Cell Bio ch 4

Why does a protein’s amino acid sequence determine its shape?

The sequence determines how the amino acids interact and fold

What happens if the amino acid sequence changes?

The protein may fold differently → change its function

What is the main evidence that amino acid sequence determines protein structure

Anfinsens experiment showed that protein can refold into its normal shape based on its amino acid sequence

What did Anfinsen’s experiment show?

The info needed for a protein to fold correctly is contained in its amino acid sequence

What does it mean for a protein to fold into its lowest energy conformation?

It folds into the most stable shape with the lowest free energy

What interactions stabilize a folded protein?

Hydrophobic interactions, hydrogen bonds, electrostatic attractions, van der Waals attractions, and disulfide bondsW

What is the role of the protein backbone?

It forms the repeating structural framework of the protein

What is the role of amino acid side chains (R groups)?

They interact with each other and the environment to determine protein shape and properties

What is an alpha helix

A coiled section of a protein stabilized by hydrogen bonds

What is a beta sheet?

A folded/ sheet like structure stabilized by hydrogen bonds

What holds alpha helices and beta sheets together?

Hydrogen bonds between the protein backbone

Primary structure?

Amino acid sequence

Secondary structures?

alpha helices and beta sheets

Tertiary structures?

Overall 3D shape of one polypeptide chain

Quaternary structure?

Multiple polypeptide chains

What is a protein domain?

A region of protein that can fold into a stable structure and has a specific function

Can one protein have multiple domains?

Yes

What does it mean when a protein has an unstructured region?

Part of the protein doesnt have one fixed shape

Are unstructured regions useless?

No. They can be important for signaling and interactions

What are chaperone proteins?

Proteins that help other proteins fold correctly

Do chaperones force proteins into one specific shape?

NO. They help prevent incorrect folding and give proteins a better env to fold

Why do chaperones require ATP?

ATP provides energy for chaperone conformational changes and cycles of binding/ releasing proteins

What is a disulfide bond?

A strong covalent bond between two cysteine amino acids

How do disulfide bonds help proteins?

They stabilize the proteins 3D structure

What is a misfolded protein?

A protein that has the wrong 3D shape

Why do proteins sometimes misfold?

Bc of mutations, cell conditions, or errors during folding

Why are misfolded proteins dangerous?

They may lose their function or form harmful aggregates

How can protein misfolding cause disease?

Misfolded proteins can damage cells or interfere with normal processes

What is a ligand?

A molecule that binds to a protein

Why is ligand binding usually reversible?

Weak interactions allow the ligand to bind and release when needed

What determines whether a protein binds a specific ligand?

The ligand’s shape and chemical properties must match the protein’s binding site

What is protein specificity?

The ability of a protein to bind a particular molecule but not others

How does an antibody bind its target?

Its binding site has a shape and chemical properties that specifically match its targetT

What do antibodies do?

They recognize and bind specific molecules/ targets, often foreign molecules

How are enzymes different from antibodies?

Enzymes catalyze reactions, antibodies mainly recognize/ bind targets

What is an enzyme’s ligand

Any molecule that binds to the enzyme

What is an enzyme’s substrate?

The molecule the enzyme acts on/ changes

What is an active site?

Region of an enzyme where the substrate binds and the reaction occurs

How do enzymes speed up reactions

Lower activation energy

Do enzymes change delta G?

NO

Do enzymes change the equilibrium position?

NO

What is a comp inhibitor?

Binds the active site and competes with the substrate

What is a noncomp inhibitor?

Binds somewhere other than the active site and reduces enzyme activity

Why do cells regulate enzyme activity?

To prevent wasted energy/materials and control cellular processesW

What is an allosteric enzyme?

An enzyme whose activity can be changed by a molecule binding at an allosteric site

What is an allosteric site?

A binding site different from the active site

What is the active site?

Where the substrate binds and reaction occurs

How can binding at one site affect another site?

Binding can cause a change in the protein’s shape, affecting another site

What is phosphorylation?

Adding a phosphate group to a proteinW

What is dephosphorylation?

Removing a phosphate group from a protein

How are phosphate groups added?

Protein kinases

How are phosphate groups removed?

Protein phosphatases

How can phosphorylation affect a protein?

It can change the protein’s shape, activity, or interactions

What happens if an important phosphorylation site is changed and be phosphorylated?

The protein may fail to turn on/off properly

How do GTP binding proteins act as molecular switches?

GTP bound =ON

GDP bound = OFF

What happens during GTP hydrolysis?

GTP → GDP, switching the protein OFF

Why are GTP switches useful?

They let cells turn signaling processes on and off

What happens if a GTP binding protein cant hydrolyze GTP

It can become stuck ON, causing continuous signaling

How does ATP make motor proteins move?

ATP binding and hydrolysis cause changes in the protein’s shape, producing movement

What happens if a motor protein can bind ATP but cant hydrolyze it?

May become stuck and unable to complete its movement cycle

What is a protein complex?

A group of proteins working together

Why are protein complexes called molecular machines?

Multiple proteins work together to perform a specific cellular task

Why do some processes require multiple proteins?

Different proteins do different parts of the same job

What is a scaffold protein?

A protein that holds other proteins togetherW

hy are scaffold proteins useful?

They bring proteins close together so they can interact efficiently

What are biochemical subcompartments?

Specialized areas where certain molecules and reactions are concentrated

How are biochemical subcompartments organized?

By proteins, membranes, and other structures that concentrate specific molecules

Why are biochemical subcompartments useful?

They keep reactions organized and efficient

Why do scientists purify proteins?

To study one protein without interference from thousands of other cell molecules

Why is isolating one protein difficult?

Cells contain thousands of different proteins with similar properties

Why are multiple purification steps needed?

Each step removes more unwanted proteins/ contaminants

What proteins can scientists use to seperate proteins

Size, charge, shape, and binding properties

How well can scientists tell if purification worked?

They can use techniques like gel electrophoresis to see if mostly one protein remains

Why is knowing a protein’s amino acid sequence useful?

It can help predict its structure, function, and relationships with other proteinsH

How can scientists determine a protein’s 3D structure?

Experimentally using methods like X-ray crystallography, NMR, or cry-EM

Why can computers predict protein structure?

Protein sequences have info about how proteins fold, and computers use bio data/models to predict structures

Why predict protein structure instead of determining it experimentally?

Prediction can be faster, cheaper, and easier

Why should predicted structures sometimes be experimentally confirmed?

Predictions arent always perfect

Why might scientists genetically engineer cells to produce a protein?

To make large amounts of a specific protein

Why might a protein made by bacteria differ from the same protein made by human cells?

Bacteria and humans have different cellular machinery and protein processing systems

What can human cells do that bacteria may not?

Perform certain post translational mods needed for some human proteins

What is feedback control?

A process where the end product affects an earlier step in a pathway

Why is feedbacl control useful?

It prevents cells from making too much of somethingW

What is negative feedback?

The end product slows or stops an earlier reaction