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2C MIDTERMS > BIOCHEM 4 & 5 > Flashcards

BIOCHEM 4 & 5 Flashcards

1
Q

Life cycle of protein

A

Translation, Post-translational modifications, Age via oxidation, Degrade into amino acids

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2
Q

Importance of Protein Purification

A

Detailed and accurate study of protein properties

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3
Q

Living organisms contain thousands of proteins in varying amounts,
so _____________ can interfere with accurate analysis

A

contaminants

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4
Q

Differences in solubility based on pH, polarity, or salt concentration

A

Selective precipitation

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5
Q

Stationary phase (beads in columns) separates proteins by size, charge, hydrophobicity, or affinity for ligands

A

Column chromatography

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6
Q

Uses small, strong silica beads for high resolution separation under high pressure

A

High-Pressure Liquid
Chromatography (HPLC)

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7
Q

Traditional column chromatography uses _______________ that ____________________
the separation process and_______________.

A

large beads, slow down, lower resolution

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8
Q

HPLC uses ______________ beads that allow better separation of
proteins due to the ______________________.

A

tiny & porous silica, higher surface area

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9
Q

In HPLC the small size of the beads means ________________________ are needed to push the liquid through the column, but this pressure results in ____________
and more ____________ protein separation.

A

higher pressures, faster, precise

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10
Q

Separation by size; larger proteins
move faster

A

Size-Exclusion Chromatography

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11
Q

In Size-Exclusion Chromatography __________ proteins cannot enter the porous beads used in the stationary phase, so they pass through the column faster than ____________ proteins, which are
delayed as they enter the pores

A

Larger, smaller

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12
Q

Separation by charge; positive proteins bind to negative beads

A

Ion-Exchange Chromatography

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13
Q

Separation by hydrophobicity; useful for membrane
proteins

A

Hydrophobic Interaction Chromatography

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14
Q

Separation of proteins by size; polypeptides
migrate based on molecular mass.

A

SDS-PAGE

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15
Q

SDS-PAGE is visualized with dyes like _______________________

A

Coomassie Blue

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16
Q

Separates proteins based on isoelectric point
(pI); used in 2D electrophoresis combined
with SDS-PAGE

A

Isoelectric Focusing (IEF)

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17
Q

SDS (sodium dodecyl sulfate) binds to proteins in a ratio that is
__________________ to the protein’s size, essentially giving each protein a uniform _______________ ratio.

A

proportional, charge-to-mass

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18
Q

The separation of proteins in SDS-PAGE depends purely on their _____, not their intrinsic _______________

A

size, charge or shape

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19
Q

First method for polypeptide
sequencing, used insulin as the model

A

Sanger Sequencing

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20
Q

Sequential removal of
amino acids from the N-
terminus

A

Edman Degradation

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21
Q

Edman Degradation is ore efficient but limited
to _________ sequences (_______ residues)

A

shorter, 5- 30

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22
Q

Edman degradation method has limitations such as its inefficiency with______________ and ___________________

A

longer peptides, low throughput

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23
Q

__________________________ is faster, more sensitive, and capable of detecting minute posttranslational modifications.

A

Mass spectrometry

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24
Q

One of the key advantages of mass spectrometry is its ability to detect modifications like _________________, ______________, and ____________________, which
are important for understanding protein function and regulation.

A

phosphorylation, methylation, glycosylation

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25
Q

Revolutionized protein sequencing, identifying proteins by
their mass and modifications.

A

Mass Spectrometry

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26
Q

Techniques to vaporize proteins for mass analysis

A

Electrospray Ionization and MALDI

27
Q

Allows for analysis of complex peptide mixtures without prior purification

A

Tandem MS (MS/MS)

28
Q

In Tandem MS Proteins are first __________ and _______________

A

ionized, fragmented

29
Q

__________________ are more susceptible to breaking than ___________________, meaning the primary fragmentation products are peptides of
varying lengths

A

Peptide bonds, carbon-carbon
bonds

30
Q

_______________ are weaker than most other bonds in a protein, making them the ________________________ during mass spectrometry.
This selective fragmentation allows for accurate sequencing.

A

Peptide bonds, primary targets for fragmentation

31
Q

Goal is to map the entire proteome under diverse
conditions, identifying proteins and their modifications

A

Proteomics

32
Q

Facilitates the understanding of protein functions by
comparing sequences and using gene arrays

A

Bioinformatics

33
Q

crucial for function, whether in catalysis, motion,
or providing structural integrity

A

PROTEINS

34
Q

involves spatial arrangement
(reversible)

A

Conformation

35
Q

requires breaking covalent bonds

A

Configuration

36
Q

Linear sequence of amino acids

A

Primary Structure

37
Q

Local folding into α-helices and β-sheets

A

Secondary Structure

38
Q

3D folding of the entire polypeptide
chain

A

Tertiary Structure

39
Q

Assembly of multiple polypeptide
chains

A

Quaternary Structure

40
Q

Twisted backbone stabilized
by hydrogen bonds, often
amphipathic

A

Alpha Helix

41
Q

Proteins are composed of __________________, and their
stereochemistry favors the
formation of ______________________

A

L- amino acids, right-handed
alpha helices

42
Q

_________________ are unstable and
rarely form due to steric hindrance and _______________ interactions between amino acids

A

Left-handed helices, less favorable

43
Q

Alpha helices are stabilized by
___________________ between the
__________________ and the ______________________ spaced _____ residues apart, giving the helix its regular, coiled structure

A

hydrogen bonds, carbonyl oxygen, amide hydrogen of amino acids, four

44
Q

_______________ lacks the hydrogen atom required to form hydrogen bonds in an alpha helix, which makes it a
“_______________________.”

A

Proline, helix breaker

45
Q

Its rigid structure introduces a kink or bend in the helix, disrupting the regular hydrogen bonding pattern

A

Proline

46
Q

due to its small size
and flexibility, can also
disrupt the helix structure,
although it does not break
the helix as dramatically as
proline

A

Glycine

47
Q

Zigzag backbone
stabilized by interstrand
hydrogen bonds

A

Beta Sheet

48
Q

Shows permissible
φ(phi) and ψ (psi)
angles for secondary
structures

A

Ramachandran Plot

49
Q

Complex 3D arrangement of helices, sheets, and loops
forming functional domains

A

Tertiary structure

50
Q

Modular units of structure within a protein, often having
specific functions

A

Domains

51
Q

are distinct structural units within a polypeptide, and
each domain can perform a specific function

A

Protein domains

52
Q

Domains are ______________, meaning they can fold independently and carry
out their function regardless of the rest of the protein’s structure

A

modular

53
Q

This modularity allows proteins to perform complex tasks efficiently

A

Independent Folding

54
Q

Proteins with multiple subunits,
such as homodimers or
heterodimers

A

Oligomeric Proteins

55
Q

Most energetically favorable and functional state

A

Native Conformation

56
Q

Folding Process is a ______________ with the aid of chaperones

A

Modular process

57
Q

Proteins fold via an ordered process involving ___________,
_________, and _______________ structures

A

secondary, tertiary, quaternary

58
Q

Stabilization Forces

A

Hydrogen bonds, van der Waals forces, Hydrophobic interactions

59
Q

are often found in the hydrophobic cores of globular
proteins because their extended structure can pack tightly and
exclude water, stabilizing the overall fold of the protein

A

Beta sheets

60
Q

Loops and turns, which are more flexible and irregular, are
typically found on the _________________, where they interact with
the aqueous environment or other molecules

A

protein surface

61
Q

Proteins like _______________ and __________________ assist
in proper folding and prevent aggregation

A

chaperones, disulfide isomerase

62
Q

High-resolution 3D structure determination

A

X-ray Crystallography

63
Q

Used to study proteins in solution

A

Nuclear Magnetic Resonance (NMR)

64
Q

Emerging technique for studying large protein complexes

A

Cryo-Electron Microscopy (Cryo-EM)

2C MIDTERMS (14 decks)

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