Biochem Final Review

Explain the problem with replicating the lagging strand

the very end of the lagging strand cannot be covered by the Okazaki fragment and will not be replicated so every time DNA replicates, the DNA gets shorter

Telomerase is a _ polymerase using _ as a template

DNA; RNA

Telomerase is composed of _ (enzymatic component) and _ (serves as the template of telomere)

telomerase reverse transciptase (TERT); telomerase RNA component (TERC)

What is a Hayflick limit?

the number of times a normal cell can proliferate before cell division stops

What is senescence?

a state in which the cell cannot process the cell cycle

Name markers of sensence.

P16,SA-β-GAL

What is the assay used to quantify the activity of telomerase?

Telomeric repeated amplification protocol (TRAP) assay

The length of telomere is _ when in space

longer

The telomere length of _ is not affected in space

B cells

_ increases in space and persists even after coming back to Earth

DNA damage

What does blood contain?

red blood cells, plasma, buffy coat (platelets and white blood cells)

Buffy coat contains both _nuclear WBCs and _morphonuclear WBCs

mono; poly

How can we isolate PBMCs from blood?

Density gradient separation

Which cells are PBMCs?

lymphocytes (T cells, B cells, NK cells) and monocytes (and macrophages), dendritic cells

What is the largest type of white blood cells?

monocytes

_ are monocytes that have migrated from the bloodstream into any tissue in the body

macrophages

Density gradient centrifugation for _Tumor Cell (CTC) isolation

Circulating

How many chromosomes do humans have?

46 chromosomes; 23 pairs

Somatic cells are _ cells (have 2 sets of chromosomes) and germ line cells are _ cells (have 1 set of chromosome)

diploid; haploid

chromosomes have a _ in the middle dividing the _ arm (small) and the _ arm (large)

centromere; p; q

What does location q21.1 mean?

q arm, region 2, band 1, sub-band 1

What causes “cri-du-chat” syndrome?

deletion of chromsome 5

How were the genes for pigments necessary for color sight developed through evolution?

gene duplication

What is a pseudogene?

a sequence of DNA that is not producing a function protein

What is the difference between pericentric inversion and paracentric inversion?

Pericentric inversion includes centromere; paracentric inversion does not include centromere

What causes Hemophilia A?

inversion of factor VIII gene

What is the difference betwwen reciprocal/non-reciprocal/Robertsonian translocation?

reciprocal → exchange

non-reciprocal → one-way

robertsonian → exchange and then one disappear

What causes Down syndrome and Patau syndrome?

Robertsonian translocation

Explain how Philadelphia chrosomes are formed

reciprocal translocation

What are the 3 steps of PCR?

denaturation, annealing, and extension

What is Southern blotting?

a method used to detect DNA (gel electrophoresis → transfer to membrane → detection)

What is Northern blotting?

a method use to detect RNA (gel electrophoresis → transfer to membrane → detection)

What is the DNA intercalating dye use for qRT-PCR?

SYBR Green I

What is the hydrolysis probe used for qRT-PCR?

TaqMan probe

What is a frame-shift mutation?

Frame-shift mutations involve a shift in the reading frame. Since a shift in the reading frame completely changes the amino acid sequence of the product, frame-shift mutations impose significant impact on the function of the gene.

What type of mutations cause a frame-shift?

deletion and insertion

What is the difference between the 2 types of point mutations, transition and transversion?

transition: purine → purine or pyrimidine → pyrimidine

transversion: purine → pyrimidine or pyrimidine → purine

what kind of point mutation does deamination cause?

C → T

What kind of data does COSMIC compile?

somatic mutations in cancer

What kind of data does TCGA compile?

genomic, transcriptomic, epigenetic, and proteomic data of cancer patients

What is cBioPortal?

a platform to analyze TCGA data

What is single nucleotide polymorphism (SNP)?

single base changes that are present in at least 1% of the population

Enzymes named _ process the cut and paste insertion of transposon

transposase

What are 2 major families of retrotransposons in human genome

L1 element; Alu sequence

Gene symbol should only contain ___/___

alphabet; arabic number

How is the hierarchy of gene families organized?

superfamily > family > subfamily

Explain what CYP1A1 means

CYP: root symbol for cytochrome 450 superfamily, family 1, subfamily A, gene identifier 1

Gene symbols are _ and protein symbols should be _

italicized; non-italicized

Some papers distinguish genes using _ letters and mouse genes using _

upper-case; lower-case

Name the species of *Mus musculus*

mouse

Name the species of *Caernorhabditis elegans*

worm

Name the speicies of *Homo sapiens*

human

Name the species of *Drosophila melanogaster*

fruit fly

Name the species of *Saccharomyces cerevisiae*

yeast

What kind of data does 1000 genomes project compiles?

whole genome sequencing, targeted exome sequencing

What is the goal of 1000 genomes project?

to find genetic variants with frequencies of at least 1%

What kind of data does exome sequencing project (ESP) compile?

exomes

What is the goal of ESP?

Discover novel genes and mechanisms contributing to heart, lung, and blood

What kind of data does exome aggregation consortium (ExAc) compiles?

exomes

What is the goal of ExAc?

create a database of normal variation

What is the method used to make point mutations?

site-directed mutagenesis

Name 2 mechanisms used for epigenetic regulation

DNA methylation (generally suppresses gene expression)

Histone acetylation (generally upregulates gene expression)

What are the 3 types of kinases?

serine/theronine kinase; tyrosine kinase; dual-specific kinase

What is the enzyme activated by Gαs?

Adenylyl cyclase

What is the secondary messenger used in the downstream of Gαs?

cAMP

What is the final enzyme activated by the Gαs pathway?

PKA

What is the enzyme activated by Gαq? What does the enzyme do?

PLC; Break down PIP2 into DAG and IP3

What are the 2 secondary messenger needed to activate PKC?

Ca2+ and DAG

What is the major protein/kinase pair that is activated by Ca2+?

Calmodulin (CaM) and CaM-kinases

What are the 2 enzymes activated by RTK? What pathways do those 2 enzymes activate?

Ras and PI 3-kinase. MAPK signaling pathway and Akt signaling pathway

What are the 4 stages of the cell cycle?

G1 phase, S Phase, G2 Phase, Mitosis

How long does G1 phase take?

6-10 hours

How long does S phase take?

2-6 hours

How long does G2 phase take?

3-6 hours

How long does mitosis take?

1-2 hours

What occurs during G1 phase?

cell growth

What occurs during S phase?

DNA replication (with multiplce origins of replication to shorten time to duplicate DNA)

What occurs during G2 phase?

DNA methylation and repair

How many initial mistakes are there per cell division?

20,000

What percent of replication errors are fixed during DNA repair?

99\.99%

After DNA repair about how many mutations are left per cell?

3

What occurs during mitosis?

splitting of the cell

What is G0?

G0 is the inactive phase that cells are in after they exit the cell cycle and are not actively preparing to divide

What are the checkpoints of the cell cycle?

G1, G2, and M

What is Rb?

a protein that binds and inactivates E2F

What is E2F?

a TF required for S phase

What happens to Rb during late G1?

It is phosphorylated and inactivated

What is necessary for the G1 checkpoint to be passed?

Rb is phosphorylated

In cancer, ___ is always on because Rb is ___

E2F; inactivated

Rb is a ___ gene

cancer

What is the multi-hit theory?

Cancer frequently increases according to the 6th power of age

What are the first 6 hallmarks of cancer?

Sustaining Proliferative Signaling, Evading Growth Supressors, Resisting Cell Death, Enabling Replicative Immortality, Inducing angiogenesis, Activating Invasion and Metastasis

What does Sustaining Proliferative Signaling mean?

uncontrolled cell growth

Rb is kept permanently off

What does Evading Growth Suppressors mean?

p21 and p53, which regulate the cell cycle even if checkpoints go wrong, are typically mutated in cancer to be inactive

What does Resisting Cell Death mean?

apoptosis (programmed cell death) does not occur

What does Enabling Replicative Immortality mean?

telomerase restores telomeres so that cells have unlimited replication potential

What does Inducing Angiogenesis mean?

blood vessels are created towards tumor to supply it with nutrients

What does Activating Invasion and Metastasis mean?

cancer starts spreading through the body

What makes p53 critical in cancer suppression?

transduces DNA damage into cell cycle arrest

can coordinate apoptosis

Within a species size ___ correlate to risk of cancer, but outside of species this does not hold.

does