon and begins translation.
What is the first step of adding the 5' cap?
The first step in adding the cap is done by an enzyme that associates with RNA polymerase II. Since RNA polymerases I and III don’t have the enzyme, RNA molecules made by these polymerases (rRNAs, tRNAs, some snRNAs) aren’t capped.
Describe the poly(A) tail.
the addition of 50-250 adenine nucleotides at the 3’ end, making a poly(A) tail. They aren’t encoded in the DNA, but they are added after transcription in a process called polyadenylation.
Describe how the poly(A) tail is added.
Many eukaryotic genes that are transcribed by RNA polymerase II are transcribed beyond the end of the coding sequence, so the extra material at the 3’ end it cut off and replaced with the tail. For some pre-mRNA molecules, more than 1000 nucleotides might be removed from the 3’ end.
What does the 3' end processing need to get a poly(A) tail?
This 3’ end processing requires sequences upstream and downstream of the cleavage site.
Give an example of 3' end processing.
The consensus sequence AAUAAA is normally 11-30 nucleotides upstream of the cleavage site, and it decides where the cleavage takes place. After cleavage the poly(A) tail is added.
What does the poly(A) tail do?
The poly(A) tail gives stability to the mRNA, helps the ribosome attach to the mRNA, and increases the time that the mRNA stays intact and available for translation before it is eaten by cellular enzymes. The stability depends on the proteins that attach to the tail.
When do transcription and translation happen in a eukaryotic cell?
In eukaryotic cells, transcription and translation take place at different times and in different spaces. Transcription is in the nucleus, translation is in the cytoplasm; this way, RNA is modified before it is translated.
What are the three main modifications to RNA before translation?
Adding the 5' cap, adding the poly(A) tail, and RNA splicing.
Describe the 5' cap.
The 5' cap is an extra nucleotide added to the 5’ end of the pre-mRNA, and methylation by adding a methyl group (CH3) to the base of the new nucleotide and to the 2’-OH group of either the sugar, or 1+ nucleotides at the 5’ end.
When is the 5' cap added, and what does it do the the RNA?
It is added after transcription, and it helps initiate translation and increases the mRNA stability, and helps remove the introns. Cap-binding proteins recognize and attach to it, and a ribosome binds to the proteins and moves downstream along the mRNA until it gets to a start codon and begins translation.
What is the first step of adding the 5' cap?
The first step in adding the cap is done by an enzyme that associates with RNA polymerase II. Since RNA polymerases I and III don’t have the enzyme, RNA molecules made by these polymerases (rRNAs, tRNAs, some snRNAs) aren’t capped.
Describe the poly(A) tail.
the addition of 50-250 adenine nucleotides at the 3’ end, making a poly(A) tail. They aren’t encoded in the DNA, but they are added after transcription in a process called polyadenylation.
Describe how the poly(A) tail is added.
Many eukaryotic genes that are transcribed by RNA polymerase II are transcribed beyond the end of the coding sequence, so the extra material at the 3’ end it cut off and replaced with the tail. For some pre-mRNA molecules, more than 1000 nucleotides might be removed from the 3’ end.
What does the 3' end processing need to get a poly(A) tail?
This 3’ end processing requires sequences upstream and downstream of the cleavage site.
Give an example of 3' end processing.
The consensus sequence AAUAAA is normally 11-30 nucleotides upstream of the cleavage site, and it decides where the cleavage takes place. After cleavage the poly(A) tail is added.
What is an Control group?
used for comparison with experimental group.

must have consisent factors - nothing is changed
What is RNA splicing?
RNA Splicing is the removal of introns from mRNA.
Where does RNA splicing happen?
It happens in the nucleus, before the RNA goes to the cytoplasm.
What does RNA splicing require in order to occur?
It requires three sequences in the intron: one end called the 5’ splice site, the other end called the 3’ splice site, and the branch point.
What is the 5' splice site?
It is a sequence in an intron needed for RNA splicing, found on the intron end closest to the 5’ molecule end; it has a short consensus sequence. Most introns begin with GU and end with AG.
What is the 3' splice site?
It is a sequence in an intron needed for RNA splicing, found on the intron end closest to the 3’ molecule end; it has a short consensus sequence. Most introns begin with GU and end with AG.
What is the branch point?
It is a sequence of an intron needed for RNA splicing. The branch point is an adenine nucleotide that is between 18-40 nucleotides upstream of the 3’ splice site.
What happens if the adenine nucleotide at the branch point is deleted or mutated?
The sequence around the branch point does not have a strong consensus, and the deletion or mutation of the adenine nucleotide at the branch point prevents RNA splicing.
Where does RNA splicing take place?
RNA splicing happens in a large structure called the spliceosome, which is very large and complex.
What is the structure of the spliceosome?
The spliceosome is made of five RNA molecules and almost 300 proteins. The RNA components are small nuclear RNAs (snRNAs) that are between 107-210 nucleotides long; they associate with proteins to make small ribonucleoprotein particles (snRNPs).
What is the structure of an snRNP?
Each snRNP has a single snRNA molecule and multiple proteins.
What is the sequence set up before pre-mRNA splicing begins?
Before splicing happens, an intron is between an upstream exon (exon 1) and a downstream exon (exon 2).
What is the first of the two steps of pre-mRNA splicing?
The pre-mRNA is cut at the 5’ splice site, which frees exon 1 from the intron, so the 5’ end of the intron folds back on itself and attaches to the branch point, which makes a structure called a lariat.
What is the lariat-forming reaction?
In the lariat-forming reaction, the guanine in the consensus sequence at the 5’ splice site bonds with the adenine at the branch point through a transesterification reaction.
What is the result of the lariat-forming reaction?
The result is that the 5’-phosphate group of the guanine is attached to the 2’-OH group of the adenine at the branch point.
What is the second of the two steps of pre-mRNA splicing?
A cut is made at the 3’ splice site and the 3’ end of exon 1 covalently attaches (splices) to the 5’ end of exon 2 at the same time. The intron is released as a lariat, and it becomes linear when the bond breaks at the branch point and then gets eaten by enzymes.
What happens to the mature mRNA made by the splicing?
The mature mRNA made of exons spliced together is exported to the cytoplasm and translated.
What do the reactions between mRNA and snRNAs depend on to occur?
The reactions depend on complementary base pairing between the different RNA molecules, and they bring the important parts of the pre-mRNA transcript and the spliceosome close together, which lets splicing happen.
What are most mRNAs made from?
Most mRNAs are made from a single pre-mRNA molecule from which exons are spliced together.
Describe the order of the nucleus.
The nucleus is very orderly, and transcription and RNA processing happen at specific locations in it. Intron removal and other processing reactions happen at the same sites as transcription does.
Describe self-splicing and the two major groups of introns that can self-splice.
Self-splicing means that the introns can remove themselves from an RNA molecule. There are two major kinds, group I introns and group II introns.
Describe Group I introns.
Group I introns are found in a variety of genes (some rRNA genes in protists, some mitochondrial genes in fungi, some bacteriophage genes). The lengths are different, but they all fold into the same secondary structure of nine looped stems that are necessary for splicing.
Describe Group II introns.
Group II introns are found in some mitochondrial genes. They fold into secondary structures too, and their splicing happens by a mechanism with similarities to the spliceosomal-mediated splicing of nuclear genes, and the splicing generates a lariat structure.
Describe alternative processing pathways.
Alternative Processing Pathways are ways that a single pre-mRNA is processed in different ways to make different mRNAs, that are translated into different amino acid sequences and different proteins.
What are the two main types of alternative processing pathways?
The two main types of alternative processing pathways are alternative splicing and splicing with multiple 3’ cleavage sites.
Describe alternative splicing.
Alternative splicing is when the same pre-mRNA is spliced in more than one way to make different mRNAs, different amino acid sequences, and then different proteins.
Describe splicing with multiple 3' cleavage sites.
Splicing with multiple 3’ cleavage sites is splicing that requires two or more sites for cleavage and polyadenylation that are present in the pre-mRNA.
Give an example of both types of alternative processing pathways existing in the same pre-mRNA transcript.
An identical pre-mRNA sequence can encode for the hormone calcitonin in the thyroid OR a calcitonin-gene-related peptide (CGRP) in the brain.
Describe calcitonin.
The mammalian gene that encodes calcitonin contains six exons and five introns. The entire gene is transcribed into pre-mRNA; there are two possible 3’ cleavage sites. In the thyroid gland cells, 3’ cleavage and polyadenylation happen after the fourth exon to make a mature mRNA made of exons 1, 2, 3, and 4. This mRNA is translated into the hormone calcitonin.
Describe calcitonin-gene-related peptides (CGRPs).
In brain cells, the identical pre-RNA is transcribed from DNA, but cleavage and polyadenylation happen after the sixth exon, which makes an initial transcript that includes all six exons. When it is translated, the mRNA makes a protein called CGRP (calcitonin-gene-related peptide), whose amino acid sequence is very different from calcitonin.