Outcome 1 Flashcards

(39 cards)

1
Q

What are the three types of RNA and their functions?

A

mRNA (messenger RNA): Carries genetic information from DNA to ribosomes.

rRNA (ribosomal RNA): Forms the ribosome and helps catalyze protein synthesis.

tRNA (transfer RNA): Delivers specific amino acids to ribosomes during translation

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2
Q

Why is the genetic code considered universal and degenerate?

A

Universal: The same codons specify the same amino acids in all organisms.
Degenerate: Multiple codons can code for the same amino acid.

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3
Q

What are the steps in gene expression?

A
  1. Transcription (in the nucleus):
    → RNA polymerase binds to the promoter region of a gene.
    DNA is unwound, and one strand is used as a template.
    Complementary RNA nucleotides pair with the template strand, forming pre-mRNA.
  2. RNA Processing (post-transcriptional modification in eukaryotes):
    → Introns (non-coding regions) are removed by spliceosomes.
    Exons (coding regions) are spliced together to form mature mRNA.
    A 5’ methyl cap and a poly-A tail are added to protect from enzyme attack and stabilise

3.Translation (at the ribosome in the cytoplasm):
→ Ribosome reads mRNA codons.
tRNA brings specific amino acids to the ribosome.
Peptide bonds form between amino acids, creating a polypeptide chain

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4
Q

What are the key regions of a gene?

A

Exons: Coding regions that determine the amino acid sequence of a protein.

Introns: Non-coding regions that are removed during RNA processing.

Promoter: The DNA sequence where RNA polymerase binds to initiate transcription.
-regulates gene expression

Operator (in prokaryotic genes): A regulatory sequence where repressor proteins can bind to control gene expression.

regulatory region:
codes for a repressor protein controls of operator gene. when a repressor protein binds to the operator it blocks the promoters binding site for RNA polymerase and prevents transcription

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5
Q

How does the trp operon regulate gene expression in prokaryotes

A

When tryptophan is absent, the repressor is inactive, and transcription occurs. Enzymes needed for tryptophan synthesis are produced.

When tryptophan is present, it binds to the repressor protein, activating it. The repressor binds to the operator, blocking RNA polymerase and stopping transcription.

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6
Q

What are the four levels of protein structure?

A

Primary: The linear sequence of amino acids in a polypeptide.

Secondary: Alpha-helices and beta-pleated sheets stabilized by hydrogen bonds.

Tertiary: The overall 3D structure of the protein due to interactions between R groups (e.g., ionic bonds, disulfide bridges, hydrophobic interactions).

Quaternary: Multiple polypeptide chains interacting to form a functional protein (e.g., hemoglobin)

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7
Q

What is a proteome?

A

The complete set of proteins expressed by a cell, tissue, or organism at a given time.

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8
Q

What is the role of the rough ER, Golgi apparatus, and vesicles in protein export?

A

Rough Endoplasmic Reticulum (RER):
-Ribosomes on the RER synthesize proteins.
-proteins intended for export from the cell at the ribosomes attached to the rough ER. From there they move through the channel network of the lumen of the rough ER toward Golgi

Golgi Apparatus:
-Further modifies proteins .
-Sorts and packages proteins into vesicles.
-proteins are delivered the cis side of the Golgi from the RER and they move through the Golgi

Vesicles:
-proteins are released from the Golgi in vesicles that bud off from the trans face
- the vesicles bud off the Golgi can diffuse to their target location over very short distances over long distances they are carried by motor proteins along the microtubules of cell cytoskeleton
-Transport proteins to their final destinations (either within the cell or for secretion via exocytosis)

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9
Q

operons

A

linked structural genes with a common promoter and operator that is transcribed as a single unit. Its expression is controlled by regulator genes that produce repressor protein

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10
Q

endonucleases and types of ends

A
  • they cut with a nucleotide sequence of DNA

endonucleases that cut specific recognition sites are known as restriction endonucleases or restriction enzyme

Cut DNA at specific recognition sites, producing blunt or sticky ends; used in gene cloning and genetic engineering.
If the restriction site is cut in the centre, the restriction enzyme leaves ‘blunt ends’. If it is cut in
any other location, the resulting ends are ‘sticky ends’

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11
Q

What are the roles of polymerases and ligases in DNA manipulation?

A

Polymerase: Synthesizes DNA strands by adding nucleotides in a 5’ to 3’ direction; used in PCR to amplify DNA.

Ligase: Joins fragments of DNA by forming phosphodiester bonds; essential in DNA recombination.

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12
Q

what is the function of CRISPER-CAS 9 in bacteria

A

is naturally occurring in bacteria and evolved as defence against invading viruses. The CAS 9 endonuclease is able to cut the invading viral DNA by recognising DNA sequences from the guide RNA. However it is important that is only cuts viral DNA and not the bacteria’s genome. In order to protect its own DNA it will only cut at sites where PAM is present.

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13
Q

what is CRISPR and how its made

A
  1. What is a CRISPR Array?
    Bacteria have a special DNA region called a CRISPR array that helps them remember past viral infections. This array is made of:

Repeats: Short palindromic DNA sequences (they read the same forward and backward).

Spacers: Pieces of viral DNA that the bacteria captured from past infections.

  1. How Does a Bacterium Capture Viral DNA?
    When a virus infects a bacterium, the bacterial defense system uses Cas1 and Cas2 enzymes to:

Cut out a small piece of the virus’s DNA (protospacer) near a sequence called PAM (which helps identify it as foreign).
- Insert this viral DNA piece into the CRISPR array as a new spacer.

  1. How Does CRISPR Help Defend Against Future Attacks?
    If the same virus attacks again, the bacterium uses the stored viral DNA to fight back:

The CRISPR array is copied into a long RNA strand (pre-crRNA).

Another RNA (tracrRNA) helps process this long strand into smaller crRNA pieces, each matching a stored viral sequence.

These crRNA pieces join with tracrRNA, forming cr:tracrRNA complexes.

These guide RNA (gRNA) molecules are picked up by Cas9, a special enzyme that can cut DNA.

  1. Destroying the Virus
    If the same virus tries to infect the bacterium again:

The gRNA in Cas9 recognizes the virus by matching its DNA.
Cas9 cuts the viral DNA, destroying the virus before it can take over

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14
Q

CRISPR Gene Editing
Type 1: Gene “Knock In”

A

A specially designed DNA sequence
is inserted into a precise location in
the genome.

Aim: To edit faulty alleles and
restore their normal function.

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15
Q

CRISPR Gene Editing
Type 2: Gene “Knock Out”

A

Re-joining that repairs the break
in the DNA

Is subject to error.

Aim: To disable or silence a gene

Can result in a random insertion
or deletion (indel) of one or two
bases, producing a frameshift
mutation.

Can disable a gene or produce a
STOP signal therefore the gene
can no longer be expressed.

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16
Q

what is polymerase chain reaction?

A

3 step process involving a sequence of DNA that is amplified or copied repeatedly, to produce large quantities of DNA

17
Q

BACTERIAL DEFENCE AGAIN VIRAL INVASION

A

1.virus invades bacterial cell
2. new spacer is deprived from virus and integrated in CRISPR sequence
3. CRISPR RNA is formed
4. CRISPR RNA guides molecular machinery to target and destroy viral genome

18
Q

Steps of PCR:

A
  1. DENATURATION: (95°C)
    the DNA to be amplified is collected and separated into two complementary strands be heating at high temp. to break the hydrogen bonds between bases.
  2. ANNEALING: (50-60°C)
    the DNA is cooled and primers (primer is a short ssDNA , usually 15-20 bases long which is synthesized in the laboratory and is complementary to the 3’ end of the target DNA.) attach to the DNA and promote replication process from the point of attachment.

3.EXTENDING: (72°C)
The DNA polymerase known as TAQ polymerase is an enzyme isolated from a bacterium. It used here because it can withstand the high temp tempatures without denaturing. Taq polymerase extends each strand beyond the primer adding free nucleotides to replicate each DNA strand. Each time this this phase is completed it will double the quantity of DNA.

—keep in mind PCR is extremely sensitive things need to be tightly controlled any contamination could ruin the whole process.

19
Q

How does gel electrophoresis separate DNA fragments?

A

DNA is placed in wells of an agarose gel and subjected to an electric field.
DNA is negatively charged and moves towards the positive electrode.
Smaller fragments travel further, while larger fragments move slower.

The distance the band travels is also influenced by the concentration or viscosity of the agarose and the specific voltage or power used.
Uses: DNA profiling, crime scene analysis, paternity testing

20
Q

what is gel electrophoresis

A

a process where nucleic acids are separated by molecular size. and electric current causes the DNA fragments to travel through the gel at different speeds.

the gel is made of agarose which is submerged in a buffer solution to maintain PH. the gel has wells across the top where the DNA is inserted. DNA is an acid but because of the phosphate groups along sugar- phosphate backbone, the DNA molecule is negatively charged.

21
Q

what is a standard ladder

A

A standard ladder of DNA fragments of known sizes is usually
run through the gel at the same time as the unknown DNA
samples. In some cases, this is referred to as an allele ladder.

The size of unknown DNA fragments can be approximated by
comparing the positions of their bands with those of the known
standards.

REMEMBER: ALWAYS check for this standard when analysing a gel. in a crime scene analysis the victim’s DNA from evidence helps eliminate

22
Q

what is STR (Short Tandem Repeat)?

A

STR (Short Tandem Repeat) sequences are short, repeating DNA sequences found in non-coding regions of the genome. They are commonly used in DNA profiling

23
Q

Plasmids: VECTORS of DNA

A

A VECTOR is a CARRIER

If a plasmid has been engineered to contain a specific piece of DNA
it becomes a ‘vector’

A SELECTABLE marker gene: Used to screen for transformed
bacteria which have taken up the plasmid; codes for an easily
identifiable trait.

Eg: Antibiotic resistance: Bacteria containing the plasmid with
the marker can be selected from among other bacteria by
exposure to the antibiotic.)

A SCREENING/REPORTER marker gene: Used to screen for
transformed bacteria which have taken up the gene of
interest; codes for an easily identifiable trait

24
Q

creating recombinant plasmids steps involved

A

Step 1: Choosing a restriction enzyme
An endonuclease is chosen to cut upstream and downstream of the gene, leaving sticky ends.

Step 2: Choosing a plasmid
A plasmid is chosen that has two genes that each encode observable traits. Of these genes, one must contain the restriction site of the restriction endonuclease being used.

Step 3: Using the restriction endonuclease
The same restriction enzyme is used to cut both the source gene, and the plasmid. As a
result, the source gene and the plasmid have complementary sticky ends.

Step 4: Making a recombinant plasmid
When the source gene and the plasmids are mixed, sometimes the source gene will incorporate into the plasmid, creating a ‘recombinant’. The bond is completed by adding ligase When the source gene and the plasmids are mixed, sometimes the source gene will incorporate into the plasmid. A plasmid containing foreign ’passenger’ DNA is called ‘recombinant’.

Step 5: Transformation
Bacteria (such as E. coli) are made competent to take up a plasmid. Only some bacteria will take up a plasmid. Only some of those will take up the recombinant plasmid.

25
Steps in the Production of Human Insulin Using Recombinant Plasmids
1. Isolating the Human Insulin Gene - Scientists extract the human insulin gene from a DNA sample. - A restriction enzyme cuts the DNA at specific sites, creating sticky ends. 2. Preparing the Plasmid Vector - A plasmid (a small, circular DNA molecule found in bacteria) is used as a vector to carry the insulin gene. - The same restriction enzyme cuts the plasmid, creating complementary sticky ends. 3. Inserting the Insulin Gene into the Plasmid - The insulin gene is inserted into the plasmid. - DNA ligase seals the human gene into the plasmid, forming a recombinant plasmid (a plasmid containing foreign DNA). 4. Transforming Bacteria with the Recombinant Plasmid - Bacteria are treated with the recombinant plasmid using heat shock or electroporation, allowing them to take up the plasmid. - The transformed bacteria now have the human insulin gene. 5. Selecting Transformed Bacteria Not all bacteria successfully take in the plasmid, so an antibiotic resistance gene is included in the plasmid. Bacteria are grown on an antibiotic-containing agar plate: Bacteria with the plasmid survive (they carry the resistance gene). Bacteria without the plasmid die. This ensures that only transformed bacteria are selected. 6. Producing and Harvesting Human Insulin The transformed bacteria express the human insulin gene, producing insulin protein. The insulin is extracted, purified, and used for diabetes treatment.
26
Why we use plasmids
✅ Efficient and Large-Scale Production: Bacteria can rapidly multiply, producing large amounts of insulin. ✅ Safer than Animal Insulin: Previously, insulin was extracted from animals (e.g., pigs), which could cause allergic reactions. ✅ Genetically Identical to Human Insulin: Reduces the risk of immune system rejection. ✅ high levels of purity ✅ reliability of supply ✅ consistency of quality between batches.
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Making Recombinant Plasmids
The DNA is cut at one point using restriction enzymes – sticky ends. The DNA passenger fragments are prepared using the same restriction enzyme. The passenger fragments are mixed and their ‘sticky ends’ pair. The joining enzyme, ligase, makes the joins permanent. Plasmids that contain the DNA passenger are then selected from the mixture. These plasmids with their passenger DNA can be reintroduced to bacterial cells using an electric pulse or heat shock.
28
what is bacterial transformation
Once recombinant plasmids have been created, plasmids need to be transferred into bacterial cells. This process is known as bacterial transformation. The bacterium needs to be able to reproduce quickly and be harmless to individuals working with it. A harmless strain of E. coli is commonly used for this purpose.
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Getting plasmids into bacterial cells Electroporation
Cells are briefly placed in an electric field Cells are shocked “Holes” are created in their plasma membranes Plasmid entry is facilitated.
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Steps involved in producing recombinant insulin
Step 1: Produce the two insulin chains separately. (As the amino acid sequence is known for each of these chains, this can be used to determine the DNA sequence that will lead to the production of insulin). Step 2: The DNA is often produced using reverse transcription. Mature mRNA is used as it no longer contains non-coding introns. With the aid of the reverse transcriptase enzyme, the DNA segments coding for insulin can be produced. Step 3: The insulin gene and plasmid are cut with an endonuclease (usually BamHI), forming sticky ends. The two DNA molecules are then inserted into plasmids using ligase. Step 4: The plasmids are then inserted into the bacterium E. coli. The plasmid contains the selectable marker the lacZ gene. LacZ encodes for β -galactosidase. Step 5: The recombinant plasmids are then mixed with the bacterial cells. Plasmids enter the bacteria in a process called transformation (using either heat shock or electroporation). The bacteria culture is incubated, allowing for the replication of bacteria and plasmids. Step 6: Bacteria are spread over culture plates containing ampicillin and X-gal. Bacteria with the recombinant plasmid are able to grow in the presence of ampicillin. They CANNOT express beta galactosidase, hence cannot digest X-gal. Colonies are therefore WHITE in colour. Step 7: The bacteria with the recombinant plasmid undergo a fermentation process. The millions of bacteria replicate roughly every 20 minutes, expressing the insulin gene. Step 8: Cells are then lysed using lysosomes, where the expressed protein is able to be extracted. The protein is then treated with cyanogen bromide, separating the insulin chains from other proteins that were also translated. Step 9: The purified samples can be tested to ensure none of the bacteria's E. coli proteins are mixed in with the insulin. This is done by using a marker protein to detect the E. coli DNA Step 10: The two chains are then mixed together and re-joined by forming disulfide bonds (or bridges). Step 11: At the end of the manufacturing process, ingredients are also added to intermediate and long-acting insulin to produce the desired duration type of insulin
31
What is the difference between genetically modified organisms (GMOs) and transgenic organisms?
Genetically Modified Organisms (GMOs): Organisms whose DNA has been altered using genetic engineering. Transgenic Organisms (TGOs): A subtype of GMOs that contain genes from a different species. - GMO = If the gene is from the same species - GMO & TGO = If the gene comes from a different species All TGOs are GMOs, but not all GMOs are transgenic.
32
How are GMOs used in agriculture?
Herbicide-resistant crops (e.g., Roundup Ready soybeans) Contain a gene that makes them resistant to glyphosate, allowing farmers to kill weeds without harming crops. Pest-resistant crops (e.g., Bt cotton & Bt corn) Produce a natural bacterial toxin (Bt toxin) that kills insect pests. Reduces the need for chemical insecticides. Disease-resistant crops Some GM bananas are resistant to Panama disease, a fungal infection that threatens global banana production.
33
Getting plasmids into bacterial cells Heat Shock
Cells are suspended in an ice-cold salt solution (~30min) Then transferred to 42 °C (<1min) Increases the fluidity of the cells’ plasma membranes Increases the chance of uptake of plasmids
34
two types of genetically modified crops that are widely grown around the world and in Australia
Group 1: Herbicide-resistant crops (glyphosate) - HERBICIDES kill weeds (or any plant material) - These crops were first altered so that they were resistant not affected by the herbicide glyphosate (active ingredient in the commercially purchased herbicide Roundup). farmers could eliminate weeds without harming their crops. This increased crop efficiency while eliminating weeds. Group 2: Natural pesticides and insecticides - These crops are altered to produce their own natural pesticides. - Protect the crops against insect infestation, as the pesticide is located within the plant and therefore needs to be ingested by the insects to have an effect. - The use of natural pesticides is environmentally friendly as it eliminates the use of sprays that could be harmful and toxic to other organisms.
35
genetic technology relating to ethical considerations
GENETIC TECH: insertion of genes into plants so they gain desirable features such as disease resistance, firmer fruits or resistance to herbicides ETHICAL CONSID: → Environmental: it is possible that genes from Gm crop plants will cross into non-GM varties via pollen or seeds it will also spread through bacterial or viral infections → evolution: greater pressure for farmers to use higher- yielding or more resistant crop varieties, thus reducing variety. → ethics: - is it right that cooperation's hold ownerships over crops that have been grown for centuries, just bc they developed one genetic variety ? - are these varieties squeezing out traditional farming in poorer communities
36
Bioethical issues
1. SOCIAL ISSUES Social issues affect society. For example, are person who is unable to work due to a genetic issue. Socially, if genetic testing were available, the individual would have less reliance on hospitals in the future. This affects more than the person therefore is a social issue. If we just stated that the person would be unwell, this affects the individual but not society as a whole. 2. LEGAL ISSUES Legal issues are often governed by legislation and government regulation. As ethical issues are often using new technologies, the laws may not be current. 3. ECONOMIC ISSUES Economic factors include areas such as bioprospecting and who owns the rights to materials. Is it the company who conducted the research or is it the locals that reside in an area? Who owns a genome, and is it fair to allow large companies to grow crops that are GM and more likely to survive, when the sole farmer
37
Approaches to bioethical issues and their pros and cons
DUTYAND/OR RULE BASED decision is aligned with a set of rules with the consequences not considered in the decision making process PROS: simple to apply CONS: rigid application VITURE BASED APPROACH: moral character of the person is considered. PROS: not binding on all people CONS: a virtue is subjective CONSEQUNCES BASED APPROACH: the outcome of the decision is considered with minimization of harm a key consideration PROS: flexible decision making CONS: hard to predict outcome
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ethical concepts and principles
Integrity (HONEST): the commitment to searching for knowledge and understanding and the honest reporting of all sources of information and communication of results, whether favourable or unfavourable, in ways that permit scrutiny and contribute to public knowledge and understanding. Justice ( FAIR ): the moral obligation to ensure that there is fair consideration of competing claims; that there is no unfair burden on a particular group from an action; and that there is fair distribution and access to the benefits of an action. Beneficence (BENEFIT): the commitment to maximising benefits and minimising the risks and harms involved in taking a particular position or course of action. For example - have considerations been taken to ensure that the planting of a new crop will benefit the farmer, the consumer, and the ecosystem ring harm Non-maleficence ( NO HARM ): involves avoiding the causations of harm. However, as positions or courses of actions in scientific research may involve some degree of harm, the concept of non-maleficence implies that the harm resulting from any position or course of action should not be disproportionate to the benefits from any position or course of action. Respect (VALUING): involves consideration of the extent to which living things have an intrinsic value and/or instrumental value
39
high trp attenuation
The leader sequence (trpL) has a small section of mRNA that the ribosome starts translating. This sequence contains two tryptophan codons (UGG-UGG). If tryptophan is abundant, the ribosome moves quickly The ribosome blocks part of the mRNA (region 2), forcing regions 3 and 4 to pair. This forms a terminator hairpin (a loop that tells RNA polymerase to stop). Transcription stops before the genes needed for tryptophan synthesis are made