Lecture 6 Review

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Questions and Answers

What drives energetically unfavorable reactions to occur?

Increasing temperature

Decreasing the concentration of products

Coupling with favorable reactions (correct)

Adding more reactants

What is the primary source of chemical energy used by cells?

FADH2

ATP (correct)

Glucose

NADH

How do nucleotides in RNA form polymers?

By ionic interactions

Through phosphodiester linkage (correct)

By peptide bonds

Via hydrogen bonding

What molecules are released during the hydrolysis of ATP?

ADP and inorganic phosphate Signup and view all the answers

Which reaction is considered unfavorable?

ATP synthesis Signup and view all the answers

What role do acyl-tRNA synthetases play in protein synthesis?

They attach amino acids to tRNA Signup and view all the answers

During RNA synthesis, where does the energy come from?

Hydrolysis of ATP Signup and view all the answers

What type of reaction occurs when monomers join to form a polymer?

Dehydration or condensation reaction Signup and view all the answers

What is the main function of glycogen in the body?

Energy storage Signup and view all the answers

Which of the following saccharides contains more than 10 monomer units?

Starch Signup and view all the answers

What is cellulose known for in plants?

Structural support Signup and view all the answers

What types of macromolecules can lysozyme specifically cleave?

Polysaccharides Signup and view all the answers

Which type of reaction is hydrolysis considered?

Decomposition reaction Signup and view all the answers

What prevents spontaneous hydrolysis of macromolecules like DNA?

Activation energy Signup and view all the answers

What is a primary role of oligosaccharides?

Modification of proteins and lipids Signup and view all the answers

Which polysaccharide can consist of up to ~50,000 glucose monomers?

Glycogen Signup and view all the answers

What role does lysozyme play in biochemical reactions?

Hydrolyzes polysaccharides in bacterial cell walls Signup and view all the answers

How do enzymes affect activation energy?

Enzymes reduce activation energy Signup and view all the answers

What is the significance of the 3D structure of proteins like lysozyme?

It allows the protein to execute specific functions Signup and view all the answers

What does the lock and key model illustrate about enzyme-substrate interactions?

Substrates perfectly fit into enzymes without modification Signup and view all the answers

Which statement is true about enzymes and reaction favorability?

Enzymes speed up reaction rates but do not change favorability Signup and view all the answers

What happens to substrates when they interact with enzymes?

They bind in a way that alters their structure Signup and view all the answers

What is the primary purpose of an enzyme-substrate complex?

To facilitate the conversion of substrates to products Signup and view all the answers

Which amino acids in lysozyme are specifically mentioned for their role in lowering activation energy?

Glu35 and Asp52 Signup and view all the answers

Which process is NOT involved in controlling the amount of protein in a cell?

Rate of protein synthesis Signup and view all the answers

What mechanism allows product F to inhibit enzyme 1 in feedback inhibition?

Allostery Signup and view all the answers

Which of the following proteins is primarily involved in phosphorylating other proteins?

Kinase Signup and view all the answers

How many kinases are approximately found in the human proteome?

518 Signup and view all the answers

What role does guanine nucleotide exchange factor (GEF) play in regulating small GTPases?

Facilitates GTP binding Signup and view all the answers

What is a consequence of the Ras G12V mutation?

Constant active Ras signaling Signup and view all the answers

Which of the following is NOT a mechanism for regulating protein activity?

mRNA degradation Signup and view all the answers

What is one of the primary functions of small GTPases?

Signal transduction Signup and view all the answers

How many phosphorylation sites are recorded in the human proteome?

51,000 Signup and view all the answers

Which type of protein modification commonly regulates protein function?

Phosphorylation Signup and view all the answers

What is the primary structure of a protein?

Sequence of amino acids in a polypeptide chain Signup and view all the answers

How do enzymes increase the rate of chemical reactions?

By lowering the activation energy barrier Signup and view all the answers

Which statement correctly describes allostery in proteins?

It refers to the regulation of protein activity through conformational changes. Signup and view all the answers

What effect do small GTPases have in cellular signaling?

They function as molecular switches in signaling pathways. Signup and view all the answers

What does the tertiary structure of a protein refer to?

Overall 3D structure of a single polypeptide chain Signup and view all the answers

What role do noncovalent interactions play in protein-ligand binding?

They are responsible for the specificity of the binding interactions. Signup and view all the answers

Which of the following statements correctly describes the quaternary structure of proteins?

It involves the assembly of multiple polypeptide chains. Signup and view all the answers

What defines the term 'ligand' in the context of protein interactions?

A small molecule or ion bound by a protein Signup and view all the answers

What is the composition of carbohydrates as described?

Molecules that include carbon and water (CH2O)n Signup and view all the answers

What type of interactions are involved in the stabilization of the enzyme-substrate complex?

Weak noncovalent interactions Signup and view all the answers

What type of biochemical reaction is performed by enzymes?

They remain unchanged after reacting with substrates. Signup and view all the answers

Study Notes

Prelim 1 Details

Exam date: Monday, September 23rd
Exams are taken on CANVAS.
Check seat assignment by Friday, September 20th. Assignments are on CANVAS/EXAM, either in Call Auditorium or Klarman G70.
Full instructions are available on CANVAS/EXAMS/Exam Instructions.
Following instructions is crucial. Failure to do so may result in a 0 on the exam and further penalties.
Material covered: Lectures 2-7 and sections 2-4.
Grading is based on material taught in class.
Practice Prelim 1 is available on CANVAS/EXAMS.
TA review sessions: Saturday/Sunday, 1-4 PM in Biotech Racker Room G01 (instructions on CANVAS/EXAMS).
Office hours with Martin Graef:
- Monday 5-6 PM in Biotech 201
- Wednesday 1:30-2:30 PM in Biotech 201

Proteins in Action Learning Objectives

Understand the specificity in binding interactions.
Understand how enzymes catalyze favorable and unfavorable reactions.
Understand the mechanisms by which proteins are regulated (allostery, phosphorylation).
Understand how "small GTPases" transmit signals as molecular switches.

Today's Topics

Proteins as Enzymes
Regulation of Protein Activity

The "Central Dogma" of Molecular Biology

DNA sequence contains genes.
Transcription: DNA → RNA (in nucleus).
mRNA sequence produced.
Translation: mRNA → protein (in cytosol).
Protein sequence consists of amino acids.
Location of cellular processes matters (compartmentalization).

Protein Structure Levels of Organization

Primary: the amino acid sequence.
Secondary: α-helices and β-sheets.
Tertiary: 3D structure of a polypeptide chain.
Quaternary: 3D structure of multiple polypeptide chains.

3D Structure of Proteins

3D structure allows proteins to execute particular functions.

Protein Binding

Effective binding of a protein to a ligand depends on weak noncovalent interactions (hydrogen bonds, van der Waals, electrostatic, hydrophobic).

Binding Sites in Proteins

Binding sites in proteins interact with specific ligands.
Folding of proteins into 3D shapes positions critical sidechains to interact non-covalently (hydrogen bonds, electrostatic attractions).

Enzymes

Enzymes catalyze chemical reactions by lowering activation energy barriers.
Enzymes remain unchanged throughout the reaction.
They form enzyme-substrate complexes (“ES”) and enzyme-product complexes (“EP”).

Activation Energy and Enzymes

Activation energy: needed energy for a chemical reaction to proceed.
Enzymes lower this activation energy.
Uncatalyzed reactions require more energy compared to enzyme-catalyzed reactions. This provides a more efficient reaction pathway.

Carbohydrates

Monomer: monosaccharides (e.g., glucose).
Macromolecule: polysaccharides (e.g., glycogen, starch, cellulose, chitin)
Sugars can form polymers via condensation reactions.
Hydrolysis is the opposite of condensation.

Hydrolysis

Hydrolysis is the opposite reaction to condensation.
It is energetically favorable.
Macromolecules like DNA are stable despite this tendency.
Activation energy prevents spontaneous hydrolysis.

Lysozyme

Lysozyme is an enzyme that cleaves polysaccharides via hydrolysis.

How Lysozyme Lowers Activation Energy

Lysozyme binds to a substrate.
The enzyme’s 3D structure precisely positions Glu35 and Asp52, creating an optimal environment for the catalytic reaction. This lowers the activation energy.

Enzyme Function (Key Idea)

Enzymes speed up reaction rates without affecting the spontaneity (favorability) of a reaction.
Shape and position of amino acid residues (like Glu35 and Asp52 in lysozyme) are crucial for catalysis.

ATP Hydrolysis

ATP is the primary source of cellular energy.
ATP hydrolysis releases energy needed to drive unfavorable reactions.
Hydrolysis of ATP to ADP and inorganic phosphate is a highly energetically favorable reaction.

RNA/Protein Synthesis Energy

Energy for RNA and protein synthesis comes from ATP, from already stored energy in the cells.

Nucleotide Condensation

Nucleotides form polymers through phosphodiester linkages via condensation reaction.

Different Ways of Regulating Protein Activity

Control of protein amount: rate of mRNA transcription, mRNA degradation, protein translation/degradation.
Control of protein activity: cellular localization, feedback inhibition, ligand-induced inhibition/activation, protein modification (such as phosphorylation).
Regulation pathways involve interactions between proteins.

Feedback Inhibition and Allostery

Feedback inhibition: a product of a pathway inhibits an earlier step.
Allostery: regulator molecules bind to a site other than the active site, changing the protein's shape and activity.

Phosphorylation

Phosphorylation is a common way to regulate protein activity by adding a phosphate group.
Kinases add phosphates; phosphatases remove them.
Phosphorylation changes how a protein interacts with other molecules.

Regulation by Phosphorylation

Many kinases and phosphatases regulate signaling pathways via phosphorylation.

Small GTP-binding Proteins

Small GTPases (e.g., Ras) are molecular switches.
They regulate downstream pathways.
GEFs activate them, and GAPs deactivate them.
GDP/GTP cycling is crucial.

Ras Protein and Cell Growth

Ras is a small GTPase involved in cell growth regulation.
Mutations in Ras can lead to uncontrolled cell growth and cancer (e.g., the G12V mutation causes Ras to be permanently "ON").

Studying That Suits You

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Description

Test your knowledge on the principles of biochemistry, focusing on energetic reactions, ATP hydrolysis, and the synthesis of nucleotides and proteins. This quiz covers essential macromolecules and their functions in biological systems, helping you understand the underlying biochemical processes that drive cellular functions.