Chapter 14 Facts - Genetics, A Conceptual Approach, V.3 By Benjamin A. Pierce

Front 1

What is a gene and its purpose?

Back 1

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.

Front 2

What is the general shape of genes?

Back 2

Genes and proteins are colinear, there is a direct correspondence between the nucleotide sequence of DNA and the amino acid sequence of a protein.

Front 3

What is the relationship between the nucleotides in a gene and amino acids?

Back 3

The number of nucleotides in a gene in proportional to the number of amino acids in the protein that the gene codes for.

Front 4

What is the weird thing with DNA-RNA hybrids?

Back 4

DNA is clearly much longer than RNA, because DNA loops out from the hybridized molecules.

Front 5

What are the two important regions in most eukaryotic genes?

Back 5

Many eukaryotic genes have coding regions called exons, and noncoding regions called “intervening sequences”, or introns.

Front 6

What are introns?

Back 6

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.

Front 7

What are the four major types of introns?

Back 7

There are four major types of introns: Group I, Group II, Nuclear mRNA introns, and Transfer RNA introns.

Front 8

Describe Group I introns.

Back 8

Group I introns are found in some rRNA genes, they are self-splicing, they can catalyze their own removal.

Front 9

Describe Group II introns.

Back 9

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.

Front 10

Describe Nuclear mRNA introns.

Back 10

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).

Front 11

Describe Transfer RNA introns.

Back 11

Transfer RNA introns are found in tRNA genes. They are spliced with enzymes to cut and reseal the RNA (enzymatic).

Front 12

What is Messenger RNA (mRNA)?

Back 12

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.

Front 13

How is messenger RNA (mRNA) transcribed in bacteria?

Back 13

In bacteria, mRNA is transcribed directly from DNA.

Front 14

How is messenger RNA (mRNA) transcribed in eukaryotes?

Back 14

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.

Front 15

Describe mature mRNA and its three primary regions.

Back 15

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”).

Front 16

Describe and give the function of the 5' untranslated region of mature mRNA.

Back 16

The 5’ untranslated region is a sequence of nucleotides at the 5’ mRNA end, doesn’t encode any amino acids for the protein.

Front 17

Describe and give the function of the protein coding region of mature mRNA.

Back 17

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.

Front 18

Describe and give the function of the 3' untranslated region of mature mRNA.

Back 18

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.

Front 19

What is the difference between the 5' untranslated regions of bacterial and eukaryotic mRNA?

Back 19

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).

Front 20

When do transcription and translation happen in bacterial cells?

Back 20

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).

Front 21

When do transcription and translation happen in a eukaryotic cell?

Back 21

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.

Front 22

What are the three main modifications to RNA before translation?

Back 22

Adding the 5' cap, adding the poly(A) tail, and RNA splicing.

Front 23

Describe the 5' cap.

Back 23

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.

Front 24

When is the 5' cap added, and what does it do the the RNA?

Back 24

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.

Front 25

What is the first step of adding the 5' cap?

Back 25

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.

Front 26

Describe the poly(A) tail.

Back 26

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.

Front 27

Describe how the poly(A) tail is added.

Back 27

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.

Front 28

What does the 3' end processing need to get a poly(A) tail?

Back 28

This 3’ end processing requires sequences upstream and downstream of the cleavage site.

Front 29

Give an example of 3' end processing.

Back 29

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.

Front 30

What does the poly(A) tail do?

Back 30

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.

Front 31

When do transcription and translation happen in a eukaryotic cell?

Back 31

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.

Front 32

What are the three main modifications to RNA before translation?

Back 32

Adding the 5' cap, adding the poly(A) tail, and RNA splicing.

Front 33

Describe the 5' cap.

Back 33

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.

Front 34

When is the 5' cap added, and what does it do the the RNA?

Back 34

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.

Front 35

What is the first step of adding the 5' cap?

Back 35

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.

Front 36

Describe the poly(A) tail.

Back 36

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.

Front 37

Describe how the poly(A) tail is added.

Back 37

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.

Front 38

What does the 3' end processing need to get a poly(A) tail?

Back 38

This 3’ end processing requires sequences upstream and downstream of the cleavage site.

Front 39

Give an example of 3' end processing.

Back 39

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.

Front 40

What is an Control group?

Back 40

used for comparison with experimental group.

must have consisent factors - nothing is changed

Front 41

What is RNA splicing?

Back 41

RNA Splicing is the removal of introns from mRNA.

Front 42

Where does RNA splicing happen?

Back 42

It happens in the nucleus, before the RNA goes to the cytoplasm.

Front 43

What does RNA splicing require in order to occur?

Back 43

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.

Front 44

What is the 5' splice site?

Back 44

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.

Front 45

What is the 3' splice site?

Back 45

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.

Front 46

What is the branch point?

Back 46

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.

Front 47

What happens if the adenine nucleotide at the branch point is deleted or mutated?

Back 47

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.

Front 48

Where does RNA splicing take place?

Back 48

RNA splicing happens in a large structure called the spliceosome, which is very large and complex.

Front 49

What is the structure of the spliceosome?

Back 49

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).

Front 50

What is the structure of an snRNP?

Back 50

Each snRNP has a single snRNA molecule and multiple proteins.

Front 51

What is the sequence set up before pre-mRNA splicing begins?

Back 51

Before splicing happens, an intron is between an upstream exon (exon 1) and a downstream exon (exon 2).

Front 52

What is the first of the two steps of pre-mRNA splicing?

Back 52

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.

Front 53

What is the lariat-forming reaction?

Back 53

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.

Front 54

What is the result of the lariat-forming reaction?

Back 54

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.

Front 55

What is the second of the two steps of pre-mRNA splicing?

Back 55

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.

Front 56

What happens to the mature mRNA made by the splicing?

Back 56

The mature mRNA made of exons spliced together is exported to the cytoplasm and translated.

Front 57

What do the reactions between mRNA and snRNAs depend on to occur?

Back 57

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.

Front 58

What are most mRNAs made from?

Back 58

Most mRNAs are made from a single pre-mRNA molecule from which exons are spliced together.

Front 59

Describe the order of the nucleus.

Back 59

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.

Front 60

Describe self-splicing and the two major groups of introns that can self-splice.

Back 60

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.

Front 61

Describe Group I introns.

Back 61

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.

Front 62

Describe Group II introns.

Back 62

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.

Front 63

Describe alternative processing pathways.

Back 63

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.

Front 64

What are the two main types of alternative processing pathways?

Back 64

The two main types of alternative processing pathways are alternative splicing and splicing with multiple 3’ cleavage sites.

Front 65

Describe alternative splicing.

Back 65

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.

Front 66

Describe splicing with multiple 3' cleavage sites.

Back 66

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.

Front 67

Give an example of both types of alternative processing pathways existing in the same pre-mRNA transcript.

Back 67

An identical pre-mRNA sequence can encode for the hormone calcitonin in the thyroid OR a calcitonin-gene-related peptide (CGRP) in the brain.

Front 68

Describe calcitonin.

Back 68

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.

Front 69

Describe calcitonin-gene-related peptides (CGRPs).

Back 69

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.