Outcome 1 Flashcards
(39 cards)
What are the three types of RNA and their functions?
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
Why is the genetic code considered universal and degenerate?
Universal: The same codons specify the same amino acids in all organisms.
Degenerate: Multiple codons can code for the same amino acid.
What are the steps in gene expression?
- 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. - 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
What are the key regions of a gene?
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
How does the trp operon regulate gene expression in prokaryotes
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.
What are the four levels of protein structure?
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)
What is a proteome?
The complete set of proteins expressed by a cell, tissue, or organism at a given time.
What is the role of the rough ER, Golgi apparatus, and vesicles in protein export?
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)
operons
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
endonucleases and types of ends
- 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’
What are the roles of polymerases and ligases in DNA manipulation?
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.
what is the function of CRISPER-CAS 9 in bacteria
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.
what is CRISPR and how its made
- 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.
- 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.
- 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.
- 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
CRISPR Gene Editing
Type 1: Gene “Knock In”
A specially designed DNA sequence
is inserted into a precise location in
the genome.
Aim: To edit faulty alleles and
restore their normal function.
CRISPR Gene Editing
Type 2: Gene “Knock Out”
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.
what is polymerase chain reaction?
3 step process involving a sequence of DNA that is amplified or copied repeatedly, to produce large quantities of DNA
BACTERIAL DEFENCE AGAIN VIRAL INVASION
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
Steps of PCR:
- 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. - 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.
How does gel electrophoresis separate DNA fragments?
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
what is gel electrophoresis
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.
what is a standard ladder
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
what is STR (Short Tandem Repeat)?
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
Plasmids: VECTORS of DNA
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
creating recombinant plasmids steps involved
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.