Proteins and DNA Flashcards
Where does DNA –> RNA occur
nucleus
what is it called for DNA to be converted to RNA
transcription
where does RNA convert to protein
cytoplasm
what is it called for RNA to be converted to protein
translation
what is the primary structure of proteins composed of
amino acids
how are amino acids in primary structures held together
peptide bonds
what kind of bonds are peptide bonds
covalent
what is the chain of amino acids called
polypeptide chain
how do secondary structure proteins come about
polypeptide chains fold into sheets
what are secondary structures due to
H-bonds
what makes the backbone of a protein
primary structure proteins
what are the 2 types of secondary structure proteins
A helix and B sheets
what is a shape characteristic of alpha helixes
corkscrew
what is a shape characteristic of beta sheets
parallel or antiparallel
where does C=O bind to N-H in alpha helixes
4 AA residues ahead
where does C=O bind to N-H in beta sheets
side by side sheets
which way do R groups point in beta sheets
in
which way do R groups point in alpha helixes
out
are tertiary structure proteins hydrophobic or hydrophilic
hydrophobic
what determines the shape of tertiary structure proteins
polar/nonpolar R groups
what 3 things determine protein shape
type of amino acid, order of amino acid, and bonds between amino acid
what are prion proteins
bad proteins
what is an amyloid
PRPsc enters protein and makes it defective
where is DNA located
in the nucleus
what kind of RNA leaves the nucleus
fully modified
is euchromatin or heterochromatin loose
euchromatin
is DNA accessible in euchromatin
yes
is DNA accessible in heterochromatin
no
what is a nucleotide
phosphate and sugar
what is a nucleoside
just sugar
what are the two types of nitrogen bases
purines and pyrimidines
what are the purines nitrogen bases
adenine and guanine (pure silver - Ag)
what are the pyrimidines nitrogen bases
cytosin, thymine, and uracil
what is the nitrogen base that is only found in RNA
uracil
what is pentose
a 5 carbon sugar (penthouse has 5 floors)
what does carbon 1 do
links bases
what does carbon 2 do
identifies sugar
what does carbon 3 and 5 do
phosphodiester bond
what is called when the hydrogen on carbon 2 contains a oxygen
ribose
what is it called when the hydrogen on carbon 2 doesn’t contain a oxygen
deoxyribose
what kind of bond is between carbon 3 and 5 on a pentose
phosphodiester bond
what is the 1st nucleotide on a pentose
OH on 3’ carbon
what is the 2nd nucleotide on a pentose
phosphate group of 5’ carbon
what does the OH on 3’ carbon bind to
phosphate group of 5’ carbon
what does the binding of OH to phosphate cause on a pentose
3rd phosphate of ATP is cut off to form backbone
what kind of bond are base pairs
H bonds
what is needed for base pairs to bond
optimal distance
how many copies of DNA does the nucleus contain
1
what does helicase do
breaks H bonds
what does primase do
create RNA primer
which way does polymerase read
3’-5’
what way does polymerase write
5’-3’
what is called when the polymerase writes the protein in segments
ozaki fragments
what happens to the ozaki fragments
they are ligated
what is ligation
to be put together
what is the base of the promoter region called
TATA box
what does the TATA box recruit
transcription factors
what do the transcription factors on the TATA box recruit
RNA polymerase
what is another function of RNA polymerase
unwinds DNA
what does U replace in RNA
T
what does A pair with
T
what does C pair with
G
what is the type of RNA for polymerase 1
rRNA
what is the type of RNA for polymerase 2
mRNA and snRNA
what is the type of RNA for polymerase 3
rRNA, tRNA, and snRNA
where on the pentose is RNA found
OH on 2’ carbon group
is RNA or DNA more stable
DNA
what is the main structure for RNA
single stranded but can fold
what is the function of rRNA
core of ribosomes
what is the function of mRNA
protein synthesis template
what is the function of tRNA
carries AA to ribosomes for protein synthesis
what is the function of snRNA
processes DNA and RNA
what is 5’ capping
attaching a nucleotide on the 5’ end
what is 3’ poly adenylation
adding a lot of A nucleotides to 3’ end
what is splicing
removing the intron, exons join together
which way is mRNA read
5’ - 3’
what is the word for 3 bases
codon
what is a codon
a specific amino acid
what is the wobble
3rd base that differs/varies
what is a point mutation
single base changed
what is a frameshift mutation
all codons after mutation are different
what is a missense mutation
changed base –> 1 changed codon
what is a nonsense mutation
stop codon made
what is a silent mutation
base change doesn’t result in anything
what do ribosomes translate mRNA to
proteins
what do rRNA bundles make
subunits
what does the small subunit do
read mRNA
what does the large subunit do
docking site for tRNA
what is the order of the initiation sites
E P A (APE)
where is tRNA found
ribosomes
what does tRNA contain
anticodons
what happens when tRNA binds to codon
it releases its amino acid
what charges empty tRNA
tRNA synthetase
in charging tRNA, what does ATP cleavage link together
amino acids and tRNA
what does tRNA drop at the ribosome
amino acids
what is elongation in translation initiation
addition of amino acid
what happens when the subunit makes a stop codon in translation initiation
proteins releases and ribosomes dissociates from mRNA
where are proteins with a signal sequence moved to
rough endoplasmic reticulum
what does the ERAD do
degrades troubled proteins
what causes ERAD to start
the cell recognizes misfolded protein
what is added to protein in the ERAD process
ubiqudin
where does ubiqudin cause the protein to move to
cytosol to cytoplasm
what degrades the protein once it moves to the cytoplasm
proteasome
what does unfolded protein response (UPR) stop
translation
what do chaperons do
folds and unfolds protein
what does UPR create more of in response to misfolded protein
chaperons
where are chaperons found
endoplasmic reticulum
what is the last resort for misfolded proteins
autophagy
what is autophagy
cell death
what does the Golgi apparatus sort
ER products
how do vesicles enter the golgi
cis face or trans face
what is cis face
part of golgi closest to nucleus
what is trans face
part of golgi furthest to nucleus
what part of the cell is the “road”
cytoskeleton
what part of the cell is the “vehicle”
motor proteins
where does the + end send stuff toward
membrane
where does the - end send stuff toward
nucleus
do microtubules carry stuff short or long distances
long distances
does f-actin carry stuff short or long distances
short distances (this man is so f-ing short)
which way does kinesin carry stuff
+ end
which was does dynein carry stuff
minus end
what is the way to remember what motor proteins carry stuff which direction
(+)K5 - D6
what is endocytosis
moving things into cytoplasm
what is phagocytosis
big particles get eaten
what is pinocytosis
fluid gets drunk (Pino like the wine)
where does COP2 carry stuff in receptor mediated endocytosis
ER –> golgi
where does COP1 carry stuff in receptor mediated endocytosis
golgi –> ER (the L in golgi looks like a 1)
where does clathrin carry stuff in receptor mediated endocytosis
to and from plasma membrane
what separates vesicle and membrane in receptor mediated endocytosis
dynamin (dynamite causes stuff to break apart)
what happens to the cage at the docking site in receptor mediated endocytosis
it sheds
what happens when V-snare binds to T-snare
water is squeezed out
what is V-snare
the vesicle
what is T-snare
the target/membrane
what are the V-snare(s)
VAMP
what are the T-snare(s)
syntaxin and snap-25 (Taylor swift) (sin and snap)
what is the calcium binding protein
synaptotagmin (tags the membrane because it’s on the vesicle)
what activates the SNARE complex
calcium binding
what is formed when V and T snares wind together
A helices
