cell biology biochemistry, Lecture notes of Zoology

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TAHIR HABIB

ZOOLOGY (BIOCHEM AND CELL BIO) FOR

LECTURER ,M.sc ,B.sc,Css

CONTENTS ( BIOCHEM & CELL BIO)

• WHAT IS GLYCOLYSIS? Sno. TOPIC PAGE NO.
• KREBS CYCLE (OR CITRIC ACID CYCLE)
• ELECTRON TRANSPORT CHAIN
• UREA CYCLE
• SYNTHESIS OF AMINO ACIDS
• FATTY ACID AND LIPID SYNTHESIS
• DNA – STRUCTURE , REPLICATION, TRANSCRIPTION 17 -
• TRANSLATION( PROTIEN SYNTHESIS)
• CELL BIOLOGY , CELL
• CELL ORGANELLES
• MITOSIS + MEIOSIS (SIGNIFICANCE)
• BIOLOGICAL MOLECULES
• CARBOHYDRATES
• PROTEINS
• LIPIDS
• Short ( Brief Answers)

Glycolysis

Glycolysis is the metabolic process that serves as the foundation for both aerobic and anaerobic cellular respiration. In glycolysis, glucose is converted into pyruvate. Glucose is a six- memebered ring molecule found in the blood and is usually a result of the breakdown of carbohydrates into sugars. It enters cells through specific transporter proteins that move it from outside the cell into the cell’s cytosol. All of the glycolytic enzymes are found in the cytosol.

Glycolysis literally means "splitting sugars" and is the process of releasing energy within sugars. In glycolysis, glucose (a six carbon sugar) is split into two molecules of the three- carbon sugar pyruvate. This multi-step process yields two molecules of ATP (free energy containing molecule), two molecules of pyruvate, and two "high energy" electron carrying molecules of NADH. Glycolysis can occur with or without oxygen. In the presence of oxygen, glycolysis is the first stage of cellular respiration. In the abscence of oxygen, glycolysis allows cells to make small amounts of ATP through the process of fermentation. Glycolysis takes place in the cytosol of the cell's cytoplasm. However, the next stage of cellular respiration known as the citric acid cycle, occurs in the matrix of cell mitochondria.

The overall reaction of glycolysis which occurs in the cytoplasm is represented simply as:

C 6 H 12 O 6 + 2 NAD+^ + 2 ADP + 2 P —–> 2 pyruvic acid, (CH 3 (C=O)COOH + 2 ATP + 2 NADH + 2 H+

Steps 1 and 3 = – 2ATP Steps 7 and 10 = + 4 ATP Net ―visible‖ ATP produced = 2.

Immediately upon finishing glycolysis, the cell must continue respiration in either an aerobic or anaerobic direction; this choice is made based on the circumstances of the particular cell. A cell that can perform aerobic respiration and which finds itself in the presence of oxygen will continue on to the aerobic citric acid cycle in the mitochondria. If a cell able to perform aerobic respiration is in a situation where there is no oxygen (such as muscles under extreme exertion), it will move into a type of anaerobic respiration called homolactic fermentation. Some cells such as yeast are unable to carry out aerobic respiration and will automatically move into a type of anaerobic respiration called alcoholic fermentation.

(1) GLYCOLYSIS ( Steps)

Glycolysis is the first and common step in both aerobic and anaerobic respiration. It consists of a complex series of enzymatically catalyzed reactions in which a 6 carbon molecule “Glucose” breaks down into 3 carbon “Pyruvic acid”. These reactions occur in Cytoplasm and doesn’t require oxygen. Following are the different steps of Glycolysis.

(I) PHOSPHORYLATION Phosphorylation is the addition of phosphate groups to the sugar molecules. Glucose is

phosphorylated by a molecule of ATP to form an activated molecule, the glucose 6 phosphate. ATP is converted to ADP.

(II) ISOMERIZATION Glucose - 6 - phosphate is converted to fructose - 6 - phosphate, an isomer of it by an enzyme.

(III) SECOND PHOSPHORYLATION Another molecules of ATP is invested which transfers its phosphate group to carbon no.1 of fructose – 6 - phosphate, forming fructose 1,6-bisphosphate and ADP.

(IV) CLEAVAGE The 6-carbon, fructose 1,6 bisphosphate molecule is break down into 2; three carbon molecules, 3-phosphoglyceraldehyde PGAL and dihydroxyacetone phosphate (DHAP). These two sugar molecules are isomers and are interconvertible. This is the reaction from which glycolysis derives its name. DHAP is converted to its isomer PGAL and then 2 PGAL will be converted to 2 pyruvic acid molecules. Since at this stage 2 ATPs are used, therefore this phase is known as Energy investment phase. In the subsequent reactions, energy is produced therefore this half is also known as Energy yielding phase

(V) DEHYDROGENATION (OXIDATION) In the next step, PGAL is acted upon by an enzyme dehydrogenase along with a co- enzyme nicotine amide adenine dinucleotide (NAD+), which convert PGAL into phosphoglyceric acid PGA or phosphoglycerate by the loss of two hydrogen atoms (2e- + 2H+). These H atoms are captured by NAD+. This is a redox reaction in which PGAL oxidized by removal of electrons and NAD is reduced by the gaining of electrons. Now phosphoglyceric acid PGA picks up phosphate group (Pi) present in cytoplasm and becomes 1,3-bisphosphoglyceric acid (DPGA)

(VI) PHOSPHORYL TRANSFER 1,3-bisphosphoglyceric acid loses its phosphate group to ADP forming ATP and 3- phosphoglyceric acid.

(VII) ISOMERIZATION The PO4 group of PGA, attaches with carbon no,3 changes its position to carbon no. forming an isomer 1-phosphoglyceric acid.

(VIII) DEHYDRATION A water molecule is removed from the substrate and forming phosphoenal pyruvate (PEP)

(IX) PHOSPHORYL TRANSFER ADP removes the high energy PO4 from PEP producing ATP and Pyruvic acid. OVERALL REACTION of glycolysis can be summarized as Glucose + 2ADP + 2NAD+ - > 2 Pyruvic acid + 2ATP + 2NADH+ H+ + 2H2O

ENERGY YIELD

Since when PGAL is produced, the cycle is counted twice because DHAP also converts into PGAL and enter the same cycle. 4ATP molecules are produced at Substrate level phosphorylation because PO4 groups are transferred directly to ADP from another molecule. 2 ATP are used in the first phase. Thus there is a net gain of 2 ATPs. 2 NADH+

H+ are produced and each gives 2 ATPs (a total of 6 ATPs). Therefore net production of ATP during glycolysis is 8 ATPs

FATE OF PYRUVIC ACID

There are 3 major pathways by which it is further processed under anaerobic conditions, pyruvic acid either forms, ethyl alcohol or lactic acid or produces CO2 and H2O from kreb’s cycle under aerobic conditions.

FERMENTA TION

Fermentatio n the alternative term for Anaerobic respiration was used by W.Pasteur and defined as respiration in absence of oxygen (air). The production of ethyl alcohol from glucose is alcoholic fermentation and that of lactic acid is lactic acid fermentation

Krebs cycle (or citric acid cycle)

The Krebs cycle (or citric acid cycle) is a part of cellular respiration. Named after Hans Krebs, it is a series of chemical reactions used by all aerobic organisms to generate energy. Its importance to many biochemical pathways suggests that it was one of the earliest parts of cellular metabolism to evolve.

The Krebs cycle comes after the link reaction and provides the hydrogen and electrons needed for the electron transport chain. It takes place inside mitochondria.

The oxidation of pyruvic acid into CO 2 and water is called Krebs cycle. This cycle is also citric acid cycle because the cycle begins with the formation of citric acid. Citric acid is a carboxylic acid containing 3 COOH groups. Hence this cycle is also called as tri carboxylic acid cycle or TCA cycle. This cycle was first described by Kreb's in 1936. This cycle occurs only in the presence of oxygen. Hence it is an aerobic process. It takes place in the mitochondria.

KREB’S CYCLE (DETaiLD STEpS)

FORMATION OF ACETYL-COA

Before entering the Kreb’s cycle, each molecule of pyruvic acid undergoes oxidative decarboxylation. During this process one of the three carbons of pyruvic acid molecule is removed to form CO2 by enzymatic reactions. Simultaneously pyruvic acid is oxidized and a pair of energy rich Hydrogen atoms are passed on to a H acceptor NAD+ to form NADH+H+. The remaining 2-carbon component is called acetyle which combines with coenzyme A to form an activated two carbon compound called acetyle CoA. ―Acetyle CoA connects Kreb’s cycle with glycolysis.‖ For each molecule of glucose that enters glycoilysis, two molecules of acetyle CoA produced, which enter in a cyclic series of enzymatically catalyzed reactions known as Kreb’s Cycle, which occurs in Mitochondria. Pyruvic acid (3C) + CoA + NAD+ -> Acetyle CoA + CO2 + NADH+H+

SERIES OF REACTIONS IN KREB’S CYCLE

Sir Hans Kreb was working over these cyclical series of reactions therefore the cycle was given the name as Kreb’s cycle. The first molecule formed during the cycle is citric acid, so it is also called as ―Citric Acid cycle.‖ This cycle is a multi step process and the steps are given below:

1. FORMATION OF CITRIC ACID In this first step of the Kreb’s cycle, bond between acetyl and CoA is broken by the addition of water molecule. The acetyl (2C) reacts with 4 carbon compound (oxalo acetic) acid to form 6- carbon compound, citric acid, and the CoA is set free. This citric acid possess 3 carboxyl groups, therefore the cycle is also recommended as Tricarboxylic Acid Cycle (TCA cycle).

2. ISOMERIZATION

A molecule of water is removed and another added back so that cirtic acid is isomerized to isocitric acid through an intermediate, Cis-aconitic acid.

3.FIRST OXIDATIVE DECARBOXYLATION First time the sugar molecules are oxidized, therefore it is also called first oxidation of the cycle. Isocitric acid is oxidized yielding a pair of electrons (2H+) that reduces a molecule of NAD+ to NADH+H+. The reduced sugar molecule is decarboxylated with the removal of CO2. It now converts into a 5 carbon compound α-Ketoglutaric acid (αKG).

4. SECOND OXIDATIVE DECARBOXYLATION αKG is oxidatively decarboxylated. A CO2 molecule is lost. The remaining 4-C compound is oxidized by transfer of a pair of electrons (2H+) reducing NAD+ to NADH+H+. This 4-C compound accepts CoA forming succinyl CoA. 5. SUBSTRATE LEVEL PHOSPHORYLATION Bond between succinyl and CoA is broken. CoA is replaced by PO4 group, which is then transferred to Guanosine diphosphate (GDP) to form Guanosine Triphosphate (GTP). GTP then transfers its phosphate group to ADP, forming ATP and with addition of 1 water molecule, succinic acid is formed. 6. THIRD OXIDATION With loss of two electrons (2H+)succinic acid is oxidized to fumaric acid and FAD+ is reduced to FADH2. 7. HYDRATION One water molecule is added to fumaric acid to convert it to Malic acid. 8. FOURTH OXIDATION AND REGENERATION OF OXALO-ACETIC ACID Oxidation of malic acid leads to the production of 1 more NADH+H+ and oxaloacetic acid is regenerated.

ENERGY YIELD

Glucose molecule breaks down into 2 pyruvic acid molecules and each will enter the Kreb’s cycle. For each pyruvic acid molecule, 3CO2 molecules are produced, four NADH+H+ are produced and 1 FADH2. Pyruvic Acid + 3H2O + 4NAD+ + FAD+ -> 3CO2 + 4NADH+H+ + 1FADH Four calculation of energy (ATPs) we will multiply the products with 2 as 2 acetyle CoA enters the Kreb’s cycle. Pyruvic Acid to Acetyl CoA…………..1NADH2 -> 3ATP x 2 = 6 ATP Kreb’s Cycle………………………………..3NADH+H+ -> 9ATP x 2 = 18 ATP

………………………………………………1FADH2 -> 2ATP x 2 = 4 ATP ………………………………………….Substrate Level Phosphorylation -> 1ATP x 2 = 2ATP Total………………………………. = 30 ATP

OVERALL ENERGY YIELD OF AEROBIC RESPIRATION

Glycolysis…………………………8ATP Pyruvic Acid to Acetyl CoA…………..6ATP Kreb’s Cycle……………………….24 ATP Total……………………………..38 ATP But actually 2 ATPs are utilizing in transporting cytoplasmic NADH+H+ to Mitochondria, which are produced during Glycolysis, so overall energy yield is only 36 ATPs.

Written by : Tahir Habib

electron transport chain

The electron transport chain is the final and most important step of cellular respiration. While Glycolysis and the Citric Acid Cycle make the necessary precursors, the electron transport chain is where a majority of the ATP is created.

The Electron Transport Chain makes energy

The simple facts you should know about the electron transport chain are:

 34 ATP are made from the products of 1 molecule of glucose.

 The process is a stepwise movement of electrons from high energy to low energy that makes the proton gradient

 The proton gradient powers ATP production NOT the flow of electrons

 This electron transport chain only occurs when oxygen is available.

This is shown by the diagram below. Complex I-IV each play a role in transporting electrons( hence the name electron transport chain), and establishing the proton gradient. The exact mechanism of each Complex can be overwhelming so I will save that for a future post.

The only thing you should be concerned with is as electrons pass from complex to complex (blue arrows) they power the movement of hydrogen atoms (red arrows) into the intermembrane space. The number of hydrogen atoms (also called proton gradient) will build up and flow back to the matrix simultaneously powering the production of ATP. We learned this principle from general chemistry. The movement of molecules from high to low concentrations requires no energy. This free source of momentum can be used as energy. In the case of the electron transport chain the momentum is used to make ATP.

But how do these protons and electrons make it inside of the mitochondria?

Both the Citric Acid Cycle and Electron Transport Chain take place in the mitochondria. NADH just floats over to the inner-membrane and can enter the ETC at complex I, while FADH2 enters the the transport chain at complex II. NADH and FADH2 are known as electron carriers. This means they are capable of donating electrons to the transport chain.

Oxygen is the final electron acceptor

While the electron transport chain’s main function is to produce ATP, another important byproduct is water. If you follow the path of electrons (blue) and protons(pink) you might notice that they follow the same basic pathway until the point where ATP is produced. At the end of the chain the electrons are taken up by oxygen molecules to make water. This is why oxygen is known as the final electron acceptor. To put things in perspective think about how we breathe in oxygen with our lungs, transport it with red blood cells in our arteries to cells, and oxygen is ultimately used inside the mitochondria of every cell to accept electrons at the end of the

ELECTRON TRANSPORT CHAIN

Summary of the Electron Transport Chain

The electron transport chain is the stepwise process of cellular respiration that is responsible for producing:

 Water (with the help of oxygen we breathe)  up to 34 ATP (thanks to the proton gradient)  NAD and FAD (which are recycled to be used again in the Citric acid cycle and glycolysis)  This process happens in the mitochondria of Eukaryotes and cell membrane of Prokaryotes The last key point to remember is this only happens in aerobic conditions( oxygen present). If there is a shortage of oxygen cellular respiration will take an alternative pathway at the end of glycolysis resulting in the the production of lactic acid and ATP.

UREA CYCLE

In humans and mammals, almost 80% of the nitrogen excreted is in the form of urea, which is produced through a series of reactions occurring in the cytosol and mitochondrial matrix of liver cells. These reactions are collectively called the urea cycle or the Krebs-Henseleit cycle.

Ammonia is a toxic product of nitrogen metabolism which should be removed from our body. The urea cycle or ornithine cycle converts excess ammonia into urea in the mitochondria of liver cells. The urea forms, then enters the blood stream, is filtered by the kidneys and is ultimately excreted in the urine.

The overall reaction for urea formation from ammonia is as follows:

2 Ammonia + CO2 + 3ATP ---> urea + water + 3 ADP

Steps in the Urea Cycle

The urea cycle is a series of five reactions catalyzed by several key enzymes. The first two

steps in the cycle take place in the mitochondrial matrix and the rest of the steps take place in the cytosol. Thus the urea cycle spans two cellular compartments of the liver cell.

 In the first step of the Krebs-Henseleit cycle, ammonia produced in the mitochondria

is converted to carbamoyl phosphate by an enzyme called carbamoyl phosphate synthetase I. The reaction can be given as follows:

NH3 + CO2 + 2ATP → carbamoyl phosphate + 2ADP + Pi

 The second step involves the transfer of a carbamoyl group from carbamoyl

phosphate to ornithine to form citrulline. This step is catalyzed by the enzyme ornithine transcarbamoylase (OTC). The reaction is given as follows:

Carbamoyl phosphate + ornithine → citrulline + Pi

Citrulline thus formed is released into the cytosol for use in the rest of the steps of the cycle.

 The third step is catalyzed by an enzyme called argininosuccinate synthetase, which

uses citrulline and ATP to form a citrullyl-AMP intermediate, which reacts with an amino group from aspartate to produce argininosuccinate. This reaction can be given as follows:

Citrulline + ATP + aspartate → argininosuccinate + AMP + PPi

 The fourth step involves the cleavage of argininosuccinate to form fumarate and

arginine. Argininosuccinate lyase is the enzyme catalyzing this reaction, which can be represented as follows:

Argininosuccinate → arginine + fumarate

 In the fifth and last step of the urea cycle, arginine is hydrolyzed to form urea and

ornithine. This is catalyzed by arginase and can be given as follows:

Arginine → urea + ornithine

The overall reaction can be given as follows:

2NH3 + CO2 + 3ATP g urea + 2ADP + AMP + PPi + 2Pi

Significance of the Urea Cycle

The main purpose of the urea cycle is to eliminate toxic ammonia from the body. About 10 to 20 g of ammonia is removed from the body of a healthy adult every day. A dysfunctional urea cycle would mean excess amount of ammonia in the body, which can lead to hyperammonemia and related diseases. The deficiency of one or more of the key enzymes catalyzing various reactions in the urea cycle can cause disorders related to the cycle. Defects in the urea cycle can cause vomiting, coma and convulsions in new born babies. This is often misdiagnosed as septicemia and treated with antibiotics in vain. Even 1mm of excess ammonia can cause severe and irreversible damages.

Diagnosis of Urea Cycle Defects

A blood aminogram is routinely used in the diagnosis of urea cycle disorders. The concentration of the nitrogen-carrying amino acids, glutamine and alanine, in plasma is elevated in the case of OTC deficiency. In babies, elevated levels of orotic acid in the urine may be an indicator of OTC deficiency. Increased levels of blood citrulline and argininosuccinate are also seen in cases of citrullinemia.

In older children, these disorders may present in the form of growth failure, psychomotor retardation and behavioral abnormalities. Hence, blood ammonia and urinary orotic acid monitoring and quantitation are crucial in patients with unexplained neurological symptoms.

SYNTHESIS OF AMINO ACIDS

Synthesis and/or collection of amino acids is critical for cell survival. They not only serve as the building blocks for proteins but also as starting points for the synthesis of many important cellular molecules including vitamins and nucleotides.

In most cases bacteria would rather use amino acids in their environment than make them from scratch. It takes a considerable amount of energy to make the enzymes for the pathway as well as the energy required to drive some of the reactions of amino acid biosynthesis. The genes that code for amino acid synthesis enzymes and the enzymes themselves are under tight control and are only turned on when they are needed.

The amino acids synthesis pathways can be grouped into several logical units. These units reflect either common mechanisms or the use of common enzymes that synthesize more than one amino acid. These categories are: simple reactions, branch chain amino acids, aromatic amino acids, threonine/lysine, serine/glycine, and unique pathways. The aromatic amino acids, threonine/lysine and serine/glycine pathways have a common beginning and then diverge to form the amino acid of interest.

Notice that each pathway begins with a central metabolite or something derived from "central metabolism". Using common compounds instead of synthesizing them from scratch saves energy and conserves genes since fewer enzymes are needed to code for the pathways.

Simple Reactions

glutamine, glutamate, aspartate, asparagine and alanine

In most cases these amino acids can be synthesize by one step reactions from central

metabolites. They are simple in structure and their synthesis is also straight forward.

Glutamate can by synthesized

by the addition of ammonia

to -ketoglutarate.

Figure 1 - The synthesis of glutamate.

Glutamine is made by the addition of another ammonia molecule to glutamate.

Figure 2 - Synthesis of glutamine

The rest of the simple reactions involve transfer of the amino group (transamination)

from glutamate or glutamine to a central metabolite to make the required amino acid.

Aspartate is synthesize by the transfer of a ammonia group from glutamate to

oxaloacetate.

Figure 3 - The synthesis of aspartate.

Asparagine is made either by transamination from glutamine or by adding ammonia

directly to aspartate.

or

Figure 4 - Formation of asparagine. Notice the use of AMP instead of ADP in this

reaction. This releases more energy which is needed to drive the synthesis.

Alanine synthesisis is a bit of a mystery. Several reactions have been identified, but it

has been impossible to generate an alanine auxotroph and therefore positively identify

a required pathway. There are several pathways and the most likely is formation of

alanine by transamination from glutamate onto pyruvate. A transamination using

valine instead of glutamate is also possible.

Figure 5 - Synthesis of alanine

Fatty Acid and Lipid Synthesis

The structure of lipids is described in the cell membrane page in the bacterial

structure chapter. Lipid synthesis consists of two phases

1. Fatty acid synthesis where the long alkyl chains are assembled using acetyl-CoA as substrate.
2. Assembly of the lipid by combining, sn - glycerol- 3 - phosphate, the finished fatty acid and the polar head group.

Fatty acid synthesis

Synthesis of fatty acids takes place in the cytoplasm and involves initiation of

synthesis by the formation of acetoacetyl-ACP and then an elongation cycle where 2

carbon units are successively added to the growing chain.

ACP

Acyl carrier protein (ACP) serves as a chaperone for the synthesis of fatty acids. The

growing fatty acid chain is covalently bound to ACP during the entire synthesis of the

fatty acid and only leaves the protein when it is attached to the glycerol backbone of

the forming lipid. ACP is one of the most abundant proteins in the bacterial cell

(60,000 molecules per E. coli cell) which makes sense given the amount of lipid that

must be synthesized to make an entire cell membrane. The formation of acetoacetyl-

ACP can be catalyzed by a number of enzymes, but in all cases the starting substrate

is acetyl-CoA.

Figure 1 - Synthesis of acetoacetyl-ACP from CoA.

Once formed, acetoacetyl-ACP enters the elongation cycle for fatty acid synthesis.

This cycle is the reverse of the -oxidation of fatty acids discussed earlier. The first

step in the elongation cycle is condensation of malonyl-CoA with a growing

acetoacetyl-ACP chain. This adds two carbons to the chain. The next three reactions

use 2 NADPH to reduce the -ketone (red in figure) and generate an acyl-ACP

molecule two carbons longer than the original substrate. The acyl-ACP molecule

continues through the cycle until the appropriate chain length is reached. In E.

coli fatty acid chains in lipids are 12-20 carbons long. The length of the fatty acid

chains and the number of double bonds (unsaturation) is dependent upon the

temperature the bacteria is growing at. The membrane must remain fluid. Using short

chain fatty acids with higher degrees of unsaturation increases the fluidity of the

membrane. As the temperature increases, longer fatty acid chains with fewer double

bonds will be more prevalent in the membrane.

Figure 2 - The elongation cycle of fatty acid biosynthesis.

Assembly of the Lipid

The enzymes of phospholipid synthesis are bound to the inside of the cytoplasmic

membrane. The glycerol backbone of bacterial lipids originate from dihydroxyacetone

phosphate (a central metabolite in glycolysis). This is reduced to sn -glycerol 3-

phosphate using NADH. In the next step fatty acids are transferred from acyl-ACP

to sn -glycerol 3-phosphate to form phosphatidic acid. Finally, the hydrophilic portion

of the lipid is added. One of the most common lipids formed (phosphatidyl serine) is

shown in the figure below.

DNA - STRUCTURE

This page, looking at the structure of DNA, is the first in a sequence of pages leading on to how DNA replicates (makes copies of) itself, and then to how information stored in DNA is used to make protein molecules. This material is aimed at 16 - 18 year old chemistry students. If you are interested in this from a biological or biochemical point of view, you may find these pages a useful introduction before you get more information somewhere else.

Exploring a DNA chain

The sugars in the backbone

The backbone of DNA is based on a repeated pattern of a sugar group and a phosphate group. The full name of DNA, deoxyribonucleic acid, gives you the name of the sugar present - deoxyribose.

Deoxyribose is a modified form of another sugar called ribose. I'm going to give you the structure of that first, because you will need it later anyway. Ribose is the sugar in the backbone of RNA, ribonucleic acid.

This diagram misses out the carbon atoms in the ring for clarity. Each of the four corners where there isn't an atom shown has a carbon atom.

The heavier lines are coming out of the screen or paper towards you. In other words, you are looking at the molecule from a bit above the plane of the ring.

So that's ribose. Deoxyribose, as the name might suggest, is ribose which has lost an oxygen atom - "de-oxy".

The only other thing you need to know about deoxyribose (or ribose, for that matter) is how the carbon atoms in the ring are numbered.

The carbon atom to the right of the oxygen as we have drawn the ring is given the number 1, and then you work around to the carbon on the CH 2 OH side group which is number 5.

You will notice that each of the numbers has a small dash by it - 3' or 5', for example. If you just had ribose or deoxyribose on its own, that wouldn't be necessary, but in DNA and RNA these sugars are attached to other ring compounds. The carbons in the sugars are given the little dashes so that they can be distinguished from any numbers given to atoms in the other rings.

You read 3' or 5' as "3-prime" or "5-prime".

Attaching a phosphate group

The other repeating part of the DNA backbone is a phosphate group. A phosphate group is attached to the sugar molecule in place of the -OH group on the 5' carbon.

ATTACHING A BASE AND MAKING A NUCLEOTIDE

The final piece that we need to add to this structure before we can build a DNA strand is one of four complicated organic bases. In DNA, these bases are cytosine (C) , thymine (T) , adenine (A) and guanine (G).

These bases attach in place of the -OH group on the 1' carbon atom in the sugar ring.

What we have produced is known as a nucleotide.

We now need a quick look at the four bases. If you need these in a chemistry exam at this level, the structures will almost certainly be given to you.

These bases attach in place of the -OH group on the 1' carbon atom in the sugar ring.

What we have produced is known as a nucleotide.

For example, here is what the nucleotide containing cytosine would look like:

JOINING THE NUCLEOTIDES INTO A DNA STRAND

A DNA strand is simply a string of nucleotides joined together. I can show how this happens perfectly well by going back to a simpler diagram and not worrying about the structure of the bases.

The phosphate group on one nucleotide links to the 3' carbon atom on the sugar of another one. In the process, a molecule of water is lost - another condensation reaction.

... and you can continue to add more nucleotides in the same way to build up the DNA chain.

Now we can simplify all this down to the bare essentials!

JOINING THE TWO DNA CHAINS TOGETHER

THE IMPORTANCE OF "BASE PAIRS"

Have another look at the diagram we started from:

If you look at this carefully, you will see that an adenine on one chain is always paired with a thymine on the second chain. And a guanine on one chain is always paired with a cytosine on the other one.

So how exactly does this work?

The first thing to notice is that a smaller base is always paired with a bigger one. The effect of this is to keep the two chains at a fixed distance from each other all the way along.But, more than this, the pairing has to be exactly...

 adenine (A) pairs with thymine (T);

 guanine (G) pairs with cytosine (C).

That is because these particular pairs fit exactly to form very effective hydrogen bonds with each other. It is these hydrogen bonds which hold the two chains together.

The base pairs fit together as follows.

The A-T base pair:

The G-C base pair: Written by : Tahir Habib

If you try any other combination of base pairs, they won't fit!

DNA REPLICATION:

Key points:

 DNA replication is semiconservative. Each strand in the double helix acts as a template for synthesis of a new, complementary strand.

 New DNA is made by enzymes called DNA polymerases , which require a template and a primer (starter) and synthesize DNA in the 5' to 3' direction.

 During DNA replication, one new strand (the leading strand ) is made as a continuous piece. The other (the lagging strand ) is made in small pieces.

 DNA replication requires other enzymes in addition to DNA polymerase, including DNA primase , DNA helicase , DNA ligase , and topoisomerase.

Introduction

DNA replication , or the copying of a cell's DNA, is no simple task! There are about 6.56.56, point, 5 \text{billion}billionb, i, l, l, i, o, n base pairs of DNA in your genome, all of which must be accurately copied when any one of your trillions of cells divides^11start superscript, 1, end superscript.

The basic mechanisms of DNA replication are similar across organisms. In this article, we'll focus on DNA replication as it takes place in the bacterium E. coli , but the mechanisms of replication are similar in humans and other eukaryotes.

Let's take a look at the proteins and enzymes that carry out replication, seeing how they work together to ensure accurate and complete replication of DNA.

The basic idea

DNA replication is semiconservative , meaning that each strand in the DNA double helix acts as a template for the synthesis of a new, complementary strand.

This process takes us from one starting molecule to two "daughter" molecules, with each newly formed double helix containing one new and one old strand.