Cells are the smallest building units of living organisms that can carry out all processes required for life. Almost all cells are too small to see without the aid of a microscope. Although glass lenses have been used to magnify images for hundreds of years, they were not enough to reveal individual cells. The compound microscope was invented in the late 1500s by the Dutch eyeglass maker Zacharias Janssen. In 1665, the English scientist Robert Hooke was the first to identify cells and name them. After long studies, the accumulated research can be summarized in the cell theory, which is considered the first unifying concept in biology. The major principles of the cell theory are:
1. All organisms are made of cells.
2. All existing cells are produced by other living cells.
3. The cell is the most basic unit of life.
Cell Types:
The variety of cell types found in living things is staggering. The human body alone is made up of trillions of cells of many different shapes, sizes, and functions. Despite this variety, the cells in the body share many similar characteristics. All cells are microscopic in size, composed of similar building blocks, and are enclosed by a membrane that controls the movement of materials into and out of the cell. Within this membrane, the cell is filled with cytoplasm and organelles. Organelles are structures specialized to perform distinct processes. Mostly, they are surrounded by a membrane, which takes us to the first classification of cells.
Prokaryotic Cells:
Prokaryotic cells are a type of cell that do not have a nucleus or other membrane-bound organelles. The cell’s DNA is suspended in the cytoplasm. Most prokaryotes are microscopic single-celled organisms, such as bacteria.
Eukaryotic Cells:
Eukaryotic cells are a type of cell that have a nucleus and other membrane-bound organelles. The nucleus is the largest organelle, enclosing the genetic information (DNA). Eukaryotes may be multi-cellular or single-celled organisms.
Prokaryotic cell.
The origin of the terms Prokaryotes” and “Eukaryotes” is the Greek root “Karuon,” which means “nuts” or “kernel.” This refers to the nucleus, where “Eu” means “true” and “pro” means “before.” The cell with a true nucleus is a Eukaryote.
General questions on the section:
- What are the major principles of the cell theory?
- What characteristics are shared by most cells?
- How do prokaryotes and eukaryotes differ?
- In what way are cells similar to atoms?
Section 3.2:
Cell Organelles:
We mentioned that eukaryotic cells share many similar structures. These structures include similar organelles involved in processing cell functions. In this chapter, we will discuss each organelle’s structure and function.
Cell internal structure:
There are some similar characteristics in all cells that shape their bodies and protect their identities. These characteristics include:
- Cell Membrane: A double-layered membrane that forms a boundary between the cell and the outside environment, controlling the passage of materials into and out of the cell.
2. Cytoskeleton:
Is a network of proteins that is constantly changing to meet the needs of a cell. It is made of small protein subunits that form long threads, or fibers that crisscross the entire cell. The cytoskeleton prevents the cell from being a random jumble of suspended organelles.
The cytoskeleton is divided into three types:
1) Microtubules: Are long hollow tubes that give the cell its shape. 2) Intermediate filaments: Smaller than microtubules and give the cell its strength. 3) Microfilaments: The smallest of the three are tiny threads that enable cells to move and divide.
3. Cytoplasm: It is the jelly-like substance that contains dissolved molecular building blocks, such as proteins, nucleic acids, minerals, and ions. Cytoplasm is the cell matrix that fills the space between the nucleus and the cell membrane, containing the organelles. The fluid portion, excluding the organelles, is called Cytosol, and it consists mostly of water, which shows the importance of water as an essential component for life.
This is the structure of plant and animal cells. You will find that they have many similar characters and organelles, with a few different organelles in each one that serve a specific function in the cell. We will discuss these differences in detail later on in the unit. For now, we will discuss the organelles according to their roles in the cell.
Organelles involved in making and processing proteins:
1. The Nucleus:
The nucleus is the storehouse for genetic information, or DNA (deoxyribonucleic acid) in the cells. The nucleus has two roles: a) DNA must be carefully protected.
b) DNA must be available for use at proper times.
The molecules that would damage DNA need to be kept out of the nucleus, while the proteins involved in turning the genes on and off have to access the DNA at certain times.
The Nucleus, Rough & Smooth Endoplasmic Reticulum.
2. Endoplasmic Reticulum and Ribosomes (ER):
Endoplasmic Reticulum (ER) is an interconnected network of thin, folded membranes. It forms a maze of enclosed spaces, with the inner side of the maze called the Lumen. Numerous processes, including the production of proteins and lipids, occur both on the surface of the ER and inside the Lumen. There are two types of ER: Smooth ER and Rough ER.
Rough ER has ribosomes on its surface, which give it a bumpy or gritty look. Ribosomes are tiny organelles that link amino acids together to form proteins. They may be bonded on the ER surface or suspended in the cytoplasm. Smooth ER doesn’t have ribosomes on its surface. It makes lipids and performs other specialized functions, such as breaking down drugs and alcohol.
3. Golgi Apparatus: It consists of closely layered stacks of membrane-enclosed spaces that package and deliver proteins.
4. Vesicles: Small membrane-bound sacs enclose some materials from the rest of the cytoplasm and transport them from place to place.
Organelles having various functions:
1. Mitochondria:
Mitochondria are the main energy suppliers to the cell. They are bean-shaped with two membranes. The inner membrane has many folds that form a compartment for many series of chemical reactions that convert food into usable energy. They have their own DNA.
2. Vacuole:
It is a fluid-filled sac used for the storage of materials needed by the cell. In a plant cell, the Vacuole takes up most of the space inside, where it is filled with watery fluid that strengthens the cell and helps to support the entire plant.
3. Lysosomes:
They are membrane-bound organelles that contain enzymes.
They defend the cell from invading bacteria and viruses. They also break down damaged or worn-out cell parts.
4. Centrosome and Centrioles:
Centrosome is a small region of cytoplasm that produces microtubules. In animal cells, it contains two small structures called Centrioles.
Centrioles are cylinder-shaped organelles made of short microtubules arranged in a circle. They double and form spindle fibers that attach to DNA during cell division. They play a role in animal cell division.
Lysosomes and centrioles.
Spindle fibers of the centrosome in a plant cell are special structures. Plant cells have two features that are not shared by animal cells. These features are cell walls, which provide rigid support, and chloroplasts, which carry out photosynthesis.
Cell walls are a rigid layer that surrounds the cell membrane of plants, algae, fungi, and most bacteria. They give protection, support, and shape to the cell. The cell walls of plants and algae are made of cellulose.
2. Chloroplasts are organelles that carry out photosynthesis, which is a series of complex chemical reactions that convert solar energy into usable energy (chemical energy). Chloroplasts are highly compartmentalized organelles, having both inner and outer membranes. Chlorophyll is the main component of chloroplasts, which is a light-absorbing molecule that gives the plant its green color. It’s found in sacs called thylakoids. Chloroplasts and mitochondria work together in plant cells to capture and convert energy, each having their own DNA.
Animal cell
Plant cell
Chapter 4
Cell Membrane and Types of Transport
Section 4.1:
Cell Membrane:
1. Structure:
The cell membrane, also known as the plasma membrane, forms a boundary between the cell and the outside environment and controls the passage of materials into and out of the cell. It consists of a double layer of phospholipids interspersed with a variety of other molecules, such as proteins and carbohydrates. As mentioned before, the phospholipid molecule consists of three basic parts: a charged phosphate group (PO₄⁻), glycerol, and two fatty acid chains. Glycerol and the phosphate group form the “head,” while the fatty acids form the “tail.” The “head” has a charge, making it polar and able to form hydrogen bonds with water molecules. This means that the polar head is soluble in water, which is a polar solvent. The fatty acid “tail” is non-polar and cannot form hydrogen bonds with water, so non-polar tails are attracted to each other and repelled by water.
The cell membrane touches the cytoplasm inside the cell and the watery fluid outside the cell (both are polar solvents), which makes the phospholipids arrange themselves in layers like a sandwich. The heads” are like bread forming the outer layer, and the “tails” are like the filling hiding from the watery environment. The “head” is called hydrophilic, which means “water-loving,” while the “tail” is called hydrophobic, which means “water-fearing.”
2. Properties:
Selective Permeability:
The cell membrane has the property of selective permeability, which means it allows some, but not all materials to cross. Therefore, the cell membrane is called semipermeable.
Selective permeability enables the cell to maintain homeostasis (balance), despite unexpected changes outside the cell. The cell only permits molecules and ions it needs to get in, whether they are at high concentration or not outside the cell. Molecules cross the membrane in several ways. Some of these methods require energy, and others do not. It depends on the molecule size, polarity, and concentration inside versus outside.
Receptors:
A receptor is a protein that detects a signal molecule and performs an action in response. It recognizes and binds to only certain molecules, ensuring that the right cell gets the right molecule. The molecule that binds to the receptor is called a ligand.
There are two types of receptors:
- Intracellular Receptors: This type of receptor is located inside the cell and binds to small, non-polar molecules that can cross the cell membrane.
- Membrane Receptors: This type of receptor is located on the cell surface and binds to molecules that cannot cross the cell membrane.
There are many types of transport across the cell membrane, and the specific type used depends on factors such as molecule size, polarity, and concentration inside versus outside the cell. Cells continually import and export substances, but if they had to expend energy to move every molecule, they would require an enormous amount of energy to stay alive. There are two main types of transport:
Passive Transport: It is a type of transport where the molecules move across the cell membrane without energy input from the cell. The molecules move from higher to lower concentration. It is also described as the diffusion of molecules across the membrane.
II. Active Transport: It is a type of transport where the cell uses energy to move a substance against the concentration gradient, i.e., move the substance from lower to higher concentration.
We will discuss every type in detail to know its subtypes and conditions.
I. Passive Transport:
It can be expressed or divided into two terms, depending on the concentration of molecules or the concentration of water. These terms are:
- Diffusion:
Diffusion is the movement of molecules in a fluid or gas from a region of higher concentration to a region of lower concentration. It results from the natural motion of particles, which causes molecules to collide and scatter. Concentration is the number of molecules of a substance in a given volume, and it can vary from one region to another (e.g. 20mg/100ml). Molecules diffuse down their concentration gradient, from a region of higher concentration to a region of lower concentration. Concentration Gradient is the difference in the concentration of a substance from one location to another. Diffusion plays an important role in moving substances across the cell membrane. Small lipids and other non-polar molecules such as carbon dioxide and oxygen easily diffuse across the membrane. Most cells continually consume oxygen, which means that the oxygen concentration is always higher outside the cell than inside. As a result, oxygen diffuses into the cell without the cell expending energy.
2. Osmosis:
It is the movement of water molecules across a semipermeable membrane from an area of higher concentration of water to an area of lower concentration. The higher the concentration of dissolved particles in a solution, the lower the concentration of water molecules in the same solution. A solution may be isotonic, hypertonic, or hypotonic relative to another solution. For example, a solution may only be described as isotonic in comparison with another solution. Hypo means less or low, Iso means equal, and Hyper means more or high.
Isotonic Solution: A solution is isotonic to a cell if it has the same concentration of dissolved particles as the cell. Water molecules move into and out of the cell at an equal rate, so the cell size remains constant.
A hypertonic solution is one with a higher concentration of dissolved particles than a cell. This means that the water concentration is higher inside the cell than outside, causing water to flow out of the cell and potentially causing it to shrink or even die.
Hypotonic Solution: It is a solution with a lower concentration of dissolved particles than a cell. This means that water molecules are more concentrated outside the cell than inside, so water diffuses into the cell, leading it to expand until it bursts.
3. Facilitated Diffusion:
Facilitated diffusion is the diffusion of molecules across the cell membrane through transport proteins. Transport proteins are openings formed by proteins that pierce the cell membrane, helping some molecules to cross the membrane where they cannot easily pass. The cell doesn’t expend energy in this process, as the molecules move down the concentration gradient. Sugar molecules are too large to cross the cell membrane, so they have to enter with the aid of transport proteins. Thus, sugar molecules cross the cell membrane by facilitated diffusion.
II. Active Transport:
Active transport is the movement of substances across the cell membrane against the concentration gradient. The cell uses energy to take its needed molecules from a region of low concentration to a region of high concentration to maintain homeostasis. Molecules pass across the membrane through transport proteins, like facilitated diffusion, but the difference here is the energy used in active transport. Some active transport proteins bind to only one type of molecule, like enzymes.
The cell uses a high-energy chemical compound called ATP as a source of energy to allow the passage of molecules against the concentration gradient. There are two other types of active transport, but they don’t depend on transport proteins. In these types of transport, materials are transported across the membrane in vesicles. This type of transport is mainly for large substances or a large amount of a substance.
1. Endocytosis:
Endocytosis is the process of taking liquids or large molecules into a cell by engulfing them in a membrane. The cell membrane makes a pocket around the substance, and the pocket breaks off inside the cell to form a vesicle. Lysosomal enzymes break down the vesicle to release its contents.
2. Phagocytosis:
Phagocytosis is a word that literally means cell eating.” It is widely used to describe the process by which cells in the immune system, called macrophages, find, engulf, and destroy foreign materials in the blood, such as bacteria.
2. Exocytosis:
Exocytosis is the opposite of endocytosis. It is the release of substances out of the cell by the fusion of vesicles with the membrane. The vesicle forms around the material to be expelled out of the cell and then moves towards the cell’s surface, where it fuses with the membrane. Exocytosis widely occurs in nerve cells (neurons) where the chemical transmitters that carry electrical signals from the brain are stored in vesicles. These vesicles fuse with the cell membrane and release these chemical transmitters outside the cell to act as a stimulus to the next cell.
General questions on Chapter 3 and 4:
1) What are the types of cytoskeleton, and what are their functions? 2) Explain the structure and function of the mitochondrion, nucleus, ER, Golgi apparatus, and lysosomes. 3) What are the roles of the cell wall and chloroplasts?
4) Describe the structure of the cell membrane and how it affects the passage of materials in and out of the cell. 5) State and compare types of transport.
6) What is the difference between diffusion and osmosis?
7) Explain what the concentration gradient is and what it means for a molecule to diffuse down its concentration gradient. 8) Why does facilitated diffusion not require energy from the cell? 9) How are receptors, transport proteins, and enzymes similar? 10) Define and give one example of endocytosis and exocytosis.
Unit 3: Cells and Energy
Chapter 1
Chemical Energy and ATP
Section 1.1:
Chemical energy used by most cells is carried by ATP.
Sometimes, you may feel that you need energy, so you eat food containing sugar. Carbohydrates and lipids are the most important energy sources in food. However, this energy is only usable after these molecules are broken down by a series of chemical reactions. All cells use chemical energy carried by ATP [adenosine triphosphate]. ATP is a molecule that transfers energy from the breakdown of food molecules to cell processes. ATP has three phosphate groups, but the bond holding the third phosphate group is unstable and easily broken. The energy carried by ATP is released when a phosphate group is removed from the molecule.
The removal of the third phosphate group usually involves a reaction that releases energy. You can think of ATP as a wallet filled with money; as long as it carries money you can spend, ATP carries chemical energy that the cell can use. Cells use ATP for functions such as building molecules and moving materials by active transport.
When the phosphate is removed, energy is released, and ATP becomes ADP (adenosine diphosphate), which is a lower energy molecule that can be converted into ATP by the addition of a phosphate group.
ADP has a nearly empty wallet, and the cell cannot spend from it.
Food and Energy:
Food that we eat does not contain ATP that cells can use.
Food must be digested to be broken down into smaller molecules that can be used to make ATP. Different types of food have different amounts of calories, which are measures of energy. Organisms break down carbon-based molecules to produce ATP.
The number of ATP molecules that are made from the breakdown of food is related to the number of Calories. A calorie is the amount of energy required to raise the temperature of 1 kilogram of water by 1 degree Celsius (i.e. an energy unit). It also depends on the type of molecule that is broken down, whether it is carbohydrate, lipid, or protein. Lipids store 80% of the energy in the body.
Plants also need ATP, but they do not eat food like animals. Instead, plants make their own food through photosynthesis. During photosynthesis, plants absorb sunlight and produce sugars that are broken down to produce ATP.
Cellular respiration:
It is the process by which the cell releases chemical energy from sugars and other carbon-based molecules to make ATP when oxygen is present. Cellular respiration is an aerobic process (aerobic respiration), where it needs oxygen to take place. Cellular respiration takes place in mitochondria.
The aerobic part of cellular respiration is called the Krebs cycle and produces 34 ATP molecules. Mitochondria cannot directly make ATP from food. First, food is broken down into smaller molecules such as glucose. Glycolysis is the process of splitting glucose into two 3-carbon molecules (pyruvate) and produces two ATP molecules. It is an anaerobic process that does not require oxygen and takes place in the cytoplasm.
When oxygen is absent, there is another anaerobic process that takes place rather than the Krebs cycle, called Fermentation. Lactic acid fermentation produces 2 ATP and allows glycolysis to continue, leading to the formation of Lactic acid at the end of the process.
Alcoholic Fermentation:
It is the same as lactic acid fermentation, but it leads to the formation of alcohol at the end of the process. It takes place in many yeasts and some plants.
General Questions on the Chapter:
1) How are cellular respiration and glycolysis related?
2) What are the steps taken by the cell to get ATP?
3) Illustrate the components of the ATP molecule and how it could be converted to ADP?
4) What do you know about aerobic and anaerobic respiration?
