Chapter 7: RNA and the Genetic Code

Question 1

terminology 5’ –> 3’

Answer 1

DNA –> DNA = replication:new DNA synthesized in 5’–>3’ direction

DNA–>RNA = transcription: new RNA synthesized in 5’–>3’ direction (template is read 3’ –> 5’ )

RNA–> protein= translation: mRNA read in 5’–> 3’

Question 2

polycistronic

Answer 2

prokaryotic cells can start transcription in different sites within the gene leads to different gene products

Question 3

Central dogma of molecular biology

Answer 3

A gene is a unit of DNA that encodes a specific protein or RNA molecule, and through transcription and translation, that gene can be expressed. Messenger RNA is synthesized in the 5’ to 3’ directions and is complementary and antiparallel to the DNA template strand. The ribosome translates the mRNA in the five to three direction as it synthesizes the protein from the amino terminus (N terminus) to the carboxyl terminus (C Terminus).

Question 3

Messenger RNA (mRNA)

Answer 3

Carries information specifying the amino acid sequence of the protein to the ribosome. mRNA is transcribed from template DNA strands by RNA polymerase enzymes in the nucleus of the cell. mRNA is the only type of RNA that contains information that is translated into protein. It is read in three nucleotide segments, termed codons. In eukaryotes the mRNA is monocistronic, meaning that each RNA molecules translates into only one protein products. In prokaryotes mRNA may be polycistronic, and staring the process of translating at different locations in M RNA can result in different proteins.

Question 4

Transfer RNA (tRNA)

Answer 4

Is responsible for converting the language of nucleic acid to the language of amino acids and peptides. It includes a 3-nucleotide anticodon. This anticodon recognizes in pairs with the appropriate codon on the mRNA in the ribosome. Amino acids are connected to specific tRNA molecules. Such tRNA molecules are said to be charged or activated with an amino acid. each type of amino acid is activated by a different aminoacyl-tRNA synthetase that requires too high energy bonds from ATP implying that the attachment of the amino acid is a high energy bond.

Question 5

Ribosomal RNA (rRNA)

Answer 5

Many rRNA molecules function as ribozymes, That is, enzymes made of RNA molecules instead of peptides. They help catalyze the formation of peptide bonds and it is important in splicing out its own introns within this nucleus.

Question 6

Codons

Answer 6

Three letter word, which translates into an amino acid. All codons are written in the five to three direction, and the cold is unambiguous in that each codon specific for one and only one amino acid.

Question 7

Anticodon.

Answer 7

The codon in the mRNA is recognized by a complementary anticodon on a transfer tRNA. The anticodon sequence allows the tRNA to pair with the codon in the mRNA.

Example: anticodon is 5’—GAU—3’ the codon for that is 5’ —AUC —3’

Question 8

What is the start codon?

Answer 8

AUG which converts to methionine.

Question 9

What are the stop codons?

Answer 9

UGA, UAA, UAG.

Question 10

Degenerate

Answer 10

The genetic code is degenerate because more than one codon can specify a single amino acid. We can see that for the amino acids with multiple codons, the first two bases are usually the same and the third base in the codon is variable. We refer to this variable third base in the cooldown as wobble position. The generosity of the genetic code allows for mutations in DNA that do not always result in an altered protein structure function. Usually a mutation within an intron will also not change the protein sequence because introns are clipped out of the M RNA transcript prior to translation.

Question 11

Silent or degenerate mutations.

Answer 11

Mutations in the wobble position tend to be called silent, which means there is no effect on the expression of the amino acid and therefore no adverse effects on the polypeptide sequence.

Question 11

Point mutation.

Answer 11

Affect only one of the nucleotides in a codon.

Question 12

Express mutations.

Answer 12

Affect the primary amino acid sequence of the protein. They can be missense or nonsense.

Question 13

Missense mutation.

Answer 13

A mutation where one amino acid substitutes for another.

Question 14

Nonsense mutation.

Answer 14

Mutation, where the codon now encodes for a premature stop codon. (Also known as a truncation mutation)

Question 15

frameshift mutation.

Answer 15

The three nucleotides of a codon are referred to as the reading frame. A frameshift mutation occur when some number of nucleotides are added to or deleted from the mRNA sequence. Insertion or deletion of nucleotide will shift the reading frame, usually resulting in changes in the amino acid sequence or premature truncation of the protein.

Question 16

Transcription.

Answer 16

Creation of mRNA from DNA template.

Question 17

Helicase

Answer 17

Involved in the unwinding the double stranded DNA and formation of supercoils.

Question 18

Topoisomerase

Answer 18

Involved in the preventing formation of supercoals in the stranded DNA.

Question 18

Promoter Regions.

Answer 18

Arena polymerase locates genes by searching for specialized DNA regions, known as promoter regions.

Question 18

Template strand

Answer 18

Transcription results in a single strand of mRNA synthesized from one of the two nucleotide strands of DNA, called the template strand. The newly synthesized mRNA strand is both antiparallel and complementary to the DNA template strain. The coding strand of DNA is not used as a template during transcription. Therefore it is identical to the mRNA transcript except that all thymine nucleotides in the DNA have been replaced with the uracil in the mRNA molecule.

Question 19

TATA Box.

Answer 19

The binding site and the promoter region is known as Tata Box, named for its high concentration of thymine and adesine bases.

Question 20

Transcription factors.

Answer 20

Help the RNA polymerase locate and bind to this promoter region of the DNA, helping to establish where transcription will start.

Question 21

RNA polymerase I

Answer 21

Locating the nucleus and synthesizes rRNA.

Question 21

RNA polymerase II

Answer 21

Locating the nucleus and synthesizes hnRNA (pre-processed mRNA) In some small nuclear RNA.

Question 22

RNA polymerase III

Answer 22

Located in the nucleus and synthesizes tRNA and some rRNA.

Question 23

How does RNA polymerase travel?

Answer 23

It travels along the template strand in the three to five direction, which allows for the construction of transcribed mRNA in the five to three direction.

Question 24

Heterogeneous nuclear RNA (hnRNA)

Answer 24

The DNA double Helix then reforms and the primary transcript form is termed heterogeneous nuclear RNA. mRNA derived from hnRNA via post transcription modification.

Question 24

Post transcriptional processing’s.

Answer 24

1) Intron/exon splicing: Splicing of the transcript to remove noncoding sequences (introns) and ligate coding sequences (exons) together. Splicing is accomplished by the spliceosome. In the spliceosome, small nuclear RNA (snRNA) is coupled with protein known as small nuclear ribonucleoproteins (snRNP). The snRNP/snRNA complex recognize both the 5’ and 3’ splice sites of the introns. These noncoding sequences are exercised in the form of lariat and then degraded.

2)5’ cap: At the 5’ end of the hnRNA molecule, a 7-methylguanylate triphosphate cap Is added. It is recognized by the ribosomes as the binding site. It also protects the mRNA from degradation in the cytoplasm.

3)3’ poly-A tail: A polyadenosyl (poly-A) tail is added to the 3’ end of the mRNA transcript and protects the message against rapid degradation. Think of the poly-A tail as a fuse for a time bomb for the mRNA transcript. As soon as the mRNA leaves the nucleus, it will start to get degraded from its three end. At this point, when only exons remain in the cap until have been added, the cell has created the mature mRNA that can now be transported into the cytoplasm and for protein translation. Untranslated region of M RNA will still exist at the five and three edges of the transcript because the ribosome initiates translations at the start codon and will end at the stop codon.

Question 25

Translation.

Answer 25

mRNA finds a ribosome to begin the process translation.

Question 26

The ribosome.

Answer 26

Is composed of protein and rRNA. The subunits only bind together during protein synthesis. There are three binding sites in the ribosome for tRNA: The A, P (peptidyl) and the E side.

Question 27

Mechanisms of translation.

Answer 27

The process translation occurred in three stages, initiation, elongation, and termination. Specialized factors for initiation (initiation factors, IF); elongation (elongation factors, EF) and termination (release factors, RF).

Question 28

Initiation.

Answer 28

In prokaryotes, the small subunit binds to the Shine Dalgarno sequence In the five untranslated region of the mRNA. In eucaryote, the small subunit binds to the 5’ cap structure.

Question 29

Post translational processing.

Answer 29

One essential step for the final synthesis of the protein is proper folding. There is specialized class of protein called chaperones, the main function of which is to assist in the protein folding process. Many proteins are also modified by cleavage events. In peptides with signal sequences, the signal sequence must be cleaved if the protein is to enter the organelle and accomplish its function. In peptides with Quaternary structure, subunits come together to form the function of protein. In some cases, biomolecules may be added to the peptide.

Question 30

Phosphorylation

Answer 30

Additional phosphate group by protein kinase is to activate or deactivate proteins. Commonly seen in Serene, Theanine and Tyrosine.

Question 31

Carboxylation

Answer 31

Addition of carboxylic acid groups, usually to serve as a calcium binding site.

Question 32

Glycosylation.

Answer 32

Addition of all oligosaccharides as protein spaced through the ER and Golgi apparatus to determine cellular destination.

Question 33

Operon structure.

Answer 33

Operon is a cluster of genes transcribed as a single mRNA. They are very common in prokaryotic cells. The Jacob Monod model describes that operon containing structural genes and operator site, promotor site and a regulator gene. The structural gene codes for the protein of interest. Upstream of the structural gene is the operator site, a non transcribable region of DNA that is capable of binding and repressor protein. Further upstream is the promoter site, which is similar in function to promoters in new karyotypes. It provides a place for RNA polymerase to bind. Furthest upstream is the regulator gene, which codes for the protein known as the repressor. There are two types of operon models, inducible and repressible.

Question 34

Prenylation

Answer 34

Addition of lipid groups to certain membrane bound enzymes.

Question 35

Inducible systems.

Answer 35

The repressors bonded tightly to the operator system and thereby acts as a roadblock. RNA polymerases unable to get from the promoter to the structural gene because the repressor is on the way. Such system, in which the binding of a protein reduces transcriptional activity, are called negative control mechanisms. As the concentration of the inducer decreases, it will pull more copies of the repair off of the operator region, freeing up those genes for transcription. This system is useful because it allows gene productions to be produced only when they’re needed. An example of this is the lac operon. It is assisted by binding of the catabolite activator protein (CAP)

Question 35

positive control mechanism.

Answer 35

The binding of a molecule increases transcription of a gene.

Question 36

Repressible systems.

Answer 36

Allow constant production of a protein product. The repressor made by the regulator gene is inactive until it binds to a corepressor. This complex then binds the operator side to prevent further transcription. An example of this is trp operon, which is a negative, repressible system. When tryptophan is high in the local environment, it acts as a corepressor.

Question 37

Histone Acetylation

Answer 37

These proteins are involved in chromatin remodeling. Because they acetylate lysine residues found in the amino terminal tail region of histone proteins. Acetylation of histone proteins decreases the positive charge on lysine residues and weakens the interaction of the histones with DNA, resulting in open chromatin confirmation that allows for easier access of transcriptional machinery to the DNA. Histone deacetylases function to remove acetyl groups from his stones, which result in a closed chromatin confirmation and overall decrease in gene expression levels in the cell.

Question 38

DNA methylation.

Answer 38

DNA methylases add methyl groups to cytosine and adenine nucleotides. Methylation of genes is often linked with the silencing of gene expression.