Cumulative
What structures of protein are affected by denaturation?
ALL but primary because covalent interactions are really strong and require a TON of energy to break
What are the key differences between a lagging and leading strand?
lagging strand has 3' end facing away the replication fork and leading strand has 3' end facing the replication fork. the lagging strand is synthesized discontinuously (okazaki fragments)
What are the three things enzymes do for reactions?
Help couple reactions, lower activation energy, stabilize the transition state
What are some common mutagens?
UV light, tobacco smoke, radiation ETC
What are the three point mutations we covered in class?
synonymous (silent mutations), missense, and nonsense
What structures of amino acids are ALWAYS the same? What is different?
Carboxyl and amino groups are the same. The r groups change (which is what tertiary structure looks at)
What way is DNA always synthesized in replication?
5' to 3'
What is Gibbs free energy?
Energy available to do work
Describe the difference between proto-oncogene and oncogenes
oncogenes are carcinogenic. code for uncontrolled cell growth
protooncogenes- can become carcinogenic but are not that way normally. code for controlled cell growth
What do frameshift mutations do?
change the reading frame. it can insert or delete an amino acid sequence (if it is not a multiple of three the length of the protein and the respective amino acids are affected)
What are the regions of noncoding on the lac operon?
lacP and lacO or the operator and promoter
Describe mismatch repair, base excision repair and nucelotide excision repair
mmr- a nucleotide is paired with its incorrect partner. So the mut proteins work to find the incorrect partner later in the line and match them back up
ber- removal of an incorrect base (uracil) and replacement of the correct one
ner-pulls out an entire section where damage is located and fixes it by recopying the line
What does delta G mean?
Change in energy
Describe recombinant DNA and the steps
Requires a fragment of double-stranded
DNA that serves as the donor. The donor
fragment may be any DNA segment of
interest.
• For protein coding genes, reverse
transcriptase is used to make double-
stranded complementary DNA (cDNA)
from mRNA.
• Requires a vector (carrier) sequence into
which the donor fragment will be inserted.
The vector must have the ability to be
maintained in the new cell.
• Involves cutting DNA (both donor and
vector) with the same restriction enzyme
(example: EcoRI isolated from E.coli) so
that the donor DNA and the vector DNA
have complementary ends for
renaturation and ligation (DNA ligase).
• The recombinant plasmid (DNA) is transformed and replicated
What are the roles of cyclins in the cell cycle?
Help to make sure the cell is able to carry the cycles it needs by checking the preparatory stages
DNA methylation occurs...
at histone tails specifically the CpG islands near the promoter region which regulates transcription
What does semi conservative mean?
One daughter strand and one parental strand are present in a newly synthesized strand
Draw an endergonic and exergonic reaction. Label the products, the reactants and draw an uncatalyzed and catalyzed version. Also include the axis.
Picture of endergonic should include progress of reaction on x axis, gibbs free on the y axis, and differing levels of reactants and products on each side
Describe PCR and the steps
Denaturation- heat the DNA to separate the strands
Annealing- when the solution is cooled the two primers anneal to their complementary sequence on the strands of the template DNA
Extension- DNA polymerase synthesizes new DNA strands (complementary to template) in the 5'-3' direction.
WE WANT TO AMPLIFY A SPECIFIC SECTION OF THE DNA so we are trying to find that by restricting a section of the DNA
What are the functions of the following three checkpoints: DNA damage checkpoint, DNA replication checkpoint, Spindle assembly checkpoint and generally where in the cell cycle do they occur?
DDC- checks for damage before synthesis phase
DRC- checks that all DNA is replicated at end of G2
SAC- checks that all spindles are attached to chromosomes before M phase
Draw out ferritin and transferrin and their response to iron. When do they bind? When do they translate? When they are not translated what do they do?
Ferritin is unbound when translated and stores iron. When it is bound ferritin cannot translate. Transferrin is translated when bound. It transfers iron to different locations and when bound covers the instability elements allowing transferrin to be translated. It degrades the protein when it is unbound
Write out EVERY SINGLE ENZYME/PROTEINS INVOLVED IN DNA REPLICATION and come up with a skit/way to remember at least 1 of them
DNA ligase, helicase, topoisomerase, single stranded binding proteins. DNA polymerase. PRIMASE
What do we need to happen to have an effectively coupled reaction?
1 endergonic and 1 exergonic reaction. The exergonic delta G must be larger than the endergonic and the delta G cannot be zero
Describe the normal role of p53. What would happen if a mutation occurred in p53 leading to overexpression? Underexpression?
Normally a tumor suppressor as it limits cell cycle growth when damage is found in the DNA. overexpression is anticarcinogenic and underexpression is carcinogenic as the cell cycle would continue and cell cycle would continue
Draw out the cell cycle and state where each phase occurs
Diagram of cell cycle should be correct and include G0, G1, G2, M and S phase and interphase