PP8

Question 1

Making a protein occurs in two stages:

Answer 1

1. Transcription (writing something down in your language)

2. Translation (translating what you wrote into another language)

Question 2

What is gene expression?

Answer 2

Gene expression: Process by which DNA directs the synthesis of proteins or various forms of RNA. A gene can be a gene that codes for a protein, or a gene can be a gene that codes for various types of RNA, which is used to make proteins.

Question 3

Transcription occurs in three stages in both bacteria and eukaryotes:

Answer 3

Initiation
Elongation
Termination

Question 4

what is transcription and where does it occur?

Answer 4

Transcription occurs in the nucleus in eukaryotic cells, and in the nucleoid of prokaryotic cells!

Transcription: genetic information in the form of DNA is used a template to generate a molecule of RNA (same language of nucleic acids).

Question 5

what is RNA polymerase II?

Answer 5

RNAP II is a large polymer. RNA is polymer, so RNA polymerase is an enzyme that makes the polymer, RNA.

Question 6

RNA polymerase II: 5 steps

Answer 6

1. Binds to specific a gene region on the chromosome.
2. Separates double helix (breaking hydrogen bonds between bases) at a specific gene region.
3. DNA is read from 3’  5’ and transcribed into messenger RNA (mRNA).
4. Transcription therefore occurs from 5’ 3’
5. mRNA strand is complementary to DNA (base pair rules). All RNA contains uracil (U) rather than thymine (T).

Question 7

what is a promotor?

Answer 7

Promoter: The DNA sequence where RNA polymerase and attaches and initiates transcription. It includes the TATA box, which is AT rich.

Question 8

describe initiation

Answer 8

The promoter leads to a transcription start point (nucleotide where RNA synthesis actually begins).

In eukaryotes, a collection of proteins called transcription factors bind to the promoter to allow the attachment of RNA polymerase (RNAP).

Prokaryotes also have transcription factors and a promoter for each gene, but it’s much simpler.

Once RNAP binds to the promoter, it splits the double helix by breaking hydrogen bonds. It has what is called “helicase” activity.

Question 9

explain elongation

Answer 9

1. RNAP moves down the DNA strand from 3’ -> 5’
   - As RNAP moves along the DNA, it continues to untwist the double helix, exposing about 10-20 DNA nucleotides at a time.
   - RNAP is said to “read” the DNA strand from 3’  5’
   - The 3’  5’ DNA strand is called the template strand
2. RNAP synthesizes a mRNA transcript in the 5’ – 3’ direction.
   - RNAP can only add nucleotides to the 3’ (-OH) end.
   - A single gene can be transcribed simultaneously by several molecules of RNA polymerase following each other like trucks on a convoy.

Question 10

explain termination.

Answer 10

1. Once the RNAP reaches the termination sequences, a special area found after the gene on the DNA template (you do not need to know what is looks like):
   - 1 rna stops transcription
   - 2 RNAP detaches from DNA template strand
   - 3 mRNA is released
2. The mRNA transcript leaves the nucleus.

Question 11

What do you need to make a protein, in other words, what is needed for the process of translation?

Answer 11

Transfer RNA (tRNA)
mRNA (product of transcription)
Ribosomes (free or bound)
Amino acids
A dictionary of the genetic code
Energy

Question 12

What is translation?

Answer 12

Translation is performed by the ribosomes which are either attached to the RER (for proteins that will be exported or embedded in the plasma membrane) or floating around in the cytosol for proteins that will remain in the cytosol or enter the nucleus or mitochondria.

Question 13

explain the 3 types of RNA:

Answer 13

tRNA (transfer RNA) is the smallest (about 90 nucleotides long) and is responsible for bringing in a specific amino acid for protein construction. The specificity is determined by the anticodon sequence at the bottom of the structure. This will match the codon.

mRNA (messenger RNA) is the product of transcription and will be read in the 5’ 3’ direction. Each triplet of 3 bases determines the amino acid that will be incorporated into the protein.

rRNA (ribosomal RNA) associates with ribosomal proteins to form ribosomes, which are not membrane bound, i.e., there is no membrane around them. Ribosomes are responsible for the coordination of protein synthesis.

Question 14

what is a Condon?

Answer 14

The triplet code found on mRNA is referred to as CODONS

They are complementary to the template strand.

Question 15

There are a total of____ codons

___ codons for ___ amino acids

____ codons stop translation

Most amino acids have ___ corresponding codon

Answer 15

There are a total of 64 codons

61 codons for 20 amino acids

3 codons stop translation

Most amino acids have > 1 corresponding codon

Question 16

___________________occurs within a ribosome.

Answer 16

The synthesis of a polypeptide occurs within a ribosome.

Question 17

A ribosome is made up of 2 subunits:
Ribosomes are composed of _______ and
___________ molecules

____ of the mass of a ribosome is rRNA, making it the most prevalent form of RNA in the cell.

Answer 17

the large subunit
the small subunit
Are composed of proteins and rRNA molecules
2/3 of the mass of a ribosome is rRNA, making it the most prevalent form of RNA in the cell.

Question 18

the rRNA is the main constituent of:

Answer 18

the rRNA is the main constituent of most of the ribosome and is the catalyst of peptide bond formation. Therefore it also acts as an enzyme

Question 19

Each ribosome contains 3 tRNA binding sites:

Answer 19

A site (Arrival)
P site (Peptide bond)
E site (Exit)

Question 20

3 steps for initiation:

Answer 20

1. The small ribosomal subunit binds to mRNA; It scans the mRNA for the start codon (AUG) and binds to the mRNA at that location.
2. The initiator tRNA binds to the mRNA at the start codon: The initiator tRNA carries the anti-codon UAC, which is complementary to the start codon (AUG).
3. Large ribosomal subunit binds: The binding of the large subunit requires energy.

Question 21

elongation step 1:

Answer 21

Codon recognition:
The anticodon of an incoming aminoacyl tRNA base pairs with the complimentary mRNA codon in the A site. This is a diffusion driven process in that many tRNAs with their amino acids enter the A site and they “try it on” to see if it’s a match. Obviously, not that many will match. Those that don’t match leave through a special tunnel, but those that match will stay and the amino acid will be connected to the previous amino acid.

Hydrolysis of GTP as the energy source is required for this step, so you see that making proteins requires chemical energy.

Question 22

elongation step 2:

Answer 22

Peptide bond formation:

A peptide bond is formed between the amino group of the incoming and the carboxyl end of the amino acid (or growing polypeptide) in the P site; this step attaches the polypeptide to the tRNA at the A site

A special rRNA is responsible for catalyzing the formation of the peptide bond. This rRNA is a ribozyme, i.e., an enzyme that is not a protein.

Question 23

elongation step 3:

Answer 23

Translocation:

• The ribosome translocates the tRNA in the A site to the P site (requiring the energy from GTP).
• The mRNA is moved through the ribosome (it is not the ribosome that is moving along the mRNA) 5’ end first.
• The empty tRNA in the P site is moved to the E site, where it is released; the mRNA moves along with its bound tRNAs, bringing the next codon to be translated into the A site.

Question 24

what is Termination?

Answer 24

Elongation occurs until the stop codon arrives at the A site (UAG, UAA, or UGA)

Proteins called release factors, which have been swimming through all along, bind to the stop codon in the A site because they “fit”.

All the factors disperse. The polypeptide is released from the last tRNA.

Question 25

What are mutations?

Answer 25

Changes in the nucleotide sequence of an organism’s DNA or in the DNA or RNA of a virus They are responsible for the huge diversity of genes found among organisms because mutations are the ultimate source of new genes

Question 26

What is silent mutation and neutral mutation?

Answer 26

Silent mutations have no effect on the amino acid produced by a codon because of redundancy in the genetic code. There will be no change in the amino acid sequence, i.e, the primary structure of the protein. Neutral mutations still code for an amino acid, but it’s one in the same R-group, so the property of the amino acid is the same. This may or may not have an effect, depending on where it is.

Question 27

what is missense mutation and nonsense mutation?

Answer 27

Missense mutations still code for an amino acid, but not for one within the same R-group, so the property of the amino acid is not the same. This will often lead to problems, i.e. sickle cell Nonsense mutations change an amino acid codon into a stop codon, nearly always leading to a nonfunctional protein because translation stops prematurely.

Question 28

what are Insertions and deletions?

Answer 28

Insertions and deletions are additions or losses of nucleotide pairs in a gene These mutations have a disastrous effect on the resulting protein more often than substitutions do

Question 29

what is frameshift mutation?

Answer 29

Insertion or deletion of nucleotides may alter the reading frame, producing a frameshift mutation

Question 30

Insertions or deletions close to the beginning of a gene have the greatest negative impact on the translation because ________________________________ If three bases are inserted or deleted, the effect ______________________________________

Answer 30

Insertions or deletions close to the beginning of a gene have the greatest negative impact on the translation because every amino acid after it will not be the correct one. If three bases are inserted or deleted, the effect may or may not matter, depending on the protein. This would mean and addition or removal of a single amino acid.

Question 31

A mutation causes cell anemia because

Answer 31

The change of 1 base, results in the amino acid glutamic acid (acidic R-group) sickle acid being substituted for valine (large hydrophobic R-group)

Question 32

What is a Mutagens? 3 types?

Answer 32

Mutagens interact with DNA in ways that cause mutatio Physical mutagens: mutagenic radiation such as UV lig Chemical mutagens: 1. Nucleotide analogues are chemicals that are similar to normal DNA nucleotide but that pair incorrectly during DNA replication. 2. Some interfere with correct DNA replication by inserting themselves into the DNA and distorting the double helix. Repair mechanisms recognize errors and fix them most of the time, but some slip through and can cause problems