molecular genetics

Question 1

list the components of a nucleotide

Answer 1

1. pentose
2. phosphate group
3. nitrogeneous base

Question 2

distinguish deoxyribose and ribose

Answer 2

deoxyribose differs from ribose in that the -OH at carbon 2 is replaced with hydrogen atom

Question 3

contrast pyrimidines and purines

Answer 3

purines: 2 rings (adenine and guanine)
pyrimidines: 1 ring (cyotsine, thymine, uracil)

Question 4

describe the formation of a nucleotide

Answer 4

condensation:
- nitrogeneous base attaches at carbon 1 of sugar
- phosphate group attaches at carbon 5 of sugar
- two molecules of water are removed in the process

Question 5

describe

formation of nucleic acids

Answer 5

nucleic acids are formed by combining nucleotides

• condensation between phosphate group of one nucleotide and sugar of the other nucleotide forms a dinucleotide.
• addition of further nucleotides produces a polynucleotide chain whose backbone consists of alternating sugar and phosphate groups with the bases projecting sideways from the sugars

Question 6

what groups are at the 5’ and 3’ end of polynucleotide chain?

Answer 6

• phosphate group attached to carbon 5
• -OH group on carbon 3

Question 7

describe the structure of a DNA molecule

Answer 7

1. two polynucleotide chains form a double helix structure
   ⭐ this part is definition of DNA according to WA3
2. two strands are anti-parallel, one strand runs in 5’ to 3’ direction whereas the other runs in 3’ to 5’ direction (MUST elaborate on anti parallel)
3. two strands are held in position by hydrogen bonds forming between nucleotide bases of opposite strands / complementary base pairing of nucleotides
4. number of nucleotides containing adenine = thymine, number of nucleotides containing cytosine = guanine
5. basic unit of DNA molecule is deoxyribonucleotide, with a deoxyribose sugar, nitrogeneous base and phosphate group
6. width between 2 sugar-phosphate backbones is constant throughout entire molecule

Question 8

why is DNA with more C and G nucleotides more heat stable?

Answer 8

3 hydrogen bonds form between cytosine and guanine nucleotides as compared to 2 between adenine and thymine nucleotides.
hence more energy required to separate the 2 strands of DNA

Question 9

why is DNA having 2 strands advantageous?

Answer 9

greater stability of DNA molecule

Question 10

outline the start of DNA replication

Answer 10

1. free nucleotides are manufactured in cytoplasm and transported into nucleoplasm via nuclear pores before DNA replication
2. specific enzymes and proteins required to initiate replication BIND to each of the origins of replication on parental DNA molecule
3. this allows helicase to disrupt the hydrogen bonds between complementary base pairs, separating the 2 parental strands

“1” happens BEFORE DNA replication

steps 2 and 3 are also the purpose of origins of replication

Question 11

suggest

why origins of replication commonly occur in A-T rich regions

Answer 11

• A pairs with T with 2 hydrogen bonds (compared to C and G with 3)
• in regions rich in A-T sequences, two strands are less tightly bonded together, hence making them easier to separate

Question 12

outline priming of DNA synthesis during DNA replication

Answer 12

1. primase joins a short sequence of RNA nucleotides complementary to first part of template strand to form a primer. this is necessary because DNA polymerase can only add free deoxyribonucleotides to the 3’ end of an existing strand
2. DNA polymerase later replaces these RNA nucleotides with DNA nucleotides

Question 13

outline DNA synthesis during DNA replication

Answer 13

each parental strand acts as templates for synthesis of complementary daughter strands
1. on each parental DNA strand, DNA polymerase reads the parental strand in 3’ to 5’ direction, recognising the bases and selecting free deoxyribonucleotides to be aligned in a sequence where they complementary base pair to those on parental strand
2. adenine pairs with thymine and vice versa, cytosine pairs with guanine and vice versa
3. DNA polymerase adds deoxyribonucleotides to growing daughter strand in 5’ to 3’ direction by adding them at 3’ -OH end
4. Since parental strands are anti-parallel, 2 daughter strands are synthesised in opposite directions by 2 DNA polymerase molecules
5. DNA polymerase catalyses the formation of phosphodiester bonds between adjacent deoxyribonucleotides
6. As DNA polymerase moves along template strand, it “proofreads” the previous region, replacing incorrectly added deoxyribonucleotides with the correct one
7. At the end of replication, the complementary parental and daughter strand rewind into a new double helix

only DNA polymerase is involved here!

Question 14

explain why DNA replication is semi-conservative

Answer 14

each resultant double helix consists of one parental strand and one daughter strand

Question 15

explain why synthesis of daughter strands happens in opposite directions

Answer 15

1. DNA consists of 2 polynucleotide chains forming a double helix that are antiparallel, where one strand runs in 5’ to 3’ direction whereas the other runs in 3’ to 5’ direction
2. DNA polymerase is an enzyme that has an active site which shape is complementary to shape of 3’ hydroxyl end of growing strand

SHAPE of active site is complementary to SHAPE of ….

Question 16

outline transcription

Answer 16

1. RNA polymerase binds to promoter of DNA causing double helix to unwind
2. template strand is used as template for mRNA production, while the non-template strand is not transcribed
3. RNA polymerase moves along template strand from 3’ to 5’ end, adding free ribonucleotides to mRNA by complementary base pairing to DNA bases on DNA template, growing the RNA strand in the 5’ to 3’ direction
4. RNA polymerase catalyses the formation of phosphodiester bonds between adjacent ribonucleotides
5. when RNA polymerase reaches end of gene, it releases newly formed mRNA and DNA rewinds
6. mRNA leaves nucleus through nuclear pores

Question 17

define transcription

Answer 17

mechanism by which base sequence in DNA template of a gene is converted to complementary base sequence of mRNA

Question 18

outline start of translation (before chain elongation)

Answer 18

1. amino acid activation : amino acid is attached to amino acid binding region at 3’ end of a tRNA which has an anticodon that is complementary to a specific mRNA codon that codes for that amino acid to form an amino acid-tRNA complex
2. binding of mRNA to ribosome : small subunit of ribosome binds to mRNA at 5’ end, and mRNA template is read in 5’ to 3’ direction
3. initiation of polypeptide chain : amino acid-tRNA complex with anticodon UAC binds to start codon AUG on mRNA, held at ‘P’ site of ribosome, and the large subunit of the ribosome also binds to small subunit after. since tRNA with anticodon UAC always carries methionine, methionine is always the first amino acid in a polypeptide chain.

Question 19

outline chain elongation of translation

Answer 19

1. the second amino acid-tRNA complex with anticodon complementary to second mRNA codon binds to the latter, held at ‘A’ site of ribosome
2. large subunit catalyses formation of peptide bond between first and second amino acids, using energy from hydrolysis of ATP
3. the ribosome then moves along the mRNA to the next codon, thus the first tRNA is now at ‘E’ site where it is released into cytoplasm, and the second amino acid-tRNA complex moves from ‘A’ to ‘P’ site, leaving ‘A’ site empty for next amino acid-tRNA complex with anticodon complementary to third codon along mRNA
4. process is repeated until ribosome reaches ‘stop’ codon (UAG, UGA, UAA) on mRNA

Question 20

outline chain termination of translation

Answer 20

1. once ‘stop’ codon reached, polypeptide is released from ribosome and it automatically assumes secondary and tertiary structures.
2. ribosome then disassembles into its subunits, and tRNA molecules are attached again to their respective amino acids in cytoplasm

Question 21

define translation

Answer 21

mechanism by which base sequence in an mRNA molecule is converted to sequence of amino acids in a polypeptide chain

Question 22

explain the role of tRNA molecule

Answer 22

• 3’ end of tRNA allows for attachment of an amino acid to form amino acid-tRNA complex, hence it carries amino acids to ribosome during protein synthesis
• every codon on mRNA has corresponding anticodon on tRNA molecule, which carries a corresponding amino acid as each tRNA molecule is specific, allowing for correct sequencing of amino acids on polypeptide chain

Question 23

describe how restriction enzymes work

Answer 23

they recognise and bind to a restriction site, (a specific sequence of 4~8 nucleotides on a DNA molecule), and acts on it by hydrolysing the phosphodiester bond at a position between 2 specific nucleotides, cutting it up into restriction fragments with sticky ends.
restriction fragments anneal by forming hydrogen bonds to complementary sticky ends from other DNA molecules cut up by SAME restriction enzyme

same restriction enzyme must be used to create complementary sticky ends, allowing complementary base pairing / annealing by formation of hydrogen bonds

Question 24

what is one characteristic of restriction sites?

Answer 24

they are palindromic, where the sequence on one strand is identical to complementary sequence on the other, when both are read in 5’ to 3’ direction, so both DNA strands share the same recognition sequence but in opposite directions

Question 25

explain how DNA ligase works

Answer 25

it **catalyses** the formation of **phosphodiester bonds** between adjacent nucleotides in a DNA molecule through **ligation**, **sealing the nicks** in the **sugar-phosphate backbone** of recombinant DNA molecules

Question 26

what are plasmid vectors? (explain each term individually)

Answer 26

a small, circular DNA molecule (plasmid) into which fragments of DNA may be inserted (vector) ## Footnote vector: small DNA molecule into which...

Question 27

what is recombinant DNA?

Answer 27

DNA formed after DNA from one source is joined to a DNA fragment from another source

Question 28

explain how to carry out genetic engineering

Answer 28

1. cut out functional **gene of interest** by cutting the two sides of the gene of interest using a **restriction enzyme** that **generates sticky ends** 2. **extract** bacterial plasmid from healthy bacterial cell (!!), then cut the DNA from it at **one point within a genetic marker** using the **same** restriction enzyme 3. **mix** the extracted gene of interest and cut bacterial plasmid to allow the restriction fragments' **complementary sticky ends** to **anneal spontaneously by forming hydrogen bonds** 4. incubate with **DNA ligase** to join the annealed strands covalently by **forming phosphodiester bonds** 5. mix the recombinant plasmid with bacterial cells and apply **temporary heat shock or electric shock**, opening up pores in cell surface membrane of each bacterium for plasmids to enter 6. culture these cells in large quantities in a suitable medium, induce the expression of inserted gene to produce protein, then extract, purify and package the protein product for mass production ## Footnote bacteria is used because they **reproduce rapidly**

Question 29

list a 1~2 benefits of genetic engineering

Answer 29

* low-cost medicine production * pesticide-resistance crops * production of crops that grow in extreme conditions * development of food designed to meet certain nutritional goals

Question 30

contrast transcription and translation

Answer 30

* transcription occurs in **nucleus**, while translation occurs in **cytoplasm** * raw materials of transcription are **ribonucleotides**, while those of translation are **amino acids** * the template strand of transcription is **DNA**, while that of translation is **mRNA** * the products formed from transcription is **mRNA**, while that of translation is **polypeptide chain**

Question 31

**compare** DNA replication and transcription

Answer 31

similarity: * both occur **in nucleus** * **complementary base pairing** occurs * template DNA is read in **3' to 5' direction** differences: * enzymes involved for DNA replication are **DNA polymerase, helicase, primase, ligase**, while that of transcription is **RNA polymerase** * site of initiation of DNA replication is **origin of replication**, while that of transcription is **promoter region**' * **both strands** of DNA molecule act as **template strands** in DNA replication, while in transcription there's only **one DNA template strand** * the product of DNA replication is **2 DOUBLE-STRANDED DNA molecules**, while that of transcription is **1 SINGLE-STRANDED mRNA molecule**

Question 32

contrast structure of DNA and RNA

Answer 32

- DNA is **double stranded** while mRNA is **single stranded** - sugar units on DNA are **deoxyribose** while those on RNA are **ribose** - bases of DNA are **adenine, thymine, cytosine, guanine**, while those in mRNA are **adenine, uracil, cytosine, guanine**

Question 33

# llst some benefits of GMOs (at least 2)

Answer 33

- low-cost production of medicines - production of crops that grow in extreme conditions - develop food designed to meet certain nutritional goals - develop crops that produce toxins to kill insect pests - develop pesticide-resistant crops

Question 34

# state a benefit and drawback of Bt Corn

Answer 34

benefit - produces Bt delta endotoxin that kills common pests, hence the use of pesticides that could damage the environment / be ingested by humans is reduced drawback - unsure if the toxin produced is completely harmless to humans

Question 35

# state a benefit and drawback of Golden Rice

Answer 35

benefit - high vitamin A content that can help people with vitamin A deficiency drawback - unsure if cross-pollination of golden rice with the wildtype could introduce genes from golden rice to the wild rice gene pool and cause long-term environmental impacts