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BIO230 Midterm > Week 4 > Flashcards

Week 4 Flashcards

1
Q

What does the proteome show?

A

differences in the proteins expressed by two human tissues
- red: common to both
- blue: tissue-specific

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2
Q

How is prokaryotic and eukaryotic translational similar?

A

both use translational control mechanisms to regulate protein expression, often in response to stressful situtations such as low nutrients, infection, or environmental stresses (temperature)

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3
Q

What is the Shine-Dalgarno (SD) sequence?

A

The Shine-Dalgarno sequence is a six-nucleotide sequence located upstream of the AUG start codon in prokaryotic mRNAs. It helps position the ribosome for translation initiation and provides translational control mechanisms

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4
Q

What is the primary focus of prokaryotic translation regulation?

A

Prokaryotic translation regulation primarily focuses on controlling the initiation of protein synthesis in response to various environmental conditions, such as nutrient availability and stress.

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5
Q

What is the role of specific RNA binding proteins in prokaryotic translation regulation?

A

Specific RNA binding proteins can block access to the Shine-Dalgarno (SD) sequence, preventing the ribosome from initiating translation. This mechanism effectively reduces protein synthesis under certain conditions. (M1)

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6
Q

How do temperature-regulated RNA structures affect translation in prokaryotes?

A

In response to temperature changes, RNA structures can form stem-loops that block the SD sequence. For example, in the virulence genes of Listeria monocytogenes, the SD sequence becomes accessible only at certain temperatures, allowing translation to occur. (M2)

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7
Q

What are riboswitches and how do they regulate translation in prokaryotes?

A

Riboswitches are segments of mRNA that can change their structure in response to small metabolite binding. This structural change can either promote or inhibit the accessibility of the SD sequence, thus regulating translation. (M3)

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8
Q

What is the function of antisense RNA in prokaryotic translation regulation?

A

Antisense RNA is produced from a different region of the genome and base-pairs with the target mRNA, blocking the SD sequence and preventing translation initiation. This mechanism is often used to regulate genes such as those involved in iron storage.

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9
Q

How does eukaryotic translation differ from prokaryotic?

A
  • no Shine-Dalgarno sequences, but there are similar mechanisms
  • translational repressors can bind near initiator AUG and inhibit translation
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10
Q

What is Ferritin?

A

Ferritin is a protein complex that stores iron in a soluble and non-toxic form, releasing it in a controlled manner when needed by the body.

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11
Q

What is the primary function of Ferritin?

A

The primary function of Ferritin is to regulate iron homeostasis by binding (storing) excess iron and releasing it when the body requires it, thus preventing iron toxicity.

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12
Q

How is Ferritin regulated in response to iron levels?

A

Ferritin translation is regulated by the availability of iron. When iron levels are low, a protein called aconitase binds to the Ferritin mRNA near the start site, blocking its translation. When iron levels are high, aconitase binds iron, causing conformational change and releases the Ferritin mRNA for translation.

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13
Q

How do small RNA molecules, such as miRNAs, regulate translation in eukaryotes?

A

Small RNA molecules can bind to complementary sequences in mRNA, leading to translational repression or degradation of the mRNA, thus controlling gene expression post-transcriptionally.

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14
Q

How do repressor proteins interact with eukaryotic initiation factors (eIFs)?

A

Repressor proteins can interfere with the interactions between the 5’ cap and the 3’ poly-A tail of mRNA, which are essential for efficient translation initiation by eIFs.

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15
Q

What is the role of eIF2 in translation initiation?

A

eIF2 forms a complex with GTP and recruits the initiator tRNA (methionyl) to the small ribosomal subunit, which then binds to the 5’ end of mRNA and scans for the first AUG codon.

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16
Q

What happens to eIF2 upon recognition of the AUG codon?

A

When the AUG codon is recognized, eIF2 hydrolyzes GTP to GDP, causing a conformational change that releases eIF2 bound to GDP, rendering it inactive.

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17
Q

How is eIF2 reactivated?

A

eIF2 is reactivated by eIF2B, which is a guanine nucleotide exchange factor (GEF) that facilitates the exchange of GDP for GTP. However, this process is regulated by phosphorylation.

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18
Q

What effect does phosphorylation have on eIF2?

A

Phosphorylation of eIF2 sequesters eIF2B as an inactive complex. Since there is more eIF2 than eIF2B in cells, this sequestration dramatically reduces translation.

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19
Q

What is the consequence of eIF2 phosphorylation on mRNA translation?

A

Not all mRNAs are equally affected by eIF2 phosphorylation; however, the overall effect is a decrease in protein synthesis due to the reduced availability of active eIF2.

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20
Q

How do eIFs contribute to translational regulation?

A

eIFs play a crucial role in the initiation of translation, and their regulation through phosphorylation or other modifications can control the rate of protein synthesis in response to cellular conditions.

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21
Q

What steps must proteins undergo to become functional?

A
  1. proteins must fold properly to adopt their 3D structure
  2. proteins are covalently modified with chemical groups
  3. proteins interact with other proteins and small molecules (cofactors)
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22
Q

During protein folding, where are the hydrophobic amino acids?

A

buried in the interior core (not surface exposed)

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23
Q

When does protein folding begin?

A
  • some being as they emerge from ribosomes
  • others are completely folded after synthesis
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24
Q

What is the primary role of molecular chaperones in protein folding?

A

Molecular chaperones assist in the proper folding of proteins by preventing misfolding and aggregation, ensuring that proteins achieve their correct three-dimensional structure.

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25
Q

What are heat-shock proteins (Hsp), and when are they typically produced?

A

Heat-shock proteins (Hsp) are a class of molecular chaperones that are synthesized in increased amounts during elevated temperatures or stress conditions to aid in protein folding and prevent aggregation.

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26
Q

How do chaperones like Hsp70 and Hsp60 assist in protein folding?

A
  • both interact with exposed hydrophobic residues of misfolded proteins
  • both use energy from ATP hydrolysis to promote proper folding
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27
Q

What happens to improperly folded proteins?

A

Improperly folded proteins can aggregate and become toxic to cells. They are marked for degradation by the proteasome, especially if they display exposed hydrophobic residues.

28
Q

What is the relationship between protein folding time and degradation?

A

The longer a protein takes to fold correctly, the higher the chance it has of being degraded by the proteasome, as misfolded proteins are targeted for destruction.

29
Q

What is the role of the proteasome in post-translational regulation?

A

The proteasome is a protein complex that degrades proteins that have been marked for destruction, particularly those that are misfolded or damaged, ensuring cellular protein quality control.

30
Q

How do chaperones and the proteasome interact in the context of misfolded proteins?

A

Chaperones compete with the proteasome for misfolded proteins; if chaperones cannot assist in proper folding, the proteins are marked for degradation by the proteasome.

31
Q

What is the proteasome?

A

The proteasome is a large protein complex found in the cytosol and nucleus, constituting about 1% of cellular protein. It functions primarily to degrade unneeded, damaged, or misfolded proteins.

32
Q

Describe the structure of the proteasome.

A

The proteasome has a hollow cylindrical shape with caps at each end that protect cellular proteins from degradation. It contains an active site in the core where protein degradation occurs.

33
Q

What role does ubiquitin play in protein degradation?

A

Ubiquitin is a small protein that is covalently attached to target proteins to mark them for degradation by the proteasome. The addition of ubiquitin signals that the protein should be destroyed.

34
Q

Explain the ubiquitin-conjugating system.

A

The ubiquitin-conjugating system consists of three enzymes:
- E1 (Ubiquitin-activating enzyme): Activates E1-bound ubiquitin in an ATP-dependent manner.
- E2 (Ubiquitin-conjugating enzyme): Accepts activated ubiquitin from E1 and exists as a complex with E3.
- E3 (Ubiquitin ligase): Selects substrates for ubiquitination and facilitates the transfer of ubiquitin from E2 to the target protein.

35
Q

What is polyubiquitination?

A

Polyubiquitination is the process where multiple ubiquitin molecules are added to a single lysine residue on a target protein, forming a polyubiquitin chain. This chain is recognized by the proteasome for degradation.

36
Q

How does the proteasome recognize ubiquitinated proteins?

A

The proteasome has specific receptors that recognize the polyubiquitin chains on target proteins, allowing these proteins to be directed for degradation.

37
Q

What is the significance of E3 ligases in the ubiquitin-proteasome pathway?

A

E3 ligases are crucial for specificity in the ubiquitination process, as they bind to specific degradation sequences in substrates and facilitate the transfer of ubiquitin from E2 to the target protein.

38
Q

What are some cellular processes regulated by ubiquitin modifications?

A
  • Protein degradation
  • Cell cycle progression
  • DNA repair
  • Signal transduction
    Depends on the number of ubiquitin molecules and types of linkages
39
Q

What are the different types of ubiquitination?

A

Monoubiquitylation: 1 ubiquitin on protein
- Histone regulation
Multiubiquitylation: ubiquitin on different sites of a protein
- endocytosis
Polyubiquitylation: ubiquitin linkage
- Lys 48 (proteasomal degradation)
- Lys 63 (DNA repair)

40
Q

How can the destruction of a protein by the proteasome be regulated?

A

Activation of a ubiquitin ligase
- phosphorylation by protein kinase
- allosteric transition caused by ligand binding
- allosteric transition caused by protein subunit addition
Activation of a degradation signal:
- phosphorylation by protein kinase
- unmasking by protein dissociation
- creation of destabilizing N-terminus

41
Q

How can multiple modifications affect a single protein?

A

A single protein can undergo various covalent modifications simultaneously, which can create a complex regulatory network that fine-tunes its functionality and response to cellular signals.

42
Q

What are some examples of gene regulatory proteins?

A
  • protein synthesis
  • ligand binding
  • covalent modification
  • addition of second subunit
  • unmasking (removed inhibitor)
  • stimulation of nuclear entry
  • release from membrane
43
Q

What is Protein Kinase A (PKA)?

A

PKA is a serine/threonine kinase that is activated by cyclic AMP (cAMP) and plays a crucial role in regulating various cellular processes, including metabolism and gene expression.

44
Q

How is PKA activated?

A

PKA is activated when cAMP binds to its regulatory subunits, causing a conformational change that releases the active catalytic subunits.

45
Q

What are the subunits of PKA?

A

PKA is composed of two regulatory subunits and two catalytic subunits (4 total). The regulatory subunits bind cAMP, leading to the activation of the catalytic subunits.

46
Q

What role does PKA play in glycogen metabolism?

A

Activated PKA promotes the breakdown of glycogen into glucose-1-phosphate and inhibits glycogen synthesis, thereby increasing glucose availability in response to hormones like adrenaline.

47
Q

What is cyclic AMP (cAMP)?

A

cAMP is a second messenger molecule that plays a crucial role in cellular signaling. It is derived from ATP and is involved in the activation of protein kinase A (PKA). (NOT A PROTEIN)

48
Q

How is cAMP produced in the cell?

A

cAMP is produced from ATP by the enzyme adenylyl cyclase, which is activated by G protein-coupled receptors in response to various extracellular signals.

49
Q

What is the primary hormone that stimulates glycogen breakdown?

A

Adrenaline (epinephrine) stimulates glycogen breakdown.

50
Q

What are the two main effects of activated PKA?

A
  1. Promotes breakdown of glycogen.
  2. Inhibits glycogen synthesis.
51
Q

What is the process of glycogen breakdown?

A

Glycogen is broken down into glucose-1-phosphate, which is then converted to glucose-6-phosphate, entering the glycolytic pathway.

52
Q

What is the role of glycogen phosphorylase in glycogen breakdown?

A

Glycogen phosphorylase is activated by PKA and catalyzes the breakdown of glycogen into glucose-1-phosphate.

53
Q

What are cAMP Responsive Elements (CRE)?

A

CRE are specific DNA sequences that are activated by phosphorylated CREB (CRE Binding Protein) in the presence of cAMP, leading to gene transcription.

54
Q

What is the significance of CREB in PKA-mediated gene transcription?

A

CREB (cAMP Response Element Binding protein) is a transcription factor that, when phosphorylated by active PKA, recruits the coactivator CBP (CREB Binding Protein) to promote the transcription of target genes.

55
Q

What is the primary role of CBP in gene expression?

A

CBP acts as a coactivator that interacts with transcription factors, such as CREB, to enhance the transcription of target genes.

56
Q

How does CBP interact with CREB?

A

CBP binds to the phosphorylated form of CREB, which is activated by Protein Kinase A (PKA) in response to cyclic AMP (cAMP) signaling.

57
Q

What is the significance of CBP in the context of PKA activation?

A

Upon activation by PKA, CREB recruits CBP to the promoter regions of target genes, facilitating the transcription process.

58
Q

What types of genes does CBP help regulate?

A

CBP is involved in the transcription of various genes, including those related to glucose metabolism, such as glucose-6-phosphatase in the liver.

59
Q

Why are protein interactions important in biological systems?

A

Protein interactions are crucial for cellular functions, as they underpin most biological processes, including signal transduction, metabolic pathways, and cellular structure maintenance.

60
Q

What types of interactions do proteins engage in?

A

Proteins can engage in static interactions (permanent complexes) and transient interactions (temporary associations) with other proteins and molecules.

61
Q

What is an interactome map?

A

the complete collection of protein-protein interactions of an organism

62
Q

What do the dots and lines represent in an interactome map?

A

dot: protein node
Line: an interaction edge

63
Q

What does “guilt by association” mean in the context of protein interactions?

A

“Guilt by association” refers to the principle that a protein’s function can be inferred based on its interactions with other proteins. If a protein interacts with known functional partners, it may be assumed to have a similar role or function.

64
Q

Can you provide an example of “guilt by association” in protein interactions?

A

An example is the DNA damage response network, where many proteins are involved in recognizing and repairing DNA damage. If a previously uncharacterized protein is found to interact with known DNA repair proteins, it may be inferred that the unknown protein also plays a role in DNA damage response.

65
Q

What are some challenges associated with the “guilt by association” approach?

A

The main challenge is that interactions do not always imply functional similarity. A protein may interact with others without sharing their function, leading to potential misinterpretations. Experimental validation is often required to confirm inferred roles.

BIO230 Midterm (6 decks)

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