SAC 1 Test

Question 1

Primary Structure of Proteins

Answer 1

the sequence of amino acids in a polypeptide chain

Question 2

Secondary Structure of Proteins

Answer 2

where acid chains naturally form alpha helixes, beta pleated sheets or random coils

Question 3

Tertiary Structure of Proteins

Answer 3

Refers to the overall 3D shape of a protein.

Formed when secondary structures fold further by forming bonds between r-groups and amino acids.

Question 4

Quaternary Structure of Proteins

Answer 4

where 2 or more polypeptide chains with tertiary structures bond together or other non-protein groups are added to form a fully functional protein

Question 5

Transcription

Answer 5

where a sequence of DNA is used as a template to produce a complementary sequence of pre-mRNA

• RNA Polymerase runs along the template strand from a 3’ to 5’ direction while it creates the mRNA in the 5’ to 3’ direction

Question 6

Process of Transcription

Answer 6

Initiation:

• transcription factors bind to promoter regions which allow RNA polymerase to bind to promoter region
• signals for the weak hydrogen bonds between DNA strands to break

Elongation:
- RNA polymerase begins to move along the template strand in a 3’ to 5’ direction synthesizing a complementary strand of pre-mRNA in a 5’ to 3’ direction

Termination:

• RNA polymerase continues until it reaches termination sequence
• RNA polymerase then de-attaches and the DNA molecule then winds up again the pre-mRNA sequence will de attach

Question 7

RNA Processing

Answer 7

involves the modification of pre-mRNA molecules into mRNA

Question 8

Process of RNA processing

Answer 8

• The addition of a 5’ Methyl- G cap: a molecule added to the 5’ end of pre-mRNA during RNA processing
  
  • The addition of a 3’ Poly- A tail: a chain of adenine nucleotides added to the 3’ end of pre-mRNA during RNA processing
  • The removal of introns: non-coding regions of DNA that do not code for proteins and are spliced out during RNA processing
    
    • The Splicing of Exons: regions of DNA that code for proteins and are not spliced out of RNA processing
    • the mRNA strand leaves the nucleus through a pore in the nuclear envelope and travel into the cytosol

Question 9

Translation

Answer 9

the reading and converting the information carried in the mRNA molecule into a polypeptide chain

Question 10

Process of Translation

Answer 10

Initiation:

• the 5’ end of the mRNA strand binds to the ribosome and is read until the start codon is recognized
• allows a tRNA molecule with a complementary anticodon to bind delivering the first amino acid in the sequence

Elongation:
- as the mRNA strand is passed through and read, tRNA molecules with complementary anticodons recognize the sequences and bring the corresponding amino acids to join to the growing chain

Termination:

• this continues until a stop codon is read
• the polypeptide chain is then released into the cytosol or the endoplasmic reticulum and the mRNA molecule de-attaches from the ribosome.

Question 11

Operon

Answer 11

a cluster of linked genes that all share a common promoter and operator and are transcribed at the same time

Question 12

Promoter Region

Answer 12

the upstream region of DNA where RNA polymerase attaches to

• can denote the starting position and direction of transcription

Question 13

Operator Region

Answer 13

A segment of DNA next to the promoter region which is the binding site for repressor and activator proteins

Question 14

Repressor Protein

Answer 14

binds to the operator region producing a conformational change which prevents RNA polymerase from moving across and transcribing the genes

Question 15

Restriction Endonuclease

Answer 15

any enzyme that acts like a molecular scissor to cut nucleic acid strands at specific recognition sites.

- Either create sticky or blunt ends

Question 16

Ligase

Answer 16

an enzyme that joins molecules, including DNA or RNA together by catalyzing the formation of phosphodiester bonds

- Lack specificity meaning they can join any blunt or sticky end. 
   	- DNA ligase: joins DNA fragments(okazaki fragments)
    - RNA ligase: joins RNA fragments

Question 17

CRISPR-Cas9

Answer 17

a complex formed between sgRNA and Cas9 which can cut a target sequence of DNA.

• Cas9 is a restriction endonuclease that is not specific, it can be coded to cut at different sequences
• CRISPR is a strand of DNA that contains clustered, regularly interspaced palindromic repeats of past viral DNA which is encoded as a formula to cut that DNA in the future
• Bacteria use this complex for protection from viruses and scientist have used it to edit genomes

Question 18

Single Guide RNA(sgRNA)

Answer 18

RNA which is single stranded and binds with a specific spacer sequence determined by CRISPR to guide Cas9 to a specific restriction site

Question 19

Protospacer Adjacent Motif

Answer 19

a sequence of 2-6 nucleotide that is found immediately and next to the DNA targeted by Cas9

- Prevents the Cas9 from accidently cutting through the cRNA sequence with all the genetic material
- PAM code = NGG(N = any nucleotide base)
- Acts as a initiation signal for Cas9(Cas9 looks for the PAM not for a match of viral genetical material)

Question 20

Spacer

Answer 20

a short sequence of DNA obtained from invading bacteriophages that are added into the CRISPR sequence

• called a protospacer before it is added into cRNA

Question 21

CRISPR-Cas9 Process

Answer 21

Exposure:
- The bacteriophage injects its viral DNA into the bacterium

- The bacterium identifies the viral DNA as foreign 
    - Cas1 and Cas2 identify and cut out a short piece of the viral DNA(approx 30 nucleotides) known as a protospacer which is then introduced into the bacteria's CRISPR genes as a spacer

Expression:
- CRISPR spacers are transcribed along with half a palindrome from the repeat and converted into a sgRNA molecule

- sgRNA binds to the Cas9 to create a CRISPR-Cas9 complex which is directed to any viral DNA inside the cell which is complementary
     - sgRNA forms a hairpin loop structure from the transcribed palindromic repeats either side of the spacer

Extermination:
- The CRISPR-Cas9 complex then scans the cell for invading bacteriophage which is complementary to the genetic material in the sgRNA

- When it does, Cas9 cleaves the phosphate-sugar backbone to inactivate the virus and as Cas 9 contains two active sites to cut both strands of DNA blunt ends are created

Question 22

What happens to Viral DNA after it has been cut by CRISPR-Cas9

Answer 22

• Enzymes within the bacterium will naturally act to repair it however the repair mechanisms are prone to errors and which can result in nucleotide additions, deletions or insertions
  
  • This is advantageous in the case of bacteriophage infiltration as mutations tend to render viral genes non-functional
  • If a mutation does not occur, the sgRNA will find the gene and repeat the process again

Question 23

How CRISPR-Cas9 is used in gene editing

Answer 23

1. Synthetic sgRNA is created in a lab that has a complementary spacer to the target DNA that scientists wish to cut
   
   2. A Cas9 enzyme is obtained with an appropriate target PAM sequence
   3. Cas9 and sgRNA are added together in a mixture and bind together to create the CRISPR-Cas9 complex
   4. The sgRNA-Cas9 mixture is then injected into a specific cell, such as a zygote
   5. The Cas9 finds the target PAM sequence and checks whether the sgRNA aligns with the DNA
   6. Cas9 cuts the selected sequence of DNA
   7. The DNA has a blunt end cut that the cell will attempt to repair
   8. When repairing the DNA, the cell may introduce new nucleotides into the DNA at this site. Scientists may also inject new nucleotide sequences into the cell with the hope that it will ligate together

Question 24

DNA polymerase

Answer 24

an enzyme used in the replication or amplification of DNA

- Synthesizes a complementary strand of DNA in a 5’ to 3’ direction

Question 25

Primers

Answer 25

a short, single strand of nucleic acids that act as a starting point for polymerase enzymes to attach

Types of Primers:
- Forward Primer: Binds to start codon at the 3’ end of template strand

• Reverse Primer: binds at the stop codon at the 3’ end of the coding strand

Question 26

Polymerase Chain Reaction

Answer 26

a DNA manipulation technique used to amplify DNA by making many identical copies of DNA from a small initial sample

- Number of DNA strands per cycle doubles

Question 27

Process of PCR

Answer 27

Denaturation:
- DNA is heated to 95 degrees to break down hydrogen bonds between bases allowing the strands to separate

Annealing:
- DNA is cooled to 55 degrees to allow DNA specific binders to join to the complementary sequences on strands

Elongation:
- DNA is heated back up to 72 degrees, the optimal temperature for Taq Polymerase, which binds to the DNA primers and synthesizes a new complementary strand in the 3’ direction

Question 28

Gel Electrophoresis

Answer 28

A technique that separates DNA fragments based on their molecular size

- Typically used after a sample of DNA has been cut up using restriction endonucleases or after a PCR
- The longer the DNA fragment, the shorter the distance it will travel and vice versa

Question 29

Process of Gel Electrophoresis

Answer 29

1. • DNA samples are placed into the wells using a micropipette alongside a standard ladder
   • sits in agarose jelly and immersed in the buffer solution
   2. • An electric current is passed throw the gel using electrodes(negative near wells, positive opposite end)
      • as DNA is negatively charged(due to phosphate backbone), it will be attracted to the positive electrode
      • means DNA fragments will move from the wells, through the pores of the agarose gel towards the positive electrode
   3. • After a few hours, the current is switched off and the DNA fragments stop moving and settle into bands
      • means DNA is now separated by size.
   4. • As DNA is difficult to see with the naked eye, the gel is stained with fluorescent dye(ethidium bromide) allowing the bands to be seen under a UV light.

Question 30

Genetically Modified Organisms(GMO)

Answer 30

an organism with genetic material that has been altered using genetic recombination technology

- To be recognized as a GMO, the altered gene must be able to be passed onto future generations

Question 31

Types of GMO’s

Answer 31

Cisgenic Organisms:
- a GMO that has genes from the same species inserted into its genome. Involves transferring genes between organisms who could otherwise be bred together.

- Process is known as cisgenesis
- Naturally occurring

Transgenic Organisms:
- a GMO that has genes from a different species inserted into its genome. Results in an organism that contains foreign DNA transplanted from a separate species.

- Process is known as transgenesis
    - Occurs only in a laboratory

Question 32

Consequence Based approach to Bioethics

Answer 32

the individual should be driven by consideration for the consequences likely to occur

• aim is to maximise benefits and minimise negatives
• sometimes allows individuals to break rules in order to achieve the greatest good for the majority of stakeholders

Question 33

Duty/Rule Based Approach to Bioethics

Answer 33

the individual should be driven by a fundamental duty to act in a certain way

• aims to follow a set of rules regardless of the consequences
• some actions have to be followed due to them being the responsibility of the individual/organisation

Question 34

Virtues Based Approach to Bioethics

Answer 34

the individual should be driven by their character rather than by any fundamental rule or consequence

• an action can be justified due to it being charitable or caring or good for example.

Question 35

Respect (GMOs)

Answer 35

it is important to promote the right of individuals to freely choose whether or not they use GMOs and be provided with equal representation of alternatives

Question 36

Integrity (GMOs)

Answer 36

manufacturers might need to clearly label their products as GMOs, allowing consumers to be better informed

Question 37

Justice (GMOs)

Answer 37

GMOs might create inequity between larger agriculture companies who have the resources to alter their crops versus a small family farm that does not

Question 38

Beneficience (GMOs)

Answer 38

there are positive health outcomes for people who consume GM foods that have nutritional enhancements in them e.g. goldren rice

Question 39

Non-maleficence

Answer 39

GMOs might cause unintended disruptions to the food web such as insect resistant crops that may alter population levels of different pests.