Chapter Review: Cells, Genomes, DNA, Proteins, and Bioenergetics

These flashcards cover key concepts from the lecture notes on Cells, Genomes, DNA, Protein Structure and Function, Bioenergetics, and DNA Replication, designed to help students prepare for their upcoming exam.

What is a universal feature of all cells regarding their hereditary information?

All cells store their hereditary information in the form of double-strand DNA molecules.

How do all cells replicate their hereditary information?

All cells replicate their hereditary information by templated polymerization.

What role do proteins play in all cells regarding catalysis?

All cells use proteins as catalysts.

What theory explains the origin of mitochondria and chloroplasts in eukaryotic cells?

The endosymbiotic theory of eukaryotic cell evolution explains their origin from symbiotic bacteria.

Why are model organisms used in biological research?

Model organisms are used because they share universal features with other organisms, are easy to maintain and reproduce in a lab, have shorter generation cycles, and can generate mutants for studying traits or diseases.

Why are viruses not considered cells?

Viruses are not considered cells because they lack the ability to make their own energy and do not have ribosomes, mitochondria, or other organelles.

Name three types of weak noncovalent bonds important in biological systems.

Van der Waals attractions, electrostatic attractions, and hydrogen bonds.

How do electrostatic attractions behave in water compared to a nonpolar environment?

Electrostatic attractions are quite weak in water because charged groups are shielded by interactions with water molecules and inorganic ions.

What is the energetic favorability of condensation reactions (building molecules)?

Condensation (building a molecule) is energetically unfavorable.

What is the energetic favorability of hydrolysis reactions (breaking apart molecules)?

Hydrolysis (breaking apart a molecule) is energetically favorable.

Which sugar is found in DNA and what is its distinctive feature at the 2' carbon?

Deoxyribose is found in DNA and has a deoxygenated hydrogen at the 2' carbon.

What type of bond joins nucleotides together in a nucleic acid chain?

Nucleotides are joined together by phosphodiester bonds.

What molecule serves as the short-term energy storage, and which one is for long-term energy storage?

Glycogen (carbohydrate) is short-term energy storage, while triglycerides (lipid) are long-term energy storage.

What are the two main types of reactions in bioenergetics and their energetic favorability?

Catabolic reactions are energetically favorable (breaking things down), and anabolic reactions are energetically unfavorable (building things).

What is the most widely used activated carrier molecule that couples energetically unfavorable reactions?

ATP is the most widely used activated carrier molecule.

Which amino acid groups have a carboxylic acid functional group (COOH)?

Acidic amino acids, such as Aspartic acid (Asp) and Glutamic acid (Glu).

Which amino acid is known for forming disulfide bonds, and what type of bond is a disulfide bond?

Cysteine (Cys) can form disulfide bonds, which are covalent bonds.

What defines the primary structure of a protein?

The primary structure of a protein is its covalently linked polypeptide chain, or amino acid sequence.

What type of bonds stabilize the secondary structure of a protein, and which parts of the amino acids are involved?

Secondary structure is stabilized by local hydrogen bonding of the polypeptide backbone (between amino and carboxyl groups), with R groups not being directly involved.

What interactions are involved in the tertiary structure of a protein, and which is the only covalent bond?

Tertiary structure involves non-covalent interactions between R groups of a single polypeptide chain (hydrophobic, hydrogen bonds, ionic interactions), and disulfide bonds are the only covalent bonds.

What factors can affect protein structure, leading to denaturation?

Heat, pH, salt concentrations, and electrolyte concentrations can affect protein structure.

What are chaperones, and what is their role in protein folding?

Chaperones are proteins that assist protein folding in the cell under physiological and stress conditions, often using ATP.

What are protein domains?

Protein domains are regions of a protein that often form a functional module with distinct structures that dictate function for that domain.

How does proinsulin become insulin, and what stabilizes the final insulin molecule?

Proinsulin undergoes proteolytic processing where a connecting peptide is removed, leaving two-chain insulin molecules stabilized by disulfide bonds.

Describe the structure of an antibody (immunoglobulin G - IgG).

An IgG antibody is Y-shaped, made up of two heavy chains and two light chains held together by disulfide bonds, with two identical antigen-binding sites formed by variable domains of heavy and light chains.

What are three common strategies used by enzymes in catalysis?

Enzymes hold substrates in precise alignment, provide charge stabilization of reaction intermediates, and apply forces that distort bonds in the substrate.

What are protein kinases and phosphatases, and what is their role in protein regulation?

Protein kinases covalently add a phosphate group to a protein, while phosphatases remove phosphate groups. This phosphorylation can increase or decrease protein activity.

What is ubiquitination, and what is its primary role in protein regulation?

Ubiquitination is the covalent addition of a ubiquitin protein to mark proteins, primarily for destruction by the proteasome, but also for signaling and trafficking.

What is the function of coenzymes?

Coenzymes are organic molecules that bind to the active sites of certain enzymes to assist in the catalysis of a reaction.

What is the charge of a DNA or RNA molecule and how is it used in gel electrophoresis?

DNA and RNA molecules have a negative charge due to their phosphate groups. In gel electrophoresis, a larger molecule (more base pairs) has a larger negative charge, allowing separation by size.

What are ‘functional RNAs’ and give two examples.

Functional RNAs are RNA molecules that do not encode proteins but perform structural or regulatory roles, such as ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs).

What happens to pre-mRNA molecules in higher eukaryotes before translation?

In higher eukaryotes, pre-mRNA molecules undergo splicing, where non-coding introns are removed and coding exons are retained to form mature mRNA.

Describe the structure and function of the nuclear envelope.

The nuclear envelope consists of two membranes, the outer one continuous with the ER membrane, and it regulates movement in and out of the nucleus through nuclear pores.

What is the nucleolus and what is its primary function?

The nucleolus is a specialized region within the nucleus (without a membrane) primarily responsible for the assembly of ribosomal subunits.

What is the difference between heterochromatin and euchromatin?

Heterochromatin is a compacted, highly condensed form of chromatin that is almost never open and less active, while euchromatin is a less condensed, loosely packed form that is more active.

What technique uses 'painted' chromosomes to identify abnormalities in number and type?

Spectral karyotyping (SKY) uses fluorescent DNA probes to 'paint' each chromosome a different color for unambiguous identification.

What three essential structures must each DNA molecule forming a linear chromosome contain?

Each linear chromosome must contain a centromere, two telomeres, and replication origins.

What is the role of the centromere during M phase?

During M phase, the centromere attaches the duplicated chromosomes to the mitotic spindle via the kinetochore to ensure proper distribution to daughter cells.

What is a nucleosome, and what is its composition?

A nucleosome is the basic unit of eukaryotic chromosome structure, consisting of DNA wound around a protein core made of eight histone molecules (two each of H2A, H2B, H3, and H4).

How do histones interact with DNA in a nucleosome and why?

Histones are positively charged, allowing them to neutralize the negatively charged DNA backbone and stabilize the interaction through hydrogen and ionic bonds.

What is the function of ATP-dependent chromatin-remodeling complexes?

These complexes use ATP hydrolysis to catalyze nucleosome sliding and histone exchanges, loosening the DNA/histone interactions to alter chromatin accessibility.

What are two types of covalent modifications to core histones that can turn gene expression on or off?

Lysine acetylation and methylation are two covalent modifications to core histones that can regulate gene expression.

What complex structures help form, maintain, and stabilize chromosome loops?

Ring structures of cohesion proteins and other proteins collectively referred to as the SMC complex (structural maintenance of chromosomes complex), which interact with proteins such as CTCF, help form and stabilize chromosome loops.

How is energy for DNA polymerization supplied?

The energy for DNA polymerization comes from the hydrolysis of a high-energy phosphate bond in the incoming nucleoside triphosphate and the release of pyrophosphate.

Why is DNA replication considered 'semiconservative'?

DNA replication is semiconservative because each daughter DNA double helix has one conserved (old) strand and one newly synthesized strand.

What synthesizes the short RNA primer molecules needed for DNA replication?

Primase synthesizes short RNA primer molecules.

What is the function of DNA helicase in DNA replication?

DNA helicase enzymes use ATP hydrolysis to separate the DNA strands and open up the double helix in front of the replication fork.

What do DNA topoisomerases do during DNA replication?

DNA topoisomerases prevent DNA tangling by relieving torsional stress that builds up ahead of the replication fork, creating transient single-strand breaks and resealing them.

When does DNA replication take place in eukaryotic cells?

In eukaryotes, DNA replication takes place during only one part of the cell cycle, known as S phase.

What enzyme is responsible for replicating the ends of chromosomes?

Telomerase replicates the ends of chromosomes, which are called telomeres.

Describe the 'pulse' stage in metabolic labeling experiments.

In metabolic labeling, the 'pulse' stage involves introducing tagged (e.g., radioactive) precursors that are incorporated into actively being synthesized macromolecules.

Describe the 'chase' stage in metabolic labeling experiments.

In metabolic labeling, the 'chase' stage follows the pulse, where the new tag is removed and the tagged molecules are tracked for post-synthesis events like modification or relocation.

What are the four major types of macromolecules in cells and their general roles?

Proteins (catalysis, structure, signaling), nucleic acids (info storage/transfer), lipids (membranes/energy), and carbohydrates (energy/recognition/structure).

How do enzymes affect chemical reactions?

Enzymes lower the activation energy (EA) and speed up the rate of a reaction, but they do not change the overall free energy change (ΔG) or the equilibrium of the reaction.

What is the fluid mosaic model of biomembranes?

The fluid mosaic model describes biomembranes as a phospholipid bilayer with embedded proteins, where amphipathic lipids self-assemble, and fluidity depends on saturation, tail length, and cholesterol.

What is the 'shape & surface' principle in protein interactions?

The 'shape & surface' principle states that complementary shapes, charges, and hydrophobic patches determine the binding affinity and specificity between proteins.

What technique is used to track biosynthesis or turnover of macromolecules by using a brief labeled period followed by an unlabeled period?

Metabolic labeling, also known as pulse-chase, is used to track biosynthesis or turnover.