Some Notes after looking at last years prelim:

Memorize the number of sizes (from first lecture ex size of a skin

cell)
Some cells can have more than 1 mitochondria or other organelle
depending on its location (changes depend on gene expression)
When talking about nucleotides- if the sugar is deoxy, or has only an
OH group at the 3, but not at the 2 end the nucleotide is written
with a d in front, but if it contains a ribose, there is no d infront
o so ATP is adenosine triphosphate, and has the adenine nuclear
base, its sugar has a free 2 and 3 OH, and at the 5 OH it has 3
phosphate groups attached
o But dAMP is deoxyribo-adenosine monophosphate, contains the
adenosine nuclear base, the sugar attached with no 2 OH, only a
free 3 OH and then at the 5 OH has 1 phosphate group attached
(and this is the way adenine appears in DNA)
Remember pyrimidines CUT a ring, so pyrimidines are C U and T and
have 1 ring whereas the purines (A and G) have 2 rings
Remember- transcription occurs adding ribonucleotides 5-3, and
since it is adding antiparallel to the DNA, it is adding based on the
DNA strand moving in the 3-5 direction
o ALSO IF NOT EXPLICITLY SHOWN, SEQUENCE IS WRITTEN 5-3
The protein polypeptide chain with N terminus on left:
o NH-CHR-CO-NH-CHR-CO just because N terminus is on the left
does not mean that the sequence shown will necessarily start
with the first atom being an N
Transcription:
o In prokaryotes, the RNA polymerase finds start with sigma factor
bound which finds the promoter region, then sigma factor leaves
and transcription begins by unwinding part of the DNA template
and adding ribonucleotides together in the 5-3 direction, when
the terminator region is reached, RNA polymerase contacts the
stop site and releases, sigma factor can then bind to RNA
polymerase again to find another promoter region to transcribe
In the end, have a complete mRNA that can be immediately
translated (even before transcription is complete sometimes)
o In eukaryotes it is more complicated, mRNA is transcribed by pol
II, and initiation begins with a set of general transcription factors
that find the promoter regions to bind to promoters and
enhancer regions (like the TATA box) after RNA polymerase II
finishes transcribing mRNA, it must be processed (adds a cap, a
tail, and splices the introns)
Alternative splicing to get proteins in the same family that
may slightly differ

Anti-codon sequence is antiparallel to the codon sequence, the

charts usually refer to the codon sequence so if given an anticodon
sequence that is 5-3 (if not specified) then first figure out the
complementary sequence which if following left to right would be 35, then flip the sequence so that you have the 5-3 code
o This are give aways just make sure to take your time and have
the sequence in the right direction
Protein translation:
o For eukaryotes initiation: the small subunit of the ribosome has
the initiator tRNA (met-tRNA) already in the P site, then the small
subunit will bind to the mRNA starting at its 5 cap, and will scan
for the start codon AUG, once found initiation factors leave and
the large subunit of the ribosome comes in to form the initation
complex.
o Elongation for both is the same: Bond formation is catalyzed by
rRNA (catalytic RNA) and puts the new peptide chain onto the
tRNA of the A-tRNA, this makes sense because then translocation
of the ribosome occurs, kicking the P tRNA out as it passes into
the E site (or exit site), leaving the peptide chain on the tRNA
that is now in the P site, so that the A site can accept a new tRNA
without losing the polypeptide chain by ejecting it. If it were to
put the polypeptide chain onto the P site, then the newly formed
protein chain would be put into the E site during translocation,
which would not make sense- so remember the chain adds to the
new tRNA in the A site, then translocation puts this tRNA into the
P site with the polypeptide chain on it and the tRNA that is now
empty from the P site is ejected out
o In eukaryotes, it is reading the ORF- open reading frame (only
part that is translated)
o Termination: ribosome enters a stop codon that a release factor
binds to (remember NOT A tRNA!) release factor binding causes
the ribosome to dissociates and the polypeptide to be released
Protein phosphorylation can turn proteins on or off, some proteins
are activated by phosphorylation whereas others may be
inactivated by phosphorylation- differing from GTP-binding proteins
which are only activated when the GTP is present, but are inactive
when GDP is bound
o Think Src- Src is a kinase itself, but must be dephosphorylated at
one site and phosphorylated at another site to be activated
Protein phosphorylation works by adding a bulky, negative
phosphate group onto a protein to change its conformation and
therefore its function
o The phosphate group comes from an ATP
o Kinase phosphorylates and puts the P onto a protein

o Phosphatase (when saying phosphatase think phosph-ATE-ase to

emphasize ATE which is like eating something)- it takes away the
P (or ate it)- just a way to remember its function from kinase
So phosphatase hyrdolyzes the P and dephosphorylates which
can function to activate or deactivate depending on the gene
GAP GTPase-Activating Protein: it has GTPase in, its name, and
works to hydrolyze the GTP to GDP that is bound to the GTP binding
protein and therefore turns OFF the protein (its putting a gap in it so
that it cannot work)
GEF- Guanine nucleotide EXCHANGE factor- GEF is exchanging the
GDP for a GTP- think about it you want to exchange GDP for GTP,
you would not want to exchange the whole nucleotide to inactivate
it, therefore it turns the protein on- think GEF as JEFF is our friend,
hes activating the protein
So the way it works with GTP binding proteins again:
o When GDP is bound, the protein is off, GEF turns on the protein
by EXCHANGING the GDP for GTP, then GAP will hydrolyze GTP to
GDP + P (P is released) turning off the protein
o This is different from phosphorylation in a few ways:
the protein is only active when GTP is bound, whereas with
phosphorylation, the protein may be activated or inactivated
with P bound
The entire nucleotide is bound, not just a phosphate group
GEF activates, and GAP inactivates the protein, whereas with
phosphorylation kinase phosphorylates (to activate or
inactivate) and phosphatase dephosphorylates (to activate or
inactivate)
Phosphorylation transfers the P onto the protein by taking it
from ATP and putting it onto the protein, just the P not the
whole nucleotide
Microtubule motors:
o Dynein- moves to negative (FOR THE MOST PART)
o Kinesin- moves to positive (FOR THE MOST PART)
So Kinesin moves AWAY from the nucleus to the positive part
of the microtubule (drags the ER away to keep it spaced out)
Dynein moves TOWARD the nucleus (pulling golgi in)
o Kinsein motion is highly coordinated between the 2 globular
heads, we do not know the way they communicate, but their
motion is like walking
o When bound to ATP, the head is tightly bound to the microtubule,
ATP binding causes the necklinker to dock and the lagging ADP
bound head to swing forward, then ATP is hydrolyzed to ADP on
the originally leading head (now lagging head) and the ATP
comes into the newly leading head to continue the cycle

o Once again this is coordinated- there is ALWAYS one head with an

ATP and one head with ADP- different from myosin
Muscle contraction:
o Myosin heads are not coordinated in their action, you do not
want a lot of the heads bound to actin at one time because it
would prevent the movement toward the plus end at the Z disc if
a lot of them are bound to actin
o Remember rigor mortis- when someone dies their muscle stiffen,
when someone dies you are not making ATP right? (unless your
like a zombie or something) so there is ADP attached to the
myosins, causing them to be tightly bound to the actin and the
muscles to be stiff
o Starting from a head with ATP ATP binds to the myosin to release it from the actin
When ATP is hydrolyzed, ADP + P are attached and the head
cocks and then docks onto the actin, weakly bound (but
bound)
P releases causes the power stroke (P=power) and pulls the
actin filament
ADP leaves and ATP comes in so that it is again not bound to
the actin and the cycle can begin again
Comparing motor molecules to muscle contraction:
o Motor molecules have 2 conditions with MT binding (with ATP
bound, with ADP weaker binding), where as myosin has 3
conditions (with ATP unbound, with ADP+P weakly bound but
bound, and with just ADP tightly bound)
o Binding is tight in motor molecules when ATP is bound, but with
myosin ATP cause the myosin to be released from actin
o Kinesin heads are highly coordinated and think about walkingalways have one head attached to the microtubule, one of the 2
heads always has ATP and the other ADP, whereas myosin heads
are not coordinated, and usually they are unattached to actin,
myosin heads are usually not bound because that would prevent
them all from collectively pulling the actin
Phospholipid membranes stiffen with:
o More saturated tails- no kinks to give them fluidity
o More cholesterol
o Lower temperatures
Phospholipid membranes are looser with:
o More unsaturated tails- kinks to loosen
o Less cholesterol
o Higher temperature
Know the phospholipid structure

The trans-membrane proteins, many times have the alpha helix

structure to tuck away the hydrogen bonds that occur from the NCC
backbone- remember inside the phospholipid membrane is
HYDROPHOBIC- part of the reason why the structure forms, to keep
the hydrophobic hydrocarbon tails away from the mostly watery
cell, therefore the side chains that are exposed on the transmembrane protein and going through the hydrophobic region are
also hydrophobic- like dissolves like
o Also shows why you know how many passes it may make by
looking at the polypeptide chain and seeing where there are
hydrophobic residues, which would be when the alpha helix is
passing through the hydrophobic membrane
Look over material from your discussion section
Make sure to read the questions carefully- be careful when you see
ALWAYS or other strong words
GOOD LUCK!