Biology Chapter on Water and Carbon Compounds

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Questions and Answers

Which property of water allows it to move against gravity in plants?

High specific heat capacity

Cohesion between water molecules (correct)

High density

Low viscosity

What is the process called that synthesizes a polymer by removing water?

Dehydration reaction (correct)

Oxidation

Reduction

Hydrolysis

Which level of protein structure consists of a linear sequence of amino acids?

Tertiary structure

Primary structure (correct)

Quaternary structure

Secondary structure

Which type of isomer has the same chemical formula but a different arrangement of atoms?

Structural isomer Signup and view all the answers

What are functional groups in organic molecules?

Reactive groups that determine properties Signup and view all the answers

Which of the following components is NOT part of a nucleotide?

Amino acid Signup and view all the answers

What type of bond links amino acids together in a protein?

Peptide bond Signup and view all the answers

Which component is part of the quaternary structure of a protein?

Multiple polypeptides working together Signup and view all the answers

What defines saturated fats?

They contain a maximum number of hydrogen atoms. Signup and view all the answers

Which statement accurately describes prokaryotic cells?

They possess one or more circular DNA strands in a nucleoid region. Signup and view all the answers

What is the main function of ribosomes?

Carrying out protein synthesis. Signup and view all the answers

What role does the nuclear envelope play?

It contains pores for molecule transport. Signup and view all the answers

Which of the following is NOT a part of the endomembrane system?

Mitochondria Signup and view all the answers

What is a key characteristic of eukaryotic cells?

They have multiple linear DNA molecules. Signup and view all the answers

What structure in the cell is responsible for synthesizing lipids?

Smooth endoplasmic reticulum. Signup and view all the answers

How do eukaryotic cells overcome the surface to volume ratio limitation?

By containing membrane-bound organelles. Signup and view all the answers

What is the primary function of lysosomes in a cell?

Digest macromolecules and recycle cellular components Signup and view all the answers

Which cellular structure acts as a microtubule organizing center and contains a pair of centrioles?

Centrosome Signup and view all the answers

How do gap junctions function in animal cells?

Allow cytoplasmic channels for communication between adjacent cells Signup and view all the answers

What is the main purpose of chloroplasts in plant cells?

Conduct photosynthesis Signup and view all the answers

What does the first law of thermodynamics state?

Total energy in a system remains constant Signup and view all the answers

Which process is described by the second law of thermodynamics?

Total disorder in a system tends to increase Signup and view all the answers

What is the role of peroxisomes in cells?

Convert hydrogen peroxide into water and oxygen Signup and view all the answers

What is one function of the cytoskeleton?

Maintain cell shape and support movement Signup and view all the answers

What is the role of intercellular chemical messengers in cellular communication?

They act as signaling molecules to influence target cell activity. Signup and view all the answers

What triggers a cellular response in signal transduction pathways?

The binding of signaling molecules to surface receptors. Signup and view all the answers

How do protein kinases function in cellular response pathways?

They amplify the signal by turning on transduction pathways. Signup and view all the answers

What is the function of protein phosphatases in cellular signaling?

They remove phosphate groups to turn off signal transduction pathways. Signup and view all the answers

What is meant by amplification in cellular response pathways?

The exponential increase in the magnitude of the signal at each step. Signup and view all the answers

What is the role of enzyme cofactors?

They are necessary for catalysis to occur. Signup and view all the answers

What happens to the rate of enzyme activity when substrate concentration is low?

The reaction rate is minimal due to infrequent collisions. Signup and view all the answers

Which factor typically has an optimal value for each enzyme?

Temperature and pH Signup and view all the answers

How does feedback inhibition function in enzyme regulation?

It uses a product of a pathway to regulate that pathway. Signup and view all the answers

What is a consequence of high temperatures on enzyme activity?

Enzymes may denature and lose activity. Signup and view all the answers

In a lipid bilayer, which of the following primarily determines its fluidity?

The saturation of phospholipid fatty acids. Signup and view all the answers

What characterizes noncompetitive inhibitors in enzyme activity?

They bind elsewhere on the enzyme. Signup and view all the answers

What occurs when the enzyme is in a low-affinity state?

It binds the substrate weakly or not at all. Signup and view all the answers

Study Notes

Water

Water is less dense than ice.
Water has a high specific heat capacity and remains a liquid at room temperature.
Cohesion, the attraction between water molecules, allows water to move against gravity.
Water is a universal solvent, meaning it can dissolve many substances.
The dissolved substance is called a solute.
Water molecules surround polar molecules and ions causing separation.

Water Ionization and pH

Water ionizes into H+ and OH- ions.
The concentration of H+ ions is measured on the pH scale.

Carbon Compounds

All living matter is organic and contains carbon.
Carbon has four bonds which allow for large, complex molecules.
Hydrocarbons contain only hydrogen and carbon.
Carbon bonds with covalent bonds.

Functional Groups

Functional groups add to carbon as active groups that enter into biological reactions.

Dehydration and Hydrolysis Reactions

Dehydration reactions create bonds through the synthesis of a polymer.
Hydrolysis reactions break down polymers by adding water to break the bond.

Isomers

Isomers have the same chemical formula but different molecular structures.
Enantiomers are mirror image isomers.
Glucose and Fructose are structural isomers.
Disaccharides contain two sugars.

Proteins

Proteins have many structures and functions.
They are the workforce of the cell and play roles in structural support, storage, transport, enzymes, communication, and movement.
A protein is one or more polypeptides (polymers made of amino acids).
Amino acids are linked by peptide bonds, which are covalent bonds created by dehydration reactions at the carboxyl end of the amino acid.

Protein Structure

Primary Structure is the linear sequence of amino acids, it is not functional and has no structure.
Secondary Structure is formed by H bonds between amino acids and carboxyl groups (with the O and H of the backbone), creating alpha helices and beta pleated sheets. It is not functional.
Tertiary Structure is formed by bonds between R groups, creating a 3D shape and ultimately functionality.
Quaternary Structure is when two or more polypeptides bond together, all bond types are functional.
Prosthetic Groups are non-protein components added to proteins to make them functional, heme is an example.

Nucleic Acids

They carry and transmit genetic information.

Nucleotides

Nucleotides have three parts joined by covalent bonds: a nitrogenous base, a pentose sugar, and one to three phosphate groups.
Uracil is only found in RNA.
Thymine is only found in DNA.
Adenine and Guanine are used in both DNA and RNA.

Structure

The structure of nucleic acids is formed by two nucleotide chains.
The sugar and phosphate backbone is on the outside, while the nitrogenous bases are on the inside with hydrogen bonds connecting the two strands.

Lipids

Lipids are defined by their monomer hydrocarbon backbone.
Saturated Fats have the maximum number of hydrogen atoms and no double bonds.
Unsaturated Fats have one or more double bonds, leading to bends or kinks in the molecule.

Cells

Cells are composed of macromolecules.
The structural organization of the macromolecules determines the function of the cells.

Chapter 2: The Cell - An Overview

The cell is the basic unit of life.
Cells were first discovered in 1665 by Robert Hooke.
All living things are composed of one or more cells.
The cell is considered the functional unit of life.

Prokaryotic vs. Eukaryotic Cells

Prokaryotic Cells lack a nucleus or membrane-bound organelles.
They have one circular strand of DNA located in an unbound region called the nucleoid.
They have a plasma membrane for respiration and photosynthesis and may have flagella, pili, or cillia.
They use a variety of substances for energy and carbon sources to synthesize organic molecules.
They outnumber and live in all regions other organisms and are extremely versatile.
Eukaryotic Cells are larger because they can overcome surface-to-volume ratio constraints as they contain membrane-bound organelles.

Parts of a Eukaryotic Cell

Nucleus:
- Contains the genes of the organism.
- Enclosed by a nuclear envelope that contains a nuclear pore complex.
- Contains DNA and proteins known as chromatin.
- Chromatin condenses into chromosomes.
- The nucleolus is located within the nucleus and is the site of ribosomal RNA synthesis.
Ribosomes:
- Made of ribosomal RNA and proteins.
- Composed of a large and a small subunit.
- Carry out protein synthesis.
- Found in the cytosol, attached to the ER, or attached to the nuclear envelope.

The Endomembrane System

A collection of interrelated membranous sacs and organelles. These include the nuclear envelope, endoplasmic reticulum, Golgi apparatus, lysosomes, vesicles, and the plasma membrane.
Endoplasmic Reticulum (ER):
- Rough ER has ribosomes attached and synthesizes proteins for the cell membrane or secretion.
- Smooth ER has no ribosomes, synthesizes lipids and breaks down toxic substances.
Golgi Apparatus:
- Modifies, sorts, and packages proteins and lipids that are secreted or embedded in the plasma membrane or lysosomes.
Lysosomes:
- Membranous sacs of hydrolytic enzymes that digest macromolecules.
- Involved in autophagy, the recycling of cell organelles and macromolecules.
- Involved in phagocytosis, the engulfing of other cells or food.
Vesicles:
- Sacs that transport substances within the cell.

Mitochondria

The site of cellular respiration.
The "powerhouse" of the cell.
They have a double membrane.
They contain mitochondrial matrix, which is where Krebs cycle enzymes are found.
They have a large surface area due to the cristae formed by the inner membrane folds which increases efficiency.
They synthesize proteins from free ribosomes.

Cytoskeleton

Composed of protein fibers: microtubules, microfilaments, intermediate filaments
Provides support and shape to the cell.
Interacts with motor proteins for cell motility.
Acts as monorails for vesicle traffic.
Regulates biochemical activities.

Centrosome and Centrioles

Microtubules grow from the centrosome.
The centrosome is the microtubule-organizing center.
The centrosome contains a pair of centrioles.

Peroxisomes

Specialized metabolic compartments bound by a single membrane.
They convert toxic hydrogen peroxide to water using catalase.

Chloroplasts

The site of photosynthesis.
They have double membranes.
They make their own proteins from free ribosomes.
They contain grana, stacks of thylakoids which contain chlorophyll – the green pigment that absorbs light energy.

Vacuoles

Large vesicles formed by phagocytosis.
Contractile Vacuoles pump excess water out of the cell.
Central Vacuoles in plants hold organic compounds and water.
They contribute to cell support, protection.
They are perforated with plasmodesmata which connect to adjacent cells.

Animal Cell Surface

Cell surface molecules aid in cell contact, communication, and organization.
Cell Adhesion Molecules (CAMs) are glycoproteins in the plasma membrane that:
- Maintain body form and function.
- Attach and detach during development.
- Aid cell recognition.
- Act as adhesion sites for pathogens.
Tight Junctions press cells together to form continuous sheets, preventing leakage of extracellular fluid.
Desmosomes: fasten cells together into sheets, providing anchoring points for cellular support.
Gap Junctions: provide cytoplasmic channels between adjacent cells, enabling communication.

Chapter 3: Energy and Enzymes

Life requires temperatures below 100°C as without enzymes life would not exist.

Energy

Energy is defined as the capacity to do work.

Thermodynamics

Thermodynamics is the study of energy and its transformations.
Open Systems: exchange both energy and matter with their surroundings.
Closed Systems: exchange energy but not matter with their surroundings.
Isolated Systems: do not exchange energy or matter with their surroundings.
First Law of Thermodynamics: Energy can be transformed but not created or destroyed. This means that the total energy in a system and its surroundings is constant.
Second Law of Thermodynamics: With every energy transformation, the total disorder of a system and its surroundings increases.
Entropy: is a measure of disorder or randomness.

Spontaneous Reactions

Spontaneous reactions release free energy and occur without external intervention.
The system becomes more ordered and stable as the potential energy decreases.

Enzymes

Enzymes are biological catalysts (proteins) that speed up chemical reactions without being consumed in the process.
Enzymes lower the activation energy which is the initial energy input required to break the bonds of the reactants.
Enzymes provide a specific, active site for specific substrates to bind to, fitting like a lock-and-key.
The induced fit model suggests that the enzyme changes shape slightly when it binds to the substrate and then reverts back to its original form.

Enzyme cofactors

Enzyme cofactors are inorganic ions or organic non-protein groups that are necessary for catalysis to occur.

Enzyme Catalysis

The active site of an enzyme is where the substrate binds.

Conditions Affecting Enzyme Activity

The activity of an enzyme is affected by:
- Influence of Enzyme and Substrate Concentration:
  - With excess substrate, the rate of catalysis is proportional to the amount of enzyme.
  - With low substrate concentration, the rate slows down, as enzymes and substrates collide infrequently.
  - With high substrate concentration, the enzymes become saturated with reactants and the reaction rate levels off.
- Enzyme Inhibitors:
  - Competitive Inhibitors: bind to the active site of the enzyme and block the substrate from binding, decreasing its activity.
  - Noncompetitive Inhibitors: bind elsewhere on the enzyme and change its shape, decreasing its activity.
- Allosteric Control:
  - Allosteric enzymes have two or more binding sites.
  - Allosteric Activators: bind to the enzyme and increase the enzyme's activity.
  - Allosteric Inhibitors: bind to the enzyme and decrease the enzyme's activity.
- Temperature and pH:
  - Each enzyme has an optimal temperature and pH for activity.
  - If the temperature or pH is not optimal, the reaction rate falls off.
  - Most enzymes have a pH optimum near the pH of cellular contents (about 7.0), but enzymes from different cells may have a pH optimum further from neutrality.
  - Changes in pH affect the charged groups in the amino acids of enzymes.
  - With temperature, two effects occur:
    - As temperature rises, the rate of reaction increases.
    - High temperatures can cause enzymes to denature, which reduces the rate of reaction.

Chapter 4: Membranes and Signaling

The cell membrane is composed of a phospholipid bilayer in which proteins are embedded and float freely.
The membrane is selectively permeable, meaning it regulates the passage of molecules between the cell and the environment.
The proteins of one half of the bilayer are structurally and functionally different from the proteins of the other half.

The Lipid Fabric

Phospholipids are the dominant lipid in the cell membrane.
Fluidity of the bilayer depends on how densely packed the individual lipid molecules are.
Saturated Fatty Acids: have no double bonds and pack tightly together, making the membrane less fluid.
Unsaturated Fatty Acids: have one or more double bonds and make the membrane more fluid.
Cholesterol: plays a role in regulating membrane fluidity.

The Endocytic Pathway

Phagocytosis: The cell engulfs another cell by creating pseudopods, which close around the prey. The prey goes into an endocytic vesicle, which moves into the cytoplasm.

Cell Communication

Cell communication is especially important in multicellular organisms.
It determines if a cell is normal or if the cell is undergoing apoptosis (cell death).

Intercellular Chemical Messengers

Controlling cells synthesize a specific molecule that acts as a signaling molecule to affect the activity of the target cell.

Surface Receptors

Signal Transduction is the process by which a signal is converted into a specific cellular response.
Signal binds to the receptor, triggering a change in the receptor that activates its molecular switch.
Molecular Switch is the internal relay system for the signal.
Cellular Response is the specific action that the target cell will perform, such as changes in gene expression or enzyme activity.

Cellular Response Pathways

Signal Transduction Pathway: The binding of a signal molecule to a surface receptor triggers a cellular response without the signal entering the cell. The signal is relayed inside by protein kinases.

Protein Kinases

Protein kinases are enzymes that transfer phosphate groups from ATP to target proteins.
This process is called phosphorylation.
Phosphorylation turns on the signal transduction pathway, activating other proteins.

Balancing Cellular Response Pathways

Protein Phosphates: are enzymes that remove phosphate groups from target proteins, which reverses the response.
Signal Transduction Pathway: is turned off by protein phosphatases.

Amplification

Amplification is the increase in the magnitude of the signal at each step.
Each enzyme can activate hundreds or thousands of proteins that then move to the next step.
This allows for a full response with only a few signal molecules.

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Explore the fascinating properties of water and its significance in biological systems. This quiz delves into water ionization, pH, carbon compounds, and their functional groups, as well as vital reactions like dehydration and hydrolysis. Test your understanding of these essential concepts in biology!