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Biochemistry > Exam 2 Review > Flashcards

Exam 2 Review Flashcards

1
Q

Def of genome:

A

complete set of genes of an organism or the set of instructions needed to create organism

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2
Q

Human genome contains how many genes that code for proteins?

A

23,000

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3
Q

What percent of the genome codes for proteins?

A

2%

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4
Q

What percent of the genome are for non-coding proteins?

A

98%

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5
Q

What does genomics tell us?

A

how genome interacts with environment

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6
Q

Copy number variation (CNV) means that there is a _____ in the number of copies of a gene

A

variation

- more than the two alleles we talked about before

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7
Q

Def of transcriptome:

A

set of expressed genes that are already transcribed

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8
Q

What happens with polymorphism?

A

alleles will produce different phenotypes

- can be detected at phenotypic level when sequence affects gene function

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9
Q

Polymorphisms should be found at a frequency greater than…

A

1% in population

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10
Q

What is a single nucleotide polymorphism (SNP)?`

A

polymorphism caused by a change in single nucleotide

  • responsible for most of the genetic variation
  • greater than 10 million are in human genome
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11
Q

A SNP occurs every….

A

1330 bases

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12
Q

T/F: most genes are expressed at a high level

A

F, should be low

- only small number of genes (specialized) are highly expressed and gives the cell its phenotypes

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13
Q

What is pharmacogenetics?

A

study of effects of gene variation on drug response

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14
Q

SNPs can affect…

A

drug efficacy and toxicity

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15
Q

Epigenetics regulation is caused by what kind of modifications?

A
  • methylation of cytosine in DNA

- modification of histone tails by methylation, acetylation, and phosphorylation

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16
Q

What are trans-acting sites?

A

usually mutant proteins, which doesn’t allow both strands to be translated

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17
Q

What are cis-acting sites?

A

mutant site only affects its own strand

- usually mutation on one DNA strand

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18
Q

Def of plasmid:

A

DNA carrier with selection and induction

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19
Q

Function of selectable markers:

A

allow selection of cells that carry plasmid

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20
Q

Def of inducible:

A

operon that allows chemical induction of expression of gene

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21
Q

Function of restriction enzymes or endonucleases:

A

sequence specific cutting of DNA

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22
Q

Def of recombinant DNA:

A

DNA from one species inserted into another

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23
Q

Def of transformation:

A

cell stress causes uptake of surrounding DNA fragments

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24
Q

How does transduction occur?

A

viral phage inserts DNA

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25
Q

What are transposons?

A

jumping genes

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26
Q

Function of PCR:

A

amplify DNA

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27
Q

Benefits of bacterial or yeast cultures:

A
  • affordable

- easy growth

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28
Q

Limitations of bacterial or yeast cultures:

A

no glycosylation

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29
Q

Benefits of mammalian production systems:

A
  • cheaper than nonculture but more expensive than bacterial

- glycosylation possible

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30
Q

Limitations of mammalian production systems:

A
  • difficulty in growth

- higher chance of contamination

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31
Q

Benefits of animal production systems:

A
  • proper folding

- proper glycosylation

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32
Q

Limitations of animal production systems:

A
  • technologically difficult
  • regulatory constraints
  • societal concern
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33
Q

Benefits of plant production systems:

A
  • high yields

- fewer societal concern

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34
Q

Limitations of plant production systems:

A
  • technologically difficulty
  • risk of pathogens
  • cross pollination
  • cost
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35
Q

What is RNA interference (RNAi) useful for?

A

studying effect of blocking specific proteins from being produced
- stops translation

36
Q

Purpose of DNA microarray chips:

A

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
37
Q

Purpose of glycolysis:

A

change pyranose to furanose to allow a second phosphorylation site

38
Q

Which steps of glycolysis need ATP?

A

kinase reactions of HK and PFK

  • step 1 of HK needs it
  • step 3 of PFK needs it
39
Q

Which steps of glycolysis produce ATP?

A

kinase reactions of phosphoglyercase kinase (PKG) and PK

  • step 7 of PKG
  • step 10 of PK
40
Q

Where does E come from in order to make ATP?

A
  • high E bond from substrate level phosphorylation

- gradient of ETC from oxidative phosphorylation

41
Q

Enzyme HK is under what kind of control?

A
  • allosteric

- G6P inhibits it

42
Q

Enzyme PFK is under what kind of control?

A
  • allosteric activation via F2,6BP

- ATP feedback inhibition

43
Q

Enzyme PK is under what kind of control?

A
  • allosteric: feedforward w/ PFK and feedback with ATP and acetyl CoA
  • hormonal: glucagon and high carbs
44
Q

Where does fructose enter and bypasses what in the liver?

A
  • G3P

- bypasses PFK

45
Q

Where does fructose enter and bypasses what in the muscle?

A
  • F6P

- doesn’t bypass PFK

46
Q

How does galactose get broken down?

A
  1. UDP swaps with galactose to create G1P
  2. phosphoglucomutase used to change G1P to G6P
  3. glucose created
47
Q

What happens to pyruvate if there’s no O2 in glycolysis?

A
  1. pyruvate reduced to lactate (anerobic exercise)

2. lactate needs Cori Cycle to create E

48
Q

How does liver HK differ?

A

has a higher Km for glucose and sigmoidal dependence on concentration

49
Q

How does glycogen get broken down?

A
  1. glycogen phosphorylase breaks alpha 1,4 and forms G1P
  2. phosphoglucomutase converts G1P to G6P
  3. debranching enzyme transfers 3 units from branch to branch and cleaves alpha 1,6
50
Q

Structure of glycogen:

A

branched at alpha 1,6 with side by sides of alpha 1,4

51
Q

How is the breakdown of glycogen controlled in the liver?

A
  • alpha receptors
  • beta receptors
  • glucagon receptors
52
Q

How is the breakdown of glycogen controlled in the muscle?

A

beta cells only

53
Q

How does the regulation of glycogen ensure survival?

A

there are multisteps to avoid mistakes of control

- can turn it off before all the glycogen is used up

54
Q

For the synthesis of glycogen, what enzymes are required?

A

glycogenin and UDP

55
Q

What controls PP1 in glycogen metabolism?

A

single and double phosphorylation of Gm

56
Q

How does PP1 alter glycogen metabolism?

A

active PP1 dephosphorylates glycogen phosphorylase and phosphorylase kinase so breakdown stops

57
Q

T/F: Glycogen is under hormonal control

A

F, should be allosteric

  • activator: AMP
  • inhibitor ATP
58
Q

Steps of glycogen synthesis:

A
  1. glucose gets phosphorylated by HK to form G6P
  2. phosphoglucomutase converts G6P to G1P
  3. glycogenin gets added (catalyzed by glycogen synthase)
  4. forms branches
59
Q

What is the most important function of the pentose phosphate pathway (PPP)?

A

make NADPH and ribulose5P

- alternative to glycolysis

60
Q

What is NADPH and how is it used?

A
  • reducing equivalent carrier

- used as reducing equiv donor for biosynthetic reactions so intermediates can be reduced using reductase

61
Q

How do we control reactive oxygen species (ROS)?

A
  • superoxide dismutase (SOD)
  • catalase
  • GPx
62
Q

What is required for GPx?

A
  • NADPH
  • glutathione
  • riboflavin
  • selenium
63
Q

Control of ROS comes from…

A
  • superoxide dismutase (SOD): inactivates reactive oxygen radical to hydrogen peroxide
  • catalase: inactivates hydrogen peroxide to water
  • GPx: same as catalase
64
Q

Gluconeogenesis provides ____ to tissues

A

glucose

65
Q

How is gluconeogenesis regulated?

A
  • reciprocal of glycolysis
  • inhibited by F2,6BP
  • activated by ATP
66
Q

What enzymes are different in gluconeogenesis compared to glucose?

A
  • G6P
  • F6P
  • F1,6BP
67
Q

What product gets formed from gluconeogenesis that can be used to replenish CAC?

A

oxaloacetate

68
Q

How much E does it cost to run gluconeogenesis?

A

6 ATP

69
Q

Function of Cori Cycle:

A

recycles lactate by exporting it to the liver where it gets converted to pyruvate

70
Q

When is the PFK-2 portion of the bifunctional enzyme active during gluconeogenesis?

A

when it gets dephosphorylated and glycolysis is active

71
Q

When is the F2,6BPase portion active during gluconeogenesis?

A

when phosphorylated and gluconeogenesis is active

72
Q

Cost of gluconeogenesis:

A
  • 2 pyruvate
  • 6 ATP
  • 2 NADPH
73
Q

What does glycolysis generate?

A
  • 2 ATP
  • 2 NADPH
  • 2 pyruvate
74
Q

When PFK-1 is activated by F2,6BP, does glycolysis or gluconeogenesis increase?

A

glycolysis

75
Q

When F1,6BPase is inhibited by F2,6BP, does glycolysis of gluconeogenesis decrease?

A

gluconeogenesis

76
Q

T/F: levels of F2,6BP are controlled allosterically

A

F, hormonally via glucagon and insulin

77
Q

PFK2/F2,6BPase is responsible for…

A

synthesis and breakdown of allosteric effector F2,6BP

78
Q

What is the main control point for the citric acid cycle?

A

PDH, which is subject to both allosteric and hormonal control

79
Q

What are the three enzyme complexes on PDH?

A
  • E1
  • E2
  • E3
80
Q

PDH needs what 5 coenzymes?

A
  • 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
81
Q

What are some allosteric PDH inhibitors?

A
  • acetyl CoA
  • NADH
  • ATP
82
Q

What are some allosteric PDH activators?

A
  • CoASH
  • NAD+
  • AMP
83
Q

What are the other control points for the citric acid cycle besides PDH?

A
  • isocitrate DH
  • alpha KG DH
  • both inhibited allosterically by NADH
84
Q

What are key reactions during the citric acid cycle?

A
  • DH reactions for NADH or FADH2

- succinylCoA synthease where ATP equiv formed

85
Q

What is made during each turn of the citric acid cycle?

A
  • 3 NADH
  • 1 ATP
  • 1 FADH2
86
Q

How much E is made per glucose during the citric acid cycle?

A
  • 6 NADH
  • 2 ATP
  • 2 FADH2

Biochemistry (9 decks)

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