BIO 203 Exam 1

Explain how hsp70 regulates protein folding

Hsp70 binds to exposed hydrophobic regions of an unfolded/misfolded protein. These regions normally become buried inside the protein when it folds.

1. Unfolded protein has exposed areas that can stick to other proteins.

2. Hsp70 binds to these exposed areas.

3. This prevents the protein from clumping with other proteins.

4. Hsp70 uses ATP → ADP to hold the protein tightly.

5. ATP binds again, causing Hsp70 to let go.

6. The protein gets another chance to fold correctly.

7. The process can repeat until the protein is properly folded.

How are macromolecules formed? (what reaction, what molecule does it involve)

Dehydration synthesis (condensation), which joins monomers together by removing water (H₂O).

Besides the conformation of the surface, what three additional molecules might be needed to

produce a functional protein?

????

How does hsp60 regulate protein folding?

• Unfolded protein enters the Hsp60 folding chamber.

• Hsp60 surrounds the protein, creating a protected space.

• ATP binds and helps Hsp60 change shape.

• A cap closes the chamber, keeping the protein isolated.

• The protein folds inside the chamber without interacting with other proteins.

• ATP is broken down, causing the chamber to open.

• The properly folded protein is released.

What type of bond usually forms the surface conformation? Why?

Hydrogen bonds usually form the surface conformation.

• They form between polar/charged amino acid side chains and water molecules (Water is polar, so it interacts strongly with other polar molecules)

• This causes hydrophilic (water-loving) amino acids to face outward toward the water.

What is the substrate of an enzyme?

The substrate is the specific molecule that an enzyme binds to and acts on during a chemical reaction.

What is the active site of an enzyme?

The active site is the specific part of an enzyme where the substrate binds and the chemical reaction occurs.

What are three mechanisms used by enzymes to decrease activation energy?

1. Bring substrates together – positions them close to each other so they can react more easily.

2. Properly orient substrates – positions the molecules in the correct way for the reaction.

3. Change the local environment – creates conditions that make the reaction easier, such as adding/removing protons or weakening bonds.

What is the Vmax of an enzyme?

Vmax is the maximum rate at which an enzyme can catalyze a reaction when all of the enzyme’s active sites are occupied by substrate.

What is the Km of an enzyme? What does low versus high Km mean for substrate affinity?

Km is the substrate concentration needed for an enzyme to reach ½ of its Vmax.
Low Km → enzyme has high affinity for substrate (doesn’t need much substrate)
High Km → enzyme has low affinity for substrate (needs more substrate)

How does the number of noncovalent interactions contribute to the Km of an enzyme?

The more noncovalent interactions an enzyme makes with its substrate, the stronger the binding and the lower the Km.

• More interactions → stronger substrate binding → lower Km

• Fewer interactions → weaker substrate binding → higher Km

How does the number of noncovalent interactions contribute to the Vmax of an enzyme?

How does the number of noncovalent interactions contribute to the Vmax of an enzyme?

What is a competitive inhibitor?

A competitive inhibitor is a molecule that competes with the substrate for the enzyme’s active site (usually binds and blocks active site)..

How does a competitive inhibitor effect Km and Vmax?

Competitive = competes for the active site
→ Km increases
→ Vmax stays the same

What is the reversibility of a competitive inhibitor?

A competitive inhibitor is reversible because it temporarily binds to the enzyme’s active site through noncovalent interactions.

How does a competitive inhibitor interact with the active site of an enzyme?

1. Inhibitor binds to the active site.

2. This blocks the substrate from binding.

3. Adding more substrate can overcome the inhibition because they are competing for the same site

What is the reversibility of a non-competitive inhibitor?

A non-competitive inhibitor is usually reversible because it typically binds to the enzyme through noncovalent interactions.

How does a non-competitive inhibitor interact with the active site of an enzyme?

• Inhibitor binds to the enzyme at an allosteric site (not the active site).

• This changes the enzyme’s shape and reduces its ability to catalyze the reaction.

• The inhibitor can unbind, allowing the enzyme to return to its functional state.

How do non-competitive inhibitors effect Vmax and Km?

Non-competitive = reversible + allosteric binding
→ Vmax decreases
→ Km stays the same (for pure noncompetitive inhibition)

What is the difference between allosteric and phosphorylation for protein enzyme regulation?

Allosteric = molecule binds → changes shape
Phosphorylation = phosphate added → changes shape/activity

How does allosteric protein enzyme regulation work?

Allosteric regulation:

1. A regulatory molecule binds to a site other than the active site (OUTSIDE).

2. This changes the enzyme’s shape.

3. The enzyme becomes more or less active.

4. The molecule can usually bind and unbind.

How does phosphorylation protein enzyme regulation work?

• A phosphate group (PO₄³⁻) is added to the enzyme.

• An enzyme called a kinase adds the phosphate.

• The phosphate changes the enzyme’s shape/activity.

• A phosphatase can remove the phosphate.

What is the function of the proteasome? What is the role of ubiquitin?

Proteasome = destroys proteins

Ubiquitin = “destroy me” tag (tells proteasome to shred certain proteins)

What is ERAD?

ERAD (ER-associated degradation) is the process cells use to identify and destroy misfolded or damaged proteins in the endoplasmic reticulum (ER).

1. Misfolded protein is recognized in the ER.

2. The protein is removed from the ER and sent to the cytosol.

3. Ubiquitin is added to tag the protein for destruction.

4. The proteasome breaks down the protein.

What is UPR?

UPR (Unfolded Protein Response) is the cell’s response to too many misfolded or unfolded proteins in the ER.

1. Misfolded proteins build up in the ER.

2. The cell detects the problem.

3. The UPR slows down new protein production to reduce the workload.

4. It increases production of chaperones to help proteins fold correctly.

5. It increases protein degradation (including ERAD) to remove misfolded proteins.

6. If the problem cannot be fixed, the cell may trigger cell death (apoptosis)

Protein folding is maintained by both noncovalent interactions (electrostatic attractions, hydrogen bonds, and van der Waals attractions) and covalent disulfide bonds. Loss of any of these will contribute to proteins unfolding at a temperature lower than they otherwise would. Generation of temperature-sensitive mutations in the yeast S. cerevisiae helped uncover genes involved in the cell division cycle and in protein secretion through the endomembrane system.

Loss of any of these will contribute to proteins unfolding at a temperature lower than they otherwise would. Generation of temperature-sensitive mutations in the yeast S. cerevisiae helped uncover genes involved in the cell division cycle and in protein secretion through the endomembrane system.

Which statement concerning feedback inhibition is false?

• A. Difficult to reverse

• B. Almost instantaneous.

• C. Regulates biosynthetic pathways

• D. Controls enzyme activity

• E. Early enzyme inhibited by a later product

A, because It can be quickly reversed when the product concentration decreases.

What maintains a stable protein–ligand interaction?:

A. A few weak, noncovalent interactions
B. Many weak, noncovalent interactions
C. Many weak, covalent interactions
D. A few weak, covalent interactions

Many weak, noncovalent interactions between the protein and ligand.

Which mutations might increase protein flexibility and lead to a temperature-sensitive phenotype? (Choose multiple)

A. A premature stop codon that truncates the protein
B. Alanine → cysteine, forming a new disulfide bond
C. Lysine → glycine, removing an ionic bond
D. Isoleucine → glycine, replacing a bulky side chain with a very small one

C & D

Consider this image depicting aspartate transcarbamoylase regulation and then answer the question; Enzymes can have both active and regulatory sites. What is the purpose of these sites?:

A. Binding of CTP at a regulatory site increases carbamoyl aspartate production.
B. Binding of CTP at a regulatory site decreases carbamoyl aspartate production.
C. Binding of CTP at the active site decreases carbamoyl aspartate production.
D. Binding of CTP at the active site increases carbamoyl aspartate production.

B. Binding of CTP at a regulatory site decreases carbamoyl aspartate production.

Which parts of the molecule are the same in every phospholipid? Are there any that would bear a negative charge?

Every standard phospholipid shares a glycerol backbone, a phosphate group, and two fatty acid tails, and the phosphate group bears a negative charge.

Shown is a schematic diagram of a membrane phospholipid. Which segment will always carry a negative charge?

B= The

How could researchers increase membrane fluidity in E. coli?

A. Decrease the temperature of the media
B. Increase the length of the fatty acid tails
C. Increase the amount of cholesterol in the bacterial membranes
D. Increase the proportion of phospholipids with unsaturated fatty acids

D. Increase the proportion of phospholipids with unsaturated fatty acids

Why must all living cells carefully regulate the fluidity of their membranes? (Choose multiple)

A. To permit membrane lipids and proteins to diffuse from their site of synthesis to other regions of the cell
B. To constrain and confine the movement of proteins within the membrane bilayer
C. To allow membranes, under appropriate conditions, to fuse with one another and mix their molecules
D. To allow cells to function at a broad range of temperatures
E. To ensure that membrane molecules are distributed evenly between daughter cells when a cell divides

A,C,E

Which membrane characteristics are more likely to apply to the ER membrane vs. the plasma membrane?”

• Increased thermal movement

• More water molecules found in the hydrophobic core

• Relatively stiffer membrane

• Relatively decreased permeability

• Relatively thicker membrane

ER membrane (lower cholesterol):

• Increased thermal movement

• More water molecules found in the hydrophobic core

Plasma membrane (higher cholesterol):

• Relatively stiffer membrane

• Relatively decreased permeability

• Relatively thicker membrane

Which organelles will become particularly active in synthesizing new membrane lipids when a B cell rapidly expands its ER and Golgi membranes?

A. Transport vesicle
B. Endoplasmic reticulum
C. Plasma membrane
D. Golgi apparatus

B

In a multipass transmembrane protein channel, what do the hydrophilic areas lining the middle of the channel represent?

A. Hydrophobic side chains of the transmembrane α helices
B. Hydrophobic lipid tails of the bilayer
C. Hydrophobic side chains of the transmembrane β barrel
D. Amphipathic side chains of the transmembrane α helices
E. Hydrophilic side chains of the transmembrane β barrel
F. Hydrophilic side chains of the transmembrane α helices

Correct answer: F

How do organisms living in cold climates adapt their membranes to low temperatures?

A. Increase saturated fatty acids to decrease membrane fluidity
B. Decrease unsaturated fatty acids to keep membranes fluid
C. Increase unsaturated fatty acids to decrease membrane fluidity
D. Increase unsaturated fatty acids to keep their membranes fluid
E. Increase saturated fatty acids to keep membranes fluid

Correct answer: D (Cold → more unsaturated fatty acids → more fluid membrane)

What are the three types of microscopes?

1. Light Microscopes

2. (Scanning)Electron Microscopes

3. Scanning Microscopes

What types of Light Microscope are there?

Stained, No Stain, Florescent

What microscope is best suited to look at the dynamic movement of molecules/organelles (like chromosomes during mitosis)?

A STAINED Light Microscope

You would use this type of microscope when viewing living cells or naturally pigmented cells; it lets you observe general shape, movement, and larger structures (such as Watching a live protist like Paramecium move around)

An UNSTAINED Light Microscope

You would use this type of microscope to when viewing cell/tissue structure and morphology with greater contrast; it’s stains make otherwise transparent structures visible

Light Microscope— Stained

You would use this microscope when locating specific molecules or structures using fluorescent dyes/tags; it’s highly specific (ex. Using an antibody to locate a particular protein inside a cell)

Florescent Light Microscope

You would use this kind of microscope in viewing the 3D surface/topography of a specimen at very high resolution to see things like the cilia and flagella of a cell.

Scanning Electron Microscopy

What are the two types of Electron Microscopy?

Transmission E.M. & Scanning E.M.

You would use this kind of microscopy to view the internal structures/ultrastructure of cells at extremely high resolution, seeing things like the mitochondria with a trained eye

Transmission Electron Microscope

What are some examples of model organisms? (CAYZEM)

• C. Elegans

• Arabidopsis

• Yeast

• Zebrafish

• E.Coli

• Mice

What is the simplest eukaryote we study (often to learn about the cell cycle)?

Yeast

What is the common plant used as a model organism?

Arabidopsis

What bacterial prokaryote is often used as a model organism as it is simple and cheap?

E. Coli

What model organism is used to learn about apoptosis?

C. Elegans

Why are model organisms beneficial?

Model organisms are beneficial because they are easy to study, reproduce quickly, and share many biological processes/genes with humans, allowing scientists to study biological mechanisms in a simpler, more controlled system.

What organelles/structures are present in bacteria?

Bacteria are prokaryotes, so they do not have membrane-bound organelles. They contain:

• Plasma membrane — controls what enters and leaves the cell

• Cell wall — provides structure and protection

• Cytoplasm — fluid interior where many reactions occur

• Ribosomes — make proteins

• DNA

Bacteria have ribosomes, but NO nucleus or other membrane-bound organelles.

Are bacteria prokaryotic or eukaryotic?

Prokaryotic.

Do bacteria have a nucleus?

No. Their DNA is located in the nucleoid region

Do bacteria have membrane-bound organelles?

No. They lack structures such as the nucleus, mitochondria, ER, and Golgi apparatus.

Do bacteria have ribosomes?

Yes. Ribosomes make proteins and are not membrane-bound.

What is the major difference between prokaryotic and eukaryotic cells?

Prokaryotes lack a nucleus and membrane-bound organelles; eukaryotes have them.

Which structures are found in both bacteria and eukaryotic cells?

DNA, ribosomes, cytoplasm, and a plasma membrane.

Which structure do bacteria have that eukaryotic animal cells do not?

A cell wall (though plant and fungal eukaryotes do have cell walls).

A scientist observes a cell with a plasma membrane, cell wall, ribosomes, and circular DNA, but no nucleus. What type of cell is it?

A prokaryotic cell (bacterium).

A cell contains a nucleus, mitochondria, ER, and Golgi apparatus. Is it prokaryotic or eukaryotic?

Eukaryotic.

A cell contains a nucleus, mitochondria, ER, and Golgi apparatus. Is it prokaryotic or eukaryotic?

Nucleus, mitochondria, ribosomes, ER, Golgi apparatus, cytoplasm, plasma membrane, cell wall, chloroplasts, and a large central vacuole.

What organelles/structures are present in animal cells?

Nucleus, mitochondria, ribosomes, ER, Golgi apparatus, cytoplasm, plasma membrane, lysosomes, and small vesicles/vacuoles.

What structures do animal cells NOT have that plant cells have?

Cell wall, chloroplasts, and a large central vacuole.

What structures are found in bacteria, plants, AND animals?

Plasma membrane, cytoplasm, ribosomes, and DNA.

Which cell type(s) has a nucleus?

Plants and animals (eukaryotes), but not bacteria.

Which cell types have mitochondria?

Plants and animals, but not bacteria.

Which cell types have a cell wall?

Bacteria and plants, but not animals.

Which cell type has a large central vacuole?

Plants.

What organelles have a double membrane?

Nucleus, mitochondria, and chloroplasts.

What is the function of the nucleus?

Stores and protects the cell's DNA and controls gene expression; has a nuclear envelope for lots of protection

What is the function of mitochondria?

Produce ATP (energy) through cellular respiration.

What is the function of chloroplasts?

Carry out photosynthesis, converting light energy into chemical energy stored in sugars.

Which double-membrane organelles are found in both plant and animal cells?

The nucleus and mitochondria.

Which double-membrane organelle is found in plant cells but not animal cells?

Chloroplasts

Which double-membrane organelle contains the cell's main DNA?

The nucleus.

What organelles have a single membrane?

The endoplasmic reticulum, Golgi apparatus, lysosomes, vacuoles, peroxisomes, vesicles, and endosomes.

What is the function of the endoplasmic reticulum (ER)?

The ER is involved in the synthesis and transport of proteins and lipids.

What is the difference between rough ER and smooth ER?

Rough ER has ribosomes and helps make/process proteins, while smooth ER lacks ribosomes and is involved mainly in lipid synthesis and other functions.

Which part of the ER doesn’t have ribosomes and makes lipids?

Smooth ER

Which part of the ER is contains ribosomes (where proteins are synthesized)?

Rough ER

What is the function of the Golgi apparatus?

Modifies, sorts, and packages proteins and lipids for transport to other locations.

What is the function of lysosomes?

Contain digestive enzymes that break down and recycle cellular materials.

What is the function of vacuoles?

Store materials such as water, ions, nutrients, or waste.

What is the function of peroxisomes?

Break down certain molecules and help detoxify harmful substances, including hydrogen peroxide.

What is the function of vesicles?

What is the function of vesicles?

Which organelles have double membranes?

Nucleus, mitochondria, and chloroplasts.

Which organelles are involved in the production and processing of proteins?

Ribosomes, rough ER, and the Golgi apparatus.

Which organelle contains digestive enzymes?

The lysosome.

Which structures are NOT membrane-bound?

Ribosomes, the cytoskeleton, centrosomes/centrioles, and the nucleolus.

What is the endomembrane system?

A group of membrane-bound organelles that work together to make, modify, transport, and process proteins and lipids within the cell.

What organelles are part of the endomembrane system?

(Connected to nucleus but it’s not included) ER, Golgi apparatus, vesicles, lysosomes, vacuoles, and plasma membrane.

What is the main function of the endomembrane system?

Making, modifying, transporting, and breaking down proteins and lipids.

What is the pathway for a protein being secreted from the cell?

Ribosome → Rough ER → Vesicle → Golgi → Vesicle → Plasma membrane → Outside cell

How does the endomembrane system work?

Organelles work together, with vesicles transporting materials between them.
Rough ER → Vesicle → Golgi → Vesicle → Destination.

What are the main protein structures in cells?

Ribosomes, cytoskeleton, and protein complexes/channels.

What is the function of ribosomes?

Make proteins by translating mRNA.