Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

BIOCHEM > CH 4 (LD) > Flashcards

CH 4 (LD) Flashcards

1
Q

Peptides and proteins

A

chains of amino acids strung together in sequence via peptide bonds
- can be very short (dipeptide (2 a.a.), tripeptide, tetrapeptide)
- can be very long (over 2000 aa)
Peptide: 2-50 aa in length
Protein: more than 50 aa in length

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What is the relative mass of a 100 aa long polypeptide and a 2000 aa long polypeptide?

A

100 aa: 100 x 110 = 11,000 Da

2000 aa: 2000 x 110 = 220, 000 Da

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Conformation

A

spatial arrangement of atoms in a 3D space dependent on the rotation of a bond or bonds is a molecule’s conformation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Configuration

A

change in protein by breaking and reforming bonds

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Protein diversity

A

we can determine the expected sequence and size of almost every polypeptide through analysis of its genome

  • e.coli: 4000 different proteins
  • fruit fly: 14,000 proteins
  • humans: 20,000 different proteins
  • diversity in their shapes
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Proteomics

A

study of a large set of proteins

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Globular Proteins

A

water-soluble, compact, roughly spherical macromolecules

ex: hemoglobin

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Fibrous Proteins

A

mechanical support

ex: collagen

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

2D Electrophoresis

A

samples are separated by two via two dimensions:

1) by molecular weight
2) by pH - proteins migrate to their isoelectric point

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Protein Structure

A
  • proteins come in many shapes and sizes

- 4 levels of organization: primary, secondary, tertiary, and quaternary

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Primary Structure

A
  • its amino acid sequence

N-terminus to C-terminus

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Secondary structure

A
  • regularities in local conformations maintained by H bonds btwn amide hydrogens and carbonyl oxygen in the peptide backbone
  • alpha helices (coils) and beta sheets (arrows)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Tertiary Structure

A
  • completely folded and compacted polypeptide chain
  • many proteins consist of multiple distinct globular units called domains
  • domains: typically 50-300 aa in length
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Quaternary Structure

A

association of two or more polypeptide chains into a multisubunit or oligomeric protein

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Ex: Hemoglobin

A
  • reaches all 4 levels of organization/ structure

- transport of oxygen through the bloodstream within red blood cells

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

X-ray crystallography

A
  • technique to determine the 3D conformation of proteins
  • a beam of collimated x-rays (parallel) is aimed at a crystal of protein molecules
  • electrons in the crystal diffract the x-rays and the pattern is recorded
  • mathematical analysis is performed on the diffraction pattern produced by the electron clouds surrounding atoms in the crystal
  • the density map allows the mapping of each atom in 3D space
17
Q

Dorothy Crowfoot Hodgkin

A

pioneer in X-ray crystallography in use for biomolecules

  • solved the structure of penicillin in 1947
  • determined the structure of Vitamin B12
  • published the structure of insulin
18
Q

Limitations of X-ray crystallography

A
  • number of calculations to determine position of atoms (solution: computers)
  • preparing crystals of suitable quality for X-ray diffraction
    Solution: robotics minimize human error and increase speed
19
Q

Protein Crystallization

A
  • similar to NaCl crystallization (solution with protein is brought to a supersaturated state to crystallize)
  • Heat is not used. Other factors are used to precipitate: pH of buffer, type of salt, cofactors
  • solution gradually is saturated with precipitant to out-compete the protein for water interaction (ammonium sulfate)
  • precipitate forms and if the conditions are correct, crystals form
20
Q

Crystallizing

A

since protein crystal contain water molecules, ligands (substrates or inhibitors) can be diffused

  • proteins will many times retain their ability to bind these
  • Why would this be important when resolving structure? confirmation of correct conformation
21
Q

Protein Data Bank

A
  • where protein structures are widely
    shared
    • Databases were created in the 1970’s which are public domain and easily accessible
22
Q

Representations

A
  • There are various ways in which peptides can be represented:
    • Space-fill models
    • Simplified cartoon emphasizing the backbone
    • Emphasizing amino acid side chains and bonds
23
Q

Space-fill model

A
  • depicts atoms as spheres
  • shows how tightly packed these molecules are
  • used to show overall shape of a protein and the surface exposed to water
24
Q

Backbone structure

A
  • typically depicted emphasizing the alpha helices and beta strands
  • shows the interior of the protein
  • easier to compare and recognize patterns
25
Q

Molecular Interactions

A
  • structure emphasizes the structure of the amino acid side chains
  • covalent bonds and weak bonds are typically shown
26
Q

Nuclear Magnetic Resonance

A
  • technique to decipher protein structures
  • protein is placed in a magnetic field in solution
  • certain atomic nuclei absorb electromagnetic radiation
27
Q

NMR structure

A
  • because the absorbance is influenced by neighboring atoms, these interactions can be recorded
  • combination with amino acid structure allows calculations of structures that fit the observations
28
Q

Domains

A
  • discrete, independently folded regions of proteins
  • some can be as small as 25-30 aa and can be greater than 300 aa
  • GODLEN RANGE: the proposed ideal for stability is 50-300aa in length

Remember:

  • Peptide: 2-49 aa
  • Protein: 50+ aa
29
Q

Zn fingers

A
  • structural motif in DNA binding domain of some proteins
  • multiple types

example: C2H2 Zn Finger with secondary structures beta-beta-alpha motif that allows DNA binding

30
Q

Pyruvate Kinase

A 
PDB 1PKM
Residues: 116-219 (top part)
 - Size of domain: 104 aa stable
Residues: 1-115 and 220-388 (middle part)
 - size of domain: 284 aa stable
Residues: 389-530 (bottom part)
 - size of domain: 142 aa stable
  • the proposed ideal for stability is 50-300aa in length
31
Q

Homology in Structure

A
  • protein structure can provide evidence for evolutionary conservation
  • cytochrome c has been studied and is highly conserved among species
32
Q

Protein families

A
  • proteins can be grouped into families according to similarities in domain structures and amino acid sequences
  • all members have descended from a common ancestral protein
  • lactate dehydrogenase and malate dehydrogenase belong to the same family
  • structure provides support for homology
  • they are present in the same species
  • protein families contain related proteins that are present in the same species that are derived from a common ancestor
33
Q

Domain Classification

A
  • domains are classified according to structure:
  • > all-α contains alpha helices
  • > all-β contains beta strands
  • > α/β class contains regions with both that arise from alternations in the peptide chain
  • > α + β class have clusters of each that arise from different regions in the peptide
34
Q

all-α

A

example:
PDB: 1BJ5
Human serum albumin (in the bloodstream: transport, osmotic pressure)
-> structures: alpha helices and bundles

35
Q

all-β

A

example:
PDB: 1VBS
Homo sapiens peptidylpropyl cis/trans isomerase
- catalyzes cis/trans of oligopeptides at prolyl residues (activation/deactivation)
- dominant features is a beta sandwich

example:
PDB: 1A45
Bos taurus gamma-crystallin
- Crystallins are the dominant structural components of the verterbrate eye lens and are believed to be very long-lived
- comprised of two beta barrel structures

example:
PDB: 1GFL
Aequorea victoria green fluorescent protein
-main feature is the beta barrel structure but contains a central alpha helix
- orientations strands anti-parallel

example:
PDB: 1AQB
Sus scrofa retinol-binding protein (RBP)
- RBPs have diverse functions including transport of Vitamin A from the liver in the form of the lipid alcohol retinol
- Retinol is shown binding in the center of the beta barrel

36
Q

α/β

A

example:
PDB 1OYA
Saccharomyces carlsbergensis (first pure culture lager yeast strain) old yellow enzyme
- roles in yeast are though to include oxidative stress programmed cell death
- central fold is an alpha/beta barrel with parallel beta strands connected by alpha helices

example:
PDB 1AHN - Escherichia coli flavodoxin
Electron transfer protein that contains the prosthetic group flavin mononucleotide
5 strand parallel twisted beta sheet surrounded by alpha helices

example:
PDB 1ERU Homo sapiens thioredoxin
The major cell protein disulfide oxidoreductase; similar to E.coli flavodoxin except this contains a single antiparallel beta strand

example:
PDB 1ABE E.coli l-arabinose-binding protein
essential component of the active transport of l-arabinose
two domain protein similar to flavodoxin
- l-arabinose is shown binding in the cavity between the two domains

BIOCHEM (8 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions