Proteins - Exam 1 Flashcards
building blocks of proteins
amino acids
amino acids linked by
peptide bonds, generate H2O
what is the amino terminus
beginning of all proteins; methyeline
what is the carboxyl terminus
end of all proteins
how are dietary proteins digested (2 steps)
first by proteolytic enzymes of the GI tract, then by cleavage by pancreatic proteases in the small intestine
3 things that make up an amino acid
amino group, an acid (carboxyl group), & side chain
amino acids with nonpolar side chains (9)
alanine, glycine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tyrptophan
bends in polypeptide chains due to
proline
characteristics of amino acids with nonpolar side chains
don’t gain or lose electrons, cluster together, hydrophobic effect,
proline characteristics
nonpolar, secondary amino group (imino acid) makes it rigid
amino acids with uncharged polar side chains (6)
asparagine, glutamine, serine, threonine, tyrosine, cysteine
disulfide bonds due to
cysteine
characteristic of amino acids with uncharged polar side chains
0 net charge
which 2 uncharged polar side chains can lose a proton at alkaline pH
cysteine & tyrosine
which 3 uncharged polar side chains can contain a polar hydroxyl group that participates in hydrogen bond formation
serine, threonine, & tyrosine
amino acids with acidic (-) side chains (2)
aspartic acid & glutamic acid
characteristic of amino acids with acidic side chains
proton donors, physiological pH fully ionized COO-
what is physiological pH
7.4
amino acids with basic (+) side chains (3)
arginine, histidine, lysine
characteristic of amino acids with basic side chains
accept protons, physiological pH fully ionized & positively charged
which amino acid with a basic side chain acts as a buffer & why
histidine; can be either positively charged or neutral depending on environment’s pH
what 2 alpha amino acids are not found within proteins & where are they found
triiodothyronine & thyroxine ; thyroid
hydroxylation of tryptophan yields ______ ; function
serotonin ; NT & paracrine hormone
acetylation and methylation of serotonin yields ______ ; function
melatonin ; reproductive activity
hydroxylation of tyrosine yields (pathway)
dopa -> dopamine -> adrenaline/norepinephrine -> alpha adrenoreceptor & beta adrenoreceptor
decarboxylation of histidine yields ______ ; function
histamine ; allergic rxns
peptide hormone produced in the hypothalamus for uterine contractions & milk secretion
oxytocin
peptide hormone produced in the hypothalamus for maintenance of water balance
ADH (antidiuretic hormone)
peptide hormone used for energy production in the muscles & cardiac cells
creatine
peptide hormone that is a vasoactive substance
bradykinin
peptide hormone that is a vasoconstrictor
angiotensin II
polypeptide hormone used for secretion of gastric glands in the stomach
gastrin
polypeptide hormone used to stimulate pancreas & liver secretion
CCK
polypeptide hormone produced by alpha cells in the pancreas
glucagon
polypeptide hormone produced in the heart for regulation of blood volume & pressure
ANP (atrial natriuretic peptide)
mutation where the base change codes for the SAME amino acid
silent
mutation where the base change codes for a DIFFERENT amino acid
missense
mutation where the base change codes for a STOP codon
nonsense
mutation where a base is added or deleted
frame-shift
mutation where base change generates a splice site
splice site
genetic code has how many combination possibilities and codes for how many amino acids
64 ; 20
what are the 3 stop codons & 1 start codon
UAG, UGA, UAA ; AUG
the first codon in the eukaryotic mRNA codes for
methionine
which cells can make mRNA in both the nucleus and the cytosol
eukaryotic
differences between DNA vs RNA
deoxyribose vs ribose ; thymine vs uracil
what are introns
noncoding sections of DNA
what is alternative splicing and what cell type uses it
removal of intron(s) ; bacteria
benefits of alternative splicing
generate different proteins isoforms, increases viability
what is tRNA and how does it work
transfer RNA “clover leaf”; attachment site for an amino acid at the 3’ end and an anticodon on the other end that pairs with a codon on the mRNA
tRNA significance
adapter for alternative splicing & codon recognition
what are the 3 sites on a ribosome
A, P, E
eukaryotic ribosomes have 2 subunits:
60 & 40
which ribosomal site binds an incoming aminoacyl-tRNA
A
which ribosomal site has peptidyl-tRNA which carries the chain of already synthesized amino acids
P
which ribosomal site has empty tRNA and is where it exits
E
RER-ribosomes function
synthesize proteins that need to be exported from the cell or put into cell membranes
cytosolic ribosomes synonym & function
“free” ribosomes ; synthesize cytosolic proteins or those meant for the nucleus , mitochondria, or peroxisomes
what are the 3 steps of protein synthesis
initiation, elongation, termination
describe initiation step
assembly before peptide bonds form
describe elongation step
adding amino acids to the carboxyl end of the chain (5’ -> 3’), bind at A site, make peptide at P site, mRNA move
describe termination step
when one of the stop codons reaches the A site
proteins in the cytosol can go where
nucleus, mitochondria, peroxisomes, plastids
proteins in the ER can go where
Golgi, endosomes, lysosomes, secretory vesicles, membrane
N-terminal signal sequence
import into the ER or mitochondria
C-terminal signal sequence
retention in the lumen of the ER
internal signal sequence
import into nucleus or peroxisomes
the ER synthesizes which 3 proteins
lysosomal, secretory, and membrane
what is the SRP and what does it do
signal recognition particle ; binds to the new protein after recognition, binds to the SRP receptor in the ER membrane, gets placed in the translocation protein using energy, SRP released (protein will be in the ER of the lumen)
type I arrangement
c terminus is in the cytosol
type II arrangement
n terminus is in the cytosol
2 examples of membrane proteins
LDL receptor & GLUT 1
what are the 4 structures of proteins
primary, secondary, tertiary, quaternary
what are the 3 folding patterns of proteins in the secondary structure
alpha helix, beta sheet, beta bend/turn (proline kink)
structure of an alpha helix & example
within membrane, every 4 amino acids = 1 hydrogen bond, side chains face outside, “spiral”; keratin
structure of a beta sheet
all amino acids make bonds “pleats”, side chains not involved, can either be parallel (c terminus same end) or antiparallel (c terminus different ends)
structure of a beta bend
proline, make a compact shape, connect alpha helix and beta sheets, can link 2 antiparallel B sheets, can link parallel B sheets by crossing over and connecting at either top or bottom
describe vesicular transport
brings proteins to larger organs
vesicular transport pathway
RER -> coated with COPII -> membrane -> microtubules -> cis Golgi (if not coated will go elsewhere)
what does SNARE stand for and why do we need it
soluble NSF attachment protein ; to recognize coated/envelope proteins
example of SNARE and it’s function
synaptobrevin ; fusion of synaptic vesicles with the plasma membrane (Botox inhibits this)
clathrin-coated vesicles
within Golgi, protein can be modified and then released into cytosol via coated vesicles (circular)
what is NLS and it’s function
nuclear transport signal ; moving protein from rER into nucleus via active transport
how does NLS work
in the middle of polypeptide chain: protein binds with importin receptor -> nuclear pore
Golgi apparatus structure consists of what 3 areas
cis, trans, medial
protein phosphorylation takes place where
cis Golgi
O-glycosylation takes place where
medial and trans Golgi
where are proteins packed into vesicles
trans Golgi net
what are chaperones and how do they work (folding cyclus)
heat stable proteins, hydrolyze ATP to bind to recognize new protein, makes ADP, stays until protein makes right shape, if protein doesn’t make right shape it will get discarded in ER
what is N-glycosylation
ER -> attach sugar to Asn
what is O-glycosylation
Golgi -> attach sugar to Ser/Thr
importance of O-glycosylation
functional conformation of protein
synthesis of glycoproteins occurs where and requires what
in ER, out cytosol; dolichol, sugar, Asn
