Biochem - cellular + labs Flashcards
Why is the genetic code considered degenerate?
Because more than 1 codon can code for a particular amino acid
(61 codons, 20 amino acids)
What is the Wobble Hypothesis?
Certain tRNA molecules can recognize multiple different codons coding for the same amino acid.
This is due to the first 2 positions on the mRNA codon require traditional (Watson-Crick) base pairing, whereas the third “wobble” nucleotide undergoes non-traditional pairing.
Which part of DNA replication is most different between the 2 daughter strands?
DNA Ligase
Since DNA synthesis can only occur in the 5’ –> 3’ direction”
1 strand is synthesized continuously (leading strand)
1 strand is synthesized discontinuously (lagging strand) in a direction away from the replication fork, resulting in the formation of Okazaki fragments which get joined together by DNA ligase
What is the function of the following in Prokaryotic DNA replication :
a. Helicase
b. Topoisomerase II (DNA Gyrase)
c. Single-Stranded DNA-Binding Protein
d. DNA Ligase
a. Unwinding of double helix
b. Removal of supercoils
c. Stabilization of unwound template strands
d. Joining of Okazaki fragments on lagging strand
What are the functions of DNA Polymerase III? (2)
- 5’ to 3’ DNA Synthesis
- 3’ to 5’ exonuclease (proofreading) activity
What are the functions of DNA Polymerase I? (3)
- 5’ to 3’ DNA synthesis
- 3’ to 5’ exonuclease (proofreading) ability
- Removes Primer
(5’ to 3’ exonuclease activity)
Which amino acid is most abundant in collagen?
What is the conformation of collagen molecules?
Glycine
A triple helical conformation
(Glycine occupies every 3rd amino acid position)
Which letter corresponds to the amino acid binding site on the tRNA molecule?
A
The 3’ CCA Tail
What does a Northern Blot detect?
RNA
What does a Southern Blot detect?
DNA
What does a Western Blot detect?
Example of a probe its used to detect?
Protein
Antibodies
What does a Southwestern blot detect?
Example of a probe it can detect?
DNA-binding Protein
c-Jun and c-Fos
Reverse Transcription Polymerase Chain Reaction (RT-PCR)
- What is it used for?
- How does it work?
1.
Detect and quantify levels of mRNA in a sample
2.
It uses reverse transcription to create a complimentary DNA template that is then amplified using standard PCR
Proteins phosphorylated with mannose residues in the Golgi are destined for which cellular location?
Lysosome
Fluorence in situ Hybridization (FISH)
What is it used to identify?
Chromosomal translocation, duplications or deletions
Flow Cytometry
- What is it used to identidy?
- What pathology is it commonly used for diagnosis?
1.
Surface Markers (eg: CD10)
2.
Leukemias
What is the function of a gap junction?
What protein is responsible for forming gap junctions?
Intercellular communication
Connexins
What proteins form tight junctions?
What is the function of a tight junction?
Claudins & Occludin
Cell Barrier
What protein forms a desmosome?
What protein forms a hemidesmosome?
Cadherins form desmosomes
Integrins form hemidesmosomes
What is the function of the CAAT & TATA boxes?
Promote Transcription
Ehlers-Danlos Syndrome
- What is the main issue?
- What are the main complications
- What step is impaired in this disease?
- Defective collagen synthesis which can cause:
- easy bruising
- hyperextendible skin
- hypermobile joints
- Berry + Aortic aneurysms, organ rupture
3.
N-terminal Peptide Removal
What enzyme removes the RNA primer?
DNA Polymerase I
(only one that has 5’ to 3’ exonuclease activity)
I-cell disease
- How/Why does it occur?
- How does it present?
- Defect in N-acetylglucosamyl-1-phosphotransferase –>
failure of golgi to phosphorylate mannose on glycoproteins
(decreased mannose-6-phosphate) —>
proteins are secreted extracellularily rather than to lysosome
2.
High plasma levels of lysosomal enzymes, coarse facial features, gingival hyperplasia
Signal Recognition Particle (SRP)
- What is its function?
- What occurs if it is dysfunctional?
1.
Traffics protein from the ribosomes to the RER
2.
Proteins accumulate in cytosol
What are the functions of the following vesicular trafficking proteins:
- COPI
- COPII
- Clathrin
COPI: - Golgi –> golgi
- cis-golgi –> ER (retrograde)
COPII: ER –> cis-golgi (anterograde)
“Two (COPII) steps forward, One (COPI) step back”
Clathrin: trans-golgi –> lysosomes
plasma membrane –> endosomes
Disuse of a muscle due to being in a case can result in atrophy.
How does this process occur?
Cytoskleton degredation via ubiquitin-proteosome pathway
What type of vitamin D do we get from:
a. Sunlight
b. Food/Plants
a. Cholecalciferol (D3)
b. Ergocalciferol (D2)
In a patient who has abnormal elastin due to defective cross-linking, what amino acid would be most different in comparison to a normal persons elastin?
Lysine
(responsible for cross-linking which gives elastin elastic propreties)
In a patient preganant with a child with Trisomy 21 how would the following serum markers be altered:
1. Nuchal Translucency
2. B-hCG
3. PAPP-A (pregnancy associated plasma protein)
4. Inhibin A
1. Increased nuchal translucency
2. Increased B-hCG
3. Decreased PAPP-A
4. Increased Inhibin A
In a patient preganant with a child with Trisomy 18 (Edwards Syndrome) how would the following serum markers be altered:
1. Nuchal Translucency
2. B-hCG
3. PAPP-A (pregnancy associated plasma protein)
4. Inhibin A
1. Normal nuchal translucency
2. decreased B-hCG
3. Decreased PAPP-A
4. normal/decreased Inhibin A
In a patient preganant with a child with Trisomy 13 (Patau Syndrome) how would the following serum markers be altered:
1. Nuchal Translucency
2. B-hCG
3. PAPP-A (pregnancy associated plasma protein)
4. Inhibin A
1. Normal nuchal translucency
2. decreased B-hCG
3. Decreased PAPP-A
4. normal Inhibin A
In patients with breast/ovarian cancers with the BRCA1 mutation, what DNA repair mechanism is damaged?
Double Stranded Recombination Repair
(A strand from the damaged dsDNA is repaired by using a complementary strand from an intact dsDNA)
What disease occurs as a result of a defect in DNA mismatch repair?
Lynch Syndrome / Hereditary Nonpolyposis Colorectal Cancer
(due to microsatelite instability)
What disease occurs as a result of having damaged nucleotide exicison repair?
Xeroderma Pigmentosum
(inability to repair DNA pyrimidine dimers caused by UV exposure)
Presents as: dry skin, extreme light sensitivity, increased risk for skin cancers
Mitochondrial Myopathies
- How do they present?
- Why do they occur?
- How do they appear on muscle biopsy?
1.Myopathy (muscle damage)
Lactic acidosis
CNS issues (migraines, seizures)
2.
Failure of oxidative phosphorylation
3.
Ragged red fibers
C-reactive protein
- What can it be used as a marker for?
- Where is it synthesized?
- Inflammation
- Liver
(like most proteins)
Nitrogen Balance
- What is it?
- What raises it?
- What lowers it?
1.
It is a measure of nitrogen input - nitrogen output
2.
Raised by food such meats, eggs, legumes
3.
Lowered by urine, feces, sweat
What are the odds that a sibling has a matching HLA type to his sibling so he can be a transplant/bone marrow donor?
1/4
(there is a 25% chance of 2 siblings inheriting the same haplotype)
What inhertiance pattern is seen in Sickle Cell disease?
Autosomal Recessive
Xeroderma Pigmentosum
- What is defective these patients ?
- What are effects?
1.
Defective Nucleotide Exicison Repair
Due to a deficiency in UV-specific Endonuclease
2.
Severe photosensitivity, hyperpigmentation is sun exposed areas, increased risk for skin cancers
Mosaicism
- What is it?
- What is the diffence between Somatic and Gonadal/Germinline Mosaicism?
- Mosaicism is when there genetically different cells in the same individual.
2.
Somatic Mosaicism is when the mutation occurs once the person is already born and presents with symptoms. Cannot be passed down to children.
Germline Mosaicism is when the mutation occurs in the sperm/egg of an indiviudal. Mutation will pass to children
What codon signals initiation of protein synthesis?
What codon signals termination of protein synthesis? (Stop codons)
Start: AUG
STOP: UGA, UAG, UAG
“U Go Away”
“U Are Away”
“U Are Gone”
What would be the anticodon for the following mRNA sequence?
5’—- UAG —-3’
5’ —- CUA —- 3’
Remember the conon-anticodon binding occurs in the opposide direction
Heterochromatin vs Euchromatin
- Where is it located?
- Is it transcriptonally active?
- Is it heavily methylated?
- Heterochromatin: periphery of nucleus
Euchromatin: Dispersed throughout
2.
Heterochromatin: no - doesnt make protein
Euchromatin: yes “euchromatin is expresssed”
- Only Heterochromatin is methylated and therefore inactive
Enhancers and Silencers
- What is their function?
- Where are they located?
1.
Enhancers: increase expression of a gene on a chromosome
Silencers: Decrease expression of a gene on a chromosome
2.
They can be located upstream, downstream or within the intron
What is the function of a promotor site?
It is another site where RNA pol II and other trancription factors can bind that is upstream from the TATA box
They increase gene transcriptiom
Do tRNAs bind stop codons?
How is protein synthesis terminated?
No tRNAs do not bind stop codons
When the ribosome encounters a stop codon, releasing factor proteins bind to the ribosome and stimulate release of the formed polypeptide
From childhood to puberty, what meiosis stage is the primary oocyte arrested in?
During ovulation, what meiosis stage is the secondary oocyte arrested in until fertilization?
Prophase of Meiosis I
Metaphase of Meiosis II
Homeobox Genes
- What do they code for?
- What is their function?
1.
Transcription factors
2.
Segmental orginization of the embryo along the cranial-caudal axis
What is the best test to see if a gene is being transcribed/expressed?
Northern Blot to test for the presence of its mRNA
What is the function of Histone H1 ?
It helps condense DNA into its heterochromatin form
What is Splicing?
It is a post-transcriptional modification process that removes introns (non-coding DNA regions) from the pre-cursor mRNA.
This leaves only the exons (DNA coding regions) in the mRNA script to be translated.
What is alternative splicing?
Can it have negative consequences?
Like regular splicing, the introns will be removed.
However, different combinations of exons are selectively included and excluded from a mRNA transcript. This allows the DNA from a single gene to code for a diverse group of proteins
Yes, it can be involved in disease processes such as cancer where it can allow cells to evade host defences
Telomerase
- What is its function?
- Which type of cell most commonly has them?
1.
Telomerase is a reverse transcriptase that lengthens telomeres by adding TTAGGG repeasts to its 3’ end to prevent cell death
2.
Stem cells (ex. epidermal basal cells)
Lesch-Nyhan Syndrome
- What enzyme is defected?
- What does it result in?
- How does it present?
- Hypoxanthine-Guanine Phosphoribosyltransferase (HGPRT)
- Defective purine salvage/rescur —> increased uric acid
3. “HGPRT”
Hyperuricemia, Gout, Pissed off (agression, self-harm), Retardation, Dystonia
HbA, HbS, HbC
- What amino acid differences are seen between them?
- What type of mutation results in HbS and HbC
- How would they differ on electrophoresis?
- HbA - normal
HbS - glutamate replaced with valine
HbC - glutamate replaced with lysine (lyCine)
- Both are Missense mutations
- HbA > HbS > HbC
snRNPs
(small nuclear ribonucleoproteins)
- What is their function?
- In what disease can they be affected?
- They are an important component of the spliceosome and are required for splicing
2. Lupus** due to its **anti-smith antibodies which are directed against snRNPs
If there is a build-up of many very long chained or branced fatty acids, which organelle is most likely not functioning?
Peroxisome
Function: oxidation of very long and brached chain fatty acids
A mutation involving the enzyme Phosphoribosyl Pyrophosphate (PRPP) sythetase gene is most likely to result in what?
Gout
Due to increased production and degredation of purines
Propionic Acidemia
- What will be elevated?
- What enzyme is deficient?
- Which amino acids can cause it?
- Propionyl Co-A
- Propionyl Co-A Carboxylase
3.
Valine, isoleucine, methionine, threonine
odd-chain fatty acids
Methylmalonic Acidemia
- What will be elevated?
- What enzyme is deficient?
- Which amino acids can cause it?
- Methylmalonyl Co-A
- Methylmalonyl Co-A Carboxylase
3.
Valine, isoleucine, methionine, threonine
odd-chain fatty acids
What is the base sequence at the 3’end of a tRNA?
CCA tail
What is the most important function of the Smooth Endoplasmic Reticulum (SER)?
Steroidgenesis
(it is involved in the processing and synthesis of hydrophobic compounds)
Which enzyme is responsible for causing bruises to appear greenish?
Heme Oxigenase
(converts heme to bilverdin)
What substance is responsible for regulating both fatty acid synthesis and breakdown (beta-oxidation)?
Malonyl-CoA
(it is the rate limiting step in FA synthesis)
(it can also inhibit B-oxidation)
Tetrahydrobiopeterin
- What is its abbreviation?
- What products require it for formation?
- BH4
2.
Tyrosine, Dopamine, Serotonin
Protein kinase B (Akt)
- What signalling pathway does it activate?
- What does it?
- mTOR pathway
2.
It translocates to nucleus and induces genes involved in cell-survival, anti-apoptosis and angiogenesis
What process causes vitamin C deficiency to result in scurvy?
Where does this process normally take place?
Vitamin C is needed for hydroxylation of proline and lysine in collagen
This takes place in Rough Endoplasmic Reticulum (RER)
Which amino acid is most likely to become essential in a patient with homocystinuria? Why?
Cysteine
Since its most commonly due to Cystathione Synthase deficinecy which results in the inability to convert homocysteine to cysteine
