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Predict potential cleavage sites cleaved by proteases or chemicals in a given protein sequence.

EXPERIMENT #13        

OBJECT:-

Predict potential cleavage sites cleaved by proteases or chemicals in a given protein sequence.

THEORY:-

Peptide cutter predicts potential cleavage sites , cleaved by proteases or chemicals in a given protein sequence.

Proteins are biological polymers , composed of aminoacids. Aminoacids, linked together by peptide bonds, form a poly peptide chains.One or more polypeptide chain twisted into a 3 dimensional shape to form a protein.

NEB cutter is also a search tool, it will take a DNA sequence and find the lare non overlapping open reading farme using E.coli  genetic code and the sites for all type 2 and commercially available type 3 restriction enzyme that cuts the sequence just once.Restriction enzymes are those enzymes , which are restricted to specific sequences,in a protein or DNA molecule.

Procedure:-

1.From expasy peptide cutter was selected.

2.Sequence of protein from fasta format was taken and pasted in input box.

3.Where the selection or the whole list of proteases and chemicals can be used.

4.By which cleavage specification of selected enzymes and chemicals can be known.

DISCUSSION:-

In this practical peptide cutter was used to observe different cleavage sites, cleaved by different available enzymes or chemicals,in a given protein sequence.The table showed list of enzymes (that cuts our protein sequence),number of cuts and position of cuts and specific sequences recognized by enzymes to make a cut.Peptide cutter returns the query sequence with the possible cleavage sites mapped on it and a table of cleavage site positions by different enzymes e.g  Protinase k,Pn-2 etc.List of enzymes were also found which do not   cleaved our protein sequence because of lack of availability of specific sequences , required for their cleavage-potential.There are some overlapping regions through which we can concluded about the complete sequence.           

Retrieve a sequence using UniprotKB.

EXPERIMENT #09

OBJECT:-

Retrieve a sequence using UniprotKB.

THEORY:

What is UniProt?

UniProt provides the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information. UniProt is a comprehensive, high-quality and freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from the research literature.

Why do we need UniProt?

As the number of completely sequenced genomes continues to increase, huge efforts are being made in the research community to understand as much as possible about the proteins encoded by these genomes. This work is critical to many areas of science including biology, medicine and biotechnology - and is generating a wealth of data. UniProt provides an up-to-date, comprehensive body of protein information. The resource facilitates scientific discovery by collecting, interpreting and organising this information, which saves researchers countless hours of work.

What can I do with UniProt?

You can use UniProt for a wide range of tasks, from finding out about your protein of interest and comparing its protein sequence with other proteins, to mapping a list of identifiers from an external database to UniProtKB or vice versa.

UniProt is a comprehensive, high-quality and freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from the research literature.

PROCEDURE:-

1.Www.uniprot.org/uniprot/P21543 was opened.

2.Name of protein was written.

3.All the information about protein was noted.

RESULTS:-

DISCUSSION:-

UniProt is a comprehensive, high-quality and freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from the research literature. It provides all the information related to that protein(amylase),the name of organism (Bacillus licheniformis), function of that protein. It showed the position of active site of protein and also its graphical view. It gives information about the position of signal peptide that was from 1-29 and functional chain that was at 30-512 position. Blue color showed alpha helix and red color showed Beta strand. There were some repeated strands which meant that in evolution perhaps there is duplication.

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To observe O-glycosylation in eukaryotic sequence.

Experiment #12   

Object:-

To observe O-glycosylation in eukaryotic sequence.

Theory:-

O- glycosylation occurs at Ser or Thr-residues, usually in sequence-stretches rich in hydroxy amino acids, but there has been no consensus sequence determined for this modification. In addition, O-glycosylation lacks a common core structure: mammalian proteins have been reported bearing O-linked N-acetylgalactosamine, fucose, glucose, and corresponding elongated structures, as well as N-acetylglucosamine. Chemical methods are used to liberate these oligosaccharides because no enzyme has been discovered that would cleave all the different O-linked carbohydrates. Glycosylation , a common PTM, plays a role in protein folding, transport and half-life, as well as being involved in cell-cell interactions and antigenicity. Glycosylation is an enzymatic process, with the exception of glycation, and involves the addition of sugars to the protein to build up glycan chains.

Procedure:-

1.NetOGly1.0 server was opened.

2. Fasta format was pasted in input box.

3.Result was noted.

DISCUSSION:-

In this experiment O-Glycosylation was observed.There is no any seqon.It has limited application.This tool is only for eukaryotic protein.O- glycosylation occurs at Ser or Thr-residues, usually in sequence-stretches rich in hydroxy amino acids, but there has been no consensus sequence determined for this modification. In addition, O-glycosylation lacks a common core structure.

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To observe N-glycosylation in eukaryotic sequence.

Experiment#11

Object:-

To observe N-glycosylation in eukaryotic sequence.

Theory:-

Most proteins do not perform their function without undergoing some form of post translational modification (PTM) . PTMs occur after the mRNA has been translated into peptide sequence and the polypeptide has begun to fold . The importance of PTMs in protein function makes their characterization of particular interest . Accurate prediction, using computational methods, of sites in a protein sequence where PTM occurs would facilitate protein annotation and would contribute to efforts in functional genomics Glycosylation , a common PTM, plays a role in protein folding, transport and half-life, as well as being involved in cell-cell interactions and antigenicity. Glycosylation is an enzymatic process, with the exception of glycation, and involves the addition of sugars to the protein to build up glycan chains. N-linked glycosylation consists of the addition of a pre-assembled glycan chain to Asn. This occurs co-translationally and influences protein folding. After its addition, the glycan chain undergoes a maturation process, which can produce a glycan of the high mannose, hybrid or complex types. The sequence motif Asn-Xxx-Ser/Thr , or in some rare cases Asn-Xxx-Cys, where Xxx is any amino acid except Pro, is required for N-glycosylation, although not sufficient on its own. This Web Service implements NetNGlyc 1.0b. It predicts N-Glycosylation sites in human proteins using artificial neural networks that examine the sequence context of Asn-Xaa-Ser/Thr sequons.The traditional server offers more detailed output (graphics), extended functionality and comprehensive documentation. It is suitable for close investigation of few proteins while this service is recommended for high throughput projects.

Procedure:-

1.NetNGly1.0 server was opened.

2. Fasta format was pasted in input box.

3.Result was noted.

DISCUSSION:-

In this experiment N-Glycosylation was observed. This Web Service implements NetNGlyc 1.0b. It predicts N-Glycosylation
sites in human proteins using artificial neural networks that examine
the sequence context of Asn-Xaa-Ser/Thr sequons.

The traditional server offers more detailed output (graphics), extended
functionality and comprehensive documentation. Glycosylation mainly depends on nature of amino acids and environment around specific aminoacids .N glycosylation occur where basic aminoacids like Asparigin is present.We observed that N glycosylation occurred at many positions of given sequence.

Discussion:-

In this experiment N-Glycosylation was observed. N-linked glycosylation consists of the addition of a pre-assembled glycan chain to Asn. This occurs co-translationally and influences protein folding. After its addition, the glycan chain undergoes a maturation process, which can produce a glycan of the high mannose, hybrid or complex types. The sequence motif Asn-Xxx-Ser/Thr , or in some rare cases Asn-Xxx-Cys, where Xxx is any amino acid except Pro, is required for N-glycosylation, although not sufficient on its own. The traditional server offers more detailed output (graphics), extendedfunctionality and comprehensive documentation.We observed that N glycosylation occurred at many positions of given sequence.

To predict signal peptide in eukaryotic sequence

EXPERIMENT#10

OBJECT:-

To predict signal peptide in eukaryotic sequence.

Theory:-

A signal peptide (some time referred to as signal sequence, targeting signal, localization signal ,transit peptide , leader sequence or leader peptide)is a short (5-30 amino acid)peptide present at the N terminal of the majority of newly synthesized proteins that are destined towards the secretary pathway. These proteins include those that reside either inside certain organelles (endoplasmic reticulum golgi bodies or   endosomes),secreted from the cells or inserted into most cellular membranes. In eukaryotes , signal sequences direct the insertion of proteins into the membrane of the endoplasmic reticulum and are usually cleaved off by signal peptidase. The resulting signal peptide are presumably rapidly degraded but some still have function on their own. SignalP 4.1 server predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks. Organism group:
It is important for performance that you choose the correct organism group — Eukaryotes, Gram-negative bacteria or Gram-positive bacteria — since the signal peptides of these three groups are known to differ from each other.
Gram-positive bacteria correspond to Actinobacteria and Firmicutes in the NCBI Taxonomy.
Gram-negative bacteria are all other eubacteria, except Tenericutes (including Mycoplasma), which seem to lack a type I signal peptidase and therefore do not have standard signal peptides You can see which cutoff values are being used in the boxes marked "D-cutoff". They will change if you change the setting for "D-cutoff values" or "Organism group".
If you want to experiment with your own cutoff values, select "User defined" and the boxes will go blank, ready for you to fill in values between 0 and 1.

PROCEDURE:-

1.In Expasy signal peptide was selected.

2. Fasta sequence of protein was pasted in input box.

3.After tat group of organism was selected (gram negative, gram positive, eukaryotes)

4.Result was noted.

Dicussion:-

In this experiment we predicted signal peptide in eukaryotic sequence, by using expasy  search tool, for that purpose , we pasted protein sequence of a eukaryotic organism in a bar of search and found a graph, we observed a peak (blue colored), it indicated site of proteolytic cleavage. In graph green line showed hydrphobicity residues.

We have to consider those lines which are above the base-line. Green and blue line played basic role in signal peptide.

We observed cleavage site between 23 and 24^th amino acids ,it indicates that signal peptide is present in given sequence. Signal peptide helps the protein to reach its destination, than through cleavage it cleaved out from protein.

Discussion:-

In this experiment we predicted signal peptide in eukaryotic sequence, by using expasy  search tool, for that purpose , we pasted protein sequence of a eukaryotic organism in a bar of search and found a graph, we observed a peak (blue colored), it indicated site of proteolytic cleavage. In graph green line showed hydrphobicity residues.

Any thing above cut off line is significant. The software looked for 3 parameters(1.short stretch of hydrophobic amino acids,2.short peptide,3.cleavage site).It only look 70 begining aminoacids because if sinal peptide present it would be in begining.In translated protein Met is first amino acid but in functional it is not the first aminoacid. By looking the graph we can predict the presence and absence of signal peptide.If signal peptide not present reason might be that protein may be cytoplasmic or there is only functional sequence uploaded or may be there is partial sequence not complete sequence.

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O LEVEL BUSINESS STUDY CHAPTER 25

Chapter 25: Business in the international community

The international dimension
In business, no manager can operate without being affected by the international community. 

Exchange rates
Exchange rates is the value of one currency compared to another. 

How are exchange rates determined?
There are two type so currencies:

• Floating rates: The exchange rate of the currency is allowed to change freely depending on market forces, i.e supply and demand of the currency.
• Fixed rates: The exchange rate of the currency is set by the country's central bank.

When the exchange rate rises, it is called appreciation. When it falls, it is calleddepreciation.
How are businesses affected by changing exchange rates?

• Appreciation:
  • Import prices fall.
    
  • Export prices rise.
    
• Depreciation:
  • Import prices rise.
    
  • Export prices fall.
    

These exchange rate movements can cause serious damage to businesses, making business endeavours that would have been profitable make losses because of changes in the currencies. The EU, for example, wants to limit these bad effects, and hence established a common currency, the Euro.

International economic organisations

• Economic and political unions. (e.g. the EU)
  
• Free trade agreements. (e.g. NAFTA)
  
• Organisations working for free trade between countries. (WTO)
  

The European Union

• Consists of 25 European countries.
• Creates a single market in the EU.
  • To tariffs, quotas or any trade boundaries.
  • This results in:
    • A huge market benefiting from economies of scale.
    • Increased competition resulting in better products.
• Common currency.
  • Issue of Euros are controlled by the European Central Bank.
  • Interest rates for the Euro become the same.
• The social charter:
  • The EU wants to improve working
    conditions and make finding
    josbs equal in the EU.
  • The main conditions include:
    • Workers can look for work anywhere in the EU.
    • Workers must be consulted on important issues.
    • Equal treatment of full/half time workers.
    • Limits on maximum working hours.
    • Improved health and safety rules at work.

Advantages for the UK to join the EU

• Lower costs because:
  • One price list throughout Europe can be used.
  • No more charge through currency conversion.
• Easier to:
  • Trade with EU countries.
  • Compare costs of supplies with EU countries.
• No risk of losing out on exchange rate changes.

Disadvantages for the UK to join the EU

• More competition from non-UK firms.
• Consumers might buy cheaper products from other EU countries.
• The rate of interest might no longer suit UK firms.

Free trade unions
Eliminates all trade barriers. Businesses within the free trade union are affected in the following ways:

• More competition from foreign firms.
  • Consumers have more choice and prices are lower.
• No 'protection' by governments.
• More opportunities for exporting. 
  • Efficient firms will be more successful.

The long-term aim of the free trade union is to encourage
trade between the member countries, ultimately improving living conditions for the people.

Globalisation
Globalisation is the word used to describe the increased worldwide competitionand business
activity. Goods and services that once can only be found in one country has spread all around the world. There are several reasons for this:

• Free trade agreements encourage international trade.
• Improved travel links and communication.
• Countries that have been undeveloped before start to develop andexport their own goods, leading to more international competition.

Globalisation results in:

• More choices and lower prices for the consumer.
• Businesses look into more ways to become more efficient.
  • Why many businesses merge to become multinationals.
• Inefficient businesses go out of business.
• Free trade results in:
  • More workers losing jobs, since governments can no longerprotect them from foreign competition.

Multinational businesses
Multinationals are businesses that have factories, services, or operations inmore than one country. It is important to note that, for a business to become multinationals, they must produce goods in more than one country.
Why do firms become multinationals

• To cut costs:
  • Labour costs.
    
  • Raw material costs.
    
• To extract raw materials not found elsewhere.
• To produce goods nearer to the market.
• To bypass trade barriers.
• To expand and spread risks.

Advantages of multinationals operating in a country

• Jobs are created.
  
• New investment increases national output.
  
• Imports are reduced since there are more goods in the country. Moreexports.
  
• More taxes are paid to the government.
  

Disadvantages of multinationals operating in a country

• Jobs created are usually unskilled jobs.
• Local firms are forced out of business since they can't compete with multinationals.
• Profits flow out of the country.
• Multinationals use up scarce resources.
• May influence the government.

O LEVEL BUSINESS STUDY CHAPTER 23

Chapter 23: Factors affecting production

What is meant by production?
Production is the provision of a product to satisfy wants and needs. The process involves businesses adding value to their products. E.g. The production process of matches involve cutting wood into matchsticks, putting phosphorus ends on them and packaging them to sell.



Productivity
Productivity is the outputs measured against the inputs used to create it. This is measured by:

Output (over a given period of time)/Number of employees

If a worker makes more products in the same amount of time, his productivity increases. Firms aim to be productively efficient to be able to make more profits and compete against their competitors.

Methods of production
Job production

• Goods are made individually, by one person.
  
• Goods are usually specialized, no two goods are the same.
  
• Usually made to order.
  

Pros

• The product meets exact requirements of the customer.
• The workers have more varied jobs.
• More job satisfaction for workers.

Cons

• Skilled labour is needed.
  
• Slower and more expensive than other methods of production.
  
• Usually labour intensive.
  

Batch production

• Products are made in batches according to order.
  

Pros

• It is flexible. You can easily change from making one product to another.
• Still gives some variety to workers jobs.
• Production is not too affected by machinery breakdown.

Cons

• Expensive to move products around the workplace.
• Storage space will be needed to store raw materials. Expensive.

Flow production

• Large quantities of a product are produced in a continuous process.
  
• Uses specialization.
  
• Benefits from economies of scale.
  
• Is capital intensive.
  

Pros

• Low costs. Low prices. High sales.
• Increased efficiency.
• Little training is needed.
• Goods are produced quickly and cheaply.
• Goods do not need to be moved around like batch production. Saves time.
• Quality is high and standardized (courtesy to Muhammad Hassaan Ayyub)

Cons

• Boring for the workers. Little job satisfaction.
• Needs a lot of capital to set up.
• If one machine breaks down then the whole production process stops.

Which type of production should be used?
The type of production that should be used varies with how the product is demanded:

• Job production: Unique and individual service is required.
• Batch production: Demand is higher but products will not be sold in large quantities. Batches are made to orders.
• Flow production: Demand for the product is high and steady.

Stock control
Stock control is important so that a business will not
run
out of stock and be unable to satisfy demands. When stock levels get to a certain point, more goods need to be reordered for the stock level to reach its maximumagain. If more goods are not reordered, stocks could run out because of anunexpected
surge in demand. However, keeping a lot of stock costs money, so the level of stock in a company should always be balanced. The following graph demonstrates how stock can be controlled:

 
Lead production

• Focuses on cutting down waste, increasing efficiency.
• It tries to reduce the time taken to produce a product and transport it the selling point.
• Includes the following methods:
  • Kaizen.
  • JIT production.
  • Cell production.
  • Kanban.

Kaizen

• Continuous improvement through the elimination of waste.
  
  • Ideas of workers.
    
  • Regular meetings of workers to discuss how to increase efficiency.
    
• The advantages of Kaizen:
  
  • Increased productivity.
    
  • Reduced amount of space needed for the production process.
    
  • Work-in-progress is reduced.
    
  • Improved layout of the factory floor may combine jobs of some employees, freeing others to do other things.
    

Just in time production

• Eliminating the need to hold stocks.
• Goods are delivered to the selling point just when they are needed.
• JIT production needs:
  • Reliable suppliers.
  • Efficient system of ordering raw materials.

Cell production

• Production line is divided into cells.
• Each cell makes an identifiable part of the finished product.
• Boosts morale.

Kanban

• A system of ordering used with JIT production.
  
• Operates with two component bins.
  
• When one is emptied, production begins to fill it.
  
• The other one is then left to be emptied.
  
• The first one is filled up when the second one is emptied.

Improvements in technology
Here are some things that technology does in the production process:

• Automation: Equipment in the production process is controlled by a computer. 
• Mechanisation: Tasks are done by machines operated by people.
• CAD (computer aided design): Used for designing 3-D objects.
• CAM (computer aided manufacture): Computers control machines in the production process.
• CIM (computer integrated manufacture): CAD and CAM are used together. The computer that uses CAD is directly linked with the one that controls the production process.

Here are some things that technology does in shops:

• EPOS (electronic point of sale): When products' bar codes are scanned and the information is printed out on a receipt. Data is also sent to a computer to keep track of stocks.
• EFTPOS (electronic fund transfer at point of sale): When the cash register is connected to the retailer's main computer and banks. The customer's credit/debit card is swiped and the money is debited from the customer's bank account. A receipt is printed out to confirm the transaction.

The advantages of new technology 

• Increased productivity.
• Boring jobs done by machines. Boosts motivation.
• Training is needed to operate new machines. Workers become moreskilled.
• Better quality.
• Better stock control.
• Quicker communication and reduced paperwork.
• Info is available faster, resulting in faster decision making (for managers).

The disadvantages of new technology

• Unemployment
• Expensive
  • To invest in new technology.
    
  • To replace outdated technology.
    
• Employees are unhappy with changes in the workplace.
  

Quality control 
There are three ways to control quality:
Quality control

• Involves checking and removing faulty products at the end of the production process.
  
• Wastes a lot of money.
  

Quality assurance

• Involves inspecting during and at the end of production.
  
• Aim to
  
  • Stop faults from happening.
    
  • Set a quality standard that all products have to achieve.
    
• Need teamworking and responsibility.
  

Total quality management

• Encourages everyone to concentrate on quality.
  
• Quality is the main aim for all staff.
  
• Products need to satisfy all customer needs.