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Comp Bio > LO9 Protein Identification and Analysis > Flashcards

LO9 Protein Identification and Analysis Flashcards

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Biology 101 flashcards
1
Q

polypeptide polymers consisting of a linear arrangement of amino acids

A

Proteins

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2
Q

3 functions of proteins

A

➢ Structural (e.g., actin contributes to the cytoskeleton)
➢ Enzymatic (e.g., hexokinase as the first catalyst of glycolysis)
➢ Transport (e.g., GLUT1 as glucose transporters)

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3
Q

large-scale determination of gene and cellular function directly at the protein level

A

Proteomics

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4
Q

method of choice for proteomics

A

Mass spectrometry

  • ion source + mass analyser =mass-to-charge ratio (m/z) of the ionized analytes
  • detector that registers the number of
    ions at each m/z value
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5
Q

2 methods to ionize protein

A
  1. Electrospray ionization
  2. Matrix-assisted laser desorption/ionization (MALDI)
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6
Q

Steps for Spectrometry

A
  1. Sample fractionation
  2. Trypsin digestion
  3. Peptide chromatography and ESI
  4. Mass spectrometry (MS)
  5. Tandem mass spectrometry (MS/MS)
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7
Q

Classic techniques cleave

A
  1. Edman degradation = chemical modification of the N-terminal AA
  2. Edman + Fluorosequencing = uses single-molecule microscopy and stable synthetic fluorophore chemistry/probes
  3. Single-molecule mass spectrometry = with a nanopore ion source delivering individual AA directly into the high-vacuum gas phase
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8
Q

DNA-facilitated protein sequencing

Relies on the transient binding of dye-labeled DNA strands (imagers) to their complementary target sequence (docking site) attached to a molecule of interest

A

DNA-PAINT = DNA-based Point Accumulation for Imaging in Nanoscale Topography

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9
Q

Strategies for Nanopore-based Sequencing

= give time-dependent and sequence-specific electrical signals

A

Biological and solid-state nanopores

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10
Q

Strategies for Nanopore-based Sequencing

A

a. single-file threading and direct sensing of the sequence
b. sensing unique fingerprints in linearized proteins
c. identification of folded proteins

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11
Q

Emerging Landscape of Protein Sequencing Techniques/Methods

A

FRET X
NEMS-MS
DNA-PAINT
N-terminal probes
Biological Nanopores
Recognition tunneling
Motor protein scanning
Single-molecule CDMS
DNA proximity recording

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12
Q

Four Perspectives of Protein Analysis

A
  1. Families (Domains & Motifs)
  2. Physical Properties
  3. Localization
  4. Function
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13
Q

Gene ontology:

A
  • cellular compartment
  • biological process
  • molecular function
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14
Q

= a broad term that denotes a protein category (domain or family or motif)

A

Signature - (largest)

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15
Q

= is a region of a protein that can adopt a particular three‐dimensional structure (fold)

A

Domains (aka modules)

*but modules are shorter than domains

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16
Q

= are short, conserved regions of proteins that typically characterize a protein family

A

Motifs (aka fingerprints) - (shortest)

17
Q

Group of proteins that share a common evolutionary origin

A

Family

18
Q

Most common domains of Homo sapiens

A

Zinc finger; C2H2
Zinc finger; C2H2-like
Immunoglobulin V-set
Immunoglobulin subtype
Immunoglobulin-like domain

19
Q

Many proteins have multiple copies of distinct domains.

The most common domain in humans is the ________, and the ______ repeat also commonly occurs. These domains are especially prevalent in the extracellular regions of proteins.

A

immunoglobulin (Ig) domain
fibronectin

20
Q

Proteins can share a common domain in a number of ways

(a) A domain may essentially extend across the length of a protein. (- Lipocalin family)
(b) Domains may contain highly related stretches of amino acids that form only a subset of each protein’s sequence. (-Transcriptional regulators)
(c) A domain may be repeated within a single protein (sometimes with many copies). (-Fibronectin III-like repeat)

A
21
Q

Physical properties of proteins

A

Amino acid motifs
Isoelectric point
Molecular weight
Sedimentation coefficient
Stokes radius
Transmembrane domain

22
Q

post‐translational modifications are added to proteins

A

Amino Acid Modification (Irreversible)
Deamidation
Eliminylation

Cleavage (Irreversible)
Proteolysis

Addition of Polypeptides (Reversible)
Ubiquitylation
UBL-protein Conjugation (e.g. SUMO)

Addition of Complex Molecules (Reversible)
AMPylation
ADP-Ribosylation
Glycosylation
Prenylation

Addition of Chemical Groups (Reversible)
Hydroxylation
Phosphorylation
Acetylation
Methylation

23
Q

= description of concepts

A

Ontology

24
Q

= a project that compiles a dynamic, controlled vocabulary of terms related to different aspects of genes and gene products (proteins)

  • standardized vocabulary of terms
A

GO Consortium

25
Q

3 main organizing principles of GO

A
  1. Molecular function = the tasks performed by individual gene products
  2. Biological process = associated broad goals of a gene product (protein)
  3. Cellular compartment = the subcellular localization of a protein
26
Q

A _____ refers to the node closer to the roots of the graph

A

Parent

27
Q

A _____ refers to the nodes closer to the leaf nodes

A

Child

28
Q

The ____ indicates the direction of the relationship

A

Arrowhead

29
Q

______ represents an inferred relationship

A

Dotted lines

30
Q

Protein localization categories based on their relationship to the plasma membrane

A

➢ Soluble = exists within PM, lumen of organelle, or extracellularly
➢ Membrane attached = direct/indirect association with PM

31
Q

is a gene product that interacts with the cellular environment in some
way to promote the cell’s growth and function

A

Protein

32
Q

Perspective on Protein Function
1. Biochemical function synonymous with its molecular function
* Enzymatic, structural, transport, etc.
2. Functional assignment is often made based upon homology
* Provisional/hypothetical assignment of function
3. Functions may be assigned based on the structure
* Related 3D folding may signify a similar function
4. All proteins function in the context of their interaction with other molecules
* Ligands to receptors; substrates to enzymes, etc
5. Many proteins function as part of a distinct biochemical pathway
6. Proteins function as part of some broad cell biological process
7. Protein function can be considered in the context of the proteome

A

Comp Bio (10 decks)

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