[STPM] [BIOLOGY] [NOTES] CHAPTER 1 : BASIC CHEMISTRY OF A CELL (PART 3.2)
Monday, May 12, 2014 | 9:21 PM | 0 comments
Fatty acids
Fatty acids can be divided into saturated fatty acids and unsaturated fatty acids.
Saturated fatty acids contain the maximum number of H atoms and do not have any double bond.
Unsaturated fatty acids contain at least one double bond. It is called “unsaturated” because the fatty acid can be still inserted some more H atoms to make it saturated.
Triglyceride formed from saturated fatty acids is normally solid at room temperature due to its compact shape and it is called fat.
Triglyceride formed from unsaturated fatty acids is liquid at room temperaturedue to the kinks caused by double bond and prevent triglyceride to form compact shape. It is called oil.
Oil can be converted to fat by the process of hydrogenation.
Phospholipids
Cells could not exist without another type of lipid – phospholipids.
Phospholipids are essential for cells because they make up cell membranes.
Phospholipids contain one glycerol and two molecules of fatty acid and a phosphate group.
Additional small molecules, which are usually charged or polar, for example choline, can be linked to the phosphate group to form a variety of phospholipids.
Lecithin is the common phospholipid which forms the cell membrane.
The two ends of phospholipids show different behaviour toward water.
The hyrocarbon tails are hydrophobic and are excluded from water while the phosphate groups and its attachments form a hydrophilic head that has an affinity for water.
When phospholipids are added to water, a micelle is formed where all the hydrophobic tails point to a point.
If phospholipids is in excess, a phospholipid bilayer is formed that shield their hydrophobic portions from water.
Steroids
Many hormones, as well as cholesterol are steroids which are lipid characterized by a carbon skeleton consisting of four fused rings.
Different steroids vary in the chemical groups attached to this ensemble of rings.
Cholesterol is a common component of animal cell membranes and is also the precursor from which other steroids are synthesized.
In vertebrates, cholesterol is synthesized in the liver.
Many sex hormones are steroids produced from cholesterol.
By : Gemini
Image from Google
[STPM] [BIOLOGY] [NOTES] CHAPTER 1 : BASIC CHEMISTRY OF A CELL (PART 5)
| 8:44 PM | 0 comments
Here is the chapter 1 of the last subtopic(nucleic acids) :)
Nucleic acids
The amino acid sequence of a polypeptide is programmed by a unit of inheritance known as gene.
Genes consists of DNA, a polymer belonging to the class of compounds known as nucleic acids.
Roles of nucleic acids
The two types of nucleic acids, deoxyribonucleic acid (DNA) and ribonucleic acid(RNA), enable living organisms to reproduce their complex components from one generation to the next.
DNA is the genetic material that organisms inherit from their parents. Each chromosome contains a long DNA molecule, usually carrying several hundred or more genes.
RNA is the intermediate between DNA and proteins which involves in the synthesis of proteins from the codes in DNA.
Structure of nucleic acids
Nucleic acids are macromolecules that exist as polymers called polynucleotide.
As indicated by the name, each polynucleotide consists of monomers called nucleotides.
A nucleotide itself composed of three parts: a phosphate group, a nitrogenous base and a five-carbon sugar (pentose).
The portion of this unit without the phosphate group is called a nucleoside.
What difference between RNA and DNA?Let's see the below of the diagram :)
 |
| DNA RNA |
Ans:The difference between RNA and DNA is the loss of one oxygen atom on the pentose sugar.
There are five types of bases present in the nucleotide
Three are single ringed called the pyrimidine and two are double-ringed called purine.
The nitrogenous bases found in DNA are adenine, guanine, cytosine and thymine.In RNA, the nitrogenous bases are adenine, guanine, cytosine and uracil instead of thymine.
Adenine is always paired with cytosine in DNA and uracil in RNA. On the other hand, cytosine is always paired with guanine in both DNA and RNA.
The phosphate group is derived from the phosphoric acid and it gives the acidic property to nucleic acid.
Deoxyribonucleic acid (DNA)
Each DNA molecule is a double-stranded polynucleotide held antiparallel to eachother by hydrogen bonds between the nitrogenous bases on both strands.
One strand runs from 5’ end to 3’ end direction and the other strand runs from 3’end to 5’ end.
The bonding between one nucleotide and the other in a strand is called the phosphodiester bond.
The backbone of DNA is made up of phosphate groups and pentose sugars.
5’ end and 3’ end mean that the fifth carbon and third carbon of the pentose sugar.
From X-ray diffraction, it is found that the diameter of DNA helix is 2nm. The distance between base pairs is 0.34nm and a complete turn of the DNA consists of 10 base pairs with a distance of 3.4nm.
The number of hydrogen bonds formed between adenine with thymine or uraciland cytosine and guanine are two and three respectively.
Ribonucleic acid (RNA)
RNA molecule is a single strand of polynucleotide chain which is much shorter than DNA.
There are three types of RNA: messenger RNA (mRNA), transfer RNA (tRNA)and ribosomal RNA (rRNA).
Messenger RNA is a linear single strand polynucleotide.
It is found during protein synthesis. It consists of a nucleotide sequence transcribed from triplet codes of the DNA in the nucleues.
Ribosomal RNA is synthesized in nucleolus. It is one of the structural components of ribosome.
Transfer RNA is a folded polynucleotide strand. It helps in the protein synthesis.
By : Gemini
Image from Google
[STPM] [BIOLOGY] [NOTES] CHAPTER 1 : BASIC CHEMISTRY OF A CELL (PART 4)
| 6:05 AM | 0 comments
Hey,let's continue our next subtopic(proteins)
Nearly every dynamic function of a living being depends on proteins.
Some protein can speed up the chemical reactions,while others play a role structural support,storage transport,cellular communication,movement and defense against foreign substances.Proteins may be composed of one or more polypeptide chains.Each polypeptide chain is a polymer consisting of many basic units of amino acids linked together,peptide bonds,through condensation reactions.
We discuss the amino acids now :)
All amino acids share a common structure.The only different is the variable R groups which determine the types of amino acids.
Amino acids are organic molecules possessing both corboxyl and amino groups.When amino acids dissolves in water,amino acids dissociate to form zwitterious,carrying a positive charge on the amino part and negative charge on the carboxyl group.Thus,amino acids show bipolar property. **still remember bipolar?**
***tips:appear in subtopic 1.1(water)***
Amino acids can be function as a pH buffer to maintain the pH level in the blood.
Can u still remember what u learn biology in form 4(chapter 4)? If forgot, never mind, here got discussed it again :)
Amino acids can be grouped into 2 groups:1.)essential amino acids
2.)non-essential amino acids
The essential amino acids are the amino acids which cannot synthesized by our body and is needed to obtain from our daily diet.
The non-essential amino acids are the amino acids which can synthesized by our body.The task is completed by liver by means of transamination.
What is polymerization of amino acids?
Polymerization of amino acids is when two amino acids are positioned so that the carboxyl group of one is adjecent to the amino group of the other,they can become joined by a dehydration reaction,with the removal of a water molecule.The resulting covalent bond is called peptide bond.Repeated over and over,this process yields a polypeptide,a polymer of many amino acids linked by peptide bonds.The polypeptide may coil and fold into a particular structure as a result of a hydrogen bonds,disulphide bonds,Van de Waal's forces or hydrophobic interaction and ionic bonds.These bonds determine the behaviour proteins and thus give a rise to form separate levels of structure.
Protein structure can be categorized into 4 types of structure:1.)primary structure.
2.)secondary structure
3.)tertiary structure
4.)Quaternary structure
Primary stucture of protein
Primary structure of protein is its unique sequence of amino acids in a linear polypeptide chain.
The sequence of amino acids in a linear polypeptide chain is determined genetically by DNA.
Secondary structure of protein
Secondary structure of a protein is the coiling and folding of a polypeptide chain that contribute to the protein’s overall shape.
One such secondary structure is alpha-helix, a delicate coil held together by hydrogen bonding between every fourth amino acids.
The other main type of secondary structure is the beta-pleated sheet, a folded sheet held together by hydrogen bonding between two or more regions of a pair of parallel polypeptides chain lying side by side.
Example: keratin, fibroin and silk.
Tertiary structure of protein
Superimposed on the patterns of secondary structure is a protein’s tertiarystructure.
Tertiary structure of protein is three dimensional, compact and globular.
The structure is maintained by the interaction of hydrogen bonds, disulphide bonds, ionic bonds and hydrophobic interaction.
Example: hormones, enzymes, antibodies and plasma proteins.
Quaternary structure of protein
Quaternary structure is the overall protein structure that results from the aggregation of several tertiary structures of proteins.
Example: haemoglobin, collagen
Classification of proteins
Structurally, proteins can be classified into three groups:
1.Fibrous proteins 2.Globular proteins 3.Intermediate proteins
Let's dicuss fibrous proteins xP
Firbrous proteins
Examples: collagen, keratin, fibrin and myosin.
Have secondary structure.
Insoluble in water.
Helical structures or pleated sheets held together by hydrogen bond.
A stable protein structure.
Globular proteins
Examples: globulin, enzymes, antibody and hormone.
Have tertiary structures.
Tightly coiled and folded to form sphere.
Structure maintained by various bonds.
Easily soluble in water.
Intermediate proteins
Example: fibrinogen.
Basically a fibrous protein but soluble in water.
If classified according to their composition, proteins are placed into two groups.
Simple proteins are considered pure proteins which do not contain any other substances except amino acids.
Conjugated protein is considered complex compound which contains protein partand a non-protein component known as prosthetic group.
Properties of proteins
Colloid formation
Globular proteins are soluble but being macromolecules, they do not dissolve completely in water but form a colloidal solution.
The electrical charges found on the bonding of the proteins prevent them from settling down and thus, they remain suspended in water.
Denaturation of proteins
Denaturation of proteins involves the loss of their specific three-dimensionalshape and is usually irreversible.
This is caused by the breaking of the bonds which hold the shape of the proteins.
Heat is the main factor that contributes to the denaturation of proteins.
Other than that, there are several factors which may denature proteins:
1.Strong acids and alkalis
2.Organic solvents and detergents
3.Heavy metals
4.Radiation
By : Gemini
Images from Google
[STPM] [BIOLOGY] [NOTES] CHAPTER 1 : BASIC CHEMISTRY OF A CELL (PART 3.1)
Sunday, May 11, 2014 | 9:55 PM | 0 comments
After part 1 and 2, finally here's the part 3~ So in part 3, we're gonna learn about lipids.
Before we start, let's revise something we've learnt during our Chemistry in SPM.
Well, lipids are organic compounds which are made up of hydrogen, carbon and oxygen atoms. The only difference between lipids and carbohydrates I think is that the ratio of C:H is not the same. Not only that, some lipids even contain phosphorus and nitrogen. Since it's organic compound, it can only dissolve in organic solvent like acetone, benzene etc.
And here, we are going to learn 3 types of lipids : -
3 types of lipids : - Triglycerides | Phospholipids | Steroids.
First, let's go to the triglyceride. We've learnt about that last year. A triglyceride is an ester formed from condensation of 1 molecule of glycerol and 3 molecules of fatty acid. [Reaction: Esterification]
Now let's go through a bit details on the reaction esterification. So, during this esterification, glycerol with 3 carbon atoms, each bearing a hydroxyl group (-OH) will neutralise with 3 molecules of fatty acids (RCOOH), each containing the carboxyl functional group (-COOH).
[R represents H or alkyl groups.]
Extra :-
Water is formed when fats are oxidised. This metabolic water can be very useful to some desert animals like camels, which store fat in their humps for this purpose.
The long and hydrophobic alkyl group forms the hydrocarbon chain of fatty acids and in most naturally occuring ones, the number of carbon atoms are even between 14 and 22.
Here's a little comparison between saturated and unsaturated fatty acid.
First, saturated fatty acid is a straight molecule while unsaturated one is a bent molecule. Why does it bend? Its due to the presence of one or more double bonds. The kinks where double bonds located prevent unsaturated fat molecules from packing together closely enough. And that's why unsaturated fat is usually in liquid form.
Fatty acids are required in very small qtt. But, if we lack of this substance, it results in :
- deterioration of nerve cells
- failure of certain groups of cells to function properly and death
Triglycerides are non-polar thus they don't form hydrogen bonds with water molecules. So, this explains why they are hydrophobic.
Some major functions of triglycerides : -
- act as energy stores : have higher calorific value than carbohydrates
- serves as an insulator : extensive in mammals living in cold climates
Plants usually store oils rather than fats. Fruits and seeds are often rich in oils.
Ohoho~~ So, finally we conclude our part 3.1, that is our triglyceride~
For the upcoming part 3.2, we are going to going for phospholipids and hopefully together with steroids :-]
Notes by WanQing
[STPM] [BIOLOGY] [NOTES] CHAPTER 1 : BASIC CHEMISTRY OF A CELL (PART 2)
Thursday, May 8, 2014 | 2:30 AM | 0 comments
Here comes our Part 2 guys!!!
In Part 1 we discuss about water, and in Part 2 we're going to learn the second subtopic, that is carbohydrates.
Okay, let's introduce our dear carbohydrates or simplify name carbs.
Well, actually carbohydrates are substance which contain element C(carbon) H(hydrogen) and O(oxygen) with a certain ratio.
So, carbohydrates can be found in 3 forms :
First is monosaccharide, which is the simple sugar.
Second is disaccharide, which is 2 simple sugars combine through process condensation.
Third is polysaccharide, and this one is the complex sugar.
After that, let us take a look at our monosaccharide. Generally, monosaccharide is the monomer for carbohydrates. They can be categorized using 2 methods.
First, by determining the number of carbon atoms. (Like what we learnt in SPM Chemistry)
Example is like triose for three carbon atoms, pentose for five carbon atoms and hexose for six carbon atoms.
Secondly, is by determining the carbonyl groups. Carbonyl groups are either aldehyde or keto group. Well, what's the difference again between these two groups? Aldehyde group is CHO, while keto group is CO. And both of them have reducing properties, making all monosaccharides reducing sugars.
Reducing means that when these sugars are tested using Benedict's solution, the copper (II) ions in this solution is reduced to copper(I) ions. Blue Benedict's solution turns brick red.
The general formula for monosaccharide is :
Pentose or hexose sugar can form ring structure which is more stable. And, ***do remember, only ring structure can be used to make disaccharides and polysaccharides.
Usually first carbon atom in aldose sugar attached to carbonyl group while in ketone sugar is attached to second carbon atom. What does that mean?
After that, it's about the importance or functions of monosaccharides.
We've done with monosaccharide, let's continue with our disaccharide.
These are formed when two monosaccharides are condensed together. One monosaccharide loses an H atom from carbon atom number 1 and the other loses an OH group from carbon 4 to form the bond.
The reaction, which is called a condensation reaction, involves the loss of water (H2O) and the formation of an 1,4-glycosidic bond. Depending on the monosaccharides used, this can be an α-1,4-glycosidic bond or a β-1,4-glycosidic bond.
The reverse of this reaction, the formation of two monosaccharides from one disaccharide, is called hydrolysis reaction and requires one water molecule to supply the H and OH to the sugars formed.
Examples of Disaccharides
Sucrose: glucose + fructose,
Lactose: glucose + galactose,
Maltose: glucose + glucose.
Sucrose is used in many plants for transporting food reserves, often from the leaves to other parts of the plant. Lactose is the sugar found in the milk of mammals and maltose is the first product of starch digestion and is further broken down to glucose before absorption in the human gut.
Finally, it's our last one, polysaccharide!!!
Examples of polysaccharides:
1.)Starch
2.)Glycogen
3.)Cellulose
Let's introduce the starch first :)
Finally, it's our last one, polysaccharide!!!
Examples of polysaccharides:
1.)Starch
2.)Glycogen
3.)Cellulose
Let's introduce the starch first :)
Function of starch:Main storage polysaccharide in plants.
Structure of starch:Made of 2 polymers - amylose and amylopectin.
Amylose: a polymer of glucoses joined by α-1,4-glycosidic bonds. Forms a helix with 6 glucose molecules per turn and about 300 per helix.
Amylopectin: a polymer of glucoses joined by α-1,4-glycosidic bonds but with branches of α-1,6-glycosidic bonds. This causes the molecule to be branched rather than helical.
Function of glycogen:Main storage polysaccharide in animals and fungi
Structure of glycogen:Similar to amylopectin but with many more branches which are also shorter.
Function of cellulose:Main structural constituent of plant cell walls
Structure of cellulose:Adjacent chains of long, unbranched polymers of glucose joined by β-1,4-glycosidic bonds hydrogen bond with each other to form microfibrils.
Functions of carbohydrates
- Substrate for respiration (glucose is essential for cardiac tissues).
- Intermediate in respiration (e.g. glyceraldehydes).
- Energy stores (e.g. starch, glycogen).
- Structural (e.g. cellulose, chitin in arthropod exoskeletons and fungal walls).
- Transport (e.g. sucrose is transported in the phloem of a plant).
- Recognition of molecules outside a cell (e.g. attached to proteins or lipids on cell surface membrane).
Notes by Gemini
Image from Google
[STPM] [BIOLOGY] [NOTES] CHAPTER 1 : BASIC CHEMISTRY OF A CELL (PART 1)
| 1:54 AM | 0 comments
Title of the first chapter in STPM Biology is Basic Chemistry of A Cell.
Let's go through the subtopic one by one.
C1 : Basic Chemistry of A CellAnd yes, today, we are going to learn the first one, water.
1.1 Water
1.2 Carbohydrates
1.3 Lipids
1.4 Proteins
1.5 Nucleic Acid : DNA and RNA
1.6 Movement of substances across membrane
1.7 Technique of analysis
As we all studied in SPM, water comes with its chemical formula :
But now in STPM, we need to learn in details. Not only we have to know it consists of 2 hydrogen atoms and 1 oxygen atom. We have to know more, how does the thing looks like?
Apart from that, water is bipolar, this is due to uneven distribution of charge within the molecule.
Below are the importance of water.
1. As universal solvent.
- Can dissolve both ionic and polar substance.
2. Has high surface tension and cohesion.
- This is due to hydrogen bonding.
- By having high surface tension, small organism is able to walk on water surface.
- Besides, it helps in translocation of water through xylem in plants.
3. Has high specific heat capacity.
- 4.2kJ/kg/K.
- Large amount of heat energy is required to raise water temperature by 1 Kelvin.
- By having this properties, our body can maintain its own normal temperature constantly.
4. Has high latent heat of vaporisation.
- 2260J/kg.
- Allows vaporisation and cooling takes place.
5. Has high latent heat of fusion.
- 340kJ/kg.
- Our cells are less likely to freeze.
6. Density decreases when below 4°C.
- When water freezes, it can float on top and insulate below.
- Aquatic life below still can stay alive without getting further cooling and freezing.
7. Medium of chemical reaction.
8. One of reactants or products in chemical reaction.
- raw material in photosynthesis.
9. Lubricant.
- mucus helps in peristalsis.
- synovial fluid at joints. ; pericardial fluid for heart. ; pleural fluid for lungs.
10. Provides moist surface.
- substance can diffuse and dissolve.
- e.g alveoli in lungs
11. As medium of transport and removal of waste substances.
- transport nutrients, hormones, mineral salts.
- remove metabolic wastes like ammonia.
12. As medium of fertilisation.
- gametes that swim
- e.g sperms
13. As support.
- hydrostatic skeleton
- exerting pressure
- e.g earthworm
14. As dispersal agent for seeds
- e.g coconut tree
That's all for part 1. Do leave comments if encounter problem or found mistakes in our notes.
Check out our Part 2 soon.
Notes by WanQing
Images from Google
Welcome~
Tuesday, May 6, 2014 | 2:53 AM | 0 comments
Thank you for stopping by. Your kind act is truly appreciated.
Are you a Pre-U student? or SPM or PMR?
Here is the first blog of mine on only studies.
Feel free to leave your introduction in the comment sections.
And if you have any questions on academics, please fill in the form in Ask tab.
Welcome~
Please treat here nice.
Labels: Welcome Note
