Exam 2 Review Flashcards
Def of genome:
complete set of genes of an organism or the set of instructions needed to create organism
Human genome contains how many genes that code for proteins?
23,000
What percent of the genome codes for proteins?
2%
What percent of the genome are for non-coding proteins?
98%
What does genomics tell us?
how genome interacts with environment
Copy number variation (CNV) means that there is a _____ in the number of copies of a gene
variation
- more than the two alleles we talked about before
Def of transcriptome:
set of expressed genes that are already transcribed
What happens with polymorphism?
alleles will produce different phenotypes
- can be detected at phenotypic level when sequence affects gene function
Polymorphisms should be found at a frequency greater than…
1% in population
What is a single nucleotide polymorphism (SNP)?`
polymorphism caused by a change in single nucleotide
- responsible for most of the genetic variation
- greater than 10 million are in human genome
A SNP occurs every….
1330 bases
T/F: most genes are expressed at a high level
F, should be low
- only small number of genes (specialized) are highly expressed and gives the cell its phenotypes
What is pharmacogenetics?
study of effects of gene variation on drug response
SNPs can affect…
drug efficacy and toxicity
Epigenetics regulation is caused by what kind of modifications?
- methylation of cytosine in DNA
- modification of histone tails by methylation, acetylation, and phosphorylation
What are trans-acting sites?
usually mutant proteins, which doesn’t allow both strands to be translated
What are cis-acting sites?
mutant site only affects its own strand
- usually mutation on one DNA strand
Def of plasmid:
DNA carrier with selection and induction
Function of selectable markers:
allow selection of cells that carry plasmid
Def of inducible:
operon that allows chemical induction of expression of gene
Function of restriction enzymes or endonucleases:
sequence specific cutting of DNA
Def of recombinant DNA:
DNA from one species inserted into another
Def of transformation:
cell stress causes uptake of surrounding DNA fragments
How does transduction occur?
viral phage inserts DNA
What are transposons?
jumping genes
Function of PCR:
amplify DNA
Benefits of bacterial or yeast cultures:
- affordable
- easy growth
Limitations of bacterial or yeast cultures:
no glycosylation
Benefits of mammalian production systems:
- cheaper than nonculture but more expensive than bacterial
- glycosylation possible
Limitations of mammalian production systems:
- difficulty in growth
- higher chance of contamination
Benefits of animal production systems:
- proper folding
- proper glycosylation
Limitations of animal production systems:
- technologically difficult
- regulatory constraints
- societal concern
Benefits of plant production systems:
- high yields
- fewer societal concern
Limitations of plant production systems:
- technologically difficulty
- risk of pathogens
- cross pollination
- cost
What is RNA interference (RNAi) useful for?
studying effect of blocking specific proteins from being produced
- stops translation
Purpose of DNA microarray chips:
DNA micro array is used to examine relative expression level of genes by using DNA micro chip
- combo is where it gets its name
- useful for studying over or under expression
Purpose of glycolysis:
change pyranose to furanose to allow a second phosphorylation site
Which steps of glycolysis need ATP?
kinase reactions of HK and PFK
- step 1 of HK needs it
- step 3 of PFK needs it
Which steps of glycolysis produce ATP?
kinase reactions of phosphoglyercase kinase (PKG) and PK
- step 7 of PKG
- step 10 of PK
Where does E come from in order to make ATP?
- high E bond from substrate level phosphorylation
- gradient of ETC from oxidative phosphorylation
Enzyme HK is under what kind of control?
- allosteric
- G6P inhibits it
Enzyme PFK is under what kind of control?
- allosteric activation via F2,6BP
- ATP feedback inhibition
Enzyme PK is under what kind of control?
- allosteric: feedforward w/ PFK and feedback with ATP and acetyl CoA
- hormonal: glucagon and high carbs
Where does fructose enter and bypasses what in the liver?
- G3P
- bypasses PFK
Where does fructose enter and bypasses what in the muscle?
- F6P
- doesn’t bypass PFK
How does galactose get broken down?
- UDP swaps with galactose to create G1P
- phosphoglucomutase used to change G1P to G6P
- glucose created
What happens to pyruvate if there’s no O2 in glycolysis?
- pyruvate reduced to lactate (anerobic exercise)
2. lactate needs Cori Cycle to create E
How does liver HK differ?
has a higher Km for glucose and sigmoidal dependence on concentration
How does glycogen get broken down?
- glycogen phosphorylase breaks alpha 1,4 and forms G1P
- phosphoglucomutase converts G1P to G6P
- debranching enzyme transfers 3 units from branch to branch and cleaves alpha 1,6
Structure of glycogen:
branched at alpha 1,6 with side by sides of alpha 1,4
How is the breakdown of glycogen controlled in the liver?
- alpha receptors
- beta receptors
- glucagon receptors
How is the breakdown of glycogen controlled in the muscle?
beta cells only
How does the regulation of glycogen ensure survival?
there are multisteps to avoid mistakes of control
- can turn it off before all the glycogen is used up
For the synthesis of glycogen, what enzymes are required?
glycogenin and UDP
What controls PP1 in glycogen metabolism?
single and double phosphorylation of Gm
How does PP1 alter glycogen metabolism?
active PP1 dephosphorylates glycogen phosphorylase and phosphorylase kinase so breakdown stops
T/F: Glycogen is under hormonal control
F, should be allosteric
- activator: AMP
- inhibitor ATP
Steps of glycogen synthesis:
- glucose gets phosphorylated by HK to form G6P
- phosphoglucomutase converts G6P to G1P
- glycogenin gets added (catalyzed by glycogen synthase)
- forms branches
What is the most important function of the pentose phosphate pathway (PPP)?
make NADPH and ribulose5P
- alternative to glycolysis
What is NADPH and how is it used?
- reducing equivalent carrier
- used as reducing equiv donor for biosynthetic reactions so intermediates can be reduced using reductase
How do we control reactive oxygen species (ROS)?
- superoxide dismutase (SOD)
- catalase
- GPx
What is required for GPx?
- NADPH
- glutathione
- riboflavin
- selenium
Control of ROS comes from…
- superoxide dismutase (SOD): inactivates reactive oxygen radical to hydrogen peroxide
- catalase: inactivates hydrogen peroxide to water
- GPx: same as catalase
Gluconeogenesis provides ____ to tissues
glucose
How is gluconeogenesis regulated?
- reciprocal of glycolysis
- inhibited by F2,6BP
- activated by ATP
What enzymes are different in gluconeogenesis compared to glucose?
- G6P
- F6P
- F1,6BP
What product gets formed from gluconeogenesis that can be used to replenish CAC?
oxaloacetate
How much E does it cost to run gluconeogenesis?
6 ATP
Function of Cori Cycle:
recycles lactate by exporting it to the liver where it gets converted to pyruvate
When is the PFK-2 portion of the bifunctional enzyme active during gluconeogenesis?
when it gets dephosphorylated and glycolysis is active
When is the F2,6BPase portion active during gluconeogenesis?
when phosphorylated and gluconeogenesis is active
Cost of gluconeogenesis:
- 2 pyruvate
- 6 ATP
- 2 NADPH
What does glycolysis generate?
- 2 ATP
- 2 NADPH
- 2 pyruvate
When PFK-1 is activated by F2,6BP, does glycolysis or gluconeogenesis increase?
glycolysis
When F1,6BPase is inhibited by F2,6BP, does glycolysis of gluconeogenesis decrease?
gluconeogenesis
T/F: levels of F2,6BP are controlled allosterically
F, hormonally via glucagon and insulin
PFK2/F2,6BPase is responsible for…
synthesis and breakdown of allosteric effector F2,6BP
What is the main control point for the citric acid cycle?
PDH, which is subject to both allosteric and hormonal control
What are the three enzyme complexes on PDH?
- E1
- E2
- E3
PDH needs what 5 coenzymes?
- TPP: accepts group from pyruvate
- lipoic acid: accepts acetyl group from TPP
- acetyl group: gets transferred from lipoamide to CoASH to form CoA
- FAD: on E3 and ox lipoamide
- FADH2: passes reducing equiv to NAD+ to form NADH
What are some allosteric PDH inhibitors?
- acetyl CoA
- NADH
- ATP
What are some allosteric PDH activators?
- CoASH
- NAD+
- AMP
What are the other control points for the citric acid cycle besides PDH?
- isocitrate DH
- alpha KG DH
- both inhibited allosterically by NADH
What are key reactions during the citric acid cycle?
- DH reactions for NADH or FADH2
- succinylCoA synthease where ATP equiv formed
What is made during each turn of the citric acid cycle?
- 3 NADH
- 1 ATP
- 1 FADH2
How much E is made per glucose during the citric acid cycle?
- 6 NADH
- 2 ATP
- 2 FADH2
