BIOCHEM 4 & 5

Question 1

Life cycle of protein

Answer 1

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

Question 2

Importance of Protein Purification

Answer 2

Detailed and accurate study of protein properties

Question 3

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

Answer 3

contaminants

Question 4

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

Answer 4

Selective precipitation

Question 5

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

Answer 5

Column chromatography

Question 6

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

Answer 6

High-Pressure Liquid
Chromatography (HPLC)

Question 7

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

Answer 7

large beads, slow down, lower resolution

Question 8

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

Answer 8

tiny & porous silica, higher surface area

Question 9

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.

Answer 9

higher pressures, faster, precise

Question 10

Separation by size; larger proteins
move faster

Answer 10

Size-Exclusion Chromatography

Question 11

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

Answer 11

Larger, smaller

Question 12

Separation by charge; positive proteins bind to negative beads

Answer 12

Ion-Exchange Chromatography

Question 13

Separation by hydrophobicity; useful for membrane
proteins

Answer 13

Hydrophobic Interaction Chromatography

Question 14

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

Answer 14

SDS-PAGE

Question 15

SDS-PAGE is visualized with dyes like _______________________

Answer 15

Coomassie Blue

Question 16

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

Answer 16

Isoelectric Focusing (IEF)

Question 17

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

Answer 17

proportional, charge-to-mass

Question 18

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

Answer 18

size, charge or shape

Question 19

First method for polypeptide
sequencing, used insulin as the model

Answer 19

Sanger Sequencing

Question 20

Sequential removal of
amino acids from the N-
terminus

Answer 20

Edman Degradation

Question 21

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

Answer 21

shorter, 5- 30

Question 22

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

Answer 22

longer peptides, low throughput

Question 23

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

Answer 23

Mass spectrometry

Question 24

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.

Answer 24

phosphorylation, methylation, glycosylation

Question 25

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

Answer 25

Mass Spectrometry

Question 26

Techniques to vaporize proteins for mass analysis

Answer 26

Electrospray Ionization and MALDI

Question 27

Allows for analysis of complex peptide mixtures without prior purification

Answer 27

Tandem MS (MS/MS)

Question 28

In Tandem MS Proteins are first __________ and _______________

Answer 28

ionized, fragmented

Question 29

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

Answer 29

Peptide bonds, carbon-carbon bonds

Question 30

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

Answer 30

Peptide bonds, primary targets for fragmentation

Question 31

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

Answer 31

Proteomics

Question 32

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

Answer 32

Bioinformatics

Question 33

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

Answer 33

PROTEINS

Question 34

involves spatial arrangement (reversible)

Answer 34

Conformation

Question 35

requires breaking covalent bonds

Answer 35

Configuration

Question 36

Linear sequence of amino acids

Answer 36

Primary Structure

Question 37

Local folding into α-helices and β-sheets

Answer 37

Secondary Structure

Question 38

3D folding of the entire polypeptide chain

Answer 38

Tertiary Structure

Question 39

Assembly of multiple polypeptide chains

Answer 39

Quaternary Structure

Question 40

Twisted backbone stabilized by hydrogen bonds, often amphipathic

Answer 40

Alpha Helix

Question 41

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

Answer 41

L- amino acids, right-handed alpha helices

Question 42

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

Answer 42

Left-handed helices, less favorable

Question 43

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

Answer 43

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

Question 44

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

Answer 44

Proline, helix breaker

Question 45

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

Answer 45

Proline

Question 46

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

Answer 46

Glycine

Question 47

Zigzag backbone stabilized by interstrand hydrogen bonds

Answer 47

Beta Sheet

Question 48

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

Answer 48

Ramachandran Plot

Question 49

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

Answer 49

Tertiary structure

Question 50

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

Answer 50

Domains

Question 51

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

Answer 51

Protein domains

Question 52

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

Answer 52

modular

Question 53

This modularity allows proteins to perform complex tasks efficiently

Answer 53

Independent Folding

Question 54

Proteins with multiple subunits, such as homodimers or heterodimers

Answer 54

Oligomeric Proteins

Question 55

Most energetically favorable and functional state

Answer 55

Native Conformation

Question 56

Folding Process is a ______________ with the aid of chaperones

Answer 56

Modular process

Question 57

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

Answer 57

secondary, tertiary, quaternary

Question 58

Stabilization Forces

Answer 58

Hydrogen bonds, van der Waals forces, Hydrophobic interactions

Question 59

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

Answer 59

Beta sheets

Question 60

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

Answer 60

protein surface

Question 61

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

Answer 61

chaperones, disulfide isomerase

Question 62

High-resolution 3D structure determination

Answer 62

X-ray Crystallography

Question 63

Used to study proteins in solution

Answer 63

Nuclear Magnetic Resonance (NMR)

Question 64

Emerging technique for studying large protein complexes

Answer 64

Cryo-Electron Microscopy (Cryo-EM)