Section 1:

1) DNA synthesis -> transcription -> translation (central dogma)

2) Energy made from food by controlled oxidation to get most energy out of it
3) Make carrier molecules from this oxidation into CO2 and O2 ie ATP, NADH
4) 3 stages of food breakdown: mechanical breakdown (chewing), glycolysis/fermentation, and Krebs
cycle/oxidative phosphorylation
5) Steps for cellular respiration
a) Breakdown of food/digestion
b) Glycolysis
i) 2 pyruvate & some ATP & NADG
ii) No O2 = fermentation, quick energy, low efficiency, lactic acid buildup
iii) With O2 = Pyruvate goes to mitochondria where there’s pyruvate dehydrogenase
iv) Makes 1 CO2, 1 acetyl group, 1 NADH
c) Coenzyme A works on acetyl group making acetyl CoA used in Kreb’s cycle
d) Makes lots of NADHs and CO2 using citric acid
e) Use these NADHs to drive electron transport chain for oxidative phosphorylation making lots of
ATP, waste is H2O, CO2, and NH3

Section 2:

1) Proteins are the most complex molecules in organisms

2) Proteins made from covalent peptide bonds, weaker bonds (hydrogen, van der waals) dictate
folding
3) Disulfide bonds are very strong, long bond length, bond proteins together
4) Serine, threonine, tyrosine are important amino acides because these can be phosphorylated
5) Hydrophobic regions fold into the center so don’t interact with H2O, the active site
6) Chaperone proteins help facilitate folding, heat shock protein example
7) Folding pattern – alpha helix (inserts into membranes, hides things well) & beta sheets (parallel and
antiparallel (more common because tighter packing, so stronger))
8) Primary structure (amino acid sequence), secondary (alpha vs beta folds), tertiary (3D structure),
quaternary (polypeptides interacting with each other)
9) Proteins are not rigid, can bind to a ligand lock & key style and change conformation resulting in
functionality
10) Equilibrium constant (k) describes binding strength, k=kon/koff
11) Kinase puts on phosphate, phosphatase removes phosphate
12) Enzyme + substrate -> ES -> EnzymeProduct -> E + P
13) When enzyme becomes saturated works at its max reaction rate, Km is the substrate concentration
needed for enzyme to work at its half max, describes efficiency
14) Enzymes stabilize intermediates & lower activation energy and have a ligand bind site and a
regulatory bind site, used for negative or positive regulation (allosteric enzymes)
15) Phosphates change conformation of protein because of the two negative charges they carry
16) Motor proteins (kinesin, dynein, myosin) use ATP to create motion
17) DNA made up of hydrogen and phosphodiester bonds
18) A+G = bump out, C+T=kink in
19) AT easier to rip apart because only 2 H bonds compared to 3 with CG, TATA box
20) DNA found in nucleolus, surrounded by nuclear envelope which is fairly impermeable, control what
goes in or out like RNA
21) DNA replication is semiconservative, always leaves a strand unedited, energy comes from
triphosphate nucleotides coming in, occurs at multiple replication forks bc otherwise too slow
22) Leading strand works on 3’ to 5’ and forms 5’ to 3’, lagging works on 5’ to 3’ and forms 3’ to 5’
23) Okazaki fragments are made on the lagging strand because polymerase cannot work that direction
so primase puts multiple RNA primers down on lagging strand, DNA ligase fuses the fragments
24) Proofreading mechanisms -> backbone is improperly aligned and polymerase can remove the
section with bad nucleotide at its editing site
25) DNA polymerase needs an RNA moiety primer to start, put in place by DNA primase, need to remove
later because of possibility of uracil screwing things up
26) Need DNA helicase to separate DNA strands because otherwise very stable
27) Helix destabilizing proteins stabilize DNA and straighten it for enzymes to work on it
28) DNA Polymerase likes to dissociate so need the sliding clamp to be loaded by the clamp loader to
hold DNAP in place
29) How to tell parent strand from new strand? Methylation of A’s
30) Topoisomerases let DNA twist as to relieve torsional stress, topoisomerase I breaks the
phosphodiester bond to let it rotate freely, topoisomerase II breaks one strand and feeds the other
over it
31) Need 3 things for origin of replication: ORC (origin recognition complex), DNA region of A’s & T’s,
and binding site for proteins that attract ORC
32) Histones need to be made for new DNA, 1 tetramer and 2 dimers
33) Telomerase adds repeating junk sequence to end of DNA (telomere) to act as a buffer

Section 3:

1) RNA can be transcribed at different rates and can translate to different amounts of proteins, so you
can’t exactly determine protein production from RNA production
2) RNA is reusable
3) RNA Polymerase makes RNA from DNA template strand by unwinding and adding triphosphates
4) RNAP has a tail region that is important for regulation
5) Multiple RNAP can work at the same time on the same gene
6) RNAP does not need a primer
7) General transcription factors needed to position RNAP at the promoter
8) TFIID is a big GTF, binds to TATA box, localizes other proteins, forms the transcription initiation
complex, made up of a lot of stuff, missing anything slows down the process
9) TFIIH has helicase as a subdomain that opens up the strand and allows RNAP tail to be
phosphorylated and begin
10) Also need transcription activator for enhancer site and mediator protein to keep everything
together
11) RNA needs modifications to be mRNA otherwise get degraded by siRNA
12) 5’ cap put on and 3’ poly-A tail shows the mRNA is intact
13) 5’ cap = phosphatase removes 5’ phosphate group, guanyl transferase adds GMP, methyl
transferase adds a methyl group
14) Also need to splice out introns by transesterifications which break the phosphodiester bonds and
makes an intron lariat
15) Introns useful because alternative splicing is possible where different splicing combinations result in
different proteins
16) Splicing location determined by common sequence at exon borders or branch point\
17) Splicing done by spliceosome, which is snRNA U1 U2 U4 U5 and U6
18) snRNP = snRNA, proteins and RNA
19) 3’ tail added by cleavage stimulation factor (CstF) and cleavage polyadenylation specificity factor
(CPSF). CPSF localizes poly-A polymerase (PAP) to add a bunch of A’s. Uses poly-A binding proteins
like helix destabilizing proteins to keep it straight
20) Nuclear export receptor bunds to mRNA to allow it to leave the nucleus through the nuclear pore,
loops to protect against degeneration
21) rRNA (ribosome) is found in the nucleolus but the 2 subunits don’t come together until they’re in
the cytoplasm with mRNA
22) mRNA decoded in sets of 3: codon, read by tRNA (clover shaped) at its anticodon site, adds proper
amino acid at its AA binding site by aminoacyl-tRNA synthetase
23) 3rd position of codon is wobble position, doesn’t totally affect what AA is placed
24) Aminoacyl-tRNA synthetase has an editing site if wrong AA is put on
25) Ribosome has large subunit (catalyzes the peptide bonds) and a small subunit (holds mRNA and
tRNA in place)
26) rRNA has 4 binding sites EPA (read backwards (E=exit, tRNA released, P=peptidyl peptide bond
formed, A=aminoacyl tRNA binds))
27) 4 steps to protein synthesis: tRNA binds, peptide bond formation, large subunit translocation, small
subunit translocation
28) ALWAYS NEED A tRNA IN TE P SITE BECAUSE OTHERWISE LOSE FRAME OF REFERENCE
29) Elongation factors help drive translocation forward
30) To start translation, need start codon AUG to be found by small rRNA subunit and tRNA complex,
large subunit attaches and process begins
31) Translation stops when it hits the stop codon UGA (2 more also), tells tRNA to add a water instead,
release factor comes in and breaks up complex
32) Polyribosome is multiple complexes working at the same time to make proteins
33) No translation if no mRNA cap or tail or improper splicing
34) Proteins can then fold with help of chaperones, can be on or off path, if too far off path =
degradation
35) Major groove vs minor groove – major groove you can tell the sequence because 4 distinct
molecules in the backbone vs 3 sometimes similar ones in minor groove
36) Proteins interact with DNA to regulate genes
37) Helix-turn-helix, 2 alpha helices, 1 recognize and 1 stabilize DNA
38) Zinc fingers, has alpha helix and beta sheet with zinc, can be scaled up easily like building blocks,
gain specificity
39) Beta sheets, two beta sheets come together kind of like helix-turn-helix
40) Leucine zipper, two alpha helices dimerize from protruding amino acids like leucine, can mix and
match helices to recognize different sequences
41) Hard to predict what sequence will be recognized because it’s almost random
42) Tryptophan repressor of operator on the promoter, when tryptophan is present, stops tryptophan
production
43) Can have positive or negative regulation on the operator and multiple operator sites can affect
promoter activation since strand tends to loop to stabilize interactions to RNAP
44) In eukaryotics, have promoter with regulatory and activator (like chromatin remodeling complex)
sequences, no one thing controls all
45) Gene activators work in concert to amplify transcription
46) Repressors can overlap or block interactions, turn off activators
47) Insulator is a sequence that blocks enhancers from working on the wrong gene since they can be
found over a wide range from the actual gene
48) RNA can be edited to add in nucleotides post transcription, possibly changing reading frame and
encoded protein

Section 4:

1) Plasma membrane is a thin film of lipids and proteins, noncovalent interactions, about 5nm
2) Lipids have a choline or serine head followed by phosphate and glycerol linker, have 2 hydrocarbon
tails
3) Sometimes lipids can flip orientation by flippase or scramblase but that usually marks it for death
4) Otherwise they tend to flex, rotate or translate throughout the membrane
5) Cholesterol is another component, keeps membrane rigid
6) Fluidity of membrane is dependent on composition, more cholesterol = more rigid, saturated vs
unsaturated tails
7) Lipid raft is an area of membrane that’s more rigid, has cholesterol, proteins and sphingolipids
8) Phospholipids can be phosphorylated and be used to relay signals
9) Glycolipids are lipids with sugars, protect the membrane and self recognize
10) Several membrane bound proteins – single pass, multipass, peripheral proteins, membrane pass
11) Peripherals aren’t connected to the membrane but are connected to other proteins on the
membrane, if they aren’t released they’re likely integral proteins
12) Beta barrel = beta sheet passive channel
13) Alpha helices = inside is hydrophilic so this channel type tends to restrict
14) Glycoproteins = similar to glycolipids, self recognize & protect
15)