Ch 4 Flashcards
what is the structure of an amino acid
amino (NH3), Hydrogen, carboxyl(COO), R-group
If amino acid has a negative charge what group should it be in?
acidic
If amino has a negative charge which group
basic
If there is no charge variation what group is it in
non-polar
If it has an oxygen or looks like it could interact with water like has a SH/Se waht is it
polar
What do chains of amino acids get linked together by?
peptide bonds
what kind of reaction is it when amino acids join
condensation reaction (aka dehydration synthesis) (water leaving)
WHat is the N-terminus?
the amino acid end, there IS directionality
What do we call amino acids when they’re linked together
residues
difference between peptide and polypeptide
peptide(below 50) are shorter
What is the antisense strand?
the template for RNA polymerase during transcription. it is the one that is read. 3’ to 5’
What is the coding or sense strand
the one that is the same as the RNA.
What are open reading frames
areas of DNA that actually encode for a gene, the coding region between start and stop codon
What are codons
combinations of 3 nucleotides in a row that dictate the amino acid. FIrst is Methionine
Can stop codons encode
yes, there is lots of exceptions when stop codons action code, like in archea
What is wobble base pairing
the third letter of the code doesn’t matter sometimes
WHat structure do amino acids need to be in for ribosomes to incorporate them?
L amino structure, not D enantiomers
How do we measure proteins
Dalton
What leads to secondary structure?
interactions of amino acids with their neighbors, H bonds, disulfide bridges, ban der walls interactions, hydrophobic contacts
WHat structures do we see in a secondary protein structure
alpha helicies, B pleated sheets (anti or paralel),
Tertiary structures
R groups interact, final folding of pollypeptide, hydrophobic interactions, h bonding, charge pair interactions, van der walls
Three main structures of tertiary structure
Globular proteins, FIbrous proteins, membrane proteins
GLobular proteins
spherical, ex. lysozyme
Fibrous proteins
long filamentous or rod-like structures, structural component of cell. like collagen or keratin, actin
Membrane proteins
hydrophilic and phobic regions. ex. G protein-coupled receptor
Quaternary structure
multiple polypeptides coming together. Functional proteins. can all be the same or different peptides
What are dimers?
2 polypeptides, homodimers or heterodimers
Multimers
multiple polypeptides like antibodies and hemoglobin
What are macromolecular assemblages
molecular machines, proteins working together. For DNA rep, repair, recom, transcrip,
WHat is a domain
functional importants, they do something and have unique functions
What is a motif
chain like bio structure made up of conectivity between secondary structural elements, supersecondary structurem
What are some Post-translational modifications
things can be added to them, they can be linked to other things, PHOSPHORYLATION of amino acid side chains
Examples of proteins being joined covalently or non-covalently
lipoproteins, glycoproteins, metalloproteins
What performs phosphorylation
kinases, they are specific to what they phosphorylate
WHat allow proteins to fold correctly
molecular chaperones,
are molecular chaperones doing work?
yes, need ATP, they also get rid of misfolded proteins
what’s another name for molecular chaperones
heat-shock proteins, aid in distructrion of misfolded proteins
Where does folding take place
endoplasmic reticulum and then they’re sent to the golgi
What is ubiquitin-proteasome system
ubiquitin targets misfolded proteins via ubiquitination to a Lys. the proteasomes finds it and degrads that protein.
what is macroautophagy
lysosomes take care of the misfolded proteins
What is the primary cause of transmissible spongiform encephalophathies
prions
types of prion diseases
sporadic, inherited, infectious (mad cow)
