Biochemistry chapter 7

Question 1

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Answer 1

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What is central dogma of molecular biology ?

Answer 3

Major steps involved in the transfer of genetic information

Question 4

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What is a gene ?

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A unit of DNA that encodes a specific protein or RNA molecule and through transcription and translation, that gene can be expressed

Question 5

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What is messenger RNA (mRNA) ?

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Carries the information specifying the amino acid sequence of the protein to the ribosome. The mRNA is transcribed from template DNA strands by RNA polymerase enzymes in the nucleus of the cells.

Question 6

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What are codons ? Monocistronic ?

Answer 6

mRNA is the only type of RNA that contains information that is translated into protein; to do so, it is read in three-nucleotide segments termed codons. In monocistronic , meaning in each mRNA molecule translates into only one protein product.

Question 7

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What is transfer RNA (tRNA) ?

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Responsible for converting the language of nucleic acids to the language of amino acids and peptides. Each tRNA molecule contains a folded strand of RNA that includes a three-nucleotide anticodon

Question 8

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What is aminoacyl-tRNA synthetase ?

Answer 8

Each type of amino acid is activated by a different synthetase that requires two high energy bonds from ATP, implying that the attachment of the amino acid is an energy-rich bond. * This is a enzyme that attaches appropriate amino acid onto its DNA * The high energy amino-acyl tRNA bond will be used to supply the energy needed to create a peptide bond during translation

Question 9

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What is Ribosomal RNA (rRNA) ? Ribozymes ?

Answer 9

It is synthesized in the nucleolus and functions as an integral part of the Ribosomal machinery used during protein assembly in the cytoplasm. Many rRNA molecules function as ribozymes ; that is enzymes made of RNA molecules instead of peptides

Question 10

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What is a codon ?

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If a gene sequence is a “sentence” describing a protein, then its basic unit is a three letter “word” known as the codon, which is translated into an amino acid

Question 11

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What is anti-codon? Start codon ? Stop codon ?

Answer 11

A sequence of three nucleotides forming a unit of genetic code in a transfer RNA molecule, corresponding to a complementary codon in messenger RNA. * Because every methionine, the codon for that is AUG for the translation of mRNA into protein * UGA, UAA, UAG

Question 12

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Degenerate ? Wobble position ?

Answer 12

A genetic code when more than one codon can specify a single amino acid. Its a evolutionary development designed to protect against mutations in the coding regions of our DNA. Mutations in the wobble position tend to be called silent or degenerate( no effect on the expression of the amino acid and therefore no adverse effects on the polypeptide sequence).

Question 13

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Point mutation ? Expressed mutations ? Missensed mutation ? Nonsense mutation ?

Answer 13

* If a mutation occurs and it affects one of the nucleotides in a codon

* When point mutations can affect the primary amino acid sequence of the protein in which they fall into two categories : the missense and nonsense

* A mutation where one amino acid substitutes for another

* Nonsense mutation: a mutation where the codon now encodes for a premature stop codon

Question 14

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Reading frame ? Frameshift mutation ?

Answer 14

Three nucleotides of a codon * When one nucleotide is changed so a mutation occurs and some number of nucleotides are added to or deleted from mRNA sequence.

Question 15

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What is Transcription ? What are the important roles in protein translation ?

Answer 15

When the DNA can’t leave the nucleus, it will be degraded, so it must use RNA to transmit genetic information. And the creation of mRNA from a DNA template would be that pretty much * Transfer RNA (tRNA) and Ribosomal RNA (rRNA)

Question 17

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What is template strand ? Promoters ? Transcription factors ?

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• Transcription results in a single strand of mRNA, synthesized from one of the two nucleotide strands of DNA or known as anti-sense strand RNA is synthesized by a DNA-dependent RNA polymerase;
• • • RNA polymerase locates genes by searching for specialized DNA regions
• • *
• Help the RNA polymerase locate and bind to this promoter region of the DNA, helping to establish where transcription will start. **** here is the DNA to hnRNA illustration {{13 0 0.png}}

Question 18

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What are the three types of RNA polymerases ?

Answer 18

• RNA polymerase I is located in the nucleolus and synthesizes rRNA
• RNA polymerase II is located in the nucleus and synthesizes hnRNA (preprocessed mRNA ) and some small nuclear RNA ( snRNA) *this is the one that involves the transcription of mRNA
• RNA polymerase III is located in the nucleus and synthesizes tRNA and some rRNA

Question 19

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What is heterogeneous nuclear RNA (hnRNA) ?

Answer 19

Transcription would continue along the DNA coding region until the RNA polymerase reaches a termination sequence or stop signal which results in the termination of transcription, and then this is where hnRNA comes in where the DNA double helix is reformed and the primary transcript is formed.

Question 20

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What is 5’ CAP ? 3’ Poly-A tail ? Alternative splicing ?

Answer 20

At the 5’ end of the hnRNA molecule, a 7-methylguanylate triphosphate cap is added. It also protects the mRNA from degradation in the cytoplasm. A polyadenosyl (poly-A) is added to the 3’ end of the mRNA transcript and protects the message against rapid degradation.

* The primary transcript of hnRNA may be spliced together in different ways to produce multiple variants of proteins encoded by the same original gene.

*** Processing Eukaryotic hnRNA to mRNA look for another notecard

Question 21

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What is translation ? Nuclear pores?

Answer 21

Once in the cytoplasm, mRNA finds a ribosome to begin the process of converting the mRNA transcript into a functional protein. * Once the mRNA transcript is created and processed, it can exit the nucleus through the pores.

Question 22

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What is a ribosome ?

Answer 22

Composed of proteins and rRNA

Question 23

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What are the three stages when it comes to the process of translation ? What is elongation factors(EFs) ?

Answer 23

Initiation, elongation, and termination * Specialized factors for initiation (initiation factor), …etc * Assist by locating and recruiting aminoacyl-tRNA along with GTP, while helping to remove GDP once the energy has been used. *Steps in translation

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This is the steps in translation

Answer 24

{{20 1 0.jpg}}

Question 25

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What is release factor ? Termination factors? Chaperones ?

Answer 25

• When any of the three codons moves into the A site and it binds to the termination codon, causing a water molecule to be added.
• * The addition of the water molecule allows peptidyl transferase and to hydrolyze the completed polypeptide chain from the final tRNA. Also its required to release the newly made nascent RNA from the transcription complex.
• * A specialized class of proteins, in which the main function is to assist in the protein-folding process

Question 26

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Biomolecules that are added to the peptide. Which are ?

Answer 26

• * Phosphorylation: addition of phosphates by protein kinases to activate or deactivate proteins.
• * Carboxylation : addition of carboxylic acid groups, usually to serve as calcium binding sites.
• * Glycosylation: Addition of oligosaccharides as protein pass through the ER and Golgi apparatus to determine cellular destination .

*

• Prenylation : addition of lipid groups to certain membrane-bound enzymes
• *Synthesis of secretory, membrane, and Lysomal proteins {{22 1 0.jpg}}

Question 27

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The three base sequences listed below are DNA sequences. Which amino acid is encoded by each of these sequences, after transcription and translation ?

Answer 27

* GAT: mRNA codon=AUC ; isoleucine * ATT: mRNA codon= AAU: Asparagine (Asn) * CGC: mRNA codon= GCG: Alanine (Alan) * CCA: mRNA codon= UGG; tryptophan (Trp)

Question 28

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Which mRNA codon is the start codon, and what amino acid does it code for ? Which mRNA codons are the stop codons ?

Answer 28

* Start codon: AUG codes for methionine; * Stop codon is UAA, UGA, and UAG

Question 29

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What is wobble and what role does it serve ?

Answer 29

Wobble refers to the fact that the third base of the codon often plays no role in determining which amino acid is translated from that codon. For example, any codon starting with “CC” codes for proline, regardless of which base is in the third (wobble) position. This is a protective mechanism because mutations in the wobble position will not have any effect on the protein translated from that gene.

Question 30

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When starting transcription, where does RNA polymerase bind ?

Answer 30

RNA polymerase II binds to the TATA box, which is located within the promoter region of a relevant gene at about -25

Question 31

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What are the roles of each site in the ribosomes ? A site, P site, and E site

Answer 31

• * A site: binds incoming amino-acyl-tRNA using codon-anticodon pairing
• * P site : Holds growing polypeptide until peptidyl transferase forms peptide bond and polypeptide is handed to A site
• * E site : Transiently(for a short time) holds uncharged tRNA as it exits the ribosomes

Question 32

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What is a Operon ?

Answer 32

This type of structure is a cluster of genes transcribed as a single mRNA; this particular cluster in E coli is known as trp Operon

Question 33

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What is a structural gene ? Operator site ? Promoter site ? Regulator gene ? Repressor?

Answer 33

• Codes for the protein of interest
• * Nontranscrible region of DNA that is capable of binding a repressor protein.
• * Similar to function in promoters in eukaryotes: it provides a place for RNA polymerase to bind.
• Codes for a protein known as repressor

Question 34

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What are the major posttranslational modification that occur in proteins ?

Answer 34

Posttranslational medications include proper folding by chaperones, formation of quaternary structure, cleavage of proteins or signal sequences, and addition of other biomolecules( phosphorylation, Carboxylation, Glycosylation, and prenylation).

Question 35

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What are two types of operons ?

Answer 35

Inducible and repressible systems

Question 36

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What is Catabolite activator protein (CAP) ?

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Assists lac operon by binding to it. Its a transcriptional activator used by E.Coli when glucose levels are low to signal that alternative carbon sources should be used.

Question 37

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What is repressible systems ? What are they also known as ?

Answer 37

Allow constant production of a protein product. In contrast to the inducible system, the repressor made by the regulator gene is inactive until it binds to a corepressor. This complex then binds the operator site to prevent further transcription. * Negative control mechanisms ( Same as negative feedback)

Question 38

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What are transcription factors ?

Answer 38

Transcription activating proteins that search the DNA looking for specific DNA-binding motifs( having a three dimensional structure that allows binding interactions to occur)

Question 39

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What are the two recognizable domains that transcription factors have ? What do they do?

Answer 39

DNA binding domain and activation domain

• DNA binding domain: binds to specific nucleotide sequence in the promoter region or to a DNA response element ( a sequence of DNA that binds only to specific transcription factors) to help in the recruitment of transcriptional machinery.
• Activation domain : allows for binding of several transcriptions factors and other important regulatory proteins, such as RNA polymerase and Histone acetylases, which function in the remodeling of the chromatin structure.

Question 40

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What is acetylation ?

Answer 40

Of Histone proteins which decrease the positive charge on lysine residues and weakens the interaction of the Histone with DNA, resulting in an open chromatin conformation that allows for easier access of the transcriptional machinery to the DNA.

Question 41

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What is DNA methylation ? DNA methylases ?

Answer 41

Involved in chromatic remodeling and regulation of gene expression levels in the cell. * Add methyl groups to cytosine and adenine nucleotides; methylation of genes is often linked with the silence of gene expression

Question 42

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In an enhancer, what are the differences between signal molecules, transcription factors, and response elements ?

Answer 42

1. Signal molecules include steroid hormones and second messengers, which bind to their receptors in the nucleus.
2. These receptors are transcription factors that use their DNA-binding domains to attach to a particular sequence in DNA called response element.
3. One bound to the response element, these transcription factors can then promote increased expression of the relevant gene.

Question 43

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By what Histones and DNA modifications can genes be silenced in eukaryotic cells ? Would these processes increase the proportion of heterochromatin or euchromatin?

Answer 43

Histone deacetylation and DNA methylation will both downregulate the transcription of a gene. These processes allow the relevant DNA to be clumped more tightly, increasing the porportion of heterochromatin.

Question 44

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What does it mean for a tRNA to be charged or activated with an amino acid ?

Answer 44

To become part of a nascent(beginning) polypeptide in the ribosomes, amino acids are connected to a specific tRNA molecule * tRNA is found in the cytoplasm and is the second most abundant type of RNA in the cell after mRNA

Question 45

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What is inducible systems ?

Answer 45

The repressor is bound tightly to the operator system and thereby acts as a roadblock. RNA polymerase is unable to get from the promoter to the structural gene because the repressor is in the way.

Question 46

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What is Histone deacetylases ?

Answer 46

Proteins that function to remove acetyl groups from Histones, which results in a closed chromatic-conformation and overall decrease in gene expression levels in the cell.