Biochemistry Quiz on Proteins and Chromosomes

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Questions and Answers

Which statement accurately describes the characteristics of peptide bonds?

Peptide bonds are planar and rigid due to double bond character. (correct)

Peptide bonds are highly flexible due to single bond character.

Peptide bonds can freely rotate around their axis without restriction.

Peptide bonds do not influence the overall stability of protein structure.

Which of the following amino acids has the single letter code 'C'?

Cyclohexyl

Cysteine acid

Cysteine (correct)

Chlorine

What type of bond links individual nucleotides in nucleic acids?

Ionic bonds

Peptide bonds

Phosphodiester bonds (correct)

Hydrogen bonds

What forces stabilize protein structure aside from covalent bonds?

Hydrogen bonding and electrostatic interactions Signup and view all the answers

How is the polarity of polypeptides oriented?

From left to right, starting from the amino N-terminus. Signup and view all the answers

Which structural feature is characteristic of alpha-helices?

They are known for their rigid spiral shape stabilized by hydrogen bonds. Signup and view all the answers

What is the basic unit of eukaryotic chromosome structure?

Nucleosome Signup and view all the answers

Which of the following is NOT one of the four levels of protein structure?

Triangular structure Signup and view all the answers

Which chemical characteristic is shared by hydrophobic effects and van der Waals forces in protein stabilization?

Both are non-covalent interactions that help stabilize folding. Signup and view all the answers

Which of the following correctly describes the 'beads on a string' structure in DNA packaging?

Nucleosomes connected by linker DNA Signup and view all the answers

During which phase of the cell cycle does chromosomal condensation primarily occur?

Prophase Signup and view all the answers

What stabilizes the interactions between histones and the DNA phosphate backbone?

Electrostatic interactions Signup and view all the answers

What is the primary structural difference between unineme and multineme chromosome forms?

Number of chromatids present Signup and view all the answers

What occurs when the standard free energy change is negative?

The reaction is exergonic. Signup and view all the answers

What role do enzymes play in the context of activation energy?

They decrease the activation energy required for reactions. Signup and view all the answers

What effect does a perfectly fitting enzyme-substrate complex have on reaction rates?

It raises the activation energy needed. Signup and view all the answers

In Michaelis-Menten kinetics, what happens at the saturation point of substrate concentration?

The reaction velocity reaches a maximum and does not increase further. Signup and view all the answers

How do allosteric regulators affect enzyme activity?

They change the enzyme's shape and can enhance or inhibit activity. Signup and view all the answers

What characterizes the environment of an enzyme’s active site?

It tends to be hydrophobic with hydrophilic amino acids embedded. Signup and view all the answers

What is the primary distinction between enzyme-catalyzed reactions and non-catalyzed reactions regarding reaction rates?

Enzyme-catalyzed reactions are subject to saturation effects. Signup and view all the answers

Which of the following is true about substrate binding at the active site of enzymes?

Substrates are bound by multiple weak non-covalent interactions. Signup and view all the answers

What type of bond stabilizes the base pairs in DNA?

H-bonds Signup and view all the answers

Which feature of DNA structure contributes to its stability due to base arrangement?

Base stacking effect Signup and view all the answers

According to Chargaff's Principle, which of the following relationships is correct?

[Cytosine] = [Guanine] Signup and view all the answers

What is the primary structural difference between DNA and RNA nucleotides?

The presence of 2' hydrogen in DNA Signup and view all the answers

How many hydrogen bonds are formed between adenine and thymine in a DNA molecule?

2 Signup and view all the answers

In DNA, the strands run in opposite directions due to their polarity. What are the polarity ends of these strands referred to?

5' and 3' Signup and view all the answers

Which component of DNA contributes to the helical structure through repulsive forces?

Negatively charged phosphate groups Signup and view all the answers

What characteristic is true of the Watson & Crick model of DNA?

The bases are perpendicular to the sugar/phosphate backbone. Signup and view all the answers

Which statement accurately describes the functional differences between heterochromatin and euchromatin?

Heterochromatin is more compact and transcriptionally silent, while euchromatin is more open and active. Signup and view all the answers

What is the primary structural difference between the solenoid model and the zigzag model of chromatin?

In the zigzag model, the linker DNA passes through the central axis while it is buried in the solenoid model. Signup and view all the answers

Which function is NOT associated with telomeres?

Facilitating the fusion of chromatids during cell division. Signup and view all the answers

What role do DNA polymerases play during DNA replication?

They catalyze the covalent addition of nucleotides to existing DNA strands. Signup and view all the answers

Which of the following statements correctly describes Okazaki fragments?

They are formed during discontinuous synthesis on the lagging strand. Signup and view all the answers

What is a key characteristic of the primase enzyme in DNA replication?

It lays down RNA primers to initiate DNA synthesis. Signup and view all the answers

Which process is primarily responsible for repairing errors missed by DNA polymerase proofreading?

Strand-directed mismatch repair (SDMMR). Signup and view all the answers

Which of the following is a false statement regarding prokaryotic and eukaryotic DNA replication?

Prokaryotic DNA is always synthesized in fragments whereas eukaryotic is continuous. Signup and view all the answers

Which statement correctly identifies the components involved in the assembly of the nucleosome core?

The core is formed by four histone types in a specific molar ratio. Signup and view all the answers

What structural feature distinguishes the sequence at centromeres?

They interact specifically with sister chromatids and spindle fibers. Signup and view all the answers

How do topoisomerases function during DNA replication?

They prevent supercoiling by introducing transient breaks in DNA. Signup and view all the answers

What is the significance of G-rich sequences at the ends of telomeres?

They allow for non-standard base pairing interactions, crucial for stability. Signup and view all the answers

Which of the following enzymes is primarily responsible for sealing nicks in the DNA backbone after replicative synthesis?

DNA ligase. Signup and view all the answers

Study Notes

Amino Acids & Proteins

20 amino acids: Know the complete structure, full name, three-letter code, and single-letter code (e.g., Aspartic acid = Asp = D).
Peptide bond structure: Planar and rigid due to double bond character.
Protein Structure Stabilization:
- Covalent forces: Peptide bonds.
- Non-covalent forces: Hydrogen bonding, hydrophobic effect, van der Waals forces, electrostatic interactions.
Polypeptide Polarity:
- N-terminus (amino group) is positive.
- C-terminus (carboxyl group) is negative.
- Proteins synthesized from N-terminus to C-terminus.
Four Levels of Protein Structure:
- Primary: Amino acid sequence.
- Secondary: Local folding patterns (alpha-helices and beta-pleated sheets).
- Tertiary: Overall three-dimensional shape of a single polypeptide chain.
- Quaternary: Arrangement of multiple polypeptide chains in a protein complex.

Enzyme Catalyzed Reactions

Free Energy: The amount of energy available to do work.
Enzyme Activity: Enzymes increase reaction rates by lowering activation energy.
Active Sites:
- Enzymes bind to substrates at specific active sites.
- Active sites are often hydrophobic but contain hydrophilic amino acids.
- Active sites are relatively small compared to the rest of the enzyme.
Allosteric Regulation:
- Allosteric sites can bind to regulatory molecules.
- Binding to allosteric sites can alter enzyme conformation and activity.

Nucleic Acids

DNA Structure:
- Double-stranded helix stabilized by hydrogen bonding between complementary bases.
- Each nucleotide consists of a sugar (deoxyribose), phosphate group, and nitrogenous base.
- Forces stabilizing DNA: hydrogen bonding, base stacking interactions, electrostatic repulsion of phosphate groups.
- Base pairing: A=T (2 hydrogen bonds), C=G (3 hydrogen bonds).
- Antiparallel strands: One strand runs 5' to 3', and the other runs 3' to 5'.
- Watson-Crick Model:
  - Right-handed double helix.
  - Bases are perpendicular to the sugar-phosphate backbone.
  - Approximately 10 bases per turn of the helix.
  - Major and minor grooves.
  - Purines (A, G) hydrogen bond with pyrimidines (T, C).
Chargaff's Principle:
- [Thymine] = [Adenine]
- [Cytosine] = [Guanine]
- [T] + [C] = [A] + [G]
RNA Structure:
- Single-stranded.
- Ribose sugar (2'-OH).
- Uracil instead of thymine.
- Can fold back on itself to form complex structures.

DNA Packaging

Levels of DNA Condensation:
- 1. DNA double helix (2 nm).
- 1. "Beads on a string" (10 nm): DNA wrapped around histone octamers (nucleosomes).
- 1. Solenoid or zigzag (30 nm): Nucleosomes packed together.
- 1. 30 nm fiber organized into loops via a chromatin scaffold.
Histones: Basic (positively charged) proteins that interact with the negatively charged phosphate groups of DNA.
Chromatin: Complex of DNA and proteins.
Uninemes vs. Multinemes:
- Uninemes: Single continuous strand of DNA.
- Multinemes: Multiple DNA strands intertwined in a chromosome.

Chromatin

Chromatin is composed of DNA, histones, and non-histone proteins.
Heterochromatin is condensed and transcriptionally inactive, resulting in low gene expression.
Euchromatin is more open and accessible, leading to higher transcriptional activity and active gene expression.
Chromatin undergoes modifications that can alter gene expression, some of which are reversible.
Changes in chromatin structure impact gene expression, influencing organismal development and cellular function activation/deactivation.
Non-histone proteins are diverse, with composition varying between cell types within an organism.
They regulate the expression of different gene sets.
The solenoid model proposes a helical structure of nucleosome discs with linker DNA buried in the center.
The zigzag model suggests a zigzag pattern of nucleosomes due to histone H1 binding, with linker DNA passing through the central axis.
Both models could be correct, depending on the length of linker DNA, which varies between species.
The final level of condensation involves non-histone proteins forming a scaffold that compacts the 30 nm chromatin fiber into loops or supercoiled domains.

Histones, Nucleosomes, and Nucleosomes Assembly

Five histone proteins exist: H1, H2A, H2B, H3, and H4.
Histones have a unique amino acid composition and are found in all eukaryotic chromosomes in quantities similar to DNA.
Specific molar ratios are observed (1 H1 : 2 H2A : 2 H2B : 2 H3 : 2 H4).
Histones form an octamer called the nucleosome core.
The N-terminal tails of histones are exposed and required for the formation of the 30 nm fiber.
Nucleosome assembly starts with an H32*H42 tetramer, which binds to DNA.
The DNA-H3H4 complex recruits two copies of H2A*H2B dimers to complete the nucleosome core.
The nucleosome core has twofold symmetry.
Histone H1 binds to linker DNA, stabilizing the structure.
Histone-DNA interactions involve 14 contact sites between the histone octamer and the minor groove of DNA.
Around 40 hydrogen bonds are involved, mainly between core proteins and DNA phosphodiester bond oxygens in the minor groove.
These bonds drive DNA bending around the nucleosome core.
Basic amino acids on the core neutralize the negatively charged phosphates of the DNA backbone, allowing DNA bending without repulsive forces.

Centromeres and Telomeres

Telomeres are the ends of chromosomes.
They prevent degradation, fusion with other DNA, and facilitate replication of linear DNA ends.
Telomerase maintains telomere length, which shortens with age in normal somatic cells.
Cancerous and germ cells maintain telomere length.
The end of a telomere has a single-stranded 3' G-rich overhang that allows for non-Watson-Crick base pairing, contributing to unique structures.
G-quartet structure: The overhang folds back and forms a four-base structure.
T-loop structure: The 3' overhang folds back and pairs with a region on the chromosome, stabilized by proteins.
The centromere is the middle of the chromosome, where sister chromatids interact.
It ensures one copy of each duplicated and condensed chromosome is pulled into each daughter cell during cell division.
The kinetochore, forming at the centromere, attaches chromosomes to the mitotic spindle, allowing for separation during cell division.
Centromeres are constricted regions of metaphase chromosomes and serve as attachment points for spindle fibers.

DNA Replication

DNA replication is a semiconservative process: each parental strand serves as a template for a new daughter strand, resulting in hybrid DNA molecules.
Synthesis occurs in the 5' to 3' direction, adding nucleotides to the 3' OH group of the previous nucleotide.
A primer, initially an RNA molecule, provides the 3' OH for polymerase activity.
DNA polymerases catalyze DNA synthesis, requiring Mg2+, dNTPs, a primer, and a template.
Pyrophosphate release provides energy for nucleotide incorporation.
DNA polymerases read template strands and synthesize new strands.

DNA Polymerases

Prokaryotic polymerases:
- Pol I: removes RNA primers and participates in DNA repair, possessing 5' to 3' exonuclease (removes RNA primer) and 3' to 5' exonuclease (removes misincorporated nucleotides) activity.
- Pol II: involved in DNA repair.
- Pol III: replicates chromosomes, acting as the main bacterial replicase.
- Pol II, IV, and V: replicate damaged DNA.
Eukaryotic polymerases (13 total):
- Pol alpha: synthesizes primers during DNA replication.
- Pol beta: involved in base excision repair.
- Pol omega: participates in lagging strand synthesis and nucleotide/base excision repair.
- Pol epsilon: involved in leading strand synthesis and nucleotide/base excision repair.
- Pol alpha, delta, and/or epsilon work together to replicate nuclear DNA.
- Pol gamma replicates mitochondrial DNA.
- Pol beta, zeta, and eta are nuclear DNA repair enzymes.
All polymerases require primers (except RNA polymerases), while DNA primase only requires a DNA template.
DNA replication uses RNA primers generated by DNA primase, which are later excised and replaced with DNA.

DNA Replication Fidelity

DNA synthesis involves multiple systems to ensure high fidelity.
These systems include 5' to 3' polymerization, 3' to 5' exonucleolytic proofreading, and strand-directed mismatch repair (SDMMR).
5' to 3' polymerization allows for the addition of nucleotides to the 3' end of the growing chain.
3' to 5' exonucleolytic proofreading removes misincorporated nucleotides.
SDMMR corrects mistakes missed by proofreading, recognizing errors in the newly synthesized strand rather than the parental strand.
In bacteria, SDMMR detects unmethylated A's on the new strand, while in humans, it uses nick detection in Okazaki fragments as a marker of newly synthesized DNA.

Prokaryotic and Eukaryotic DNA Replication

Both prokaryotic and eukaryotic DNA replication occur at origins, but prokaryotes have a single origin while eukaryotes have multiple origins, facilitating faster replication in large eukaryotic genomes.
AT-rich regions are found at origins, facilitating DNA separation.
DNA replication is bidirectional in both prokaryotes and eukaryotes, occurring in both directions simultaneously.
The use of denaturation mapping in phage lambda provides evidence for bidirectional replication.
Leading strand: continuously synthesized, moving 5' to 3'.
Lagging strand: discontinuously synthesized, with multiple 5' to 3' stretches (Okazaki fragments) that are later joined together.

DNA Replication Enzymes - Ligase, Primase, Helicases, and Topoisomerases

DNA ligase joins adjacent Okazaki fragments by creating a phosphodiester bond between them, requiring ATP or NAD.
DNA primase synthesizes RNA primers for initiation of DNA synthesis.
DNA helicases unwind DNA using ATP hydrolysis, moving ahead of the polymerase and producing two single-stranded DNA molecules.
Single-stranded DNA binding proteins (SSBs) keep unwound DNA extended, preventing reannealing and facilitating access for polymerase.
Topoisomerases prevent overwinding by introducing transient breaks in DNA:
- Topo I: removes supercoils one at a time, introducing a single-stranded break.
- Topo II: introduces negative supercoils, introducing a double-stranded break.

Accessory Proteins

In prokaryotes, single-stranded DNA binding protein (SSB) keeps the unwound strands extended, preventing reannealing.
The replication fork utilizes a "sliding clamp" that holds DNA polymerase on the template strand.
Eukaryotic replication uses replication protein A (RPA) to keep unwound strands extended, PCNA proteins to form the clamp, and various ribonucleases to excise RNA primers.
Pol alpha initiates replication at origins and primes Okazaki fragments, working in complex with primase.
Pol omega or epsilon completes Okazaki fragment synthesis, responsible for processive synthesis of chromosomal DNA.
These polymerases require interaction with PCNA and replication factor C for activity.
Prokaryotic clamps are formed by two beta subunits, while eukaryotic clamps are formed by PCNA proteins.

DNA Replication: Eukaryotes vs. Prokaryotes

Eukaryotic DNA replication:
- More complex than prokaryotic replication.
- Shorter RNA primers.
- Shorter Okazaki fragments.
- Occurs only during the S phase of the cell cycle.
- Multiple origins of replication per chromosome.
- Multiple polymerases at the replication fork.
- Involves nucleosomes, telomeres, and centromeres.
The DNA clamp in eukaryotes is PCNA, while in prokaryotes, it is the β subunit of Pol III.

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Description

This quiz covers essential concepts related to peptide bonds, amino acids, and protein structure. Additionally, it explores the fundamental aspects of chromosome structure and packaging in eukaryotic cells. Test your knowledge on these vital biochemical topics!