Week 00 Asssumed knowledge / revision (excluding material covered later)

Question 1

What are the three parts of a nucleotide?

Answer 1

1. A sugar: pentose has a hydrogen atom at the 2’ carbon (deoxyribose)
2. A phosphate: phosphorus atom bonded to 4 oxygen atoms
3. A nitrogen-containing base: purine or pyrimidine

Question 2

What are the four bases in DNA? Which does each pair with?

Answer 2

Adenine - Thymine

Guanine - Cytosine

Question 3

What is a pyrimidine? Two examples?

Answer 3

Pyrimidine nitrogenous base: six member ring only; cytosine (C) and thymine (T)

Question 4

What is a purine? Two examples?

Answer 4

Purine nitrogenous base: six member ring attached to a five-member ring; adenine (A) and guanine (G)

Question 5

What kind of bonds form between complementary bases on a DNA strand?

Answer 5

Hydrogen bonds

Question 6

What does it mean to say that the two complimentary strands of DNA are antiparallel?

Answer 6

The two polynucleotide strands run parallel to each other but with opposite directionality (alignments) regarding their 3’ and 5’ ends

Question 7

DIRECTIONALITY

• In what direction is a DNA (or RNA) strand read during transcription?
• What gives DNA strands the 5’ and 3’ ends?
• To which end of a DNA/RNA strand can more nucleotides be easily added?

Answer 7

• 3’-5’ direction refers to the orientation of nucleotides of a single strand of DNA or RNA and it is read in this direction (read 3’-5’, written 5’-3’)
• The 5’ and 3’ specifically refer to the 5th and 3rd carbon atoms in the deoxyribose/ribose sugar ring. The phosphate group attached to the 5’ end of one nucleotide and the hydroxyl group at the 3’ end of another nucleotide have the potential to form phospodiester bonds, and hence link adjacent nucleotides. This linkage provides the sugar-phosphate backbone that gives DNA its structural rigidity. Any single strand of DNA/RNA will always have an unbound 5’ phosphate at one end and an unbound 3’ hydroxyl group at the opposite end.
• Nucleotides are added at the 3’ end

Question 8

The [sugar/phosphate] is the 3’ end, and the [sugar/phosphate] is the 5’ end of each nucleiotide

Answer 8

The sugar is the 3’ end, and the phosphate is the 5’ end of each nucleiotide

Question 9

The phosphate group attached to the 5’ carbon of the sugar on one nucleotide forms an ester bond with the free hydroxyl on the 3’ carbon of the next nucleotide. What is this bond called?

Answer 9

phosphodiester bond

Question 10

The sugar-phosphate backbone is [positively/negatively**] charged and [**hydrophilic/hydrophobic], which [prevents/allows] the DNA backbone [to form/from forming] bonds with water.

Answer 10

The sugar-phosphate backbone is negatively charged and hydrophilic, which allows the DNA backbone to form bonds with water.

Question 11

What is the name of the enzyme that joins nucleotides to synthesise the new complementary strand duirng DNA replication and also proofreads each new DNA strand to make sure that there are no errors?

Answer 11

DNA polymerase

Question 12

During DNA replication, the leading strand, runs [3’/5’ to 3’/5’] [towards/away from] the fork and is made [continuously/in small pieces called *Okazaki fragments*].

Answer 12

During DNA replication, the leading strand, runs 5’ to 3’ towards the fork and is made continuously.

Question 13

During DNA replication, the lagging strand, runs [3’/5’ to 3’/5’] [towards/away from] the fork and is made [continuously/in small pieces called Okazaki fragments].

Answer 13

During DNA replication, the lagging strand runs 5’ to 3’ away from the fork and is made in small pieces called Okazaki fragments

Question 14

What is the central dogma of genetics about (broadly speaking)?

Answer 14

The central dogma of molecular biology explains the flow of genetic information, from DNA to RNA, to make a functional product, a protein

Question 15

What are the three major pathways of genetic information flow within the cell?

Answer 15

1. Replication: information from one DNA molecule passes to another
2. Transcription: information passes from DNA to RNA
3. Translation: information passes from RNA to protein

Question 16

________ __________ is the enzyme-mediated synthesis of a DNA molecule from an RNA template. The enzyme involved is called a ________ ___________.

Answer 16

Reverse transcription is the enzyme-mediated synthesis of a DNA molecule from an RNA template. The enzyme involved is called a reverse transcriptase.

Question 17

What is the difference (from DNA) in the sugar structure that gives RNA its name?

Answer 17

RNA’s sugar, called ribose, has a hydroxyl group (-OH) attached to the 2’-carbon atom. DNA, on the other hand, is missing the O and has only a H attached (hence Deoxyribose).

Question 18

The additional oxygen atom in the RNA nucleotide makes it [more/less] reactive and [more/less] chemically stable than DNA.

Answer 18

The additional oxygen atom in the RNA nucleotide makes it more reactive and less chemically stable than DNA.

Question 19

Both DNA and RNA contain 2 purines; adenine and guanine (A and G). Cytosine is found in both DNA and RNA, however the pyrimidine ________ is found only in RNA. The sugar in RNA does not contain a phosphorus atom.

Answer 19

Both DNA and RNA contain 2 purines; adenine and guanine (A and G). Cytosine is found in both DNA and RNA, however the pyrimidine uracil is found only in RNA. The sugar in RNA does not contain a phosphorus atom.

Question 20

What are the three main types of RNA?

Answer 20

1. Transfer (tRNA)
2. Ribosomal (rRNA)
3. Messenger (mRNA)

Question 21

What does transfer RNA (tRNA) do?

Answer 21

reads the code and carries the amino acid to be incorporated into the developing protein

Question 22

Describe the function of ribosomal RNA (rRNA)

Answer 22

Combines with protein to form a nucleoprotein called a ribosome

The ribosome serves as the site of and carries the enzymes necessary for protein synthesis.

The ribosome attaches itself to mRNA and provides the stabilising structure to hold all substances in position as the protein is synthesised

Question 23

What does messenger RNA (mRNA) do?

Answer 23

synthesised from a gene segment of DNA which contains the information on the primary sequence of amino acids in protein to be synthesised

The mRNA carries the code into the cytoplasm where protein synthesis can occur

Question 24

Define transcription. How does this differ from DNA replication?

Answer 24

Transcription is the synthesis of an RNA molecule from a DNA template.

In replication all the nucleotides in the DNA template are copied but in transcription only a single gene or a few genes are transcribed into RNA. Constant transcription of all genes is highly inefficient therefore individual genes are transcribed as their products are needed.

Question 25

What are the three main elements needed for transcription?

Answer 25

1. A DNA template 2. Ribonucleotide triphosphates to build a new RNA molecule 3. Proteins needed for catalysing the synthesis of RNA

Question 26

What is the ***template strand*** in transcription?

Answer 26

The DNA template is a single strand of the DNA double helix (template strand) that is used to synthesise a complimentary and antiparallel RNA molecule.

Question 27

In the context of DNA transcription, what is a ***promoter***?

Answer 27

The promoter is a DNA sequence to which proteins and enzymes bind that initiate transcription of a single RNA from the DNA downstream of it. It indicates which of the two DNA strands is to be read as the template and the direction of transcription. The promoter determines the transcription start site, the first nucleotide to be transcribed into RNA.

Question 28

What is the ***RNA coding region***?

Answer 28

The RNA coding region is a sequence of DNA nucelotides that is copied into an RNA molecule.

Question 29

What is the ***terminator*** region of a DNA strand?

Answer 29

The terminator is a sequence of nucleotides that signals where transcription is to end.

Question 30

Define ***translation***.

Answer 30

Translation is the second major step in gene expression, where the mRNA strand that has been transcribed from the DNA is used to assemble an amino acid sequence into proteins

Question 31

What are *ribosomes* and what role do they play in *translation*?

Answer 31

mRNA is translated into proteins on ribosomes. Ribosomes consist of proteins and RNA molecules with a large and small subunit. A ribosome attaches near the 5’ end of a mRNA strand and moves towards the 3’ end translating the codons as it goes. Synthesis begins at the amino acid end of the protein where the protein is elongated by the addition of new amino acids to the carboxyl end.

Question 32

What are the four stages of protein synthesis?

Answer 32

1. tRNA charging 2. Initiation 3. Elongation 4. Termination

Question 33

What is (1) ***tRNA charging***? What is it also known as?

Answer 33

**Amino acid activation** (also known as **aminoacylation** or **tRNA charging**) refers to the attachment of an amino acid to its Transfer RNA (tRNA). ## Footnote Amino acids are attached to specific tRNAs by aminoacyl-tRNA synthetases in a 2 step reaction that requires ATP.

Question 34

What is the (2) ***initiation*** stage of protein synthesis?

Answer 34

Initiation occurs when mRNA binds to the small subunit of the ribosome. The initiator tRNA binds to the mRNA through base pairing between the codon and anticodon, and the large ribosomal subunit joins to form the i*nitiation complex*. The necessary components for protein synthesis are; mRNA, small and large subunits of the ribosome, intiation factors, initiator tRNA and GTP.

Question 35

What is involved in the (3) ***elongation*** phase of protein synthesis?

Answer 35

Elongation joins amino acids to create a polypeptide chain. Elogation requires the 70s complex, tRNA charged with their amino acids, elongation factors and GTP.

Question 36

What is the ***termination*** stage in protein synthesis?

Answer 36

Protein synthesis terminates when the ribosome reaches a termination codon. Proteins called release factors bind to the ribosome.

Question 37

What is a ***codon***?

Answer 37

A codon is a series of 3 nucelotides ( a triplet) that encodes a specific amino acid residue in a polypeptide chain or for the termination of translation. A total of 20 different amino acids can be translated. The abundance in codons allows many amino acids to be encoded by more than one codon.

Question 38

What is the difference between chromosome number and copy number?

Answer 38

**Chromosome number** is a combination of how many chromosomes the organism has, multiplied by how many copies of the chromosome there are. So a human somatic cell will be diploid (2 copies) and there are 23 chromosome pairs, giving a chromosome number of 46. chromosomes = # functional centromeres **Copy number** refers to how many copies of the genome there are. So in a human somatic cell after the DNA has been replicated and before it has divided (mitosis), the copy number will be 4C because there are two copies of the two homologous chromosomes.

Question 39

What is a ***zygote***?

Answer 39

A zygote is a eukaryotic cell formed by a fertilisation event between two gametes (g.e. egg and sperm).

Question 40

What is a ***bivalent***?

Answer 40

A bivalent is one pair of chromosomes (sister chromatids) in a tetrad. A tetrad is the association of a pair of homologous chromosomes (4 sister chromatids) physically held together by at least one DNA crossover. This physical attachment allows for alignment and segregation of the homologous chromosomes in the first meiotic division.