FOM Module 0-2 Extras

Question 1

Key interactions of primary structure

Answer 1

Peptide bonds

Question 2

Key interactions of secondary structure

Answer 2

Hydrogen bonds
Electrostatic (Ionic)

Question 3

Key interactions of tertiary structure

Answer 3

Hydrophobic
Disulfide bonds

Question 4

Key interactions of quaternary structure

Answer 4

Subunit interactions
Salt bridges

Question 5

Essential amino acids

Answer 5

Phenylalanine (F)
Valine (V)
Tryptophan (W)
Threonine (T)
Isoleucine (I)
Methionine (M)
Histidine (H)
Leucine (L)
Lysine (K)

Question 6

Hydrophobic amino acids

Answer 6

Glycine (G)
Alanine (A)
Proline (P)
Valine (V)
Leucine (L)
Isoleucine (I)
Methionine (M)
Phenylalanine (F)
Tryptophan (W)

Question 7

Hydrophilic amino acids

Answer 7

Serine (S)
Tyrosine (Y)
Glutamine (Q)
Asparagine (N)
Cysteine (C)
Threonine (T)

Question 8

Acidic amino acids

Answer 8

Aspartate (D)
Glutamate (E)

Question 9

Basic amino acids

Answer 9

Arginine (R)
Lysine (K)
Histidine (H)

Question 10

Examples of chaperone proteins

Answer 10

Disulfide isomerase (PDI)
Calnexin (Glycoprotein)
Calreticulin (Glycoprotein)
Heat shock proteins (HSP)

Question 11

Components of aging that lead to proteostasis imbalance

Answer 11

Altered posttranslational modification of amino acids
Decreased chaperone activity
Altered ubiquitin activity
Increased protein oxidation

Question 12

Downrange effects of proteostasis imbalance

Answer 12

Misfolded proteins ->
Protein aggregation ->
Alzheimer disease, Parkinson disease, heart disease, cancer

Question 13

What is the function of PINK1

Answer 13

PINK1 activates PARKIN to degrade damaged mitochondria

Question 14

Defects in what genes causes Parkinson disease

Answer 14

PINK1 or PARKIN

Question 15

What is the function of enzymes

Answer 15

Decrease activation energy

Question 16

What is the most common relationship of the inhibitor molecule to the allosteric enzyme in feedback inhibition of enzyme activity (negative feedback)

Answer 16

The inhibitor is the final product of the metabolic pathway

Question 17

When is glucose diffused through facilitated diffusion (GLUT4)

Answer 17

After eating when the glucose concentration is higher in the intestinal lumen than inside the cells

Question 18

What receptors are examples of ligand-gated channels?

Answer 18

Nicotine acetylcholine
GABA

Question 19

What receptors are examples of GPCR

Answer 19

Adrenoreceptors
Muscarinic (mushrooms)

Question 20

What other name is PKB known as

Answer 20

AKT

Question 21

2nd messenger cAMP is released by

Answer 21

Adenylate cyclase

Question 22

2nd messenger IP3 is released by

Answer 22

Phospholipase C

Question 23

2nd messenger IP3 precursor is

Answer 23

PIP2

Question 24

2nd messenger calcium is terminated by

Answer 24

Extrusion pumps

Question 25

Competitive inhibitors

Answer 25

Increase Km Don't change Vmax Can be reversed with extra substrate

Question 26

Noncompetitive inhibitors

Answer 26

Don't change Km Decrease Vmax Cannot be reversed

Question 27

Do allosteric regulators participate in enzyme kinetics

Answer 27

No

Question 28

Primary factor in migration of proteins in SDS-PAGE

Answer 28

Molecular weight

Question 29

What is PAGE used for

Answer 29

Separate proteins by weight or charge

Question 30

Why use SDS-PAGE instead of native

Answer 30

When you want to denature proteins Purify proteins for western blot

Question 31

What samples are used in ELISA

Answer 31

Measurement of a specific protein, hormone, antibodies, or known biomarkers (ng-pg) in tissue homogenates, cell lysates, serum, saliva, synovial fluid

Question 32

What is IHC used to find

Answer 32

Expression of specific protein in cells tissues Tissue pathology in biopsy samples, fixed tissue and cells

Question 33

What does IHC give you as a result

Answer 33

Qualitative visual identification

Question 34

What do kinases do

Answer 34

Add phosphate (activate)

Question 35

What do phosphatases do

Answer 35

Remove phosphate (inactivate)

Question 36

Adapter proteins in insulin signaling

Answer 36

Grb2 MYD88

Question 37

Ligand for JAK/STAT

Answer 37

Cytokines

Question 38

Ligand for GPCR pathway

Answer 38

GABA Serotonin Acetylcholine

Question 39

Scaffold proteins in insulin pathway

Answer 39

MEKK1 BCL-10

Question 40

What are upstream enhancers and silencers

Answer 40

Regulatory elements that can enhance or repress gene transcription from a distance by interacting with transcription factors and other proteins.

Question 41

What are exons

Answer 41

Coding sequences within a gene that are transcribed and translated into protein

Question 42

What is the terminator region

Answer 42

A sequence that signals the end of transcription, ensuring the proper release of the RNA transcript

Question 43

What are downstream enhancers and silencers

Answer 43

Regulatory elements that can enhance or repress gene transcription by interacting with transcription factors and other proteins

Question 44

Point mutations

Answer 44

None Silent Nonsense Conservative missense Nonconservative missense

Question 45

Nonconservative missense

Answer 45

Amino acid is changed to one with different properties

Question 46

Nonsense mutation

Answer 46

Amino acid is changed to a STOP

Question 47

When do you use PCR

Answer 47

When you want to amplify a desired gene Diagnostic for neonatal HIV, herpes encephalitis

Question 48

What does Southwestern blot do

Answer 48

Detects DNA binding proteins

Question 49

When do you use Southwestern blot

Answer 49

Identifying DNABP using dsDNA probes Explores transcription factors

Question 50

What does is situ hybridization (ISH) do

Answer 50

Detect DNA and RNA

Question 51

When do you use ISH

Answer 51

Detecting nucleic acids within tissue sections or whole cells (FISH) Detects chromosomal abnormalities (FISH) Detects infectious disease

Question 52

What does Next-Generation Sequencing (NGS) do

Answer 52

Detailed genetic profiling

Question 53

When do you use NGS

Answer 53

Genetically profile cancer Rare diseases Personalized medicine Vaccine development

Question 54

When do you use Restriction endonuclease treatment

Answer 54

Generating restriction fragments

Question 55

What does Restriction endonuclease treatment do

Answer 55

Detects mutations Gene structure Mostly genetic engineering

Question 56

Function of the A site

Answer 56

Bind aminoacyl-tRNA

Question 57

Role of A site

Answer 57

Ensure correct amino acid is added

Question 58

Function of P site

Answer 58

Hold tRNA with growing polypeptide chain

Question 59

Role of P site

Answer 59

Facilitate peptide bond formation between chain and new aa

Question 60

Function of E site

Answer 60

Release deacylated tRNA

Question 61

Role of E site

Answer 61

Allow tRNA to exit

Question 62

What does blocking E site do

Answer 62

Inhibits translocation

Question 63

What does tRNA do

Answer 63

Matches anticodon with codon on mRNA to ensure correct sequence

Question 64

What is mRNA's function

Answer 64

Carry genetic information from DNA to ribosomes

Question 65

Where is mRNA made

Answer 65

Nucleus but active in cytoplasm

Question 66

Where is rRNA made

Answer 66

Nucleolus but active in the cytoplasm

Question 67

Stability level of rRNA

Answer 67

Very stable

Question 68

Key features of rRNA

Answer 68

Integral to ribosomes Catalyzes peptide bond formation

Question 69

What is snRNA's funciton

Answer 69

Form snRNP (small nuclear ribonucleoproteins) to make spliceosomes to splice RNA

Question 70

Where is snRNA active

Answer 70

Nucleus

Question 71

What is miRNA's function

Answer 71

Regulate gene expression by binding 3' end of untranslated region (UTR) of mRNA leading to repression or degradation

Question 72

Where is miRNA active

Answer 72

Cytoplasm

Question 73

What is siRNA's function

Answer 73

RNA interference leading to degradation of specific mRNA

Question 74

Activity level of RNA polymerase I

Answer 74

High activity due to high ribosome demand

Question 75

Function of RNA polymerase II

Answer 75

Synthesize mRNA, snRNA, miRNA, and IncRNA Codes most protein-coding genes

Question 76

What is the function of SRP

Answer 76

Binding of SRP temporarily halts translation into ER, which pauses the elongation of the polypeptide chain to prevent premature folding

Question 77

Disease relating to untranslated repeats (specifically CTG)

Answer 77

Myotonic dystrophy

Question 78

What is DNA methylation

Answer 78

Addition of a methyl group (CH3) to cytosine residues in DNA, typically at CpG dinucleotide

Question 79

How does histone methylation affect gene expression

Answer 79

Associated with either gene activation or repression