Chapter 7: From DNA to Protein: How Cells Read the Genome

Question 1

Define the following terms:

Gene Expression:

RNA Polymerase II:

Transcription:

RNA Processing:

Start Site:

Start Codon:

Translation:

Codon:

Anticodon:

Answer 1

Gene Expression: The process by which a gene makes a product that is useful to the cell or organism by directing the synthesis of a protein or an RNA molecule with a characteristic activity.

RNA Polymerase II: Enzyme that catalyzes the synthesis of an RNA molecule from a DNA template using ribonucleoside triphosphate precursors.

Transcription: Process in which RNA polymerase uses one strand of DNA as a template to synthesize a complementary RNA sequence.

RNA Processing: Broad term for the modifications that a precursor mRNA undergoes as it matures into an mRNA. It typically includes 5′ capping, RNA splicing, and 3′ polyadenylation.

Start Site: is the location where transcription starts at the 5’-end of a gene sequence from the end of termination.

Start Codon: is the initiation signal for translation that is found on a messenger RNA (mRNA) strand usually the triplet codon is AUG that starts the process close to TATA box.

Translation: Process by which the sequence of nucleotides in a messenger RNA molecule directs the incorporation of amino acids into protein.

Codon: Group of three consecutive nucleotides that specifies a particular amino acid or that starts or stops protein synthesis; applies to the nucleotides in an mRNA or in a coding sequence of DNA.

Anticodon: Set of three consecutive nucleotides in a transfer RNA molecule that recognizes, through base-pairing, the three-nucleotide codon on a messenger RNA molecule; this interaction helps to deliver the correct amino acid to a growing polypeptide chain.

Question 2

What is the Central Dogma of Molecular Biology?

Answer 2

The central dogma of molecular biology describes the flow of genetic information from DNA to RNA, RNA to protein. The central dogma follows the two step process, transcription and translation. The process is given below.

DNA → RNA → Protein

The information in the DNA of every cell is converted into small portable RNA messages in transcription. During translation, the RNA messages travel from the DNA to the ribosomes to make specific proteins.

Question 3

Protein Conformation Primary Structure-? Secondary Structure-? Tertiary Structure-? Quaternary Structure-?

Answer 3

order of amino acids alpha helix, beta sheet lowest energy folded state protein complexes

Question 4

How many different amino acids are commonly used in making proteins?

Answer 4

20

Question 5

Which parts of amino acids are involved in a peptide bond?

Answer 5

amino group of one amino acid and carboxyl group of the other

Question 6

Which part of an amino acid gives it its unique properties

Answer 6

side chain

Question 7

What is the best type of model visualizing the surface of a protein

Answer 7

space-filling

Question 8

What are two types of β sheets?

Answer 8

parallel and anitparallel

Question 9

What does the primary structure of a protein refer to?

Answer 9

the linear amino acid sequence of the protein

Question 10

Consider the thermodynamic properties of chemical reactions. Even though enzymes do not affect the overall energy of the reactants or the products (i.e., the thermodynamics), they alter the speed of the reaction. Enzymes accomplish this by doing which of the following?

Answer 10

Reducing the activation energy of a reaction.

Question 11

RNA Polymerase RNA Pol1 makes-? RNA Pol2 makes-? RNA Pol3 makes-?

Answer 11

rRNA mRNA rRNA, tRNA, snRNA

Question 12

RNA Pol II is a protein complex that ___ DNA into ___

Answer 12

RNA Pol II is a protein complex that transcribes DNA into mRNA

Question 13

Transcriptional Control (TF)

Answer 13

Bind to gene’s promoter by DNA-binding domain Regulate Transcription.

Question 14

2 major types of Transcription Factors

Answer 14

1. General Transcription Factors 2. Specific Transcription Factors

Question 15

General Transcription Factors

Answer 15

Required for TXN at all genes. At every gene that is being transcribed.

Question 16

Specific Transcription Factors

Answer 16

Activators and Repressors Required for TXN only at some genes AND regulate TXN of those genes.

Question 17

Regulated genes

Answer 17

1. Cell type specific 2. Expressed during development and differentiation. 3. Expressed in response to environmental changes.

Question 18

What Translation requires?

Answer 18

mRNA transcript Many tRNA One Ribosome

Question 19

Transcription ->(?) -(?)-> (?) -> (?)

Answer 19

Transcription -> Primary mRNA -(RNA processing) -> Mature mRNA transcript -> Translation

Question 20

What makes one type of cell different from another type of cell, even if they have the same genome?

Answer 20

It has to do with the expression of the gene although they are comprised of the same gene, and DNA as it is expressed differently from one another.

Question 21

How is DNA different from RNA? (Name four ways that they are different.)

Answer 21

Various ways DNA and RNA is different:

-DNA is double stranded and RNA is single stranded.

-DNA has deoxyribose and RNA has ribose sugars.

-DNA has adenine, Guanine, cytosine and thymine bases.

-RNA has adenine, guanine, cytosine and uracil bases.

-DNA and RNA both has sugar phosphate backbones, the difference is in the type of the sugar they have. DNA has deoxyribose and RNA has ribose sugar.

-DNA is immense in bulk and has a larger strand while RNA is much smaller in comparison.

Question 22

Define the following:

mRNA:

tRNA:

rRNA:

snRNA:

Answer 22

mRNA: RNA molecule that specifies the amino acid sequence of a protein.

tRNA: Small RNA molecule that serves as an adaptor that “reads” a codon in mRNA and adds the correct amino acid to the growing polypeptide chain.

rRNA: RNA molecule that forms the structural and catalytic core of the ribosome.

snRNA: RNA molecule of around 200 nucleotides that participates in RNA splicing.

Question 23

Describe Transcription. What is needed for Transcription to happen? How does Transcription begin? How does Transcription end?

Answer 23

Process in which RNA polymerase uses one strand of DNA as a template to synthesize a complementary RNA sequence. Transcription begins when RNA polymerase binds to a promoter sequence near the beginning of a gene (directly or through helper proteins). RNA polymerase uses one of the DNA strands (the template strand) as a template to make a new, complementary RNA molecule. Transcription ends in a process called termination.

Question 24

Describe the three parts of RNA processing. (What happens to make a primary transcript into a mature transcript?)

Answer 24

Splicing, adding of the cap and tail, and the exit of the mRNA from the nucleus.

A 5’ cap is added to the beginning of the RNA transcript, and a 3’ poly-A tail is added to the end.

In splicing, some sections of the RNA transcript (introns) are removed, and the remaining sections (exons) are stuck back together.

Some genes can be alternatively spliced, leading to the production of different mature mRNA molecules from the same initial transcript.

Question 25

What structure is responsible for selecting and transporting only properly processed eukaryotic mRNAs into the cytoplasm?

Answer 25

nuclear pore complex

Question 26

The assembly of general transcription factors at a eukaryotic promoter typically begins at what site?

Answer 26

the TATA box

Question 27

To begin transcription, eukaryotic RNA polymerase recognizes nucleotide sequences in what region of the DNA?

Answer 27

promoter region.

Question 28

Which part of a protein is synthesized by a ribosome first?

Answer 28

the N-terminus

Question 29

Describe Translation. What is needed for Translation to happen? How does Translation begin? How does Translation end?

Answer 29

Initiation

In order for translation to start, we need a few key ingredients. These include:

A ribosome (which comes in two pieces, large and small)

An mRNA with instructions for the protein we’ll build

An “initiator” tRNA carrying the first amino acid in the protein, which is almost always methionine (Met)

During initiation, these pieces must come together in just the right way. Together, they form the initiation complex, the molecular setup needed to start making a new protein. they bind to the 5’ end of the mRNA by recognizing the 5’ GTP cap (added during processing in the nucleus). Then, they “walk” along the mRNA in the 3’ direction, stopping when they reach the start codon (often, but not always, the first AUG).^6

Elongation

methionine-carrying tRNA starts out in the middle slot of the ribosome, called the P site. Next to it, a fresh codon is exposed in another slot, called the A site. The A site will be the “landing site” for the next tRNA, one whose anticodon is a perfect (complementary) match for the exposed codon.

the formation of the peptide bond that connects one amino acid to another. This step transfers the methionine from the first tRNA onto the amino acid of the second tRNA in the A site.

Termination

Translation ends in a process called termination. Termination happens when a stop codon in the mRNA (UAA, UAG, or UGA) enters the A site.

Stop codons are recognized by proteins called release factors, which fit neatly into the P site (though they aren’t tRNAs). Release factors mess with the enzyme that normally forms peptide bonds: they make it add a water molecule to the last amino acid of the chain. This reaction separates the chain from the tRNA, and the newly made protein is released.

Question 30

What are the E, P, and A sites? What happens at each?

Answer 30

Each ribosome contains three binding sites for tRNA molecules, called the A site, the P site, and the E siteTo add an amino acid to a growing peptide chain, a charged tRNA enters the A site by base-pairing with the complementary codon on the mRNA molecule. Its amino acid is then linked to the growing peptide chain, which is held in place by the tRNA in the neighboring P site. Next, the large ribosomal subunit shifts forward, moving the spent tRNA to the E site before ejecting it (Figure 7–37). This cycle of reactions is repeated each time an amino acid is added to the polypeptide chain, with the new protein growing from its amino to its carboxyl end until a stop codon in the mRNA is encountered and the protein is released.

Question 31

Transcribe the top strand of this DNA into RNA. Label the 3’ and 5’ ends.

DNA: ^3’ TAC CCC GGG AAA TTT ACT ^5’

_5’ ATG GGG CCC TTT AAA TGA _3’

Answer 31

^3’ TAC CCC GGG AAA TTT ACT ^5’

5’ UAG GGG CCC UUU AAA UGA 3’

Question 32

Now translate your mRNA into Protein. Label the C-term and N-term.

Answer 32

5’ UAG GGG CCC UUU AAA UGA 3’

N-terminus H3N + -Stop-Gly-Pro-Phe-Lys-Stop- COO- C-terminus