Protein Biology Lecture: Key Terms and Concepts (Ch 1–7)

A comprehensive set of vocabulary flashcards covering feedback regulation, allostery, covalent modifications, protein design, and methods for studying protein structure and function, based on the provided lecture notes.

Feedback inhibition

A regulatory mechanism where accumulation of a downstream product inhibits an earlier step in the pathway, slowing or stopping production.

Allosteric enzyme

An enzyme with two or more binding sites; binding at one site causes a conformational change that alters activity.

Conformation (conformational change)

The three-dimensional shape of a protein; changes in conformation regulate enzyme activity.

Open vs. closed conformation (allosteric regulation)

Two shapes of an allosteric enzyme; one allows substrate binding (open) and the other (closed) alters activity, often via effector binding.

ADP-induced activation

Binding of ADP promotes the active conformation of some enzymes, increasing their activity.

CTP (negative regulation)

CTP binding to an enzyme can cause conformational changes that reduce active sites and decrease activity.

Methionine

An essential amino acid produced in the pathway; excess can trigger feedback inhibition.

Threonine–to–isoleucine feedback

Threonine is converted to isoleucine and participates in feedback regulation of the pathway.

Isoleucine

A downstream amino acid product that participates in feedback regulation of its biosynthetic pathway.

Homoserine

An intermediate in amino acid biosynthesis that can be involved in feedback control of its pathway.

Lysine feedback

Lysine exerts feedback on its own biosynthetic pathway, influencing earlier steps such as conversion from aspartate semialdehyde.

Aspartate semialdehyde

An intermediate in amino acid biosynthesis involved in branched pathways including lysine production.

Active site

The region of an enzyme where the substrate binds; its accessibility depends on the enzyme’s conformation.

Phosphorylation

Addition of a phosphate group to a protein, often changing its shape and activity; reversible by phosphatases.

Protein kinase

An enzyme that transfers a phosphate from ATP to a protein, causing phosphorylation.

Protein phosphatase

An enzyme that removes a phosphate group from a protein (dephosphorylation).

Covalent modification

Attachment of chemical groups (e.g., phosphate, acetyl, ubiquitin) to a protein to alter function or location.

Acetylation

Addition of an acetyl group to a protein, affecting activity or interactions.

Ubiquitin

A small protein covalently attached to other proteins to modify function or stability.

p53 (tumor suppressor)

A key tumor suppressor protein with a DNA-binding domain and a transcription activation domain; regulated by covalent modifications.

DNA-binding domain

The region of p53 that interacts with DNA to regulate transcription.

Transcription activation domain

The part of p53 that activates transcription of target genes.

GTP-binding proteins

Proteins that switch on/off by binding GTP or GDP; hydrolysis toggles their activity.

GDP–GTP cycle

GTP-bound is active; GDP-bound is inactive; exchange and hydrolysis cycle controls activity.

ATP hydrolysis and motor proteins

Hydrolysis of ATP provides energy for conformational changes that drive directed movement along cellular tracks.

Scaffold protein

A protein that brings together other proteins into a complex, often via unstructured regions and structured domains.

Unstructured regions

Flexible parts of scaffold proteins that help bind multiple partners.

Structured domains

Rigid regions of scaffold proteins with specific shapes that interact with partner proteins.

Rosetta

A computer program used to design new proteins from scratch and predict folding.

Synthetic gene

A gene designed and synthesized artificially to encode a designed, novel protein.

Fold It

An online protein-folding game that crowdsources problem-solving for protein structure.

Rosetta@Home

A distributed computing project where volunteers’ computers assist in protein design problems.

Protein design vaccine concept

Designing protein particles to present viral proteins and boost immune responses (e.g., RSV-based designs).

Five grand challenges of protein design

Big goals: universal flu vaccine, expanding the amino acid alphabet, targeted delivery vehicles, smart therapeutics, and novel protein-based materials.