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Biochemistry General Study > Master Flashcard Deck > Flashcards

Master Flashcard Deck

1
Q

Draw out the precursers to the amino acids

A
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2
Q

What is the reaction linking glycolysis to the citric acid cycle? What enzyme catalyzes the reaction?

A

Reaction catalyzed by the pyruvate dehydrogenase complex.

Pyruvate + CoA + NAD+ —–> Acetyl-CoA + CO2 + NADH + H+

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3
Q

What complex are the following enzymes a part of?

  1. Pyruvate Dehydrogenase
  2. Dihydrolipoyl transacetylase
  3. Dihydrolipoyl dehydrogenase

What do they catalyze? what are their coenzymes/prosthetic groups?

A
  1. Pyruvate Dehydrogenase
    1. Prosthetic group: TPP
    2. Oxidative decarboxylation of pyruvate
  2. Dihydrolipoyl transacetylase
    1. Prosthetic group: Lipoamide
    2. Transfer of acetyl group to CoA
  3. Dihydrolipoyl dehydrogenase
    1. Prosthetic group: FAD
    2. Regeneration of the oxidized form of lipoamide.
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4
Q

Draw out the Citric Acid Cycle

A
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5
Q

How is the citric acid cycle regulated?

A
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6
Q

Draw out Gluconeogenesis

A
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7
Q

Draw Out Glycolysis

A
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8
Q

How are glycolysis and gluconeogenesis regulated in the liver and muscle?

A

Glycolysis:

  1. Liver:
    1. also regulated by ATP, not as important as in muscle
    2. Citrate inhibits phosphofructokinase
    3. Fructose 2,6-bisphosphate increases affinity phosphofructokinase for Fructose 6-phosphate
  2. Muscle
    1. High levels of ATP inhibit phosphofructokinase, Higher levels of AMP stimulate it.
    2. glucose 6-phosphate inhibits hexokinase
    3. Fructose 1,6-bisphosphate stimulates pyruvate kinase.
    4. low pH inhibits
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9
Q

What are the glucose transporters?

A
  1. GLUT1: Basal glucose uptake
  2. GLUT2:
    1. in pancreas, plays role in regulation of insulin.
    2. In liver, removes excess glucose from the blood
  3. GLUT3: Basal glucose uptake
  4. GLUT4: Amount in muscle plasma membrane increases with endurance training.
  5. GLUT5: Primarily a fructose transporter
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10
Q

Draw out Oxidative Phosphorylation

A
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11
Q

Draw out Purine Biosynthesis

A
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12
Q

Draw out Pyrimidine Biosynthesis

A
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13
Q

Draw the Watson-Crick base pairing for Adenine and Thymine.

A
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14
Q

Draw the Watson-Crick base pairing for Guanine and Cytodine.

A
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15
Q

Draw the Watson-Crick base pairing for Adenine and Uracil.

A
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16
Q

Draw ATP

A
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17
Q

Draw GTP

A
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18
Q

Draw cAMP

A
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19
Q

Draw cGMP

A
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20
Q

Draw alpha D glucopyranose (glucose)

A
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21
Q

List the essential/nonessential amino acids

A

Essential

  1. Isoleucine (Ile)
  2. Leucine (Leu)
  3. Valine (Val)
  4. Phenylalanine (Phe)
  5. Tryptophan (Trp)
  6. Histidine (His)
  7. Lysine (Lys)
  8. Threonine (Thr)
  9. Methionine (Met)

Nonessential

  1. Alanine
  2. Arginine
  3. Asparagine
  4. Aspartate
  5. Cysteine
  6. Glutamate
  7. Glutamine
  8. Glycine
  9. Proline
  10. Serine
  11. Tyrosine
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22
Q

Draw Alanine and Include:

3 letter name

1 letter name

Category

A

Alphatic, Hydrophobic/Nonpolar, Nonessential

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23
Q

Draw Glycine and Include:

3 letter name

1 letter name

Category

A

Aliphatic, Hydrophobic/Nonpolar, Nonessential

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24
Q

Draw Isoleucine and Include:

3 letter name

1 letter name

Category

A

Aliphatic, Hydrophobic/Nonpolar, Essential

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25
Q

Draw Leucine and Include:

3 letter name

1 letter name

Category

A

Aliphatic, Hydrophobic/Nonpolar, Essential

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26
Q

Draw Proline and Include:

3 letter name

1 letter name

Category

A

Aliphatic, Hydrophobic/Nonpolar, Nonessential

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27
Q

Draw Valine and Include:

3 letter name

1 letter name

Category

A

Aliphatic, Hydrophobic/Nonpolar, Essential

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28
Q

Draw Phenylalanine and Include:

3 letter name

1 letter name

Category

A

Aromatic, Hydophobic/Nonpolar, Essential

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29
Q

Draw Tryptophan and Include:

3 letter name

1 letter name

Category

A

Aromatic, Hydrophobic/Nonpolar, Essential

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30
Q

Draw Tyrosine and Include:

3 letter name

1 letter name

Category

A

Aromatic, Polar, Nonessential

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31
Q

Draw Aspartic Acid (Aspartate) and Include:

3 letter name

1 letter name

Category

A

Acidic, Negatively Charged, Nonessential

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32
Q

Draw Glutamic Acid (Glutamate) and Include:

3 letter name

1 letter name

Category

A

Acidic, Negatively Charged, Nonessential

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33
Q

Draw Arginine and Include:

3 letter name

1 letter name

Category

A

Basic, Positively Charged, Nonessential

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34
Q

Draw Histidine and Include:

3 letter name

1 letter name

Category

A

Basic, Positively Charged, Essential

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35
Q

Draw Lysine and Include:

3 letter name

1 letter name

Category

A

Basic, Positively Charged, Essential

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36
Q

Draw Serine and Include:

3 letter name

1 letter name

Category

A

Hydroxylic, Polar, Nonessential

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37
Q

Draw Threonine and Include:

3 letter name

1 letter name

Category

A

Hydroxylic, Polar, Essential

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38
Q

Draw Cysteine and Include:

3 letter name

1 letter name

Category

A

Sulfur-Containing, Polar, Nonessential

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39
Q

Draw Methionine and Include:

3 letter name

1 letter name

Category

A

Sulfur-Containing, Hydrophobic/Nonpolar, Essential

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40
Q

Draw Asparagine and Include:

3 letter name

1 letter name

Category

A

Amidic, Polar, Nonessential

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41
Q

Draw Glutamine and Include:

3 letter name

1 letter name

Category

A

Amidic, Polar, Nonessential

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42
Q

Draw the generic structure of a tripeptide at pH 7, label R groups R1, R2, R3.

A
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43
Q

Draw Tripeptide Met-Phe-Ser at pH 7.

A
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44
Q

Draw a Diagram of DNA Replication

A
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45
Q

What are the pKas of the amino acid side chains? What pH are they protonated/deprotonated?

A
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46
Q

Draw a diagram depicting the conversion of glycogen to glucose 6-phosphate.

A

The Glucose 1-phosphate —-> Glucose 6-phosphate reaction is catalyzed by Phosphoglucomutase

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47
Q

What Molecules and which hormone regulated glycogen breakdown in the liver and the muscle?

A

Inhibiting

  1. ATP - muscle
  2. Glucose - Liver
  3. Glucose 6-phosphate - Muscle

Stimulating

  1. Epinephrine - muscle
  2. Glucagon - Liver
  3. AMP - Muscle
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48
Q

Draw a diagram depicting glycogen synthesis starting with glucose 1-phosphate.

A

Note: the enzyme catalyzing the conversion of glucose 1-phosphate to UDP-Glucose is: UDP-glucose pyrophosphorylase

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49
Q

Which molecules regulate glycogen synthesis?

A
  1. Molecules:
    1. Glucose 6-phosphate activates b form (usually not active)
    2. Insulin stimulates glycogen synthesis.
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50
Q

Draw a diagram depicting the control of glycogen metabolism by Glucagon and/or Epinephrine as well as insulin.

A

FIGURE 21.19 Coordinate control of glycogen metabolism. Glycogen metabolism is regulated, in part, by hormone-triggered cyclic AMP cascades. The sequence of reactions leading to the activation of protein kinase A ultimately activates glycogen degradation. At the same time, protein kinase A along with glycogen synthase kinase inactivates glycogen synthase, shutting down glycogen synthesis.

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51
Q

Draw a diagram depicting the control of glycogen metabolism via insulin

A

FIGURE 21.22 Insulin inactivates glycogen synthase kinase. Insulin triggers a cascade that leads to the phosphorylation and inactivation of glycogen synthase kinase and prevents the phosphorylation of glycogen synthase. Protein phosphatase 1 (PP1) removes the phosphates from glycogen synthase, thereby activating the enzyme and allowing glycogen synthesis. IRS, insulin-receptor substrate.

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52
Q

Draw a diagram depicting the Urea Cycle. Include enzymes and cofactors.

A
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53
Q

Draw a diagram depicting the basic pathways of Protein degradation

A
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54
Q

What are the 2 ways in which Nitrogen is transported from the muscles to the liver in a non toxic way?

A
  1. Glucose-Alanine cycle (see picture).
    1. Nitrogen from glutamate transferred to pyruvate to form alanine
    2. Alanine transferred to liver through blood
    3. transformed back to pyruvate and glutamate
    4. Pyruvate is used for gluconeogenesis
    5. Nitrogen eventually turned into urea
  2. Glutamine synthetase
    1. NH4+ + Glutamate + ATP —> Glutamine + ADP + Pi
    2. nitrogens of glutamine can be converted to urea in the liver.
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55
Q

Draw a diagram depicting the creation of acyl-CoA and the Beta-Oxidation Pathway

A
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56
Q

When are fatty acids oxidized in the peroxisome and why?

A

The peroxisome oxidizes long chain and branched chain fatty acids.

It does this to shorten them for easier Beta-oxidation in the mitochondrion.

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57
Q

Draw a diagram depicting the synthesis of fatty acids starting with acetyl-CoA

A

Make sure to include something about elongating by condensing Malanoyl-ACP with butyryl ACP.

When chain is finished, a thioesterase hydrolyzes C16-Acyl ACP to yield Palmitate and ACP.

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58
Q

Under what kind of conditions are Glucagon and Epinephrine present? What about Insulin?

A

1) Glucagon and Epinephrine: Under conditions of fasting and exercise.
2) Insulin: Present under fed conditions

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59
Q

How is acetyl CoA carboxylase regulated?

A

Inhibited by:

  1. Phosphorylation by AMP activated Kinase (AMPK)
  2. Glucagon
  3. Epinephrine
  4. Palmitoyl CoA

Stimulated by:

  1. Dephosphorylation
  2. Citrate
  3. Insulin
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60
Q

What are the 3 major regulatory transitions in the cell cycle?

A
  1. Start/Restriction Point
    1. in late G1 phase
    2. Cell Commits to cell cycle entry and chromosome duplication.
    3. Yeast Check for nutrients
    4. metazoan cells check for mitogens.
  2. G2/M transition
    1. control system triggers the early mitotic events that lead to chromosome alignment on the mitotic spindle in metaphase.
    2. checks that replication has finished
  3. Metaphase-anaphase transition
    1. Checks for spindle assembly.
    2. Control system stimulates sister-chromatid separation
    3. leads to the completion of mitosis and cytokinesis
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61
Q

Draw a basic diagram depicting the 4 phases of the cell cycle. Mark the control points and what they check for.

A
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62
Q

Draw all pathways regulating cell cycle associated with S-Cyclin

A
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63
Q

Draw all regulation pathways associated with G1/S-Cyclin

A
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64
Q

Draw all cell cycle regulatory pathways having to do with M-Cyclin

A
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65
Q

Draw all cell cycle pathways having to do with G1/S and S-CDK regulation

A
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66
Q

Draw all pathways having to do with M-CDK regulation

A
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67
Q

Draw all pathways having to do with APC/C regulation of cell cycle

A
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68
Q

Draw a diagram depicting control of the cell cycle. Should include cyclin levels as well as other molecules.

A
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69
Q

Name the 4 classes of cyclins and what they regulate. When are their levels high/low?

A
  1. G1/S-Cyclins
    1. activate Cdks in late G1 phase
    2. help trigger progression through start
    3. results in commitment to cell cycle entry
    4. levels fall in S phase
  2. S-Cyclins
    1. binds Cdks soon after progression through start
    2. help stimulate chromosome duplication
    3. levels remain elevated until mitosis
    4. also contribute to control of early mitotic events
  3. M-Cyclins
    1. Activate Cdks that stimulate entry into mitosis at the G2/M transition
    2. levels fall-mid mitosis
  4. G1-Cyclins
    1. Exist in most (but not all) cells
    2. Help govern activites of G1/S-Cyclins, which control progression through start/restriction point in late G1
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70
Q

Name 4 types of regulation in the cell cycle.

A
  1. Phosphorylation/dephosphorylation of Cdks
    1. CdK activating Kinase (CAK) - activates Cdks by phosphorylating activation site.
    2. Wee1 Kinase - inhibits through phosphorylation
    3. Cdc25 phosphatase - removes inhibitory phosphates
  2. Inhibition of Cdks
    1. Cdk inhibitor proteins (CKIs) - inactivates Cyclin-Cdk complexes by rearranging active site.
  3. Ubiquitylation of cell cycle associated proteins
    1. Anaphase promoting complex (APC/C)
      1. Ubiquitylates and causes destruction of:
        1. Securin - causing separation of sister chromatids in metaphase
        2. S- and M- cyclins - causing inactivation of most Cdks in the cell.
    2. SCF
      1. Ubiquitylates and causes destruction of:
        1. CKI proteins - helping to control the activation of S-Cdks and DNA repplication.
        2. G1/S-Cyclins - in early S phase.
  4. Transcriptional regulation
    1. Example: Changes in cyclin gene transcription can help control cyclin levels.
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71
Q

What are the phases of mitosis in order?

A
  1. Prophase
  2. Prometaphase
  3. Metaphase
  4. Anaphase
  5. Telophase
  6. Cytokinesis (not really a phase of mitosis)
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72
Q

Give a brief description of Prophase and draw a simple diagram of it.

A
  1. Chromosomes (each consisting of 2 closely associated sister chromatids) condense
  2. Outside nucleus, mitotic spindle assembles between the 2 chromosomes
  3. the centrosomes have been replicated and moved apart.
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73
Q

Give a brief description of Prometaphase and draw a simple diagram of it.

A
  1. Starts with breakdown of nuclear envelope
  2. chromosomes can now attach to spindle microtubules via kinetochores and undergo active movement.
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74
Q

Give a brief description of Metaphase and draw a simple diagram of it.

A
  1. Chromosomes are aligned at equator of spindle
  2. kinetochore microtubules attach sister chromatids to opposite poles of the spindle.
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75
Q

Give a brief description of Anaphase and draw a simple diagram of it.

A
  1. Sister chromatids separate to form 2 daughter chromosomes
  2. The daughter chromosomes are pulled apart towards the spindle poles
  3. kinetochore microtubules shorten
  4. spindle poles move apart
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76
Q

Give a brief description of Telophase and draw a simple diagram of it.

A
  1. Daughter chromosomes arrive at poles of spindle and decondense
  2. a new nuclear envelope reassembles around each set
    1. this completes the formation of 2 nuclei, marking end of mitosis.
  3. Division of cytoplasm begins with contraction of the contractile ring.
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77
Q

Give a brief description of Cytokinesis and draw a simple diagram of it.

A
  1. Cytoplasm is divided in 2 by contractile ring
    1. made of actin and myosin II filaments
  2. Cell pinched in two to create 2 daughter cells
  3. each daughter cell has 1 nucleus.
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78
Q

What is a chromosome and how many do humans have? What is the difference between a chromosome and a chromatid?

A
  1. A chromosome is a single, long, double stranded DNA molecule and the associated proteins.
    1. Humans have 23 pairs of chromosomes (46 total).
    2. 22 are non-sexual chromosome pairs (autosomes).
    3. There is 1 sexual chromosome pair (allosome)
  2. A chromatid is an exact copy of a chromosome that is made during cell division. The copy of the chromosome and the original chromosome are referred to as sister chromatids until they are separated. Then they are referred to as daughter chromosomes.
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79
Q

Give a brief summary of what happens in each phase of the cell cycle.

A
  1. G1 phase
    1. Gap phase/growth phase
    2. proteins and number of organelles are built up
    3. Cell grows in size
    4. The restriction point is at end of G1 phase
  2. S phase
    1. DNA replication occurs
  3. G2 phase
    1. more cell growth and biosynthesis of proteins and other structures in preparation for mitosis
    2. Another checkpoint, the G2/M-phase checkpoint, is at the end of G2 phase
  4. M-phase
    1. mitosis Happens
      1. Sister chromatids are pulled apart to opposite poles by the mitotic spindle.
    2. Cytokinesis happens
      1. the contractile ring splits the cell into 2 daughter cells.
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80
Q

What is meiosis and how is it different from mitosis?

A
  1. Meiosis is the development of haploid (only one set of chromosomes, so 23 rather than 46 in humans) gametes (sexual cells, like sperm or eggs)
  2. produces 4 gametes
  3. is a chance for homologous recombination between homolog chromosomes, contributing to genetic diversity.
  4. Different from mitosis because there are two rounds of chromosome separation, as opposed to 1 in mitosis
    1. 1st separation separates the homologous chromosomes (that have had a chance to exchange genes)
    2. 2nd separation separates the chromatids, making 4 different sets.
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81
Q

Draw out the cholesterol biosynthetic pathway (drawings of molecules are not necessary)

A
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82
Q

What does HMG-CoA Reductase do?

A
  1. Catalyzes the comitted step of converting Acetyl CoA and acetoacetyl CoA to Mevalonate in the cholesterol syntheic pathway.
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83
Q

What are the 4 basic ways that HMG-CoA reductase is regulated?

A
  1. Control of Transcription
  2. Control of Translation
  3. Ubiquitination
  4. Phosphorylation in response to ATP levels.
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84
Q

How is HMG-CoA Reductase regulated by transcription?

A

Control of transcription

  1. Happens when Cholesterol levels are low
  2. Sterol regulatory element binding proteins (SREBPs) bind to Sterol regulatory element (SRE) on DNA
  3. This causes transcription of reductase mRNA
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85
Q

How is HMG-CoA reductase regulated by control of translation?

A

Control of translation

  1. Non-sterol metabolites derived from Mevalonate inhibit translation of reductase mRNA
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86
Q

How is HMG-CoA Reductase Regulated by Ubiquitination?

A

Degredation of reductase by ubiquitination

  1. membrane domain of reductase senses signals from increasing concentration of sterols
  2. causes it to become polyubiquitinated and ejected from membrane
  3. it is then degraded by proteosome
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87
Q

How is HMG-CoA reductase regulated by phosphorylation?

A

Phosphorylation in response to ATP levels

  1. Phosphorylation of reductase switches it off
  2. phosphorylated by an AMP-activated protein kinase
  3. Thus, cholesterol synthesis stops when ATP level is low (and AMP level is high)
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88
Q

Draw a diagram depicting receptor mediated endocytosis, use LDL as the example.

A

FIGURE 26.20 Receptor-mediated endocytosis. The process of receptor-mediated endocytosis is illustrated for the cholesterol-carrying complex, low-density lipoprotein (LDL):

  1. (1) LDL binds to a specific receptor, the LDL receptor;
  2. (2) this complex invaginates to form an endosome;
  3. (3) after separation from its receptor, the LDL-containing vesicle fuses with a lysosome, leading to the degradation of the LDL and the release of the cholesterol.
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89
Q

Name the lipoproteins and their roles

A
  1. Chylomicron - Dietary fat transport
  2. Very Low density lipoprotein (VLDL) - Endogenous fat transport
  3. Intermediate-density lipoprotein (IDL) - LDL-precurser
  4. Low-density lipoprotein (LDL) - Cholesterol transport
  5. High-density lipoprotein (HDL) - Reverse cholesterol transport
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90
Q

Draw the steroid synthesis pathway

A
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91
Q

Draw a diagram depicting pathway integration of synthesis of Triacylglycerols and Phospholipids

A
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92
Q

In what 2 ways is phosphatidate formed?

A
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93
Q

How are Triacylglycerols formed from phosphatidate? Which enzyme is a key regulating enzyme in lipid synthesis?

A

Phosphatidic acid phosphatase is a key regulatory enzyme since it converts phosphatidate to DAG, which is used in lipid creation.

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94
Q

Draw a diagram depicting the regulation of lipid synthesis

A
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95
Q

Draw a diagram depicting sphingolipid synthesis.

A
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96
Q

Draw a diagram depicting the activated phosphatidate pathway of lipid synthesis. Use inositol as the alcohol. (there is no need to draw molecular diagrams).

A
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97
Q

Draw a diagram depicting the activated alcohol pathway of lipid synthesis. Use ethanolamine as the alcohol. (no need to draw molecular structures)

A
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98
Q

In what 2 ways can phosphatidylcholine be synthesized? Why is it important?

A
  1. Activated alcohol method of lipid synthesis, with dietary choline being converted to UDP-choline by CTP-phosphocholine cytidyltransferase (CCT) - a rate limiting step
  2. In the liver, an enzyme called phosphatidylethanolamine methyl transferase converts phosphatidylethanolamine to phosphatidylcholine by 3 methylation reactions.
    1. S-adenysylmethionine is the methyl donor.
    2. only happens if there are low levels of dietary choline
  3. Phosphatidylcholine is important because around 50% of membrane mass is made of it.
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99
Q

What does cytochrome P450 do?

What is it important for?

A
  1. It catalyzes hydroxylations by using NADPH and O2
  2. Importance:
    1. Steroid hormone synthesis
    2. Drug metabolism
    3. Metabolism of polyunsaturated fats
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100
Q

Draw a diagram depicting the distinction between the types of inhibitors

A
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101
Q

Draw a michaelis menton graph and label it, and know what each thing stands for.

A
102
Q

Draw a Lineweaver Burke Plot and label it. Know what each thing stands for and means.

A
103
Q

How do the different inhibitors affect Michaelis menton plots? Draw or describe.

A
104
Q

How do the different inhibitors affect Lineweaver Burke plots? Draw or describe.

A
105
Q

What enzyme catalyzes the attachement of amino acids to tRNA? What does the reaction look like?

A

Aminoacyl tRNA-synthetase

106
Q

Draw prokaryotic initiation

A
107
Q

Name 6 Differences between eukaryotic and prokaryotic translation.

A
  1. Eukaryotic 80S ribosome is bigger than prokaryotic 70S ribosome.
  2. Eukaryotic mRNA usually encodes for just 1 protein, prokaryotic mRNA can potentially encode for more than 1.
  3. Eukaryotic translation initiation begins at the 5’ cap since there is just one start site. Prokaryotic translation initiation begins at the start site following the Shine-Dalgarno sequence since there can be multiple start sites.
  4. Eukaryotic first amino acid is Met, prokaryotic is fMet.
  5. Eukaryotic mRNA forms a circle by having 5’ Cap connect to Poly(A) tail. Prokaryotic does not.
  6. Eukaryotic translation only has 1 release factor. Prokaryotic has 2.
108
Q

Draw prokaryotic elongation

A
  1. EF-Tu-GTP brings new aminoacyl-tRNA to A site
    1. leaves as EF-Tu-GDP and is regenerates by EF-Ts
  2. Peptide bond formation
    1. old amino acid transfered to C side of new one on new tRNA
    2. catalized by Peptidyl transferase
  3. Translocation of mRNA
    1. EF-G uses hydrolysis of GTP to move mRNA by 3 base pairs forward through ribosome
  4. tRNA in exit site dissociates.
109
Q

Draw prokaryotic termination

A
110
Q

Draw eukaryotic initiation

A
111
Q

Draw eukaryotic circularization

A
112
Q

Name the components of the prokaryotic ribosome.

A
  1. Entire thing: 70S ribosome complex
  2. Large subunit: 50S subunit made up of:
    1. 23S RNA - The peptidyl-transferase center is located here, which catalyzes teh formation of peptide bonds.
    2. 5S RNA
  3. Small Subunit: 30S subunit
    1. 16S RNA: associates with the Shine-Dalgarno sequence, which moves the start codon and anti-codon into position with each other to begin protein synthesis.
113
Q

Name the components of the Eukaryotic ribosome

A
  1. Whole thing: 80S ribosome complex
  2. Large subunit: 60S subunit made up of:
    1. 5S RNA: homologous to prokaryotic 5S RNA
    2. 28S RNA: homologous to prokaryotic 23S RNA
    3. 5.8S RNA: homologous to 5’ end of prokaryotic 23S RNA.
  3. Small Subunit: 40S subunit
    1. 18S RNA: homologous to 16S RNA in prokaryotes.
114
Q

Name the prokaryotic inititation elongation, release factors and their function.

A

Initiation factors

  1. IF1:
    1. attaches to 30S subunit at same time as IF3 to form 30S initiation complex.
    2. Binds near A site and directs fMet-tRNAf to P site.
  2. IF2 - a member of the G-protein family
    1. binds GTP, allowing association with fMet-tRNAf
    2. Also stimulates associateion with 50S subunit to form 70S inititation complex
  3. IF3
    1. Attaches to 30S Subunit at the same time as IF1 to form the 30S initiation complex
    2. helps to preven premature formation of 70S complex.

Elongation factors:

  1. EF-Tu - a member of the G-protein family
    1. Delivers non-initiation aminoacyl-tRNA to A site.
    2. Protects the ester linkages in aminoacyl-tRNA from hydrolysis.
    3. Contributes to accuracy of protein synthesis since GTP hydrolysis and expulsion of EF-Tu-GDP can’t happen until a correct pairing between codon and anti-codon ocurrs.
  2. EF-Ts - Resets EF-Tu to GTP form
  3. EF-G (translocase)
    1. Using GTP hydrolysis, it catalyzes movement of mRNA by 3 nucleotides through ribosome.

Release factors

  1. RF1 - Recognizes UAA or UAG stop codons
    1. catalyzes hydrolytic cleavage of ester linkage holding polypeptide chain to tRNA in P site.
  2. RF2 - Recognizes UAA or UGA stop codons
    1. does same thing as RF1, just with different codon.
  3. RF3
    1. catalyzes release of RF1 or RF2 from ribosome upon release of newly synthesized protein.
  4. Ribosome Release factor (RRF)
    1. causes dissociation of entire 70S complex.
115
Q

Name the Eukaryotic inititation, elongation, release factors and their function.

A

Initiation Factors

  1. eIF-2
    1. associates with 40S ribosome and Met-tRNAi to form the 43S preinititation complex (PIC).
  2. eIF-4E
    1. Binds to 5’ cap of mRNA
    2. helps PIC bind to mRNA
    3. Linked by eIF-4G to PABPI to make mRNA circular.
  3. eIF-4G
    1. Links eIF-4E to poly(A) binding protein I (PABPI) at the Poly(A) tail to make circular mRNA.

Elongation factors

  1. EF1-alpha - homologous to EF-Tu
    1. delivers aminoacyl-tRNA to A site
  2. EF1-By (beta-gamma) - homologous to EF-Ts
    1. catalyzes exchange of GTP for bound GDP
  3. EF2 - homologous to EF-G
    1. mediats GTP-driven translocation, moving mRNA through ribosome.

Release factors

  1. eRF-1 - only 1 release factor for eukaryotes
    1. binds to all stop codons.
  2. eRF-3
    1. accelerates the activity of eRF-1
116
Q

What are the 2 mechanisms of protein sorting and which organelles or structures do they send proteins to?

A
  1. General mechanism - synthesized in cytoplasm.
    1. Nucleus
    2. Chloroplasts
    3. Mitochondria
    4. Peroxisomes
  2. Secretory pathway - ribosomes moved to rough ER
    1. secretory proteins
    2. Residents of ER
    3. Golgi Complex
    4. Lysosomes
    5. Integral membrane proteins for these organelles.
    6. Integral plasma membrane proteins.
117
Q

Draw a diagram depicting the secretory pathway.

A
  1. Ribosome in cytoplasm synthesizes protein with a hydrophobic signal sequence attached at N-terminal end.
  2. SRP (signal recognition protein) binds to signal sequence.
    1. stops translation
    2. is a GTP bound protein
  3. SRP brings ribosome to SRP receptor on ER and binds to it
    1. Receptor is also GTP bound.
  4. This causes the translocon to open
    1. SRP and receptor hydrolyze GTP to GDP and Pi
    2. SRP dissociates from mRNA and receptor and goes back into cytoplasm.
    3. the nascent protein is now inside translocon.
  5. Signal peptidase cleaves off signal sequence
  6. Protein synthesis continues
    1. goes into ER lumen
    2. Keeps translocon open.
  7. Once protein synthesis is finished, ribosome dissociates and translocon can close.
118
Q

Draw a diagram depicting prokaryotic translation. Mark initiation, elongation, and termination parts of it.

A
119
Q

Draw a basic diagram of a chloroplast.

A
120
Q

Draw a diagram depicting the light reactions of photosynthesis.

A

Note: in diagram, it lists photosystem 2 as the one that catalyzes NADP+ to NADPH, it should be photosystem 1.

PS I and PS II are swapped in the picture.

121
Q

What is the difference between bacterial and plant photosynthesis?

A

Bacteria

  1. 1 special pair: P960
  2. Does cyclic electron flow to generate proton gradient.
  3. Basically 1 photosystem and a cytochrome

Plant

  1. 2 special pairs: P680, P700
  2. normally not doing cyclic phosphorylation
  3. 2 photosystems and 1 cytochrome.
122
Q

What are accessory pigments and what do they do?

A
  • Accessory pigments are pigments in addition of chlorophyll a that assist in gathering light energy.
  • two main ones are:
    • Chlorophyll b
    • caratenoids
  • gather in light harvesting complexes and use resonance energy transfer to send energy to reaction centers in photosystems.
123
Q

Which components of light reactions are on stacked and unstacked regions of thylakoid membrane and what advantages are there to being in one region or another? How do protons get from unstacked region to stacked?

A

Unstacked:

  1. Photosystem I: allows direct access to stroma for reduction of NADP+ to NADPH
  2. ATP Synthase: Gives room for its large CF1 globule and gives access to ADP.

Stacked:

  1. Photosystem II: Tight quarters of stacked are no problem since it interacts with small polor electron donor (H2O) and highly lipid soluble electron carrier (plastiquinone).

Both:

  1. Cytochrome bf: Present in both regions

Protons can get from one region to another because both the stacked and unstacked regions are on the same Thylakoid space, meaning that the proton gradient is the same for both.

124
Q

In what ways are the light reactions regulated?

A
  1. ATP Synthase
    1. Thioredoxin
  2. need more on this. But I assume it is similar to how oxidative phosphorylation is regulated. Based on energy and NADPH needs.
125
Q

Draw a diagram depicting the calvin cycle (the simple version).

What is the main purpose of the calvin cycle?

A

Carbon fixation

The complex version has basically the entire reverse pentose phosphate pathway going from fructose 6-phosphate to ribulose 5-phosphate.

126
Q

Name 7 pathways that require NADPH?

A

Synthesis:

  1. Fatty acid metabolism
  2. cholesterol synthesis
  3. neurotransmitter biosynthesis
  4. Nucleotide biosynthesis
  5. calvin cycle

Detoxification

  1. reduction of oxidized glutathione
  2. Cytochrome P450 monooxygenases
127
Q

Describe the C4 pathway. What environment do plants need it in? Why is it needed?

A
  • It is a pathway of carbon fixation
  • needed in hot climate
  • needed because increased temperature increases photorespiration.
  • Having the carbon be transported to site of calvin cycle, away from site of carbon absorption, means that less wasteful photorespiration happens.
128
Q

What are C4, C3, CAM plants? What environments are they found in?

A
  1. C4 plants
    1. hot, tropical environment. Use C4 pathway to prevent wasteful photorespiration.
  2. C3 Plants
    1. temperate environments, don’t need C4 pathway since photorespiration not as much of a problem.
  3. CAM plants
    1. hot arid environment. Collect carbon as malate during day with stomata closed.
    2. Do carbon fixation at night to avoid losing water.
129
Q

Draw the pentose phosphate pathway including:

Enzymes of non-oxidative phase

Don’t have to draw out complete phase 1 components and enzymes (doesn’t really seem necessary)

A
130
Q

What are the 4 modes of pentose phosphate pathway?

A
  1. Much more Ribose 5-phosphate than NADPH is required.
  2. The needs for NADPH and for Ribose 5-phosphate are balanced.
  3. Much more NADPH than Ribose 5-Phosphate is required
  4. Both NADPH and ATP are required.
131
Q

Name 7 tissues have active pentose phosphate pathways, and what is their function?

A
  1. Adrenal gland - Steroid synthesis
  2. Testes - Steroid synthesis
  3. Ovary - Steroid synthesis
  4. Liver - Fatty acid and cholesterol synthesis
  5. Adipose tissue - Fatty acid synthesis
  6. Mammary gland - Fatty Acid Synthesis
  7. Red blood cells - maintanance of reduced glutathione
132
Q

Why is Glutathione important and how does it tie into the pentose phosphate pathway?

A
  1. Reduced Glutathione (GSH) reduces Reactive Oxygen Species (ROS) which are dangerous to us.
  2. After reducing an ROS, it is in its oxidyzed form (GSSG).
  3. It needs to be regenerated back to its GSH form by being reduced.
  4. NADPH provides reducing power to do this.
  5. The NADPH generated by glycerol 6-phosphate dehydrogenase provides the reducing power to regenerate it.
133
Q

What is the difference between an aldose and a ketose?

A
  1. Aldose
    1. has an aldehyde group (in red on diagram)
  2. Ketose
    1. has a keto group (in red on diagram)
134
Q

Define isomers

A
  1. Isomer - have the same molecular formula, but different structures.
135
Q

What kind of isomers are these? Why are they these isomers?

A

Constitutional isomers

They Differ in the order of attachement of atoms

136
Q

Define Stereoisomers, what kinds of isomers are stereoisomers?

A

Atoms are connected in the same order but with different spatial arrangement.

  1. Enantiomers
  2. Diastereoisomers
  3. Epimers
  4. Anomers
137
Q

What kind of isomer is this? Why?

A

Enantiomers

Nonsuperimposable mirror images

138
Q

What kind of isomers are these? Why?

A

Diastereoisomers

Isomers that are not mirror images

139
Q

What kind of isomers are these? Why

A

Anomers

Isomers that differ on at a new asymmetric carbon atom formed on the ring enclosure

140
Q

What kind of isomers are these? Why?

A

Epimers

Differ at one of several asymmetric carbon atoms

141
Q

Name 2 types of glycosidic bonds and what they link.

A
  1. O-glycosidic bond - links monosaccharides together
  2. N-glycosidic bond - links to the nitrogen of an amine, such as linking a ribose sugar to a nitrogenous base.
142
Q

What are the 2 forms of starch and what is the difference between them?

A
  1. Amylose - unbranched form, alpha-1,4-linkages between glucose residues only.
  2. Amylopectin - branched form, has 1 alpha-1,6-linkage per 30 alpha-1,4-linkages between glucose residues.
143
Q

What is a glycoprotein? What are the 3 classes of glycoproteins?

A

Glycoprotein - A carbohydrate group covalently attached to a protein.

Classes:

  1. Glycoproteins:
  2. Proteoglycans:
  3. Mucins or Mucoproteins:
144
Q

What are the characteristics of the Glycoprotein class of glycoproteins?

  1. Is the protein or carbohydrate larger?
  2. What are they generally components of?
  3. What do they have to do with secretion?
  4. What is an example?
A
  1. potein larger than carbohydrate
  2. Are components of cell membranes, taking part in cell adhesion and binding of sperm to eggs
  3. many proteins secreted from cells are glycosylated, including many in serum of blood.
  4. Erythropoietin (EPO) is a vital hormone that stimulates the production of red blood cells
145
Q

What are the characteristics of the Proteoglycan class of glycoproteins?

  1. Is the protein or carbohydrate larger?
  2. What is the polysaccharide it is attached to?
  3. What is its general function?
  4. What is an example?
A
  1. Carbohydrate larger than protein
  2. Polysaccharide = glycosaminoglycan
  3. Structural compenents and lubricants
  4. Aggrecan is an important part of Cartilage
146
Q

What are the characteristics of the Mucin/Mucoprotein class of glycoproteins?

  1. Is the protein or carbohydrate larger?
  2. What is the carbohydrate it is attached to?
  3. What is its general function?
A
  1. Carbohydrate larger than protein
  2. Carbohydrate: N-Acetylgalactosamine, an amino sugar,
  3. Abundant in mucus and saliva, serving as lubricants.
147
Q

What is cellulose, and what purpose does it serve?

A
  1. Cellulose is a major polysaccharide of glucose found in plants.
  2. Is unbranched, joined by beta-1,4-linkages as opposed to alpha-1,4-linkages.
  3. Is one of the most abundant organic compounds in the biosphere.
  4. Serves a strucutural role in plants, rather than a nutritional role like starch.
148
Q

How can oligosaccharides be sequenced?

A

Cleaving bonds and MALDI-TOF mass spectrometry.

149
Q

What reactions do glycosyltransferases catalyze?

A

catalyze the formation of glycosidic bonds, and the synthesis of complex carbohydrates.

150
Q

What are lectins? Why are they important?

A
  1. Lectins: a type of glycan-binding protein (proteins that bind specific carbohydrate structures on neighboring cell surfaces).
  2. Chief function of lectins is to facilitate cell-cell contact.
151
Q

What are the 3 major classes of membrane lipids?

A
  1. Phospholipids - made from 4 components
    1. Example: Phosphatidylcholine
  2. Glycolipids - sugar containing lipids
    1. example: Cerebroside
  3. Cholesterol - is a large part of membrane in certain nerve cells.
152
Q

Draw the basic phospholipid structure schematic.

Draw phosphatidylserine.

A
153
Q

What are the properties of phospholipids that allow them to form membranes? What are two kinds of structures that form?

A

Properties:

  • Polar head groups favor contact with water
  • hydrocarbon tails interact with one another in preference to water.

Structures:

  1. Micelle:
    1. ​Polar heads form outside of globular structure.
    2. Tails point inwards.
    3. readily formed by ionized fatty acids.
  2. Lipid bilayer or bimolecular sheet:
    1. Tails point towards each other
    2. Heads point out.
    3. Form a lipid bilayer.
154
Q

What is a liposome/lipid vesicle?

A
  1. A synthetic bilayer with liquid inside
  2. can be used to study membrane permeability or deliver chemicals to cells.
155
Q

What kinds of structures are found in membrane spanning proteins? In channel proteins?

A
  1. Membrane spanning - Alpha helices do to hydrophobic residues pointing out.
  2. Channel proteins - Beta strands form hollow cylinders
156
Q

What are the types of groups are used by proteins to attach to membranes?

A
  1. A Palmitoyl group - Is attached to a specific cysteine residue by a thioester bond
  2. A Farnesyl group - attached to a cysteine residue at the carboxyl terminus.
  3. GPI anchor - Glycolipid structure (glycosylphosphatidylinositol) attached to carboxyl terminus.
157
Q

What is the difference between active and passive transport?

A
  1. Passive Transport - molecules move across membranes with the concentration gradient. Energy not requred.
    1. Facilitated diffusion is an example of this.
  2. Active transport - molecules move against a concentration gradient. Requires input of free energy.
158
Q

What does chiral mean in the context of amino acids?

A

Means that they may exist in one or the other of two mirror-image forms. The L-isomer and D-isomer. Can’t simply be rotated to change between forms.

159
Q

What isomer do amino acids that make up protein have?

A

All amino acids that make up protein are L-Amino acids.

160
Q

What are torsion angles and why are they important? What are phi and psi angles?

A
  1. Torsion angle - the rotation around the bonds to the alpha-carbon in an amino acid.
  2. Important because the freedom of rotation around these bonds allows proteins to fold in many different ways.
  3. Phi angle - the angle of rotation around the bond between the alpha carbon and the nitrogen.
  4. Psi angle - the angle of rotation around the bond between the alpha-carbon and the carbonyl carbon.
161
Q

What is a Ramachandron plot and how is it used?

A
  • Not all combinations of Phi and Psi angles are allowed due to Steric Occlusion (the fact that two atoms cannot be in the same place at the same time).
  • A Ramachandron plot is a 2D plot that shows which combinations are possible or not due to steric clashes.
  • Can be used to determine the likelihood of certain kinds of 2ndary structures.
162
Q

What are the 3 RNA polymerases, where are they located, what kind of RNA do they transcribe, how sensitive are they to the effects of alpha-amanitin?

A
163
Q

Draw the anticancer drug targets diagram that targets thymidylate.

A
164
Q

What does thymidylate synthase do?

A

It catalyzes the formation of TMP from dUMP

165
Q

Which enzymes convert and interconvert Nucleoside monophosphate, diphosphate, and triphosphates?

A
  1. Nucleoside monophosphate kinases convert nucleoside monophosphates to diphosphates.
    1. example: UMP Kinase
    2. UMP + ATP <—-> UDP + ADP
  2. Nucleoside diphosphate kinases interconverts nucleoside diphosphates and triphosphates.
    1. Has broad specificity
    2. XDP + YTP <—–> XTP + YDP
166
Q

What reaction is catalyzed by cytidine triphosphate synthetase

A

The transformation of Uridine triphosphate (UTP) into cytidine triphosphtate (CTP)

UTP + NH3 + ATP —-> CTP + ADP + Pi

167
Q

Describe the salvage pathway of Thymine released from degraded DNA

A
  1. Thymine converted to nucleoside thymidine
    1. Reaction catalyzed by Thymidine phosphorylase
    2. Thymine + Deoxyribose 1-phosphate <——> Thymidine + Pi
  2. Thymidine converted into a nucleotide
    1. Reaction catalyzed by Thymidine kinase
    2. Thymidine + ATP <—–> TMP + ADP
168
Q

What is the committed step in purine synthesis?

A
  1. The conversion of PRPP to 5-phosphoribosyl-1-amine by Glutamine phosphoribosyl amidotransferase
  2. Requires the hydrolysis of Gln to create ammonia for the reaction, catalyzed by the same enzyme. Is a potential regulating thing.
169
Q

Which enzymes catalyze the formation of AMP and GMP from IMP

A
  1. Adenylosuccinate synthetase
    1. ​AMP
  2. GTP synthetase
    1. ​GMP
170
Q

Why is ribose 5 phosphate imporatant? How is it produced? What enzyme and product are used?

A
  1. Produced in pentose phosphate pathway, and during calvin cycle.
  2. Is important because it can be turned into phosphoribosyl pyrophosphate (PRPP) which is used in nucleotide synthesis.
    1. this reaction is catalyzed by PRPP synthetase
171
Q

What enzyme catalyzes the conversion of NDPs to dNDPs?

A

Ribonucleotide reductase

172
Q

What is the enzyme and reaction that creates PRPP? Why is PRPP important?

A

Enzyme = PRPP Synthetase

PRPP is an activated ribose that accepts nucleotide bases.

173
Q

What is a suicide inhibitor? What is an example of one?

A

An inhibitor that traps an enzyme in a form that cannot proceed down the reaction pathway.

An example is fluorodeoxyuridylate trapping Thymidylate synthase in its active form.

174
Q

4 things that happen in the nucleolus?

A
  1. rRNA synthesis
  2. Ribosome biogenesis
  3. Assembly of signal recognition particles (SRP)
  4. Plays a role in how cell responds to stress
175
Q

4 things that happen in the nucleus?

A
  1. Transcription of genes.
  2. Replication of DNA.
  3. Contains cells genetic material
  4. Splicing and pre-mRNA processing
176
Q

3 things about a vesicle?

A
  1. Fluid enclosed in lipid bilayer, seperating it from the cytoplasm.
  2. Can store food and other stuff
  3. Can be used for transport
177
Q

What happens in the rough ER (8),

A
  1. Site of protein synthesis at ribosomes attached to it
  2. Secretory pathway happens here
  3. Works with golgi to target proteins to destinations.
  4. Key in manufacture of lysosomal enzymes
  5. Manufacture of secreted proteins
  6. Integral membrane proteins as vesicles exit and bind to new membranes.
  7. N-linked glycosylation - lumen
  8. Disulfide bond formation - lumen
178
Q

What happens in the Smooth ER (6)?

What does it synthesize?

What does it metabolize?

else does it do?

A

Smooth ER

  1. Synthesizes
    1. Lipids
    2. Phospholipids
    3. Steroids
  2. Carries out metabolism of:
    1. carbohydrates
    2. Steroids
    3. Lipids
  3. Detoxification
  4. Attachment of receptors on cell membrane proteins
  5. Regulates Ca2+ ion concentration in muscle
  6. Converts glucose-6-phosphate to glucose with glucose-6-phosphatase in gluconeogenesis.
179
Q

2 things that happen at the golgi apparatus?

A
  1. Proteins packaged in ER modified by golgi and destined for secretion via endocytosis or use in the cell.
  2. Protein glycosylation
180
Q

What are 3 components of the cytoskeleton?

A
  1. Actin microfilaments
  2. Intermediate filaments
  3. Microtubules
181
Q

What are 9 things that happen at the Mitochondria?

A
  1. Energy conversion/production
  2. Pyruvate transported to matrix for
  3. citric acid cycle, also in matrix
  4. Oxidative phosphorylation and the electron transport chain
    1. Is located at the inner mitochondrial membrane
  5. Heat production in case of mitochondrial uncoupling.
  6. Storage of calcium ions in matrix
  7. Beta oxidation of fatty acids - outer membrane
  8. Apoptosis
  9. Has a role in steroid synthesis
182
Q

What are 6 things that happen in the cytoplasm?

A
  1. Signal transduction
  2. Glycolysis
  3. Gluconeogenesis
  4. Protein biosynthesis
  5. Pentose phosphate pathway
  6. Sucrose synthesized here
183
Q

What is the lysosome? (3 things)

What are the molecules it interacts with?

A
  1. Contain enzymes to break down various biomolecules
    1. Peptides
    2. Nucleic acids
    3. Carbohydrates
    4. Lipids
  2. Can cooperate with phagosomes to conduct autophagy, clearing out damaged structures
  3. Can help break down virus particles or bacteria in phagocytosis of macrophages.
184
Q

What is the centrosome? (3 things)

A
  1. Associates with nuclear membrane in mitosis
  2. Nucleates microtubules for use in mitosis
  3. Interact with chromosomes in building mitotic spindle.
185
Q

Describe the cell membrane, what happens at it? (5 things)

A
  1. Lipid bilayer
  2. Endo/exocytosis
  3. Selectively-permeable
  4. Passive osmosis and diffusion
  5. Transmembrane protein channels and transporters
186
Q

What happens in the chloroplast? (5 things)

What is synthesized?

A
  1. Key player in pathogen defense
  2. Calvin cycle/dark reactions - in stroma
  3. Light reactions of photosynthesis - thylakoid stacks in stroma
  4. Convert nitrate into ammonia
  5. Synthesis
    1. starch (also stored in chloroplasts)
    2. Amino acids (except S-containing) - Stroma
    3. Nucleotide synthesis
    4. Complex lipid synthesis
187
Q

What reaction is catalyzed by an aminotransferase?

A

The transfer of an alpha-amino group from an alpha-amino acid to an alpha-keto acid

Example:

Aspartate + Alpha-ketoglutarate <——> Oxaloacetate + Glutamate

188
Q

Name types of DNA damage

A
  1. Incorrect base insertion during replication
  2. Base mismatch
  3. mutagens
    1. oxidizing agents
      1. reactive oxygen species, can convert bases to other bases that match with wrong base
    2. alkylating agents
      1. can lead to something like a G-C to T-A transversion
    3. light
      1. covalently links adjacent pyrimidine residues
  4. Double stranded DNA breaks
189
Q

How would incorrect base insertion during replication be repaired?

A
  1. Proofreading by DNA polyemrase
    1. incorrect base moved to exonuclease site and excised.
190
Q

How would a DNA base mismatch be repaired?

A

DNA mismatch-repair systems

  1. 2 proteins:
    1. 1 recognizes mismatch, calls for other one
    2. 2nd protein is an exonuclease that removes a section of DNA
    3. DNA polyermase remakes section correctly
191
Q

How would a UV induced pyrimidine dimer be repaired?

A

Direct repair by photolyase

  1. DNA photolyase uses photoenergy to cleave the dimer
192
Q

How would bases modified by something like a ROS be repaired?

A

base-excision repair/nucleotide excision repair

  1. an enzyme detects damaged DNA
  2. flips affected base out of double helix and into active site
  3. acts as a glycosylase, releasing damaged base.
193
Q

How would a break in the double stranded DNA be repaired?

A

Nonhomologous end joining (NHEJ)

  1. free ends of doubles strand brought close together so that enzymes can seal the break.
194
Q

What does RecA do and how?

A
  1. Homologous recombination
  2. Strand invasion
195
Q

What does Cre-Recombinase do and how?

A
  1. Homologous recombination
  2. Holliday junciton intermediates
196
Q

What is the basic process of prokaryotic transcription?

A
  1. Initiation
    1. RNA polymerase binds to promotor sites
    2. the -10 sequence and -35 sequence
      1. -35 = TTGACA
      2. -10 = TATAAT
    3. Sigma subunit of RNA polymerase allows it to recognize promotor site.
  2. Elongation
    1. RNA polymerase synthesizes mRNA using template strand.
  3. Termination
    1. sequences in new RNA signal termination
    2. termination signal forms a stable stem-loop structure.
    3. Rho factor helps to terminate.
197
Q

What is the basic process of eukaryotic transcription?

A
  1. Inititation
    1. different prmotors for different RNA polymerases
  2. Elongation
    1. Transcription factors interact with promotors and assemble transcription complex
  3. Termination
    1. pre-mRNA post processing
198
Q

What are the 3 steps in pre-mRNA processing?

A
  1. 5’ capping
  2. 3’ Polyadenylation (poly(A) tail)
  3. Splicing
    1. remove introns, connect exons
199
Q

What do the different snRNPs in the spliceosome do?

A
  1. U1 recognizes 5’ splice site by base- pairing with 5’ region of intron;
  2. U2 recognizes branch point and loops out adenosine for nucleophilic attack of 5’ splice site
200
Q

What are the basic ways that transcription is regulated in Eukaryotes?

A
  1. Promotors
  2. Enhancers
  3. Histone remodelling
  4. alternative splicing
  5. transcription factors
201
Q

What is chromatin?

A

Chromatin is the DNA tightly wrapped around a histone core.

202
Q

How is chromatin used to control gene expression?

A
  1. DNA can bind more or less tightly to chromatin based on its charge.
  2. methylation of DNA can be used to control gene expression
  3. Chromatin structure is modulated by covelant modifications of histone tails.
203
Q

What is a promotor site?

A
  1. A specific sequence of DNA,
  2. usually just upstream of a gene
  3. specifies the site and extent of transcription of the associated gene.
204
Q

What is an operator site?

A
  1. A regulatory DNA sequence that is part of the operon model.
  2. A repressor can bind to it
205
Q

What is an enhancer?

A
  1. DNA sequences which have no promoter activity themselves.
  2. Can greatly enhance the activity of other promoters.
  3. Enhancers can exert their stimulatory effect over a distance of several thousand nucleotides.
206
Q

What is the catabolite activator protein (CAP)?

A
  1. The cAMP response protein;
  2. when bound to cAMP, CAP binds to an inverted repeat of the lac operon,
  3. near position -61 relative to the start site of transcription,
  4. Stimulates transcription.
207
Q

Outline the principle regulatory components of the E.Coli Lac operon!

A
  • Make sure that underlined ones are mentioned.
  • P - Promotor: site that directs RNA polymerase to correct transcription inititiation site.
  • i gene - encodes the lacl repressor
  • o site - operator site - repressor attaches here to prevent transcription of the structural genes by RNA polymerase.
  • Lacl repressor: binds to operator site and prevents transcription of LacZYa genes. Binds tightly in absence of lactose, releases in presence of lactose.
  • Structural genes (Lac-ZYa) - Code for mRNA that creates 3 proteins (known as a polycistronic transcript)
    • LacZ - codes for beta-galactosidase
    • LacY - codes for galactoside permease
    • Laca - codes for thiogalactoside transacetylase
  • Cyclical nature of the operon: In the presence of lactose, the repressor releases and allows beta-galactosidase gene (LacZ) to be expressed. This enzyme cleaves lactose, and then the lack of lactose causes repressor to bind again. This way, beta-galactosidase is only expressed when needed.
208
Q

What is a transcription factor?

A
  1. A protein that assists RNA polymerase in the initiation of RNA synthesis.
  2. Transcription factors bind to specific promoter elements.
209
Q

What is a repressor?

A
  1. A protein that binds to an operator sequence
  2. inhibits the transcription of the structural genes in the operon.
210
Q

What is an inducer?

A
  1. A small molecule that binds to a repressor.
  2. Alters its interaction with an operator.
211
Q

What is a mediator?

A
  1. A complex of 25 to 30 subunits conserved from yeast to human beings,
  2. Acts as a bridge between transcription factors and promoter-bound RNA polymerase II.
212
Q

Draw the activated methyl cycle. Why is it important?

A

It shows the synthesis of methionine, the fact that SAM is a methyl donor and the activation of methyl groups.

213
Q

Draw pyruvate structure

A
214
Q

Draw the lambda phage alternative infection modes.

A
215
Q

How can the lambda phage be used as a cloning vector? Draw or describe.

A
216
Q

How can plasmids be used as cloning vectors? Draw or describe insertional inactivation.

A
217
Q

What are plasmids? What are characteristics of plasmids?

A
  1. Circular duplex DNA molecules.
  2. Replicate autonomously
  3. Act as accessory chromosomes in bacteria;
  4. they carry useful genes but are disposable under certain conditions.
  5. Bacteria can transfer plasmids between themselves by horizontal gene transfer.
  6. Often confer benefits like antibiotic resitance or other things.

Picture description:

There are two types of plasmid integration into a host bacteria: Non-integrating plasmids replicate as with the top instance, whereas episomes, the lower example, can integrate into the host chromosome.

218
Q

List the important functional elements of an E. coli plasmid vector (3)

A
  1. Origin of replication,
  2. antibiotic resistance gene,
  3. multiple cloning site or recombinase target sequences
219
Q

Origin of replication:

A
  1. In general, the site on a chromosome where replication is initiated.
  2. The origin of replication site in E. coli has a length of 245 bp and contains a tandem array of three nearly identical 13-nucleotide sequences and five binding sites for the DnaA protein.
220
Q

Draw the chemical structure of the second messenger cyclic-AMP and the Watson-Crick base pair adenine-uracil!

A
221
Q
A
  • A) Replication
    • 2) DNA Polymerase
    • 4) dNTP
    • 8) Primer
  • B) Transcription
    • 1) RNA polymerase
    • 6) NTP
    • 7) mRNA
    • 9) Promotor
  • C) Translation
    • 3) Ribosome
    • 5) tRNA
222
Q
A
  • A) T-State - 4) Less active state of an allosteric protein
  • B) R-State - 3) More active state of an allosteric protein
  • C) Preprotein - 1) Protein with signal sequence
  • D) Kinase - 6) Protein phosphorylation
  • E) Phosphatase - 5) Removes phosphates
  • F) Zymogen - 2) Proenzyme
223
Q
A

Answer:

D) Polymer of Glucose

224
Q
A

Answer:

C) Lipids

225
Q
A
  • In principle, 16 amino acids could be encoded by doublet codons (4x4=16) (1.5 points)
  • However, 16 amino acids plus stop codon (17) requires triplets (1.5 points)
226
Q
A
  • A retrovirus is a virus that has RNA as its genetic material.
  • information flow:
    • retrovirus: RNA –> DNA –> RNA
    • Normal cell: DNA –> RNA
227
Q
A
  • A) Transcribes tRNA genes
    • RNA Polymerase III
  • B) Is localized in nucleolus
    • RNA Polymerase I
  • C) Transcribes most protein coding genes
    • RNA Polymerase II
228
Q
A

Answer to A)

  1. Treat the complex with RNAse to digest RNA.
  2. Rebind proteins to affinity matrix.
    1. or native PAGE, Size Exclusion
  3. The proteins will only elute together if they are still associated with each other.
  4. If they elute together, RNA does not hold them together, if they elute seperatly it does.

Answer to B)

  1. Incubate the heterodimer in beta-mercaptoethanol to break disulfide bonds.
  2. Rebind proteins to affinity matrix.
    1. or native page/size exclusion
  3. If they elute together, they are still associated with each other, if they elute seperatly, then they are not.
  4. Eluting together indicates that disulfide bridges were not holding them together. Eluting seperatly indicates that they were in fact held together by disulfide bridges.
229
Q
A
  1. A) NMR spectroscopy at near atomic resolution
    1. Membrane protein means its bad for x-ray
    2. Small, so good for NMR
    3. In large amounts, so good for NMR
  2. B) Cryo-EM single particle analysis at near atomic resolution
    1. Native complex - not good for x-ray
    2. Not much sample - not good for NMR
  3. C) X-ray Crystallography at atomic to near atomic resolution
    1. Large amounts - good for X-ray
    2. Is stable - good for crystallization
    3. Thermophilic makes it bad for cryo-EM
230
Q
A
  1. Translation initiation (0.5 points)
  2. Prokaryotes (0.5 points)
  3. Base pairing with 3’-end of 16S rRNA, thereby properly positioning the AUG start codon on the 30S ribosomal subunit.
231
Q
A
  • SRP and SRP receptor (0.5 points)
  • Hydrophobic signal sequence (0.5 points)
  • SecA ATPase in prokaryotes (1 point)
  • Hsp70 ATPases in eukaryotes (1 point)
    • Bip
    • Kar2P
232
Q
A
  1. mRNA Splicing - The Nucleus
  2. Citric acid cycle (krebs cycle) - The mitochondrial matrix
  3. Beta-oxidation of fatty acids - The Mitochondrial matrix
  4. Photosynthesis - Thylakoid stacks in stroma of chloroplasts.
  5. Electron transport (respiration) chain - Inner mitochondrial membrane.
  6. Disulfide bond formation - ER
233
Q
A
  1. Protein kinases catalyze:
    1. Unphosphorylated —-> Phosphorylated protein
  2. GTPases catalyze:
    1. GDP-bound protein —> GTP-bound protein
  3. Lead to Conformational change
    1. allows switch of activity
    2. downstream signaling
    3. pathway is Off when there is no signal
    4. pathway is on when there is signal
    5. Molecular switches are prefect for this
234
Q
A

Cell Growth

  1. Increase in protein mass
  2. Occurs in G1, followed by S phase and Mitosis

Cell Division

  1. The replication of DNA in and then mitosis.

Checkpoints

  1. G1 check:
    1. based on growth (nutrients) in yeast
    2. Based on mitogens in metazoan cells.
  2. G2-M-Check:
    1. replication has to be finished
  3. M-Checkpoint:
    1. Spindle assembly.
235
Q

Draw the complete structure for the tripeptide Met-Phe-Ser, as it would appear at pH 7!

A
236
Q
A
  1. F-2,6-BP activates the glycolytic enzyme phosphofructokinase and inhibits gluconeogenesis eznyem fructose-1,6-bisphosphatase. (0.5 points each)
  2. Glycolysis is stimulated and at the same time gluconeogenesis is inhibited. Thus anaerobic energy consumption is increased. (1 point)
  3. Tumors often grow in hypoxix conditions because blood vessels are insufficient. Anerobic generation of ATP is thus an advantage. (1 point)
237
Q
A
  1. HMG-CoA reductase is the enzyme that catalyzes the comitted step in cholesterol synthesis. (1 point)
  2. Inhibition of HMG-CoA reductase will lower blood cholesterol levels. (1 point)
  3. This reduces the formation of atheroscleretic plaques (1 point, but exact term can be replaced by explanation)
238
Q
A

Part A

  1. The Ribonucleotide reductase catalyzed reaction
    1. This is a critical enzyme in dNTP creation
  2. The Thymidylate synthase reaction
    1. Makes T from U
  3. (1 point for reaction, 1 point for reason why this is specific)

Part B

  1. Ribonuclease reductase reaction
    1. can be inhibited by hydroxy-urea at the radical in the active site.
  2. Thymidylate synthase
    1. Anticancer drug fluorouracil forms a suicide inhibitor in vivo for thymidylate synthase.
      1. Suicide inhibitor is fluorodeoxyuridylate.
    2. Thymidylate synthase can also be inhibited by methotrexate which stops the regeneration of methylene tetrahydrofolate by inhibiting dihydrofolate reductase.
  3. (1 point for mechanism)
239
Q

Origin of replication complex (ORC):

A
  1. A complex of DnaA, DnaB and DnaC proteins
  2. Bind at the origin of replication on the E. coli chromosome
  3. Make single-stranded DNA accessible to other proteins required for replication.
240
Q

What does inhibition of HMG-CoA reductase stop the formation of?

A

Atherosclerotic plaques

241
Q

How is energy provided for post translational protein translocation via the canonical Sec pathway in prokaryotes and eukaryotes?

A
  1. Prokaryotes:
    1. SecA ATPase
  2. Eukaryotes
    1. HSP70 ATPases
      1. BiP
      2. Kar2p
242
Q

Cytoskeleton:

A
  1. Internal scaffolding of cells,
243
Q

Myosin:

A
  1. A protein that forms the thick filaments of striated muscle;
  2. displays ATPase activity at its globular head,
    1. which, in conjunction with the ability to reversibly bind actin at its fibrous region, provides the power stroke of muscle contraction.
244
Q

Kinesin:

A
  1. A protein with ATPase activity
  2. Moves cellular organelles along microtubule tracks in anterograde transport.
245
Q

Dynein:

A
  1. A large protein with ATPase activity
  2. Is a component of microtubules;
  3. the ATPase activity provides the power for the movement of cilia and flagella.
  4. In cytoplasm, a motor protein that is related to the dynein in flagella and cilia and powers retrograde transport.
246
Q

Actin:

A
  1. A highly conserved protein found in all eukaryotes;
  2. in striated muscle, it forms the thin filaments of the sarcomere
  3. activates the ATPase of myosin.
247
Q

Microtubule:

Major component of: (3)

Composed primarily of: (2)

A
  1. A cytoskeleton element that is a major component of:
    1. cilia,
    2. eukaryotic flagella, and
    3. the mitotic spindle;
  2. composed primarily of:
    1. alpha-tubulin
    2. beta-tubulin;
  3. capable of rapid assembly and disassembly.
248
Q

What does the cytoskeleton enable cells to do?

A
  1. Enables cells to:
    1. transport vesicles,
    2. change shape
    3. migrate.
249
Q

What is teh cytoskeleton made up of?

A
  1. made up of:
    1. microfilaments,
    2. intermediate filaments
    3. microtubules,
250
Q

Draw a diagram of double helical DNA with T-A pairing and G-C pairing. Label 5’ and 3’ ends.

A
251
Q

Draw oxaloacetate structure

A

Biochemistry General Study (16 decks)

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