Protein Structure Flashcards
What is the shape of proteins determined by?
Noncovalent bonds (hydrogen, van der Waals interactions, ionic)
What determines the flexibility or rotation of proteins?
Covalent bonds between amino acids
What role do hydrophobic forces play in protein structure?
They push hydrophobic molecules together and keep hydrophilic together, therefore shaping the protein to accommodate these attractions.
Lowest energy protein confirmation
Proteins will do they least they can to fold. If something like urea is introduced, it will only effect or break the noncovalent bonds.
This way, only side chains are broken and the backbone of the protein remains.
When the urea is washed away, proteins fold back to original shape.
Molecular chaperone
Help protein to fold properly
Molecular chaperones place a chamber cap on to a protein and do not release it until the protein is correctly folded.
Clinical examples of misfolded proteins
Alzheimer’s, Huntington’s, Creuzfeldt-Jakob Disease
Types of folding patterns and their location
Alpha helix - found in keratin; examples = hair, nails, horns; found all over the membrane
Beta sheets - fibroin; first discovered in silk; example = antifreeze proteins
Alpha helix
Curled ribbon
Hydrogen bond every 4th peptide bond
Can be right- or left-handed
In the membrane, hydrophobic particles curl around hydrophilic core
Beta sheets
Laying side-by-side with hydrogen bonds between each peptide
Parallel (longer to loop around) or anti-parallel (relatively short)
Levels of protein organization
Primary, secondary, tertiary, quaternary, protein domain
Primary
Amino acid sequence
Secondary
Alpha helices and beta sheets
Tertiary
Polypeptide with a-helices, b-sheets, and random coils
Quaternary
More than one polypeptide chain
Protein domain
Independently folding polypeptide chain from which other proteins are constructed
Define unstructured protein regions
- Larger proteins w/ multiple domains connected by polypeptide chains
- disordered sequences
- tether one protein to another to provide movement
Define and give examples of protein families
Groups of proteins w/ similar amino acid sequences
Ex.- serine proteases (trypsin, elastase)
Aggregate
If a protein folds onto itself, it is called an aggregate and is dangerous.
Forms the backbone of DNA
Sugar and phosphate
mRNA vs. rRNA vs. tRNA
mRNA - messenger RNA
rRNA - ribosomal
tRNA - brings protein to mRNA as an adaptor
RNA structure is
Single stranded
Promoter vs. terminator
signals RNA polymerase where to begin/end transcribing on DNA
Post-transcriptional processing
Process where primary RNA transcript is converted to mRNA
- 5’ capping (modified guanine)
- 3’ polyadenylation
- RNA splicing
RNA splicing
Removal of introns, remaining extrons joined together
Subunits of RNA and their function
- Small subunit — put mRNA w/ tRNA and provide a binding site for them
- Big subunit - enzyme that makes peptides that will become proteins
Aminoacyl tRNA synthetases
- link tRNA to amino acid
- each RNA has its own synthetase
How does protein synthesis begin?
With AUG - methionine
- small ribosomal subunit binds to 5’ cap and moves along RNA
- at AUG, large subunit translates to mRNA
Stopping translation
- Stop codons (UAG, UAA, UGA)
- if tRNA does not match those, water is added
- water terminates the end of the protein
Results of reading frame being off
Creates nonsense proteins
Polyribosomes
Multiple ribosomes that simultaneously translate the same mRNA into a protein
Protein synthesis inhibitors include
Antibiotics
Proteolysis
- Proteases break proteins down into peptide bonds
- then into amino acids
- used on proteins w/ short life spans or improperly folded
Proteasomes and ubiquitin
Breakdown proteins in cytosol
Factors that determine protein shape
- Amino acid sequence
(Proteins, side chain, polar/nonpolar, polypeptides) - lowest energy confirmation
- molecular chaperones`
Hydrophobic forces
- role in shaping proteins
- pushes hydrophobic molecules together
Diseases as a result of improperly folded proteins
Alzheimer’s, Huntington’s, Creuzfeldt-Jakob disease
Unstructured protein regions
- the loops on beta sheets
- allows larger proteins to fold around one another
- tether one protein to another to provide movement (flexible tethers)
- targets for proteases
Flexible tethers
- provide movement and flexibility
- help scaffold proteins bring proteins together in intracellular signaling pathways
- assist elastin in forming fibers
Function of disulfide bonds in extracellular proteins
To fortify and protect the protein shape between 2 cysteine side chains
Functions of proteins
- Enzymes as catalysts
- antibody binding sites
- protein binding
Antibody binding sites
- specific between antibody and antigens
- due to looped ends on antibody
- binding triggers an immune response
How proteins are controlled
Allosteric enzymes, phosphorylation, GTP binding
Allosteric enzymes
- have 2 binding sites
- shift confirmations to inactive enzymes
Phosphorylation
- attachment of a phosphate group to an amino acid side chain
- protein kinases: adds phosphate
- phosphotases: removes phosphate
GTP binding
- GTP binds
- becomes GDP when it loses a phosphate
- leaves when a new GTP approaches
