Genetics Chapter 14

gene

all sequences in DNA that are transcribed into a single RNA molecule

colinear

there is a direct correspondence between the nucleotide sequence of DNA and the amino acid sequence of a protein; the number of nucleotides in a gene should be proportional to the number of amino acids in the protein encoded by that gene

True or false: All genes are collinear.

False. Colinear genes are found in prokaryotic cells, but not eukaryotes.

What revealed that nuclear RNAs undergo change before they are exported to the cytoplasm?

many large molecules observed in the nucleus were absent from the cytoplasm

What demonstrates that eukaryotes are not co-linear?

coding sequences were interrupted by nucleotides that did not specify amino acid

Describe the experiment that revealed that the coding sequence in a gene is not always continuous.

1.) DNA was paired with complementary mRNA
2.) Non-coding regions of DNA were seen as loops

exons

RNA coding regions

intron

non-coding regions; intervening sequences

What are the difference between introns and exons?

while all introns and exons are initially transcribed into RNA, after transcription, the introns are removed and the exons are joined

True or false: Sizes and numbers of introns appear to be directly related to organismal complexity.

True. Most eukaryotes have a large number of introns.

Group I/ Group II introns

self-splicimg

spell-splicing introns

can catalyze their own removal ; possess the ability to remove themselves from an RNA molecules without the aid of enzymes of other proteins; fold into secondary structures (hairpins)

nuclear pre-mRNA introns

introns located in the protein-encoding genes of the eukaryotic nucleus

What is required for the removal of nuclear pre-mRNA introns?

a splice some that includes small nuclear RNAs

transfer RNA introns

tRNA that use enzymes for splicing

Where does the splicing of all pre-mRNA introns take place?

in the nucleus

True or false: The order of exons in DNA is maintained.

True. Once the introns are spliced, the order of exons in DNA is usually maintained in the spliced RNA

True or false: All nucleotides encode amino acids.

False. Introns as well as nucleotides that encode the 5' to 3' ends of an mRNA molecules do not specify amino acids

What are the main components that make up a gene?

exons, introns, and sequences at the beginning and end of the RNA, rRNAs, tRNAs, and other nn-mRNAs

True or false: DNA can not directly encode proteins.

True. RNA needs to be copied from RNA and then directed to synthesize proteins.

What is most RNA in a cell used for?

to make up ribosomes

Describe the experiment that showed that ribosomes carry genetic information.

1.) Ecoli were grown in a medium containing heavy isotopes that became incorporated into its ribosomes.
2.) Cells were then moved into a medium containing light isotopes with infected phages.
3.) Phage proteins were then produced and ribosomes are separated via centrifuge
4.) The ribosomes were then analyzed.

How did the experiment show that ribosomes carry genetic information?

ribosomes were not produced in phage production; if ribosoms carried the genetic information for the synthesis of proteins the new ribosomes should contain light isotopes (b/c the phages would reproduce genetic material which would then be absorbed by the bacteria)

What was the main conclusion of the ribosome experiment?

short-lived RNA carries genetic information for proteins to the ribosome were translation occurs

messenger RNA (mRNA)

functions as the template for protein synthesis; carries genetic information from the DNA to the ribosome; helps assemble amino acids in the correct order

What is the difference between mRNA in prokaryotes versus eukaryotes?

mRNA is transcribed directly from DNA in prokaryotes, but in eukaryotes, pre-mRNA is first transcribed from DNA and then processed intro mature mRNA

codon

a set of nucleotides that specify each amino acid of a protein

5' untranslated region

a sequence of nucleotides at the 5' end of the mRNA that does not encode any of the amino acids of a protein

What is present at the 5' consensus sequence in bacterial mRNA?

the Shine Dalgarno sequence

Shine Dalgarno sequence

a consensus sequence that serves as the ribosome-binding site during translation

How does the ribosome bind to the Shine-Dalgarno sequence?

the Shine-Dalgarno sequence is complementary to a sequence in rRNA and pairs with it during translation

True or false: Eukaryotes have an analogue for the Shine-Dalgarno sequence.

False. In eukaryotic cells, ribosomes just bind to the modified 5/ end of mRNA.

protein-coding region

compromises the codons that specify the amino acid sequence of the protein

Where does the protein coding region begin and end?

it begins with the start codon and ends with a stop codon

3' untranslated region

a sequence of nucleotides at the 3' end of the mRNA that is not translated into amino acids; affect the stability of mRNA and helps regulate the translation of the mRNA protein-coding sequence

Why is eukaryotic transcription differ than prokaryotes?

in eukaryotes take place in the nucleus and translation takes place in the cytoplasm, unlike bacteria who have transcription and translation simultaneously

What are the main parts of editing mRNA?

1.) Addition of 5' cap
2.) 3' cleavage and addition of poly-A tail
3.) RNA splicing
4.) RNA editing
5.) Internal RNA modifications

addition of 5' cap

facilitates the binding of ribosomes to the 5' end of mRNA; increases mRNA stability and RNA splicing

3' cleavage and addition of the poly-A tail

increases the stability to mRNA; aids in export of mRNA from the nucleus; facilitates the binding of the ribosome to mRNA

How is the 5' cap formed?

addition of an extra guanine nucleotide at the 5' end of the mRNA and the addition of methyl groups (CH3)

Describe the addition of the poly-A tail.

1.) One of three phosphate groups at the 5' end of the mRNA groups at the 5' end
2.) A guanine nucleotide with its phosphate group is added
3.) Methyl groups are aded to the position 7 of the base of the terminal guanine nucleotide.

How is the 5' cap added?

a 5' 5' bond

What is the role of 5' cap?

increases the stability of mRNA and influences the removal of introns

poly(A) tail

addition of adenine nucleotides at the 3' end

polyadenylation

the process of adding the poly-A tail

Describe the process of adenylation.

1.) Pre-mRNA is cleaved
2.) addition of adenine nucleotides takes place at the 3' en of the pre-mRNA generating poly(A)

5' end of the mRNA binds to the 5' end of the cap

True or false: The amount of protein produced by a cell depends only on the amount of mRNA transcribed.

the amount of protein produced by a cell dependent not only on the amount of mRNA transcribed but also on the stability of the mRNA that is transcribed

RNA splicing

removal introns

When and where does RNA splicing take place?

it takes place in the nucleus before the RNA moves to the cytoplasm

5' splice site

one end of the intron

3' splice site

another end of the intons

Branch point

an adenine nucleotide

What happens is if the branch point is deleted or. stated?

splicing is prevented

What determines the separation between the intron and exon?

consensus sequences

Where does splicing take place?

within the splice some

What are the function of small nuclear RNAs?

the associate with proteins and comprise the splicisome

Describe the process of splicing.

1.) mRNA is cut at the 5' splice site
2.) the 5' end of the intron attaches to the branch point
3.) A cut us made at the 3' splice site
4.) The intro is released as a lariat
5.) Two exons are spliced together
6.) the spliced mRNA is exported to the cytoplasm and translated

cap binding proteins

recognize and attach to the cap; ribosome bind to these proteins to initiate translation

Describe the assembly process of the RNA processing and mRNA association.

1.) U1 attaches to the 5' splice site
2.) u2 attaches to the branch point
3.) A complex of U4, U5, and U6 joins the splicis`ome
4.) U1 and U4 are released
5.) base pairing between sequences in the mRNA and snRNAs hold the splicisome together
6.) The exons are joined together and the intron is released as the lariat

When (and where) is pre-mRNA cleaved?

a few nucleotides past the consensus sequence at the cleavage site

GU/ AG

5'/3'

alternative processing paathyways

a single pre-mRNA can be processed in different ways to produce alternative types of mRNA

What is the result of alternative processing pathways?

the production of different proteins from the same DNA sequence

alternative splicing

the same pre-mRNA can be spliced into more than one way to yield different mRNAs that are translated into different amino acid sequences and thus different proteins

What does alternative splicing require?

multiple 3' cleavage sites

multiple 3' cleavage sites

two or more potential sites for cleavage and polyadenylation are present in pre-mRNA

What is the result of having multiple 3' cleavage sites?

a different protein may or may not be produced, depending on whether the site is located before or after the stop codon

What is another affect of alternate cleavage sites?

the stability and translation of the mRNA is influenced

RNA editing

the coding sequence of an mRNA molecule is altered after transcription, so that the translated protein has an amino acid sequence that differs from that encoded from the gene

guide RNAs

contain sequences that are partly complementary to segments of the unedited mRNA and the two molecules undergo base paring at these sequences; the mRNA then undergoes cleavage and nucleotides are added, deleted, or altered according to the template provided by the guide RNA

Describe the process of DNA editing.

1.) The unedited mRNA pairs with the guide RNA.
2.) The guide RNA serves as a template for the addition, deletion, or alteration of bases
3.) The mature mRNA is released

Describe alternative splicing.

Different combinations of exons are cleaved. For example, two introns can be removed to yield one mRNA or two introns and an exon can be removed to yield a different mRNA.

Describe multiple 3' cleavage sites.

Multiple 3' cleavage sites use different locations for 3' cleavage on the same exon. As a result, mRNA products of different lengths are produced after splicing.

transfer RNA (tRNA)

serves as a link between the genetic code in mRNA and the amino acids that make up a protein; attaches to a particular amino acid and carries it to the ribosome, where the tRNA adds the its amino acid to the growing polypeptide chain at the position specified by the genetic instructions in the mRNA

What type of mRNA has modified bases?

tRNA molecules have modified bases

How do tRNA molecules form its structure?

by forming hairpin loops (secondary structures) via a string of complementary nucleotides

acceptor arm

includes the 5' and 3' ends of the tRNA molecule

3' end of tRNA

where amino acid attaches to the tRNA

Describe how tRNAs are produced.

1.) A large precursor tRNA is cleaved to produce an individual tRNA molecule.
2.) An intron is removed by splicing
3.) bases are added to the 3' end
4.) Bases are modified to produce mature tRNA

What are the 2 main parts of the ribosome?

1.) large ribosomal subunit
2.) small ribosomal subunit

What makes up the ribosome?

rRNA and proteins

When is ribosomal RNA processed?

after transcription

Describe the creation of rRNA in prokaryotes?

1.) Methyl groups are added to specific bases and sugars
2.) RNA is cleaved into intermediates by an enzyme
3.) RNA is trimmed
4.) Mature rRNA is created

Describe the creation of rRNA in eukarotes.

a precursor is methylated

RNA interference

single-stranded RNA molecules that are complementary to a gene's DNA sequence , leading to gene silencing

What types of mRNA are involved in gene interference?

1.) small interfering RNAs (siRNAs)
2.) microRNAs (miRNAs)

What is the purpose of RNA interference?

1.) to limit the invasion of foreign genes
2.) to censor the expression of own genes

Describe how microRNAs work.

1.) Transcription through an inverted repeat occurs, producing a primary RNA with a hairpin.
2.) The hairpin is cleaved to produce a short RNAand a smaller hairpin
3.) A dicer removes the terminal loop of the shorted hairpin
4.) The RNA combines with a protein that expels one strand of the RNA
5.) an RNA-induced silencing complex is produced
6.)the silencing complex pairs with a mRNA and inhibits translation

Describe how small interfering RNAs work?

1.) A double stranded RNA arises from a RNA virus.
2.) The double stranded RNA is cleaved by Dicer
3.) SiRNAs a produced
4.) The siRNA combines with proteins to form a silencing complex
5.) The complex then pairs with and cleaves mRNA, leading to degradation

How did RNA interference molecules evolve?

as a defense mechanism against RNA viruses (the immune system of the genome)

What is the general difference between miRNA and siRNAs?

each miRNA is cleaved from a single-stranded RNA precursor that forms small hairpins, while siRNAs are produced from the cleavage of an RNA duplex consisting of 2 different RNA molecules.

What is the difference between the origin and targets of miRNAs and siRNs?

miRNAs are from an RNA molecule transcribed from a distinct gene that attack genes other than those transcribed, while siRNAs are from viruses and attack genes of that virus

What is the difference between the purpose of miRNAs and siRNs?

miRNAs are mainly used to inhibit translation, whereas siRNAs are for the deviation of mRNA

What is the difference in relationship between the composition of miRNAs and siRNAs and their targets?

siRNAs are exactly complementary with their target mRNA or DNA sequences, whereas miRNAs often have limited complementary with their target mRNs

Why is there a difference in relationship between the composition of miRNAs and siRNAs and their targets?

miRNAs need to inhibit translation, whereas siRNAs need to degrade the mRNA (the matching serves as a "tag" for degration)

RNA-induced silencing complex (RISC)

iRNA combining with proteins

What is the purpose of dicer in iRNAs?

1.) Removes terminal loop of the hairpin in order to create miRNAs
2.) Cleaves double stranded RNA to create siRNA

Where miRNAs formed?

within the organism's own genome from miRNA genes that are usually found in regions of noncoding DNA or within introns

What is the function of small nuclear RNAs (snRNAs)?

participate in the post transcriptional processing of RNA (ex. splicing/ stabilizing lariat in eukaryotes)