Biochemistry L5/6 - Gene structure and function

Question 1

What type of bonds exist between complimentary bases of the 2 anti parallel DNA strands in a DNA double helix? How do these protect DNA?

Answer 1

Hydrogen bonds

They keep the charged phosphate sugar backbone facing the water environment, protecting the bases in the middle.

Question 2

Which enzyme catalyses the addition of nucleotides during replication of DNA

Answer 2

DNA polymerase III

Question 3

In what direction does DNA synthesis always occur, and how do you distinguish between the two ends?

Answer 3

5’ to 3’. The 5’ end is the amino end, while the 3’ end features a hydroxyl group from the carboxyl group

Question 4

Where DNA contains thymine, RNA contains which base?

Answer 4

Uracil

Question 5

At which part of a gene is the promoter located?

Answer 5

5’ to the transcription start site

Question 6

What are the two main types of RNA processing (to make mature mRNA)

Answer 6

5’ capping, addition of a polyA tail (for nuclear export and stability)

Question 7

Which amino acid always initiates translation

Answer 7

Methionine (AUG)

Question 8

What are the 3 stop codons and do they code for an amino acid

Answer 8

UAA, UAG, UGA.

Don’t code for an amino acid

Question 9

What end of tRNA is the amino acid attached to and what is tRNA with an amino acid attached referred to as

Answer 9

3’ end, aminoacyl-tRNA

Question 10

What are the four stages of protein synthesis

Answer 10

Amino acid activation, initiation, elongation, termination

Question 11

What is an example of a general transcription factor

Answer 11

Housekeeping gene. General TF are expressed in all cells

Question 12

What are the 3 main constituents of a nucleotide

Answer 12

Nitrogenous base, pentose sugar, phosphate

Question 13

What does a nucleoside consist of

Answer 13

Base, sugar

Question 14

Which two bases are purines

Answer 14

Guanine and adenine

Question 15

What is the building block of DNA synthesis

Answer 15

Nucleoside triphosphate (dNTP)

Question 16

What are the 4 steps (include enZymes involved) in synthesis of the lagging strand

Answer 16

Lagging strand synthesis is discontinuous

1. Primase synthesizes RNA primer
2. DNA pol III elongates RNA primers with new DNA a
3. DNA pol I removes RNA at 5’ end of neighboring fragment plus fills the gap
4. DNA ligase connects adjacent fragments

Question 17

What is an exon?

Answer 17

A coding region of DNA, separated from each other by non-coding regions called introns

Question 18

Do regulatory regions contain information about the structure of a gene product?

Answer 18

No. They contain sequences that are recognised and bound to by proteins that make a gene’s RNA, and also by proteins that influence how much of the gene should be made

Question 19

What is the difference between DNA and RNA sugars?

Answer 19

The ribose sugar has an extra alcohol group where a deoxyribose sugar has a hydrogen

Question 20

What are Nucleic Acids?

Answer 20

Polymers of nucleotides, linked by phosphodiester bonds

Question 21

Which bases are pyrimidines and how many rings to they have?

Answer 21

PyCT - pyrimidines are Cytosine and Thymine. These are ONE ringed structures

Question 22

What is a regulatory sequence?

Answer 22

A binding site for gene regulatory proteins that affects transcription rates. These DO NOT have to be close to promotor regions, and can even be in introns

Question 23

Do purine bind to other purines, or to pyrimidines and why?

Answer 23

Purines bind to pyrimidines, which keeps an even radius to the DNA double helix - purines are big (double rings) and pyrimidines are small (single rings). This is Complementary Base Pairing - Adenosine binds to Thymine, Cytosine binds to Guanine

Question 24

What do the terms degenerate, and unambiguous refer to in regards to DNA and amino acids?

Answer 24

Degenerate: every amino acid is coded for by at least one codon
Unambiguous: one codon codes for only one amino acid

Question 25

What is the charge on a:

1. nucleic acid
2. amino acid

Answer 25

1. Negative

2. Positive

Question 26

Which enzyme unwinds DNA for replication, and which nucleotides feature strongly in origin of replication regions?

Answer 26

DNA helicase

A-T regions

Question 27

When are introns spliced out?

Answer 27

After the formation of mRNA