The Structure of the Universe :Challenge to the Plasma Theory (Part-III)

     Author : Rumana Reza    

[My previous chapters were basically focused on particle physics. Here I've focused on some biological terms. You may get confused that how  the structure of the universe and some biological terms could be connected with each other. Hold your breathe please .....Time's there. This chapter is dedicated to those readers who had no science background before, to those who had once but now lil forgotten and to those readers who want to understand my findings,analysis and conclusion on this topic clearly,smoothly. ]

What is a cell

Cells are the basic building blocks of all living things. The human body is composed of trillions of cells. They provide structure for the body, take in nutrients from food, convert those nutrients into energy, and carry out specialized functions. Cells also contain the body’s hereditary material and can make copies of themselves.

Cells have many parts, each with a different function. Some of these parts, called organelles, are specialized structures that perform certain tasks within the cell. Human cells contain the following major parts, listed in alphabetical order:

Cell of human liver 

Cytoplasm 

Within cells, the cytoplasm is made up of a jelly-like fluid (called the cytosol) and other structures that surround the nucleus.

Microfilaments - Stringy Proteins

You will find microfilaments in most cells. They are the partner of microtubules. They are long,  thin, and stringy proteins (mainly actin) compared to the rounder, tube-shaped microtubules. We'd like to say you can find them here or there, but they are everywhere in a cell. They work with microtubules to form the structure that allows a cell to hold its shape, move itself, and move its organelles.

Microtubules - Thick Protein Tubes

Microtubules are usually discussed with microfilaments. Although they are both proteins that help define cell structure and movement, they are very different molecules. While microfilaments are thin, microtubules are thick, strong spirals of thousands of subunits. Those subunits are made of the protein called tubulin. And yes, they got their name because they look like a tube.

Cytoskeleton

The cytoskeleton is a network of long fibers that make up the cell’s structural framework. The cytoskeleton has several critical functions, including determining cell shape, participating in cell division, and allowing cells to move. It also provides a track-like system that directs the movement of organelles and other substances within cells.

Making the Cytoskeleton

All of the microfilaments and microtubules combine to form the cytoskeleton of the cell. The cytoskeleton is different from cytoplasm (cytosol). The cytoskeleton provides structure. Cytoplasm is just a fluid. The cytoskeleton connects to every organelle and every part of the cell membrane. Think about an amoeba. All of the pieces work together so that the foot might reach out towards the food. Then lysosomes and peroxisomes are sent to begin digestion. The movement of the cell membrane, organelles, and cytoplasm is all related to the tubules and filaments.

You will also find many microfilaments in muscle tissue. They are called myofibrils when you find them in muscles. The two proteins myosin and actin work together to help the muscle cells relax and contract. The two proteins need each other and together they are called actomyosin. Combine those protein threads with some ions in the muscle cell and you get a huge contraction. The groups of actomyosin contracting are called sarcomeres. All of the muscle cells work together to make a muscle contract.

Endoplasmic reticulum (ER) 

This organelle helps process molecules created by the cell. The endoplasmic reticulum also transports these molecules to their specific destinations either inside or outside the cell.

Golgi apparatus 

The Golgi apparatus packages molecules processed by the endoplasmic reticulum to be transported out of the cell.

Foundation of Vesicles

The Golgi apparatus gathers simple molecules and combines them to make molecules that are more complex. It then takes those big molecules, packages them in vesicles, and either stores them for later use or sends them out of the cell. It is also the organelle that builds lysosomes (cell digestion machines). Golgi complexes in the plant may also create complex sugars and send them off in secretory vesicles. The vesicles are created in the same way the ER does it. The vesicles are pinched off the membranes and float through the cell.

The Golgi apparatus is a series of membranes shaped like pancakes. The single membrane is similar to the cell membrane in that it has two layers. The membrane surrounds an area of fluid where the complex molecules (proteins, sugars, enzymes) are stored and changed. Because the Golgi complex absorbs vesicles from the rough ER, you will also find ribosomes in those pancake stacks.

Working with the Rough ER

The Golgi complex works closely with the rough ER. When a protein is made in the ER, something called a transition vesicle is made. This vesicle or sac floats through the cytoplasm to the Golgi apparatus and is absorbed. After the Golgi does its work on the molecules inside the sac, a secretory vesicle is created and released into the cytoplasm. From there, the vesicle moves to the cell membrane and the molecules are released out of the cell.

Lysosomes and peroxisomes 

These organelles are the recycling center of the cell. They digest foreign bacteria that invade the cell, rid the cell of toxic substances, and recycle worn-out cell components.

Lysosome Action

Mitochondria 

Mitochondria are complex organelles that convert energy from food into a form that the cell can use. They have their own genetic material, separate from the DNA in the nucleus, and can make copies of themselves.

Mitochondria Structure

Mitochondria are shaped perfectly to maximize their productivity. They are made of two membranes. The outer membrane covers the organelle and contains it like a skin. The inner membrane folds over many times and creates layered structures called cristae. The fluid contained in the mitochondria is called the matrix.

The folding of the inner membrane increases the surface area inside the organelle. Since many of the chemical reactions happen on the inner membrane, the increased surface area creates more space for reactions to occur. If you have more space to work, you can get more work done. Similar surface area strategies are used by microvilli in your intestines.

What’s in the matrix? It's not like the movies at all. Mitochondria are special because they have their own ribosomes and DNA floating in the matrix. There are also structures called granules which may control concentrations of ions. Cell biologists are still exploring the activity of granules.

Using Oxygen to Release Energy

How does cellular respiration occur in mitochondria? The matrix is filled with water and proteins (enzymes). Those proteins take organic molecules, such as pyruvate and acetyl CoA, and chemically digest them. Proteins embedded in the inner membrane and enzymes involved in the citric acid cycle ultimately release water (H₂O) and carbon dioxide (CO₂) molecules from the breakdown of oxygen (O₂) and glucose (C₆H₁₂O₆). The mitochondria are the only places in the cell where oxygen is reduced and eventually broken down into water.

Mitochondria are also involved in controlling the concentration of calcium (Ca²⁺) ions within the cell. They work very closely with the endoplasmic reticulum to limit the amount of calcium in the cytosol. 

Nucleus 

The nucleus serves as the cell’s command center, sending directions to the cell to grow, mature, divide, or die. It also houses DNA (deoxyribonucleic acid), the cell’s hereditary material. The nucleus is surrounded by a membrane called the nuclear envelope, which protects the DNA and separates the nucleus from the rest of the cell.

Life Before a Nucleus

Not all cells have a nucleus. Biology breaks cell types into eukaryotic (those with a defined nucleus) and prokaryotic (those with no defined nucleus). You may have heard of chromatin and DNA. You don't need a nucleus to have DNA. If you don't have a defined nucleus, your DNA is probably floating around the cell in a region called the nucleoid. A defined nucleus that holds the genetic code is an advanced feature in a cell.

Important Materials in the Envelope

The things that make a eukaryotic cell are a defined nucleus and other organelles. The nuclear envelope surrounds the nucleus and all of its contents. The nuclear envelope is a membrane similar to the cell membrane around the whole cell. There are pores and spaces for RNA and proteins to pass through while the nuclear envelope keeps all of the chromatin and nucleolus inside.

When the cell is in a resting state there is something called chromatin in the nucleus. Chromatin is made of DNA, RNA, and nuclear proteins. DNA and RNA are the nucleic acids inside of the cell. When the cell is going to divide, the chromatin becomes very compact. It condenses. When the chromatin comes together, you can see the chromosomes. You will also find the nucleolus inside of the nucleus. When you look through a microscope, it looks like a nucleus inside of the nucleus. It is made of RNA and protein. It does not have much DNA at all.

Mixing and Matching Amino Acids

When are ribosomes used in the process of protein synthesis? When the cell needs to make a protein, mRNA is created in the nucleus. The mRNA is then sent out of the nucleus and to the ribosomes. When it is time to make the protein, the two subunits come together and combine with the mRNA. The subunits lock onto the mRNA and start the protein synthesis.

The process of making proteins is quite simple. First, you need an amino acid. Another nucleic acid that lives in the cell is transfer RNA. tRNA is bonded to the amino acids floating around the cell. With the mRNA offering instructions, the ribosome connects to a tRNA and pulls off one amino acid. The tRNA is then released back into the cell and attaches to another amino acid. The ribosome builds a long amino acid (polypeptide) chain that will eventually be part of a larger protein.

Special Fluids in the Nucleus

Nucleoplasm has a little different composition. Nucleoplasm can only be found inside of the nucleus. It doesn't have big organelles in suspension. The nucleoplasm is the suspension fluid that holds the cell's chromatin and nucleolus. It is not always present in the nucleus. When the cell divides, the nuclear membrane dissolves and the nucleoplasm is released. After the cell nucleus has reformed, the nucleoplasm fills the space again.

Ribosomes

Ribosomes are organelles that process the cell’s genetic instructions to create proteins. These organelles can float freely in the cytoplasm or be connected to the endoplasmic reticulum .

Plasma membrane 

The plasma membrane is the outer lining of the cell. It separates the cell from its environment and allows materials to enter and leave the cell.

Flexible Containers

The cell membrane is not a solid structure. It is made of millions of smaller molecules that create a flexible and porous container. Proteins and phospholipids make up most of the membrane structure. The phospholipids make the basic bag. The proteins are found around the holes and help move molecules in and out of the cell. There are also proteins attached to the inner and outer surfaces of the membrane.

Scientists use the fluid mosaic model to describe the organization of phospholipids and proteins. The model shows you that phospholipid molecules are shaped with a head and a tail region. The head section of the molecule likes water (hydrophilic) while the tail does not (hydrophobic). Because the tails want to avoid water, they tend to stick to each other and let the heads face the watery (aqueous) areas inside and outside of the cell. The two surfaces of molecules create the lipid bilayer.

Ingrained in the Membrane

What about the membrane proteins? Scientists have shown that many proteins float in the lipid bilayer. Some are permanently attached while others are only attached temporarily. Some are only attached to the inner or outer layer of the membrane while the transmembrane proteins pass through the entire structure. The transmembrane proteins that cross the bilayer are very important in the active transport of ions and small molecules.

Cell_membrane detailed diagram

Different Membranes of the Cell

As you learn more about cell organelles, you will find that they all have a membrane. Organelle membranes do not have the same chemical makeup as the cell membrane. They have different lipids and proteins that make them unique. The membrane that surrounds a lysosome is different from the membrane around the endoplasmic reticulum.

Some organelles have two membranes. A mitochondrion has an outer and inner membrane. The outer membrane contains the mitochondrion parts. The inner membrane holds digestive enzymes that break down food. While we talk about membranes all the time, you should remember they all use a basic phospholipid bilayer structure, but you will find many variations throughout the cell.

Membrane Proteins - Bumpy Surfaces

We have a page on the basic structure of the cell membrane and other membranes within the cell. They are basic bilayers made of lipids that surround the cell and organelles. The lipid bilayer is not smooth because there are a variety of proteins attached to the surface and embedded in the membrane. You will find millions of embedded protein molecules when you look at the cell membrane. Each type of protein has a specific purpose. Examples of membrane proteins include ion channels, receptor proteins, and proteins that allow cells to connect to each other.

A Tale of Two Types

You will learn about two types of membrane proteins: peripheral proteins and integral proteins. Peripheral proteins have weaker and temporary connections to the membrane. Some just sit on the surface, anchored with a few ionic bonds while others might have small sections that dip into the hydrophobic section of the bilayer. When you look at the entire membrane, there are more peripheral proteins when compared to the number of integral proteins.

As you can guess from the name, integral proteins are permanently connected to the cell membrane. They are hard workers and have large sections embedded in the hydrophobic (middle) layer of the membrane.

Transmembrane proteins are integral proteins that cross the membrane and can act as pathways for ions and molecules. Polytopic transmembrane proteins cross the membrane several times. Some are receptor proteins while others form channels. Ion movement that does not require work is called passive transport while active transport systems use work to move molecules. Active transport is regularly used when membrane proteins pump ions against the concentration gradient.

Discovering Structures

This structure of the membrane with embedded proteins and a lipid bilayer , first developed the theory of the "Fluid Mosaic Model." It was described in several different methods, such as the freeze-fracture technique and electron micrographs, to look closely at the cell membrane and its structure. It was identified as the proteins that sat on the surface, were sunk into the membrane, and the others that crossed the membrane.  

Cell Wall 

Cell membranes surround every cell you will study. Cell walls made of cellulose are only found around plant cells and a few other organisms. Cellulose is a specialized sugar that is classified as a structural carbohydrate and not used for energy. If a plant cell is like a water balloon, the cell wall is like a cardboard box that protects the balloon. The balloon is protected from the outside world by a structure that provides protection and support.

While many sugars, such as glucose, can dissolve in water (H₂0), cellulose will not dissolve in water and can form long chains to support plants. When you eat plant material, you can’t even digest and break down cellulose for energy. Cows and other herbivores have special bacteria in their stomachs to digest the cellulose polymers.

While cell walls protect the cells, they also allow plants to grow to great heights. You have a skeleton to hold you up. A 100-foot tall redwood tree does not. It uses the strong cell walls to maintain its shape. For overall support, dense cells in the core of the trunk can let a tree grow very high. Cell walls are slightly elastic for smaller plants, leaves, and thin branches. Winds can push them from side to side and they bounce back. Big redwoods need strength in high winds and sway very little (except at the top).

Another Hole in the Wall

A cell wall is not an impenetrable fortress around the delicate plant cell. There are small holes, called plasmodesmata, in the cell walls between plant cells. The cell membranes of neighboring cells are able to connect through these holes. The connections allow the transfer of nutrients, waste, and ions (symplastic pathways). Molecules can also pass through the spaces within the cell walls, avoiding the cells completely (apoplastic pathways).

It is great that nutrients can move from cell to cell, but there is also a problem with all the holes. Cells can lose water. Plants lose large amounts of water in the middle of the day or on very hot days. When the air heats up and the water vapor pressure decreases, plants lose water through the process of transpiration. The water escapes through pores on the surface of the plant called stomata. Even when the plant cells lose water, the basic shape is maintained by the cell walls. The plant may droop or wilt, but it can recover when water returns to the system. It will look just the same as when it started.  

Cell Connections and Communication

All living things communicate in one way or another. When you start looking at the world on a cellular level, you won't find communication in writing or words. Cellular communication is on a molecular level. This section talks about cells in a larger organism that are near each other. We don't cover the communication between single-celled organisms. They behave in different ways.

Gap Junctions

Gap junctions are one type of cell connection. When two cells are right next to each other, their cell membranes may actually be touching. A gap junction is an opening from one cell to another. It's not a big opening, but it is large enough for cytoplasm to move from one cell to another. The connections are called channels and they act like tunnels for the movement of molecules.

Desmosomes

Desmosomes are a second type of cell connection. They physically connect cells like the gap junction, but no opening is created. Proteins that bond the membrane of one cell to its neighbor create the desmosomes. You will find desmosomes in your skin cells. All of those proteins hold your skin together. The distance between the cells, however small, is about 10 times wider than the gap junction connections.

Tight Junction

The last type of connection we will introduce is the tight junction. Tight junctions happen when two membranes actually bond into one. It makes a very strong barrier between two cells. Cells have some distance with a desmosome. Gap junctions allow molecules to pass. Tight junctions form solid walls. These types of connections are often found where one area needs to be protected from the contents of other areas.

by Twooars

To Be Continued..........

Copyright © 2015 by Rumana Reza (Aurny)