Biochem Random

Question 1

Where does de novo purine/pyrimidine synthesis take place?

Answer 1

Cytosol

Question 2

Purine de novo pathway

Answer 2

Ribose5P -> PRPP -> IMP -> either GMP or AMP

Question 3

How do you make uracil?

Answer 3

Deamination of cytosine

Question 4

Which nucleotides have a higher melting point and why?

Answer 4

C and G do bc they are connected via 3 hydrogen bonds while A and T are only connected by 2 H bonds

Question 5

Which histones make up the core in the nucleosome?

Answer 5

H2A, H2B, H3, H4: two of each of these

Question 6

What is the role of H1?

Answer 6

to link different nucleosomes together

Question 7

Which AAs are needed to make purines? What additional substances are needed to make purines?

Answer 7

Glycine Aspartate Glutamine (GAG) are the AAs

You also need tetrahydrofolate and CO2

Question 8

What is needed to make pyrimidines?

Answer 8

ASPARTATE, Glutamine, CO2, ATP

Question 9

Pyrimidine de novo pathway

Answer 9

glutamine + CO2 + ATP -> carbamoyl phosphate THIS IS RATE LIMITING STEP -> orotic acid + PRPP -> UMP -> UDP -> CTP or dUDP -> dUMP + THF -> dTMP

Question 10

Purine salvage pathways: what is the purpose

Answer 10

HGPRT is able to recycle purines so you don’t have to always make them from scratch

If they aren’t recycled they will end up as uric acid

Question 11

Silent mutations

Answer 11

Nucleotide substitution codes for the SAME amino acid, usually has to do with change in the Wobble position

Question 12

Transition mutation

Answer 12

purine to purine or pyrimidine to pyrimidine

Question 13

Transversion mutation

Answer 13

purine to pyrimidine or pyrimidine to purine

Question 14

Missense mutation

Answer 14

Nucleotide substitution resulting in changed AA

Question 15

Nonsense mutation

Answer 15

Nucleotide substitution resulting in early STOP codon, usually creates a nonfunctional mutation

STOP THE NONSENSE

Question 16

Frameshift mutation

Answer 16

Deletion/insertion that results in misreading of all nucleotides downstream

Protein can be shorter/longer, function may be altered

Question 17

Splice site mutation

Answer 17

Mutation at a splice site that causes the INTRON to remain in the mRNA: causes protein to have impaired/altered function

Question 18

Nucleotide excision repair: what is it? when does it occur?

Answer 18

Repairs bulky lesions that distort the helix, endonucleases remove sections of nucleotides that contain the bulky damage, DNAP and ligase fill in and seal the gap

Occurs during G1 phase of cell cycle

Question 19

Base excision repair: what is it? when does it occur?

Answer 19

Occurs when a specific base was damaged: ex. due to spontaneous deamination, during any phase of cell cycle

1. Base-specific glycosylase removes damaged base leaving a blank space
2. Endonucleases come in and remove additional nucleotides at the 5’ end
3. Lyase cleaves the 3’ end
4. DNAP beta fills in gap
5. Ligase seals gap

Question 20

Mismatch repair: what is it? when does it occur?

Answer 20

Occurs when new strand base does not match with parent strand, usually during G2 phase of cell cycle

1. New strand is recognized
2. Mismatched nucleotides are removed
3. Gap is filled and seals

Question 21

Nonhomologous end joining

Answer 21

2 ends of DNA fragments brought together to repair ds-breaks

Question 22

Start codons

Answer 22

AUG (CUG is rare alternative)

Question 23

Stop codons

Answer 23

UGA, UAA, UAG

U Go Away
U Are Away
U Are Gone

Question 24

PCR

Answer 24

Used to amplify a fragment of DNA

1. Denature DNA by heating it
2. Add primer that will bind to the sequence that you want to amplify
3. Heat-stable DNAP replicates sequence after primer

Question 25

Southern Blot

Answer 25

Used to ID a piece of DNA

1. DNA sample is cleaved into smaller pieces that are separated on a gel by electrophoresis and then transferred to a filter
2. Filter exposed to radiolabeled DNA probe that will bind to complementary strand
3. Expose filter to film so you can see the DNA probe

“SNOW DROP”

Question 26

Northern Blot

Answer 26

Used to ID RNA

Similar to southern blot except RNA

“SNOW DROP”

Question 27

Western Blot

Answer 27

Used to ID a protein

Sample protein separated via gel electrophoresis and then transferred to a membrane

Labeled antibody is used to bind to the protein

“SNOW DROP”

Question 28

Southwestern Blot

Answer 28

identifies DNA-binding proteins using labeled oligonucleotide probes

Question 29

Flow cytometry

Answer 29

Used to assess size, granularity, protein expression of individual cells in a sample

Cells are tagged with specific antibodies, a laser focuses on the cell and then measures the intensity of the fluorescence

Data plotted on histogram or scatter plot

Question 30

Microarrays

Answer 30

Nucleic acid sequences arranged in grids on glass or silicon

DNA or RNA probes are hybridized to a chip and a scanner is used to determine the amt of complementary binding

Used to profile gene expression of THOUSANDS of genes simultaneously to study certain diseases and treatments

Able to detect SNPs

Question 31

ELISA

Answer 31

Immunologic test used to detect the presence of a specific antigen or antibody

You have antibody bound to an enzyme, then you add substrate that will react with the enzyme to produce a color

Question 32

FISH: Fluorescence in situ hybridization

Answer 32

Fluorescent DNA/RNA probe binds to specific gene site of interest on chromosomes

Allows you to view microdeletions, translocations, duplications on chromosomes

Question 33

Cloning method

Answer 33

1. Isolate eukaryotic mRNA of interest
2. Exposed mRNA to reverse transcriptase to produce cDNA which does not have introns
3. Insert cDNA fragments into bacterial plasmids that contain antibiotic resistance genes
4. transform the recombinant plasmid into bacteria
5. Plate on antibiotic medium: the ones that survive have cloned copies of DNA in them

Question 34

Microsatellite testing

Answer 34

Test for genetic differences btw people, looks at length of microsatellite repeats

Paternity test