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UNIT 1: CELLS AND TISSUES GROUP 1 THE CELL Almost everything in the world is made up of smaller things.. A cell can make copies of everything it has inside it, then divide itself in two,

ENGLISH FOR BIOLOGY

Ho Chi Minh City University of Industry - HUI Institute of Biotechnology and Food Technology

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UNIT 1: CELLS AND TISSUES

GROUP 1

THE CELL

Almost everything in the world is made up of smaller things Houses are built out of individual bricks and pieces of wood Cars are built out of pieces of metal, plastic, and rubber Think about your cell What parts make up your cell?

The Cell Theory

One very important similarity among all living things is that they are made of cells, the smallest units of life

In 1838, two biologists, Schleiden and Schwann, studied many cells and made some conclusions From their observations they developed what is known as the Cell Theory Since then, this theory has been central to our understanding of biology This theory states that:

1 All life forms are made from one or more cells Some organisms, like bacteria or paramecium, are only one cell big These are called unicellular organisms (uni-=one) Other organisms are multicellular: that means

they are made up of more than one cell (multi-=more than one) For example, the human body consists of billions of cells!

2 Cells only arise from pre-existing cells A cell can make copies of everything it has inside it, then divide itself in two, making two new cells This process is called mitosis, or cell division In this way, organisms can

keep growing or replace damaged or old cells For example, the formation of new cells is what allows your body to grow, or what replaces your damaged skin when you fall and skin your knee, making you good as new!

3 The cell is the smallest form of life There is nothing smaller that is alive, and life requires what is inside

a cell For example, the molecules that make up the parts of the cell, such as sugars, fats and proteins are not alive The separate regions of the cell are not alive on their own Life can only be reduced down to the cellular level-thus cells are the smallest unit of life!

The Cell and Its Organelles

Even the cell is made up of smaller parts These parts are called organelles (little organs) They divide up all the work that the cell has to do In the human body, we have different organs to do different jobs that help us live: for example, our lunges help us breathe while our brain helps us think It’s the same in a cell: the different organelles have different jobs, and together they help the cell live

In a unicellular organism, one cell does all the jobs the being needs to survive, and the cell divides up these jobs among its organelles In multicellular organisms, many cells come together to make a living being Just like in unicellular organisms, the cells of a multicellular organism have organelles which divide up the cell’s work

1 Nucleus The nucleus is the control center of the cell It houses all

the genetic information, DNA in the form of chromatin, that tells the

cell what to do DNA is like the recipe for the cell: all the instructions

are there, and the organelles of the cell help to read it and build the

final products: proteins! When the cell reads its DNA recipe in its

nucleus, it converts these instructions to another form called

messenger RNA (mRNA), which is like translating from one language to another in a process called transcription.

2 Endoplasmic reticulum (ER) The ER is like a little maze of tubes that are hollow inside Add a few cake sprinkles right next to the ER These are ribosomes After mRNA is made in the nucleus, it is sent to the

ribosomes on the ER The ribosomes are responsible for reading the mRNA message and making the proper protein according to its instructions This process is called

translation As a protein is made, or “translated,” the ribosomes

pushes it into the maze of the ER A second type of ER, called the

smooth ER is where fats are formed It is called smooth ER

because it has no ribosomes on it

3 The Golgi body The proteins made by the ribosomes that are

inside the ER are sent to the Golgi for finishing touches and

distribution Here, the protein may be packaged or changed: it’s

like putting the paint on a car being made in a factory before it is sent out to the car dealer!

4 Mitochondria are often referred to as the powerhouses of the cell, for it is within them that energy is

released from organic molecules by the process of Cellular respiration This energy is needed to keep

the individual cells and the plant functioning as a

whole Carbon skeletons and fatty acid chains are also

rearranged within mitochondria, allowing for the

building of a wide variety of organic molecules

Mitochondria are numerous and tiny, typically

measuring from 1 to 3 or more micrometers in length and having a width of roughly one half micrometer; they are

barely visible with light microscopes They appear to be in constant motion in living cells and tend to accumulate in groups where energy is needed

5 To the lysosome, which is full of molecules that can break down cellular waste Lysosomes are the garbage

dumps of the cell—they break down waste and dispose of it properly Lysosomes are relatively large vesicles formed by the Golgi They contain hydrolytic enzymes that could destroy the cell

6 How does the cell stay together? They are housed in a double-layered coating called the plasma membrane that gives the cell its shape This membrane helps control what goes in and out of the cell, and

helps protect the cell from damaging things in the environment The cell membrane functions as a

semi-permeable barrier, allowing a very few molecules across it while fencing the majority of organically produced chemicals inside the cell Electron microscopic examinations of cell membranes have led to the development

of the lipid bilayer model (also referred to as the fluid-mosaic model) The most common molecule in the model is the phospholipid, which has a polar (hydrophilic) head and two nonpolar (hydrophobic) tails These

phospholipids are aligned tail to tail so the nonpolar areas form a hydrophobic region between the hydrophilic heads on the inner and outer surfaces of the membrane

7 Ribosomes are the sites of protein

synthesis They are not membrane-bound

and thus occur in both prokaryotes and

eukaryotes Eukaryotic ribosomes are

slightly larger than prokaryotic ones

Structurally the ribosome consists of a small

and larger subunit Biochemically the

ribosome consists of ribosomal RNA

(rRNA) and some 50 structural proteins

Often ribosomes cluster on the endoplasmic

reticulum, in which case they resemble a

series of factories adjoining a railroad line

UNIT 2: DNA STRUCTURE

GROUP 2:

INTRODUCTION

Our genes are made of deoxyribonucleic acid (DNA) This remarkable molecule contains all the information

necessary to make a cell, and DNA is able to pass on this information when a cell divides This chapter describes the structure and properties of DNA molecules, the way in which our DNA is packaged into chromosomes, and how the information stored within DNA is retrieved via the genetic code

THE STRUCTURE OF DNA

Deoxyribonucleic acid is an extremely long polymer made from units called deoxyribonucleotides, which are often simply called nucleotides Figure 4.1 shows one deoxyribonucleotide, deoxyadenosine triphosphate Note that deoxyribose, unlike ribose, has no OH group on its 2’carbon Four bases are found in DNA; they are the two purines adenine (A) and guanine (G) and the two pyrimidines cytosine (C) and thymine (T) (Fig 4.2) The combined base and sugar is known as a nucleoside to distinguish it from the phosphorylated form, which is called a nucleotide Four different nucleotides join to make DNA They are 2’-deoxyadenosine-5’-triphosphate (dATP), 2’-deoxyguanosine-5’-triphosphate (dGTP), 2’-deoxycytidine-5’-triphosphate (dCTP), and 2’-deoxythymidine-5’-triphosphate (dTTP)

DNA molecules are very large The single chromosome of the bacterium Escherichia coli is made up of two

strands of DNA that are hydrogen-bonded together to form a single circular molecule comprising 9 million nucleotides Humans have 46 DNA molecules in each cell, each forming one chromosome We inherit 23

chromosomes from each parent Each set of 23 chromosomes encodes a complete copy of our genome and

is made up of 6 × 109 nucleotides (or 3 × 109 base pairs—see below) We do not yet know the exact number

of genes that encode messenger RNA and therefore proteins in the human genome The current estimate is in the range of 30,000 Table 4.1 compares the number of predicted messenger RNA genes in the genomes of different organisms In each organism, there are also approximately 100 genes that code for ribosomal RNAs and transfer RNAs

Figure 4.3 illustrates the structure of the DNA chain As nucleotides are added to the chain by the enzyme

DNA polymerase, they lose two phosphate groups The last (the α phosphate) remains and forms a

phosphodiester link between successive deoxyribose residues The bond forms between the hydroxyl group

on the 3’carbon of the deoxyribose of one nucleotide and the α-phosphate group attached to the 5’ carbon of

the next nucleotide Adjacent nucleotides are hence joined by a 3’–5’phosphodiester link The linkage gives rise to the sugar–phosphate backbone of a DNA molecule A DNA chain has polarity because its two ends are different In the first nucleotide in the chain, the 5’ carbon of the deoxyribose is phosphorylated but otherwise

free This is called the 5’ end of the DNA chain At the other end is a deoxyribose with a free hydroxyl group

on its 3’carbon This is called the 3’end

The DNA Molecule Is a Double Helix

In 1953 Rosalind Franklin used X-ray diffraction to show that DNA was a helical polymer James Watson and Francis Crick demonstrated, by building three dimensional models, that the molecule is a double helix (Fig 4.4) Two hydrophilic sugar–phosphate backbones lie on the outside of the molecule, and the purines and pyrimidines lie on the inside of the molecule There is just enough space for one purine and one pyrimidine in the center of the double helix The Watson–Crick model showed that the purine guanine (G) would fit nicely with the pyrimidine cytosine (C), forming three hydrogen bonds The purine adenine (A) would fit nicely with the pyrimidine thymine (T), forming two hydrogen bonds Thus A always pairs with T, and G always pairs with C The three hydrogen bonds formed between G and C produce a relatively strong base pair Because only two hydrogen bonds are formed between A and T, this weaker base pair is more easily broken The difference in strengths between a G–C and an A–T base pair is important in the initiation and termination of RNA synthesis The two chains of DNA are said to be antiparallel because they lie in the opposite orientation with respect to one another, with the 3’-hydroxyl terminus of one strand opposite the 5’-phosphate terminus of the second strand The sugar–phosphate backbones do not completely conceal the bases inside There are two grooves along the surface of the DNA molecule One is wide and deep—the major groove—and the other is narrow and shallow—the minor groove (Fig 4.4) Proteins can use the grooves to gain access to the bases

The Two DNA Chains Are Complementary

A consequence of the base pairs formed between the two strands of DNA is that if the base sequence of one

strand is known, then that of its partner can be inferred A G in one strand will always be paired with a C in the other Similarly an A will always pair with a T The two strands are therefore said to be complementary Different Forms of DNA

The original Watson–Crick model of DNA is now called the B-form In this form, the two strands of DNA form a right-handed helix If viewed from either end, it turns in a clockwise direction B-DNA is the predominant form in which DNA is found Our genome, however, also contains several variations of the B-form double helix One of these, Z-DNA, so-called because its backbone has a zig-zag shape, forms a left-handed helix and occurs when the DNA sequence is made of alternating purines and pyrimidines Thus the structure adopted by DNA is a function of its base sequence

GROUP 3: DNA AS THE GENETIC MATERIAL

Deoxyribonucleic acid carries the genetic information encoded in the sequence of the four bases—adenine, guanine, cytosine, and thymine The information in DNA is transferred to its daughter molecules through replication (the duplication of DNA molecules) and subsequent cell division DNA directs the synthesis of proteins through the intermediary molecule RNA The DNA code is transferred to RNA by a process known as transcription The RNA code is then translated into a sequence of amino acids during protein synthesis This is the central dogma of molecular biology: DNA makes RNA makes protein

Retroviruses such as human immunodeficiency virus, the cause of AIDS, are an exception to this rule As their name suggests, they reverse the normal order of data transfer Inside the virus coat is a molecule of RNA plus

an enzyme that can make DNA from an RNA template by the process known as reverse transcription.

PACKAGING OF DNA MOLECULES INTO CHROMOSOMES

Eukaryotic Chromosomes and Chromatin Structure

A human cell contains 46 chromosomes (23 pairs), each of which is a single DNA molecule bundled up with

various proteins On average, each human chromosome contains about 1.3 × 108 base pairs (bp) of DNA If the DNA in a human chromosome were stretched as far as it would go without breaking it would be about 5

cm long, so the 46 chromosomes in all represent about 2 m of DNA The nucleus in which this DNA must be

contained has a diameter of only about 10μm, so large amounts of DNA must be packaged into a small space

This represents a formidable problem that is dealt with by binding the DNA to proteins to form chromatin

As shown in Figure 4.5, the DNA double helix is packaged at both small and larger scales In the first stage, shown on the right of the figure, the DNA double helix with a diameter of 2 nm is bound to proteins known

as histones Histones are positively charged because they contain high amounts of the amino acids arginine

and lysine and bind tightly to the negatively charged phosphates on DNA A 146 bp length of DNA is wound around a protein complex composed of two molecules each of four different histones—H2A, H2B, H3, and

H4—to form a nucleosome Because each nucleosome is separated from its neighbor by about 50 bp of linker

DNA, this unfolded chromatin state looks like beads on a string when viewed in an electron microscope Nucleosomes undergo further packaging A fifth type of histone, H1, binds to the linker DNA and pulls the nucleosomes together helping to further coil the DNA into chromatin fibers 30 nm in diameter, which are

referred to as 30-nm solenoids The fibers then form loops with the help of a class of proteins known as

nonhistones, and this further condenses the DNA (panels on left-hand side of Fig 4.5) into a higher order set of

coils in a process called supercoiling.

In a normal interphase cell about 10% of the chromatin is highly compacted and visible under the light

microscope This form of chromatin is called heterochromatin and is the portion of the genome where

no RNA synthesis is occurring The remaining interphase chromatin is less compacted and is known as

Chromatin is in its most compacted form when the cell is preparing for mitosis, as shown at the top left of Figure 4.5 The chromatin folds and condenses further to form the 1400- nm-wide chromosomes we see under the light microscope Because the cell is to divide, the DNA has been replicated, so that each chromosome

is now formed by two chromatids, each one a DNA double helix This means the progeny cell, produced by

division of the progenitor cell, will receive a full set of 46 chromosomes Figure 4.6 is a photograph of human

chromosomes as they appear at cell division

Prokaryotic Chromosomes

The chromosome of the bacterium E coli is a single circular DNA molecule of about 4.5 ×106 base pairs

It has a circumference of 1 mm, yet must fit into the 1-μm cell, so like eukaryotic chromosomes it is coiled,

supercoiled, and packaged with basic proteins that are similar to eukaryotic histones However, an ordered nucleosome structure similar to the “beads on a string” seen in eukaryotic cells is not observed in prokaryotes Prokaryotes do not have nuclear envelopes so the condensed chromosome together with its associated proteins

lies free in the cytoplasm, forming a mass that is called the nucleoid to emphasize its functional equivalence to

the eukaryotic nucleus

Plasmids

Plasmids are small circular minichromosomes found in bacteria and some eukaryotes They are several

thousand base pairs long and are probably tightly coiled and supercoiled inside the cell Plasmids often code for proteins that confer resistance to a particular antibiotic In Chapter 7 we describe how plasmids are used by scientists and genetic engineers to artificially introduce foreign DNA molecules into bacterial cells

Viruses

Viruses rely on the host cell to make more viruses Once viruses have entered cells, the cells’ machinery is used to copy the viral genome Depending on the virus type, the genome may be single- or double-stranded DNA, or even RNA A viral genome is packaged within a protective protein coat Viruses that infect bacteria

are called bacteriophages One of these, called lambda, has a fixed-size DNA molecule of 4.5 × 104 base pairs In contrast, the bacteriophage M13 can change its chromosome size, its protein coat expanding in parallel to accommodate the chromosome This makes M13 useful in genetic engineering

UNIT 3: VIRUSES

GROUP 4:

The Discovery of Viruses

The border between the living and the nonliving is very clear to a biologist Living organisms are cellular and able to grow and reproduce independently, guided by information encoded within DNA the simplest

creature living on earth today that satisfy these criteria are bacteria Even simpler than bacteria are viruses

As you will learn in this section, viruses are so simple that they do not satisfy the criteria for “living.” Viruses

possess only a portion of the properties of organisms Viruses are literally parasitic” chemicals, segments of DNA or RNA wrapped in a protein coat They cannot reproduce on their own, and for this reason they are not considered alive by biologists They can, however, reproduce within cells, often with disastrous results to the host organism Earlier theories that viruses represent a kind of halfway point between life and nonlife have largely been abandoned Instead, viruses are now viewed as detached fragments of the genomes of organisms

due to the high degree of similarity found among some viral and eukaryotic genes Viruses vary greatly in

appearance and size The smallest are only about 17 nanometers in diameter, and the largest are up to 1000 nanometers (1 micrometer) in their greatest dimension (figure 33.2) The largest viruses are barely visible with

a light microscope, but viral morphology is best revealed using the electron microscope Viruses are so small

that they are comparable to molecules in size; a hydrogen atom is about 0.1 nanometer in diameter, and a large protein molecule is several hundred nanometers in its greatest dimension

Biologists first began to suspect the existence of viruses near the end of the nineteenth century European scientists attempting to isolate the infectious agent responsible for hoof-and-mouth disease in cattle concluded that it was smaller than a bacterium Investigating the agent further, the scientists found that it could not multiply in solution—it could only reproduce itself within living host cells that it infected The infecting agents were called viruses The true nature of viruses was discovered in 1933, when the biologist Wendell Stanley

prepared an extract of a plant virus called tobacco mosaic virus (TMV) and attempted to purify it To his great

surprise, the purified TMV preparation precipitated (that is, separated from solution) in the form of crystals This was surprising because precipitation is something that only chemicals do—the TMV virus was acting like

a chemical off the shelf rather than an organism Stanley concluded that TMV is best regarded as just that—chemical matter rather than a living organism

Within a few years, scientists disassembled the TMV virus and found that Stanley was right TMV was not cellular but rather chemical Each particle of TMV virus is in fact a mixture of two chemicals: RNA and protein The TMV virus has the structure of a Twinkie, a tube made of an RNA core surrounded by a coat of protein Later workers were able to separate the RNA from the protein and purify and store each chemical Then, when they reassembled the two components, the reconstructed TMV particles were fully able to infect

healthy tobacco plants and so clearly were the virus itself, not merely chemicals derived from it Further

experiments carried out on other viruses yielded similar results

Nearly all viruses form a protein sheath, or capsid, around their nucleic acid core The capsid is composed

of one to a few different protein molecules repeated many times (figure 33.3) In some viruses, specialized

enzymes are stored within the capsid Many animal viruses form an envelope around the capsid rich in proteins, lipids, and glycoprotein molecules While some of the material of the envelope is derived from the

host cell’s membrane, the envelope does contain proteins derived from viral genes as well

Viruses occur in virtually every kind of organism that has been investigated for their presence However, each type of virus can replicate in only a very limited number of cell types The suitable cells for a particular virus

are collectively referred to as its host range The size of the host range reflects the coevolved histories of the

virus and its potential hosts A recently discovered herpes virus turned lethal when it expanded its host range from the African elephant to the Indian elephant, a situation made possible through cross-species contacts between elephants in zoos Some viruses wreak havoc on the cells they infect; many others produce no disease

or other outward sign of their infection Still other viruses remain dormant for years until a specific signal triggers their expression A given organism often has more than one kind of virus This suggests that there may be many more kinds of viruses than there are kinds of organisms—perhaps millions of them Only a few thousand viruses have been described at this point

Viral Replication

An infecting virus can be thought of as a set of instructions, not unlike a computer program A computer’s operation is directed by the instructions in its operating program, just as a cell is directed by DNA-encoded instructions A new program can be introduced into the computer that will cause the computer to cease what

it is doing and devote all of its energies to another activity, such as making copies of the introduced program The new program is not itself a computer and cannot make copies of itself when it is outside the computer, lying on the desk The introduced program, like a virus, is simply a set of instructions Viruses can reproduce only when they enter cells and utilize the cellular machinery of their hosts Viruses code their genes on a single

type of nucleic acid, either DNA or RNA, but viruses lack ribosomes and the enzymes necessary for protein

synthesis Viruses are able to reproduce because their genes are translated into proteins by the cell’s genetic machinery These proteins lead to the production of more viruses

Viral Shape

Most viruses have an overall structure that is either helical or isometric Helical viruses, such as the tobacco mosaic virus, have a rodlike or threadlike appearance Isometric viruses have a roughly spherical shape whose geometry is revealed only under the highest magnification.

The only structural pattern found so far among isometric viruses is the icosahedrons, a structure with 20 equilateral triangular facets, like the adenovirus shown in figure 33.2 Most viruses are icosahedral in basic structure The icosahedron is the basic design of the geodesic dome It is the most efficient symmetrical arrangement that linear subunits can take to form a shell with maximum internal capacity

UNIT 4: STEM CELL

GROUP 6:

Since the isolation of embryonic stem cells in 1998, labs all over the world have been exploring the possibility

of using stem cells to restore damaged or lost tissue Exciting results are now starting to come in What is a stem cell? At the dawn of a human life, a sperm fertilizes an egg to create a single cell destined to become

a child As development commences, that cell begins to divide, producing a small ball of a few dozen cells

At this very early point, each of these cells is identical We call these cells embryonic stem cells Each one

of them is capable by itself of developing into a healthy individual In cattle breeding, for example, these cells are frequently separated by the breeder and used to produce multiple clones of valuable offspring The exciting promise of these embryonic stem cells is that, because they can develop into any tissue, they may give us the ability to restore damaged heart or spine tissue (figure 19.24) Experiments have already been tried successfully in mice Heart muscle cells have been grown from mouse embryonic stem cells and successfully integrated with the heart tissue of a living mouse This suggests that the damaged heart muscle of heart attack

victims might be reparable with stem cells, and that injured spinal cords might be repairable These very

promising experiments are being pursued aggressively They are, however, quite controversial, as embryonic stem cells are typically isolated from tissue of discarded or aborted embryos, raising serious ethical issues

Tissue-Specific Stem Cells

New results promise a neat way around the ethical maze presented by stem cells derived from embryos Go

back for a moment to what we were saying about how a human child develops What happens next to the

embryonic stem cells? They start to take different developmental paths Some become destined to form nerve

tissue and, after this decision is taken, cannot ever produce any other kind of cell They are then called nerve stem cells Others become specialized to produce blood, still others muscle Each major tissue is represented

by its own kind of specific stem cell Now here’s the key point: as development proceeds, these

tissue-specific stem cells persist Even in adults So why not use these adult cells, rather than embryonic stem cells?

Transplanted Tissue-Specific Stem Cells Cure

MS in Mice

In path finding 1999 laboratory experiments by Dr Evan Snyder of Harvard Medical School, tissue-specific stem cells were able to restore lost brain tissue He and his coworkers injected neural stem cells (immediate descendants of embryonic stem cells able to become any kind of neural cell) into the brains of newborn mice

with a disease resembling multiple sclerosis (MS) These mice lacked the cells that maintain the layers of