Biochemistry: Protein Structure and Function

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Questions and Answers

What does the term 'affinity' refer to in the context of protein binding?

  • How readily the protein binds its target (correct)
  • The strength of the protein's conformational change
  • The speed at which a protein performs its function
  • The range of targets a protein binds to

Which protein plays a crucial role in muscle contraction by interacting with actin?

  • Kinesin
  • Actin-Binding Protein
  • Myosin (correct)
  • Dynein

How does an enzyme accelerate a biological reaction?

  • By increasing the concentration of substrates
  • By converting substrates into products rapidly
  • By consuming substrate in the reaction
  • By stabilizing the transition state and lowering activation energy (correct)

What characteristic of antibodies allows them to effectively bind to specific antigens?

<p>Their unique and specific binding site (C)</p> Signup and view all the answers

What type of transport does dynein facilitate in neurons?

<p>Retrograde transport (A)</p> Signup and view all the answers

What role does ATP hydrolysis play in the function of motor proteins?

<p>It provides energy for conformational changes (D)</p> Signup and view all the answers

Which type of bond is primarily responsible for forming dimers of cysteine?

<p>Covalent disulfide bonds (A)</p> Signup and view all the answers

What are the two key types of interactions that comprise salt bridges in proteins?

<p>Electrostatic interactions and hydrogen bonds (B)</p> Signup and view all the answers

Which of the following statements about enzyme function is correct?

<p>Enzymes can be reused after a reaction (C)</p> Signup and view all the answers

What effect does a conformational change in a protein have?

<p>It alters affinity and specificity (B)</p> Signup and view all the answers

What is the main role of proline in protein structure?

<p>Creates kinks in the polypeptide chain (A)</p> Signup and view all the answers

Which type of proteins are characterized by their diverse functions such as acting as enzymes and hormones?

<p>Globular proteins (A)</p> Signup and view all the answers

How does a protein's conformation influence its stability regarding hydrophobic residues?

<p>Hydrophobic residues buried inside reduce entropic penalties (B)</p> Signup and view all the answers

What does the solvation layer refer to in protein chemistry?

<p>The organization of solvent around a solute like a protein (B)</p> Signup and view all the answers

Which statement about the isoelectric point is correct?

<p>It is influenced by the charge of the protein's amino acid side chains (B)</p> Signup and view all the answers

Which protein is known as the most abundant type in the body, providing structural support?

<p>Collagen (C)</p> Signup and view all the answers

What is the primary purpose of using a semi-log graph?

<p>To visualize data that are related according to an exponential relationship (D)</p> Signup and view all the answers

Which of the following is essential for using dimensional analysis properly?

<p>Balancing equations using units (C)</p> Signup and view all the answers

In what situation is it appropriate to estimate square roots?

<p>When seeking an approximate answer for simplicity (D)</p> Signup and view all the answers

What is true about the basic trigonometric functions sine, cosine, and tangent?

<p>They help relate angles to the ratios of sides in right triangles (C)</p> Signup and view all the answers

What is a common use of significant digits in calculations?

<p>To reflect the precision of measured values (C)</p> Signup and view all the answers

Which mathematical concept assists in visualizing relationships between different variables on a single graph?

<p>Logarithmic scales (D)</p> Signup and view all the answers

When evaluating a scientific explanation, what reasoning method is employed?

<p>Analyzing patterns in data to draw conclusions (C)</p> Signup and view all the answers

What type of enzymes are specifically targeted for regulation within a metabolic pathway?

<p>Regulatory enzymes (D)</p> Signup and view all the answers

What type of calculations are primarily involved in using probability effectively?

<p>Calculating ratios and proportions (D)</p> Signup and view all the answers

What key factor contributes to maintaining a constant internal environment in living organisms?

<p>Homeostasis mechanisms (C)</p> Signup and view all the answers

What characterizes allosteric enzymes during regulation?

<p>They undergo conformational changes upon effector binding. (C)</p> Signup and view all the answers

In homotropic allosteric regulation, what is the role of the effector molecule?

<p>It is the same as the substrate. (D)</p> Signup and view all the answers

Which mathematical understanding is crucial to solve simultaneous equations?

<p>Competence in algebraic manipulation (C)</p> Signup and view all the answers

What is the main function of zymogens in enzyme regulation?

<p>They are inactive precursors that require activation. (C)</p> Signup and view all the answers

Which of the following statements about nucleotides is true?

<p>Nucleotides are composed of a sugar, base, and phosphate group. (B)</p> Signup and view all the answers

What maintains the structural stability of DNA compared to RNA?

<p>The double-stranded structure of DNA. (D)</p> Signup and view all the answers

What type of bond links nucleotides together in a nucleic acid strand?

<p>Phosphodiester bonds (C)</p> Signup and view all the answers

How does RNA differ structurally from DNA?

<p>RNA contains ribose sugar, whereas DNA contains 2'-deoxyribose. (A)</p> Signup and view all the answers

What is the significance of DNA being semi-conservative during replication?

<p>Each new DNA molecule retains one original strand and includes one newly synthesized strand. (C)</p> Signup and view all the answers

Which enzyme is responsible for unwinding the DNA helix at the replication fork?

<p>DNA helicase (B)</p> Signup and view all the answers

Which role does DNA ligase play during DNA replication?

<p>Joins Okazaki fragments (B)</p> Signup and view all the answers

What problem do linear chromosomes face during DNA replication?

<p>Inability to synthesize the ends due to the telomere's structure (D)</p> Signup and view all the answers

How do single-stranded binding proteins (SSBPs) function during DNA replication?

<p>Prevent reannealing of separated DNA strands (A)</p> Signup and view all the answers

Which statement correctly describes the role of DNA polymerase 1?

<p>Removes RNA primers and replaces them with DNA nucleotides (B)</p> Signup and view all the answers

In prokaryotic cells, how many origins of replication typically exist?

<p>A single origin for their circular DNA (D)</p> Signup and view all the answers

What is the primary function of primase in the DNA replication process?

<p>Synthesizes RNA primers for DNA polymerase (A)</p> Signup and view all the answers

What is a characteristic feature of Prophase I in meiosis?

<p>Crossing over occurs forming chiasmata (B)</p> Signup and view all the answers

During which phase do homologous chromosomes remain attached and line up at the metaphase plate in meiosis?

<p>Metaphase I (A)</p> Signup and view all the answers

What is the result of cytokinesis during Telophase I of meiosis?

<p>Two haploid cells with replicated chromosomes (A)</p> Signup and view all the answers

What distinguishes meiosis from mitosis in terms of genetic material segregation?

<p>Meiosis results in the random selection of one gene copy for each gamete (C)</p> Signup and view all the answers

What is the main outcome during Anaphase I of meiosis?

<p>Homologous chromosomes separate (A)</p> Signup and view all the answers

Which type of nondisjunction occurs during Anaphase I?

<p>Primary nondisjunction (D)</p> Signup and view all the answers

What appearance do chromosomes take during Metaphase I of meiosis?

<p>Tetrads (D)</p> Signup and view all the answers

How does the genetic variability of gametes produced by meiosis differ from that of mitosis?

<p>Meiosis creates genetic diversity through random assortment (C)</p> Signup and view all the answers

Flashcards

Protein Affinity

The tendency of a protein to bind specifically to its target molecule.

Protein Specificity

The ability of a protein to bind preferentially to its target molecule over other molecules.

Antibody

A protein that has a unique and very specific binding site that recognizes and inactivates or tags its target.

Antigen

The target molecule that an antibody binds to.

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Enzyme

A biological catalyst that speeds up chemical reactions in living organisms.

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Enzyme Substrate

The molecules that an enzyme interacts with and converts into products.

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Transition State (‡)

The unstable intermediate state that molecules pass through during a reaction.

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Activation Energy (Ea)

The minimum amount of energy needed for a reaction to occur.

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Disulfide bond

A strong, flexible bond between two cysteine amino acids, formed by the oxidation of their sulfhydryl groups. This type of bond is important in protein structure and stability, particularly in enzymes and structural proteins.

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Tertiary structure

The specific 3-dimensional arrangement of a polypeptide chain, including interactions between side chains. This intricate arrangement determines the protein's function.

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Tertiary structure forces

Interactions between protein side chains that shape its structure. These include electrostatic interactions, hydrogen bonds, van der Waals forces, and hydrophobic interactions.

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Quaternary structure

The arrangement of multiple polypeptide chains in a protein complex. Each polypeptide chain maintains its own tertiary structure, while interacting with other chains.

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Solvation layer

The structured organization of solvent molecules (like water) around a solute (like a protein). This organization is influenced by the protein's surface properties.

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Isoelectric point

The point at which a protein has no net charge. This property is used in techniques like electrophoresis to separate proteins based on their charge.

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Globular proteins

Proteins that have a compact, globular shape and are usually involved in various biological functions.

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Structural proteins

Proteins that form long, fibrous structures and provide support and strength to cells and tissues.

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Semi-log graph

A graph with one axis plotted on a logarithmic scale, used to visualize data with an exponential relationship.

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Dimensional analysis

A technique for converting measurements from one unit to another, using factors to maintain dimensional consistency.

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Significant digits

The number of digits in a measurement that are known with certainty plus one uncertain digit.

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Exponential function

A mathematical expression where a variable is raised to a power.

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Logarithm

A mathematical function that reverses the effect of an exponential function.

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Scientific notation

A method used to represent very large or very small numbers. It expresses a number as a product of a decimal number between 1 and 10 and a power of 10.

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Solving simultaneous equations

Solving two or more equations with two or more unknowns, finding values that satisfy all equations simultaneously.

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Tangent (tan)

The ratio of the opposite side to the adjacent side of a right triangle.

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Inverse tangent (tan-1)

A method used to find the angle in a right triangle given two sides.

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Vector

A quantity that has both magnitude and direction.

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Semi-conservative DNA Replication

DNA replication is called semi-conservative because each new DNA molecule contains one original strand from the parent molecule and one newly synthesized strand.

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DNA Helicase

An enzyme that unwinds the DNA double helix at the replication fork, separating the two strands.

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Topoisomerases

Enzymes that relieve the tension created by unwinding the DNA double helix.

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Single-stranded binding proteins (SSBPs)

Proteins that bind to single-stranded DNA, preventing them from re-pairing.

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Primase

An enzyme that synthesizes short RNA primers, which are necessary for DNA polymerase to start replication.

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DNA Polymerase

An enzyme that adds nucleotides to the new DNA strand, following the replication fork.

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DNA Ligase

An enzyme that joins Okazaki fragments, which are short segments of DNA synthesized on the lagging strand.

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Telomerase

An enzyme that adds repetitive sequences to the ends of chromosomes, protecting them from degradation during replication.

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Allosteric enzymes

Enzymes that can be activated or deactivated by regulatory molecules binding to a specific site on the enzyme, leading to conformational changes.

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Effector molecule

A small molecule that binds to an allosteric site of an enzyme, influencing its activity without being a substrate.

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Homotropic allosteric regulation

The binding of the enzyme's substrate itself acts as a regulator, promoting enzyme activity.

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Heterotropic allosteric regulation

A regulator molecule that is not the enzyme's substrate binds to the enzyme and influences its activity.

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Covalent modification

Enzyme regulation through the addition or removal of a small molecular modifier, often a phosphate group.

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Zymogen

An inactive precursor of an enzyme that is activated by a specific event, such as proteolytic cleavage or a change in environment.

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Nucleic Acid

A biological polymer composed of nucleotides linked by phosphodiester bonds, crucial for information storage and transfer.

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Nucleotide

The basic building block of nucleic acids, consisting of a sugar, a phosphate group, and a nitrogenous base.

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Meiosis

The process of cell division that produces gametes (sperm and egg cells), which have half the number of chromosomes as the parent cell.

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Mitosis

A type of cell division that results in two daughter cells that are genetically identical to the parent cell.

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Crossing Over

The exchange of genetic material between homologous chromosomes during prophase I of meiosis. This process leads to greater genetic diversity.

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Chiasma

A point where homologous chromosomes are connected during crossing over.

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Nondisjunction

The failure of homologous chromosomes or sister chromatids to separate properly during meiosis. This can result in gametes with abnormal chromosome numbers.

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Synapsis

A process where homologous chromosomes line up alongside each other during prophase I of meiosis.

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Homologous Chromosomes

Chromosomes that contain the same genes but may have different alleles. They pair up during meiosis.

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Gene

A unit of heredity that is responsible for a particular trait.

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Study Notes

General Math

  • Recognize and interpret linear, semilog, and log-log scales and calculate slopes from data found in figures, graphs, and tables
  • Demonstrate a general understanding of significant digits and the use of reasonable numerical estimates in performing measurements and calculations
  • Use metric units, including converting units within the metric system and between metric and English units (conversion factors will be provided when needed), and dimensional analysis (using units to balance equations)
  • Perform arithmetic calculations involving the following: probability, proportion, ratio, percentage, and square-root estimations
  • Demonstrate a general understanding (Algebra II-level) of exponentials and logarithms (natural and base 10), scientific notation, and solving simultaneous equations
  • Demonstrate a general understanding of trigonometry: functions (sine, cosine, tangent) and inverse functions (sin⁻¹, cos⁻¹, tan⁻¹), sin and cos values of 0°, 90°, and 180°, relationships between side lengths of right triangles containing 30°, 45°, and 60° angles
  • Demonstrate a general understanding of vector addition and subtraction and the right-hand rule

Scientific Inquiry and Reasoning Skills

  • Demonstrate understanding of scientific concepts and principles
  • Identify the relationships between closely-related concepts
  • Reason about scientific principles, theories, and models
  • Analyze and evaluate scientific explanations and predictions
  • Demonstrate understanding of important components of scientific research
  • Reason about ethical issues in research
  • Interpret patterns in data presented in tables, figures, and graphs
  • Reason about data and draw conclusions from them

Biological and Biochemical Foundations of Living Systems

  • This section tests processes unique to living organisms (growth, reproduction, maintaining internal environment, acquiring materials and energy, responding to environmental changes, and adapting)
  • It tests how cells and organ systems work independently and in concert to maintain life, at different biological levels
  • Biomolecules have unique properties that determine how they contribute to the structure and function of cells; participating in functions necessary to maintain life

Amino Acids (Biological Context)

  • Amino acids have a general structure with an amino group (-NH₂), a carboxyl group (-COOH), and a variable side chain (R group)
  • Amino acids are classified as: nonpolar, polar, acidic, or basic based on the chemical properties of their R groups
  • Amino acids are building blocks of proteins
  • Understanding the structure and function of amino acids is foundational to understanding proteins

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