Protein Structure Flashcards
What is the 3D structure of Proteins
- Determined by amino acid sequence
- determines function of protein
- unique for each protein
- maintained by non-covalent interactions
- Has several recurring motifs
What are the 4 levels of protein architecture
- Primary: Amino acid sequence + disulfide bond
- Secondary: Regular recurring arrangements of adjacent amino acids.
- Arrangements of the total protein, the complete 3D structure
- Arrangement of multiple protein subunits
The primary structure can be derived from ____sequence
gene
The primary structure includes _____ and ____bonds
peptide; disulfide
The primary structure can give important clues to probable _____
protein function
Contigous regions of a protein with a distinct function or structure is called a
domain
Peptide bonds and disulfide bonds are both ____bonds
covalent
Peptide bonds are ____and ____
planar; rigid
What includes the secondary structure
- alpha helix
- beta sheet
- beta turn
What do alpha helices consist of
- Peptide bonds align along long axis
- R groups stick out of sides
- each turn -3.6 aa
- every 3-4 aa in close proximity and stabilize through H bonding
What are alpha helix destabilizers
- String of several basic or acidic aa’s
- String of several aa with bulky side groups
- aa 3-4 residues apart which cannot interact
- Proline residues (“helix breakers”)
- String of glycine residues
What are the characteristics of beta pleated sheets
- Extended arrangement of polypeptides
- H bonds hold adjacent chains together
- Chains may be arranged in parallel or anti parallel fashion.
What are characteristics of Beta turn
Contain proline in the cis conformation; requires proline isomerase to convert it
What are characteristics of tertiary structure
- 3D arrangement
2. Brings distant regions into close proximity
What are the two major groups of tertiary structure
- Globular
2. Fibrous
What are fibrous proteins
- Primarily water insoluble
- Structural proteins
- Simple arrangement
- Usually long chains or sheets
What do fibrous proteins consist of
Alpha and beta keratin
What are fibrous proteins found in
Hair, nails, feathers
What are characteristics of fibrous proteins
- Classic, right handed a helix
- Many hydrophobic aa
- 2 stranded superhelix= protofilament
- Crosslinks via disulfide links
- Permanent wave solution breaks, reforms disulfide bonds
How many types of keratin are found in the skin
18
What are cytokeratins
components of the intermediate filaments of the cytoskeleton
What are the characteristics of globular proteins
- All other proteins
- Most enzymes and protein hormones
- Secondary structure is more complex
- Multiple arrangements of folding into a “spherical” shape
How do water molecules arrange themselves
in an orderly manner to form “cages” around hydrophobic groups
____groups tend to be sequestered internally.
Hydrophobic
____regions interact with water.
Hydrophilic
What are the tertiary structure bond types
- H bonds: an EN atom (usually O or N) acts as a H acceptor
- Ionic bonds: Attraction bet oppositely charged atoms
- Hydrophobic interactions
- Van der Waals: Weak attractions resulting from transient dipole formation.
What is the tertiary structure folding
Proteins dont fold randomly. Most proteins use chaperone proteins to assist in folding
What are the most famous chaperone proteins
Heat shock proteins
What does Iatrogenic refer to
of or relating to illness caused by medical exam or treatment
What are prion diseases caused by
improper folding of Prp protein
What is Mad Cow Disease
Bovine spongiform Encephalitis
What is Scrapie
Spongiform encephalitis found in sheep
What is Kuru
human spongiform disease limited to Fore tribe of New Guinea
What is Creuzfeldt-Jacob
sporadic, hereditary, acquired
What is cystic fibrosis
Caused by defective protein folding
-chloride channel protein (CFTR) is missing a single amino acid (Phe- 508) due to a triplet deletion in the coding sequence of the gene.
What are the characteristics of quaternary structure
Only found in proteins with more than 1 protein subunit
What are some proteins with quaternary structure
- pyruvate dehydrogenase
- ribosomes
- RNA polymerase
What is the best way to study proteins?
X-ray crystallography
What is protein denaturation
Disrupts weak interactions; destabilizes the structure and becomes less thermodynamically stable
Protein denaturation does NOT disrupt ____bonds
covalent (peptide and disulfide)
What are some protein denaturants
- heat
- pH extremes
- detergents
- organic solvents (alcohol, acetone, urea)
What is protein hydrolysis
Disruption of primary structure by hydrolysis to single aa by boiling in strong acid or base
What are proteases enzymatically?
enzymes that cleave proteins at specific dipeptide sites
T/F denatured proteins can be renatured
True
AA’s critical for proper folding are _____ which means that mutations in codons for these aa are very deleterious (harmful_
invariant
Urea ____proteins
denatures
BME ____disulfide bonds
reduces
Primary structure dictates ____structure
tertiary
What two 3D protein structures are important in the progression of Eale’s Disease and are current targets for drug design
retinal s antigen and interphotoreceptor retinoid binding protein
