Chapter 7.1

Question 1

What is the central dogma of biology?

Answer 1

The central dogma refers to the way proteins are made in our body. First, DNA is transcribed into RNA, then RNA is translated into protein.

Question 2

What are the three main types of RNA?

Answer 2

1. mRNA
2. tRNA
3. rRNA

Question 3

What is a codon?

Answer 3

A codon is any three nucleotides in a row. Codons are what the ribosome reads to translate mRNA into Amino Acids.

Question 4

What is mRNA?

Answer 4

mRNA is the link between DNA and proteins. DNA is transcribed into mRNA, which travels out of the nucleus to the ribosomes where it can be translated into proteins.

Question 5

What does it mean for eukaryotic mRNA to be monocistronic?

Answer 5

Monocistronic RNA is mRNA that can only be translated into one protein product. That means every single on of the thousands of proteins we contain has its own mRNA strand.

Question 6

What does it mean for prokaryotic mRNA to be polycistronic?

Answer 6

Polycistronic mRNA is mRNA that can be translated into more than one protein product. This means that 10 different proteins in a bacteria may all be made from the same strand of mRNA. This is possible because you can get a different protein product if you don’t translate all of the mRNA or don’t start the translation in the same place.

Question 7

What is tRNA?

Answer 7

tRNA is responsible for translating the language of nucleic acids into amino acids at the ribosome. Each tRNA molecule contains a folded strand of RNA that includes a three nucleotide anticodon and an amino acid. The anticodon of tRNA binds to the codon of mRNA and brings with it the appropriate amino acid.

Question 8

What does it mean when someone says a tRNA molecule is charged or activated?

Answer 8

tRNA molecules don’t always have an amino acid attached. A charged or activated tRNA molecule is a tRNA with an amino acid attached.

Question 9

What is aminoacyl-tRNA synthetase?

Answer 9

Aminoacyl-tRNA Synthetases are a class of enzymes that attach specific amino acids to specific tRNA molecules (based on the anticodon). Each type of amino acid is activated by a different aminoacyl-tRNA synthetase. Amino Acids are always added to the free hydroxyl at the 3’ end of the tRNA.

The new bond is high in energy which is used to make a peptide bond in translation

Question 10

What is rRNA?

Answer 10

rRNA is synthesized in the nucleolus and functions as an important structural component of ribosomes (and catalyzes the formation of peptide bonds in the growing AA chain). rRna molecules can also act as ribozymes. (detail: can also splice out its own introns)

Question 11

What is a ribozyme?

Answer 11

A ribozyme is a strand of RNA with enzymatic properties.

Question 12

What are the three stop codons?

Answer 12

-UAA
-UGA
-UAG

Question 13

What is the start codon?

Answer 13

AUG

Question 14

Describe start and stop codons

Answer 14

Start and stop codons are the codons that start and stop protein translation respectively. In other words, ribosomes will not start translating mRNA into amino acids unless it sees an AUG codon. On the other hand, translation will not stop until a UAA, UGA, or UAG codon appears.

Question 15

What is translation?

Answer 15

Translation is the process of protein synthesis in the ribosome using an mRNA template.

Question 16

What does it mean when we say codons are specific?

Answer 16

Codons are specific because each individual only codes for one amino acid.

Question 17

What does it mean when we say codons are degenerate?

Answer 17

Codons are degenerate because there are multiple different codons that code for the same amino acid. This is most notably seen in third base wobble.

Question 18

What is third base wobble?

Answer 18

Third base wobble is the tendency for the third base in a codon to not be as important in determing the amino acid for which the codon codes. Third base wobble is an evolutionary development designed to protect our body from mutations.

Question 19

What are the three types of point mutations?

Answer 19

1. Silent Mutation
2. Missense Mutation
3. Nonsense Mutation

Question 20

What is a silent/degenerate mutation?

Answer 20

A silent mutation is when the third codon of a nucleotide is swapped out for another, but the same amino acid is coded, resulting in no actual change in the protein product.

Question 21

What is a missense mutation?

Answer 21

A missense mutation is a mutation where an altered codon substitues a different amino acid. The effect on the protein product is variable. If the new amino acid is very different from the unmutated amino acid than the protein’s function can be affected.

If the new amino acid is not very different from the unmutated amino acid, than the protein’s function is less likely to be affected.

Question 22

What is a nonsense mutation?

Answer 22

A nonsense mutation is a mutation where an altered codon results in a premature STOP codon. These mutations almost always lead to non-functional proteins.

Question 23

What is the reading frame?

Answer 23

The reading frame refers to the way the entire strand of DNA and RNA is framed in terms of triplets (codons). The reading frame is important for understanding frameshift mutations.
By adding or substracting a base, you don’t just affect that one base, you shift the ENTIRE reading frame.

Question 24

What is a frameshift mutation and what are the two types?

Answer 24

A frameshift mutation is a mutation that shifts the entire reading frame of the genetic information.

1. Frameshift Deletion - a base is deleted and the frame shifts down one base.
2. Framsehift Insertion - a base is added and the frame shifts up one base.

Notice, if three bases were removed at once, the frame would actually be conserved.

Question 25

Are frame-shift of point mutations more likely to result in nonfuntional proteins?

Answer 25

frameshift

Question 26

What is transcription?

Answer 26

Transcription is the process by which mRNA is synthesized by RNA polymerase from a strand of template DNA.

Question 27

What needs to happen before RNA pol can access DNA and transcribe it?

Answer 27

Just like in DNA replication, helicase needs to unwind the DNA and Topoisomerase nicks the strand further down to prevent super coiling.

Question 28

What is the template strand and other name?

Answer 28

The template strand (also called the antisense strand) is the DNA strand that is read by RNA pol to create the mRNA transcript. The bases of the mRNA Transcript will be antiparallel and complementary to the template strand.

Question 29

What is the coding strand and other name?

Answer 29

The coding strand (sense strand, + strand) is the DNA strand that is not read by RNA pol. The bases of the mRNA Transcript will be parallel and equivalent to the bases in the coding strand, it's just that there will be U's instead of T's. This also protects RNA pol

Question 30

Does RNA polymerase just randomly transcribe segments of DNA as they open up?

Answer 30

No. RNA polymersase searches for specializeed DNA regions known as promoter regions and only transcribes starting at those.

Question 31

What are the three types of RNA pol in eukaryotes?

Answer 31

1. RNA pol 1 - Located in Nucleolus, synthesizes most rRNA. 2. RNA pol 2 - Located in the nucleus, synthesizes hnRNA (pre mRNA) and some small nuclear RNA (snRNA). This is the transcription RNA pol. 3. RNA pol 3 - Located in the Nucleus, synthesizes tRNA and some rRNA. and some snRNA

Question 32

What is the TATA box?

Answer 32

The TATA box is the binding site within the promoter region in eukaryotic DNA to which RNA pol binds. The TATA box is able to be separated easily because of the relative weakness of T-A bonds compared to G-C bonds.

Question 33

What are transcription factors?

Answer 33

Transcription factors are proteins that bind to DNA and either help or hurt the transcription of certain genes. In the case of helping, transcription factors help RNA pol find and bind to the DNA of interest.

Question 34

In what direction does RNA polymerase read and synthesize?

Answer 34

RNA pol reads in the 3'->5' direction so that it can synthesize nucleotides in the 5'->3' direction. Nucleotides are always synthesized in the 5' -> 3' direction!

Question 35

What is hnRNA?

Answer 35

hnRNA is heterogenous nuclear RNA. hnRNA is RNA after it has been transcribed from DNA but before it has been post-transcriptionaly modified. Because the hnRNA has not been processed yet, it will be a perfect RNA version of the DNA strand.

Question 36

What is postranscriptional processing?

Answer 36

anscriptional processing is a series of modifications made to hnRNA to make into mRNA. The three most important post transcriptional processes are... 1. Intron/Exon Splicing 2. 5' Cap 3. 3' Poly-A tail

Question 37

Describe Splicing

Answer 37

Splicing is the process of cutting out non-coding sequences of DNA (introns) and reconnecting the coding sequences (exons)

Question 38

What is a lariat?

Answer 38

A lariat is a name for a lasso shaped structure. In the context of biochemistry, it refers to the way introns are spliced out of the rna transcript.

Question 39

What is the spliceosome and what is it made of?

Answer 39

The spliceosome is the specialized complex that handles the splicing of rna. It is comprised of small nuclear RNA (snRNA) and small nuclear ribonucleoproteins (snRNPS).

Question 40

Why do we even have introns? What is the point of chunks of rna that don't code for anything?

Answer 40

To this day, the evolutionary function of introns in eukaryotic cells is not well understood. However, scientists hypothesize that introns play an important role in maintaining the appropriate size of our genome and for regulating gene expression. Detail: Also may allow for rapid protein evolution (sequences swapped in and out depending on need of cell)