FOM Module 0-2 Extras Flashcards
Key interactions of primary structure
Peptide bonds
Key interactions of secondary structure
Hydrogen bonds
Electrostatic (Ionic)
Key interactions of tertiary structure
Hydrophobic
Disulfide bonds
Key interactions of quaternary structure
Subunit interactions
Salt bridges
Essential amino acids
Phenylalanine (F)
Valine (V)
Tryptophan (W)
Threonine (T)
Isoleucine (I)
Methionine (M)
Histidine (H)
Leucine (L)
Lysine (K)
Hydrophobic amino acids
Glycine (G)
Alanine (A)
Proline (P)
Valine (V)
Leucine (L)
Isoleucine (I)
Methionine (M)
Phenylalanine (F)
Tryptophan (W)
Hydrophilic amino acids
Serine (S)
Tyrosine (Y)
Glutamine (Q)
Asparagine (N)
Cysteine (C)
Threonine (T)
Acidic amino acids
Aspartate (D)
Glutamate (E)
Basic amino acids
Arginine (R)
Lysine (K)
Histidine (H)
Examples of chaperone proteins
Disulfide isomerase (PDI)
Calnexin (Glycoprotein)
Calreticulin (Glycoprotein)
Heat shock proteins (HSP)
Components of aging that lead to proteostasis imbalance
Altered posttranslational modification of amino acids
Decreased chaperone activity
Altered ubiquitin activity
Increased protein oxidation
Downrange effects of proteostasis imbalance
Misfolded proteins ->
Protein aggregation ->
Alzheimer disease, Parkinson disease, heart disease, cancer
What is the function of PINK1
PINK1 activates PARKIN to degrade damaged mitochondria
Defects in what genes causes Parkinson disease
PINK1 or PARKIN
What is the function of enzymes
Decrease activation energy
What is the most common relationship of the inhibitor molecule to the allosteric enzyme in feedback inhibition of enzyme activity (negative feedback)
The inhibitor is the final product of the metabolic pathway
When is glucose diffused through facilitated diffusion (GLUT4)
After eating when the glucose concentration is higher in the intestinal lumen than inside the cells
What receptors are examples of ligand-gated channels?
Nicotine acetylcholine
GABA
What receptors are examples of GPCR
Adrenoreceptors
Muscarinic (mushrooms)
What other name is PKB known as
AKT
2nd messenger cAMP is released by
Adenylate cyclase
2nd messenger IP3 is released by
Phospholipase C
2nd messenger IP3 precursor is
PIP2
2nd messenger calcium is terminated by
Extrusion pumps
Competitive inhibitors
Increase Km
Don’t change Vmax
Can be reversed with extra substrate
Noncompetitive inhibitors
Don’t change Km
Decrease Vmax
Cannot be reversed
Do allosteric regulators participate in enzyme kinetics
No
Primary factor in migration of proteins in SDS-PAGE
Molecular weight
What is PAGE used for
Separate proteins by weight or charge
Why use SDS-PAGE instead of native
When you want to denature proteins
Purify proteins for western blot
What samples are used in ELISA
Measurement of a specific protein, hormone, antibodies, or known biomarkers (ng-pg) in tissue
homogenates, cell lysates, serum, saliva, synovial fluid
What is IHC used to find
Expression of specific protein in cells tissues
Tissue pathology in biopsy samples, fixed tissue and cells
What does IHC give you as a result
Qualitative visual identification
What do kinases do
Add phosphate (activate)
What do phosphatases do
Remove phosphate (inactivate)
Adapter proteins in insulin signaling
Grb2
MYD88
Ligand for JAK/STAT
Cytokines
Ligand for GPCR pathway
GABA
Serotonin
Acetylcholine
Scaffold proteins in insulin pathway
MEKK1
BCL-10
What are upstream enhancers and silencers
Regulatory elements that can enhance or repress gene transcription from a distance by interacting with transcription factors and other proteins.
What are exons
Coding sequences within a gene that are transcribed and translated into protein
What is the terminator region
A sequence that signals the end of transcription, ensuring the proper release of the RNA transcript
What are downstream enhancers and silencers
Regulatory elements that can enhance or repress gene transcription by interacting with transcription factors and other proteins
Point mutations
None
Silent
Nonsense
Conservative missense
Nonconservative missense
Nonconservative missense
Amino acid is changed to one with different properties
Nonsense mutation
Amino acid is changed to a STOP
When do you use PCR
When you want to amplify a desired gene
Diagnostic for neonatal HIV, herpes encephalitis
What does Southwestern blot do
Detects DNA binding proteins
When do you use Southwestern blot
Identifying DNABP using dsDNA probes
Explores transcription factors
What does is situ hybridization (ISH) do
Detect DNA and RNA
When do you use ISH
Detecting nucleic acids within tissue sections or whole cells
(FISH) Detects chromosomal abnormalities
(FISH) Detects infectious disease
What does Next-Generation Sequencing (NGS) do
Detailed genetic profiling
When do you use NGS
Genetically profile cancer
Rare diseases
Personalized medicine
Vaccine development
When do you use Restriction
endonuclease treatment
Generating restriction fragments
What does Restriction
endonuclease treatment do
Detects mutations
Gene structure
Mostly genetic engineering
Function of the A site
Bind aminoacyl-tRNA
Role of A site
Ensure correct amino acid is added
Function of P site
Hold tRNA with growing polypeptide chain
Role of P site
Facilitate peptide bond formation between chain and new aa
Function of E site
Release deacylated tRNA
Role of E site
Allow tRNA to exit
What does blocking E site do
Inhibits translocation
What does tRNA do
Matches anticodon with codon on mRNA to ensure correct sequence
What is mRNA’s function
Carry genetic information from DNA to ribosomes
Where is mRNA made
Nucleus but active in cytoplasm
Where is rRNA made
Nucleolus but active in the cytoplasm
Stability level of rRNA
Very stable
Key features of rRNA
Integral to ribosomes
Catalyzes peptide bond formation
What is snRNA’s funciton
Form snRNP (small nuclear ribonucleoproteins) to make spliceosomes to splice RNA
Where is snRNA active
Nucleus
What is miRNA’s function
Regulate gene expression by binding 3’ end of untranslated region (UTR) of mRNA leading to repression or degradation
Where is miRNA active
Cytoplasm
What is siRNA’s function
RNA interference leading to degradation of specific mRNA
Activity level of RNA polymerase I
High activity due to high ribosome demand
Function of RNA polymerase II
Synthesize mRNA, snRNA, miRNA, and IncRNA
Codes most protein-coding genes
What is the function of SRP
Binding of SRP temporarily halts translation into ER, which pauses the elongation of the polypeptide chain to prevent premature folding
Disease relating to untranslated repeats (specifically CTG)
Myotonic dystrophy
What is DNA methylation
Addition of a methyl group (CH3) to cytosine residues in DNA, typically at CpG dinucleotide
How does histone methylation affect gene expression
Associated with either gene activation or repression
