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Noorda FOM > FOM Module 0-2 Extras > Flashcards

FOM Module 0-2 Extras Flashcards

1
Q

Key interactions of primary structure

A

Peptide bonds

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2
Q

Key interactions of secondary structure

A

Hydrogen bonds
Electrostatic (Ionic)

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3
Q

Key interactions of tertiary structure

A

Hydrophobic
Disulfide bonds

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4
Q

Key interactions of quaternary structure

A

Subunit interactions
Salt bridges

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5
Q

Essential amino acids

A

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

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6
Q

Hydrophobic amino acids

A

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

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7
Q

Hydrophilic amino acids

A

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

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8
Q

Acidic amino acids

A

Aspartate (D)
Glutamate (E)

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9
Q

Basic amino acids

A

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

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10
Q

Examples of chaperone proteins

A

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

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11
Q

Components of aging that lead to proteostasis imbalance

A

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

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12
Q

Downrange effects of proteostasis imbalance

A

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

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13
Q

What is the function of PINK1

A

PINK1 activates PARKIN to degrade damaged mitochondria

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14
Q

Defects in what genes causes Parkinson disease

A

PINK1 or PARKIN

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15
Q

What is the function of enzymes

A

Decrease activation energy

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16
Q

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

A

The inhibitor is the final product of the metabolic pathway

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17
Q

When is glucose diffused through facilitated diffusion (GLUT4)

A

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

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18
Q

What receptors are examples of ligand-gated channels?

A

Nicotine acetylcholine
GABA

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19
Q

What receptors are examples of GPCR

A

Adrenoreceptors
Muscarinic (mushrooms)

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20
Q

What other name is PKB known as

A

AKT

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21
Q

2nd messenger cAMP is released by

A

Adenylate cyclase

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22
Q

2nd messenger IP3 is released by

A

Phospholipase C

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23
Q

2nd messenger IP3 precursor is

A

PIP2

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24
Q

2nd messenger calcium is terminated by

A

Extrusion pumps

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25
Q

Competitive inhibitors

A

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

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26
Q

Noncompetitive inhibitors

A

Don’t change Km
Decrease Vmax
Cannot be reversed

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27
Q

Do allosteric regulators participate in enzyme kinetics

A

No

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28
Q

Primary factor in migration of proteins in SDS-PAGE

A

Molecular weight

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29
Q

What is PAGE used for

A

Separate proteins by weight or charge

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30
Q

Why use SDS-PAGE instead of native

A

When you want to denature proteins
Purify proteins for western blot

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31
Q

What samples are used in ELISA

A

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

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32
Q

What is IHC used to find

A

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

33
Q

What does IHC give you as a result

A

Qualitative visual identification

34
Q

What do kinases do

A

Add phosphate (activate)

35
Q

What do phosphatases do

A

Remove phosphate (inactivate)

36
Q

Adapter proteins in insulin signaling

A

Grb2
MYD88

37
Q

Ligand for JAK/STAT

A

Cytokines

38
Q

Ligand for GPCR pathway

A

GABA
Serotonin
Acetylcholine

39
Q

Scaffold proteins in insulin pathway

A

MEKK1
BCL-10

40
Q

What are upstream enhancers and silencers

A

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

41
Q

What are exons

A

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

42
Q

What is the terminator region

A

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

43
Q

What are downstream enhancers and silencers

A

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

44
Q

Point mutations

A

None
Silent
Nonsense
Conservative missense
Nonconservative missense

45
Q

Nonconservative missense

A

Amino acid is changed to one with different properties

46
Q

Nonsense mutation

A

Amino acid is changed to a STOP

47
Q

When do you use PCR

A

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

48
Q

What does Southwestern blot do

A

Detects DNA binding proteins

49
Q

When do you use Southwestern blot

A

Identifying DNABP using dsDNA probes
Explores transcription factors

50
Q

What does is situ hybridization (ISH) do

A

Detect DNA and RNA

51
Q

When do you use ISH

A

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

52
Q

What does Next-Generation Sequencing (NGS) do

A

Detailed genetic profiling

53
Q

When do you use NGS

A

Genetically profile cancer
Rare diseases
Personalized medicine
Vaccine development

54
Q

When do you use Restriction
endonuclease treatment

A

Generating restriction fragments

55
Q

What does Restriction
endonuclease treatment do

A

Detects mutations
Gene structure
Mostly genetic engineering

56
Q

Function of the A site

A

Bind aminoacyl-tRNA

57
Q

Role of A site

A

Ensure correct amino acid is added

58
Q

Function of P site

A

Hold tRNA with growing polypeptide chain

59
Q

Role of P site

A

Facilitate peptide bond formation between chain and new aa

60
Q

Function of E site

A

Release deacylated tRNA

61
Q

Role of E site

A

Allow tRNA to exit

62
Q

What does blocking E site do

A

Inhibits translocation

63
Q

What does tRNA do

A

Matches anticodon with codon on mRNA to ensure correct sequence

64
Q

What is mRNA’s function

A

Carry genetic information from DNA to ribosomes

65
Q

Where is mRNA made

A

Nucleus but active in cytoplasm

66
Q

Where is rRNA made

A

Nucleolus but active in the cytoplasm

67
Q

Stability level of rRNA

A

Very stable

68
Q

Key features of rRNA

A

Integral to ribosomes
Catalyzes peptide bond formation

69
Q

What is snRNA’s funciton

A

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

70
Q

Where is snRNA active

A

Nucleus

71
Q

What is miRNA’s function

A

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

72
Q

Where is miRNA active

A

Cytoplasm

73
Q

What is siRNA’s function

A

RNA interference leading to degradation of specific mRNA

74
Q

Activity level of RNA polymerase I

A

High activity due to high ribosome demand

75
Q

Function of RNA polymerase II

A

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

76
Q

What is the function of SRP

A

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

77
Q

Disease relating to untranslated repeats (specifically CTG)

A

Myotonic dystrophy

78
Q

What is DNA methylation

A

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

79
Q

How does histone methylation affect gene expression

A

Associated with either gene activation or repression

Noorda FOM (18 decks)

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