Ch 4 Flashcards
Satellite RNA
ssRNA genome, needs another virus to replicate, ex hepatitis
Virusoids
SsRNA genome, like viroids with capsid, need helper virus to replicate
Proteins are made of
Amino acids, chain like polymer
Four types of Amino acid
Acidic, basic, polar, and non polar
Amino acids are bound by
Peptide bonds with a condensation reaction
Residues
When amino acids are joined in a series ofpeptide bonds
Peptide
Short chain of amino acids
Coding/sense strand
Same as RNA, but U is used instead of T
Antisense strand/ template strand is read
3’to 5’, read by RNA polymerase
How many codons possible
64
Synonymous codon
Two diff codons with the same amino acid associated
Degenerate code
Some codons can mean the same thing
One tRNA can recognize more than one codon with
Wobble
Wobble
tRNA specific to a particular amino acid recognize multiple codon triplets that differ only in the third letter
Modified bases on tRNA anti codon allow for
Recognition of more codons by one tRNA
What amino acid isomer do living organism usually use
L-amino acids for protein making
Dalton unit
Molecular weight of protein, average amino 110 da
Protein primary structure
Amino acids
Secondary structure
Amino acids reacting to fold, stabilized with hydrogen bonds
Three protein secondary structures
A helix, b pleated sheet, unstructured turn
A helix
Most common, helical structure stabilized with h bonds with aminos, proline prevents helix
Beta pleated
Secondary common, h bonds between backbone, can be parallel or antiparrallel
Unstructured turns
Allow for helix and pleats to interact, short loops
Tertiary structure of protien
3D shape of one polypeptide,
Stabilized with hydrophobic interactions, hydrogens bonds, van Dee walls, just non covalent stuff
Disulfide bridges
Bridges between cysteines, main and strongest covalent bond with polypeptide
Tertiary structure types
Globular, fibrous, membrane
Globular proteins
Rough sphere, most common
Ex. Lysozyme
Fibrous protiens
Rod like, structural components of cells and tissues,
Made of: coils, anti parallel pleated sheets, trip helical arrangement
Ex. Collagen, keratin
Membrane protein
Interact with membrane, ex seven transmembrane helix structure, hydrophobic and hydrophilic parts
Quaternary structure
Multiple polypeptide subunits, same non covalent stabilizers as tertiary structure
Dimer
2 polypeptides
Multimers
More than 2 polypeptides,
Ex. Hemoglobin
Macro molecular assemblages
Hella polypeptides,
For: DNA replications, repair, recombination, and yea
Intrinsically disordered protiens
Lack secondary and tertiary structure, fucked up
Ex. Amyloid beta and synuclein, linked with Alzheimer’s and stuff
Domains (tertiary)
Larger proteins (20+ kDA), perform specific functions like DNA binding, can have patterns and shit, usually made with a continuous amino acid sequence
Protiens functions as
Enzymes (catalysts),
Post translational modifications
Amino acid mods, add lipids, metals, and phosphorylation and others
Kinases
Catalyze addition of phosphate group
Phosphatase
Remove phosphates, less specific
Two kinase types (euk)
Serine or Threonine side chains, tyrosine side chains
Need specific substrate
Allosteric regulation
Change of shape to regulate protien activity, can increase or decrease activity
Heat shock protiens
molecular chaperones, promote proteins folding and aid in destruction of misfolded proteins
HSP 70 and HSP 40
Common heat shock protiens
Endoplasmic reticulum “quality control”
protiens are sent to ER to fold from Golgi apparatus (chaperones here), missfolded are then taken care of
Ubiquitin proteasome system
Protein degradation in eukaryotes
Ubiquitin
Tags a protein to an amino acid
After Ubiquitin tags amino acid
A chain of Ubiquitin forms, Proteasome targets the protiens, Ubiquitin is released, protiens destroyed
Chaperones mediated autophagy
Protein degradation, HSP 70 targets misfolded protiens to lysosome
Macroautophagy
Proteins degradation process, atuopphagosome formed
Amyloid fibrils
Normally soluble proteins turn insoluble and accumulate
Human protein misfolding diseases
Alzheimer’s, Parkinson’s, huntingtons, type II diabetes, creuzfeldt Jakob
codon bias
Multiple ways to construct a set of tRNAs able to recognize all codons
ex. wobble baes pairing and modded bases
allosteric regulation induced by
ligands
molecular chaperones are independent of
ATP
proteasome
degrades ubiquitin tagged protien
