12 BIOLOGY, CH 1 1melba12biology.weebly.com/uploads/1/0/9/9/10997732/biol_3_ch_1... · 12 BIOLOGY,...

1 12 BIOLOGY, CH 1

2 12 BIOLOGY, CH 1

“Almost all aspects of life are engineered at the molecular level, and without understanding molecules we can only have a very sketchy understanding of life itself.”

‘What Mad Pursuit’ (1988, Ch.5)

Francis Crick (1916 – ) British molecular Biologist

Presenter

Presentation Notes

Watson and Crick discovered the structure of DNA in the 1950s.

3 12 BIOLOGY, CH 1

There are new fields in biological science: • Genomics – the study of the genome (an organism’s

entire DNA sequence)

• Proteomics – the study of the structure and function of proteins

• Bioinformatics – the science of managing and analysing biological data using advanced computing techniques.

Presenter

Presentation Notes

Watson and Crick discovered the structure of DNA in the 1950s.

4 12 BIOLOGY, CH 1

THE NATURE OF MATTER Matter has mass and takes up space. Matter is composed of atoms.

Atoms are made up of a nucleus which contains protons (+) and neutrons (0). Electrons (-) spin around the nucleus in paths called orbitals. An atom is neutral if electrons = protons

The number of protons defines an element.

Presenter

Presentation Notes

Atomic number = number of protons Mass number = protons + neutrons

5 12 BIOLOGY, CH 1

ORGANIC CHEMICALS

Carbon is found in all compounds (except water) that make up living things on Earth. Organic compounds are complex carbon-containing compounds such as: Carbohydrates Lipids (fats & oils) Proteins Nucleic acids (DNA, RNA)

Carbon dioxide is not complex and is grouped with inorganic compounds.

Presenter

Presentation Notes

List some other inorganic compounds.

6 12 BIOLOGY, CH 1

OTHER ELEMENTS

Besides carbon, there are many other elements that are essential for making organic compounds: Oxygen (O), Hydrogen (H) Nitrogen (N), Phosphorus (P) Iron (Fe), Calcium (Ca) Sodium (Na), Potassium (K) Magnesium (Mg), and many others in very small

quantities

7 12 BIOLOGY, CH 1

ISOTOPES Some atoms of an element can have more neutrons in their nucleus than others. Such atoms are called isotopes of the element eg. Carbon-14 The nucleus of the isotope is unstable and breaks apart giving off energy, which we call radiation. When this happens we say that the element ‘decays’. By giving off radiation, atoms reach a more stable state. Radioactive isotopes are useful tools in the study of many areas of science, including biochemical reactions and medical research (Biobox 1.1, pg 6) because their presence can be detected by the radiation they release.

Presenter

Presentation Notes

Atomic number stays the same. Mass number is different in isotopes. Decay of radioisotopes is measured in half-life (the time taken for half of the isotope to reach the more stable state). Eg. Carbon-14 has a half-life of 5730 years, Potassium-40 has a half-life of 1.25 billion years.

8 12 BIOLOGY, CH 1

ISOTOPES

9 12 BIOLOGY, CH 1

10 12 BIOLOGY, CH 1

11 12 BIOLOGY, CH 1

Review Questions – Set 1

Presenter

Presentation Notes

Answers: They are all made up of matter. Living things can take in nutrients, give out wastes, grow, reproduce and respond to stimuli. A neutral atom with 6 protons would have 6 electrons. The proton defines a particular element. Phosphorus is written in standard notation as 32 15 P. The neutron varies in number in isotopes. The 4 major elements found in living things are C, H, O and N. Radioactive isotopes are used in biomedical research to trace biochemical pathways and treat cancers.

12 12 BIOLOGY, CH 1

Chemical Bonds

The number and arrangement of electrons in an atom’s outer shell determine its chemical behaviour or reactivity. Outer shell electrons are called valence electrons.

13 12 BIOLOGY, CH 1

Chemical Bonds

Atoms accept, give away or share their valence electrons with other atoms, thereby achieving chemical stability. Compounds are stable combinations of atoms of different elements that are held together by chemical bonds. The nature of the bonds differs according to the type of atoms involved.

14 12 BIOLOGY, CH 1

Ionic Compounds

15 12 BIOLOGY, CH 1

Electrolytes

Salts are ionic compounds that dissolve in water as the bonds holding the ions together weaken and break, releasing them. These particles in solution are called electrolytes.

Presenter

Presentation Notes

In plants, the transport system carries mineral ions (electrolytes) in solution from where they are absorbed to where they are required. Generally, we obtain all the electrolytes we need from our diet. At times we can suffer dehydration due to excessive diarrhoea, vomiting or strenuous exercise for long periods. Have you licked your lips and tasted salt? Under these conditions you will need to replenish the electrolytes and water you have lost. Many sports drinks contain electrolytes together with carbohydrates for energy, but unless you are an endurance athlete, it is not necessary to replenish electrolytes in this fashion.

16 12 BIOLOGY, CH 1

Molecular Compounds

Instead of losing or gaining electrons, atoms of non-metals combine with other non-metal atoms by sharing pairs of valence electrons, thus forming molecular compounds. The bonds holding the atoms in these molecules together are covalent bonds.

Ionic and Covalent bonding animation

http://www.youtube.com/watch?v=QqjcCvzWwww

17 12 BIOLOGY, CH 1

Molecular Compounds - water

In the water molecule, oxygen and the two hydrogens share outer electrons. Oxygen now has 8 outer electrons (stable) Each hydrogen now has 2 outer electrons (stable)

18 12 BIOLOGY, CH 1

Presenter

Presentation Notes

The size of each atom, the arrangement of its outer electrons and any charge will determine the shape of the molecule.

19 12 BIOLOGY, CH 1


Presenter

Presentation Notes

9. A compound is a substance that is made up of more than one element.� 10, 11 MOLECULARIONIC non-metal to non-metalmetal to non-metal sharing of electrons gaining or losing electrons ions not formedions formed stronger bondweaker bond A chemical bond is a force of attraction between two atoms or molecules. Polar molecules are partly charged, non-polar molecules are not charged.

20 12 BIOLOGY, CH 1

Acids, Bases and Buffers An acid is a substance that produces hydrogen ions (H+) in solution. The acidity of a solution is measured by its pH. The lower the pH, the more acidic the solution. A buffer is a substance that can react with an acid or a base and maintain a steady pH.

21 12 BIOLOGY, CH 1 From Jacaranda Biology 3&4

22 12 BIOLOGY, CH 1

Water

About 75-85% of a cell by weight is water. Most reactions occur in a watery medium. Many organisms live in water. Water molecules are polar and form hydrogen bonds with each other. More substances dissolve in water than in any other substance. Polar substances dissolve in water and are Hydrophilic (water loving). Non-polar substances (eg. Oil, petrol) do not dissolve in water and are Hydrophobic. Most gases dissolve in water.

Opposites attract

23 12 BIOLOGY, CH 1

Properties of Water

24 12 BIOLOGY, CH 1

25 12 BIOLOGY, CH 1


Presenter

Presentation Notes

Cohesion (water – water) is important because it causes water tension. This allows some insects to walk on water. It also helps in � capillary action.� Hydrophilic substances are attracted to water because they are either polar or ionic, and water is polar (slight charges on it).� a) Water has a high heat capacity (it can hold a lot of heat). When dogs pant they are evaporating water and therefore lose a lot of � heat in the process.� b) Adhesion between water molecules and the glass surface allows the water molecules to creep up the tube.� pH is a measure of the concentration of H+ ions in solution. Buffers are liquids that can either take up or release H+ ions and therefore � help to maintain a steady pH in the solution.� Solid water (ice) has a crystalline structure where the water molecules are further apart than in liquid water. Therefore ice is less dense � than water and floats.�� If ice did not float, it would sink to the bottom of oceans and eventually most of the oceans would freeze from the bottom up. It would � greatly reduce the available space for the marine organisms. The same would apply to lakes and rivers.

26 12 BIOLOGY, CH 1

BIOLOGICAL MACROMOLECULES

Macromolecules are large molecules involved in many processes in the cell. The four main groups of macromolecules are:

PROTEINS NUCLEIC ACIDS CARBOHYDRATES LIPIDS (fats and oils)

Each of the macromolecules is made up of smaller components.

27 12 BIOLOGY, CH 1

BIOLOGICAL MACROMOLECULES

Presenter

Presentation Notes

See flipchart on macromolecules. (grouping of lipids and CHOs, and proteins and nucleic acids with reference to specificity.

28 12 BIOLOGY, CH 1

MACRO-MOLECULE

MAIN ELEMENTS

SUBUNITS EXAMPLE

CARBOHYDRATE C, H, O Saccharides Glucose, starch, cellulose, sucrose

LIPID C, H, O Fatty acids Vegetable oil

PROTEIN C, H, O, N Amino acids enzymes

NUCLEIC ACID C, H, O, N, P Nucleotides DNA, RNA

29 12 BIOLOGY, CH 1

Functional groups in Hydrocarbons

30 12 BIOLOGY, CH 1


Presenter

Presentation Notes

1. Hydrocarbon molecules are composed of Carbon and Hydrogen atoms. They originally came from living organisms such as plants (coal) and animals (crude oil, natural gas).� Functional groups attached to the hydrocarbons can give them different properties, including the ability to dissolve in water.� Alcohol molecules have the hydroxyl functional group (-OH).

31 12 BIOLOGY, CH 1

Polymerisation

32 12 BIOLOGY, CH 1


Presenter

Presentation Notes

The 4 main types of macromolecules are:� CARBOHYDRATES�LIPIDS�PROTEINS�NUCLEIC ACIDS� Carbohydrates, Proteins and Nucleic Acids are polymers made up of many repeating units. �Lipids are not polymers because they are made up of distinct groups of atoms.� See diagram on page 17.� Autotrophs synthesise glucose during photosynthesis. � They then convert glucose to other building blocks of macromolecules. � Heterotrophs take their food in, break it down and absorb it. � They use these building blocks to make their own macromolecules.

33 12 BIOLOGY, CH 1

Carbohydrates Each molecule consists of carbon, hydrogen and oxygen atoms in the ratio of 1:2:1, giving the general formula for carbohydrates of nCH2O. Carbohydrates are classified as: monosaccharides (eg. glucose) disaccharides (eg. sucrose) and polysaccharides (eg. cellulose)

Run Molworks

34 12 BIOLOGY, CH 1 From

Jac

aran

da B

iolo

gy 3

&4

35 12 BIOLOGY, CH 1

Carbohydrates Make models of glucose

Join 2 glucose molecules at 1,4 to show cellulose bonds, and at 1,6 to show starch & glycogen

Demonstrate condensation

Make ribose models

36 12 BIOLOGY, CH 1

37 12 BIOLOGY, CH 1

Carbohydrates


Jac

aran

da B

iolo

gy 3

&4


Jac

aran

da B

iolo

gy 3

&4

40 12 BIOLOGY, CH 1

Carbohydrates

Organisms use carbohydrates as an energy source (eg. starch and glycogen) and for structural components (eg. cellulose and chitin). Most animals do not have the enzymes to break down cellulose in their diet, but have to rely on bacteria in their gut to do it for them. Carbohydrate molecules can combine with other atoms or groups to form important compounds, eg. glycoproteins, which are a combination of carbohydrate and protein molecules.

41 12 BIOLOGY, CH 1


Presenter

Presentation Notes

23. Carbohydrates are composed of Carbon, Hydrogen and Oxygen. Chitin also contains Nitrogen.� 24. Monosaccharides (eg. Glucose) are single monomer molecules. They are easily absorbed and broken down.� Disaccharides (eg. Sucrose) are made up of two monomers joined together. They are a good store of energy and are easily broken � down.� Polysaccharides (eg. Starch, Cellulose, Glycogen, Chitin) are composed of long chains of monomers. They have different bonding and � branching which gives them different properties including energy storage and structural strength.� 25. a) Glycogen is found in animals.� b) Starch is found in plants.� 26. Lettuce has a lot of cellulose which humans cannot digest and absorb. We only obtain some energy from the cytoplasm of the cells, � which are mostly water.� 27. (see SRAM 2010, page 19)

42 12 BIOLOGY, CH 1

Lipids

Lipids are a diverse group of molecules and include: fats and oils, terpenes, waxes, phospholipids, glycolipids and steroids

whose various functions relate to their hydrophobic nature.

43 12 BIOLOGY, CH 1

Lipids

In cells, lipids have three important functions: 1 energy storage

they have twice the amount of energy as carbohydrates

2 structural component of membranes

3 specific biological functions, such as the transmission of chemical signals both within and between cells (hormones).

44 12 BIOLOGY, CH 1

Lipids

The fats and oils of plants and animals are typically composed of triglyceride molecules – three fatty acid chains attached to a glycerol backbone.

GLYCEROL

45 12 BIOLOGY, CH 1

Lipids

46 12 BIOLOGY, CH 1

Lipids in the membranes of cells

Phospholipids form when a phosphate group is added to the glycerol backbone rather than a third fatty acid chain. Glycolipids form when a carbohydrate group attaches to the glycerol backbone rather than a third fatty acid chain. They are vital for communication and detect, and bind with, signalling molecules. Cholesterol is a component of cell membranes and of myelin sheaths around nerve cells. It belongs to the group of lipids collectively known as steroids.

47 12 BIOLOGY, CH 1

Steroids

From Jacaranda Biology 3&4

48 12 BIOLOGY, CH 1


Presenter

Presentation Notes

28.

49 12 BIOLOGY, CH 1

Proteins

Virtually everything a cell is or does depends on the proteins it contains. Keratin is a protein found in your hair, feathers of birds, the rattle of a rattlesnake and the spines of an echidna. The whole set of proteins produced by a cell is called its proteome and the study of proteomes is proteomics.

50 12 BIOLOGY, CH 1

Proteins

Proteins are large complex molecules and are the most important molecules in living organisms. As enzymes they control the thousands of chemical reactions that maintain life processes. This diversity of proteins can be explained by the way their subunits, the 20 amino acids, are sequenced in various combinations (like arranging 20 kinds of beads in different ways to make different necklaces of different lengths and the necklace chains can then be arranged differently in loops and folds to give each its characteristic features).

51 12 BIOLOGY, CH 1

Proteins

52 12 BIOLOGY, CH 1

Proteins - amino acids Amino acids are small molecules that have the same basic structure: a central carbon atom a hydrogen atom a carboxyl acid group (COO- ) an amine group (NH3

+ ) and an R group.

It is the difference in the R group that distinguishes one amino acid from another and gives them their particular chemical properties. There are only 20 different amino acids found in the proteins of living organisms

53 12 BIOLOGY, CH 1

Proteins - amino acids

Some of the R groups are non-polar, some are polar and others are charged.

Run Molworks

54 12 BIOLOGY, CH 1

Isomerisation in amino acids

55 12 BIOLOGY, CH 1

Proteins - structure Primary structure DNA determines the sequence of amino acids in the polypeptide. Secondary structure various parts of the polypeptide undergo coiling and folding due to interactions between the various amino acids that are present.

Hydrogen bonding Ionic bonding Disulfide bridges Hydrophobic Interactions (van der Waals’ interactions)

Tight coils are known as α-helices and the folding forms β-sheets.

56 12 BIOLOGY, CH 1

Proteins – structure: α-helix

57 12 BIOLOGY, CH 1

Proteins – structure: β-sheet

58 12 BIOLOGY, CH 1

Proteins - structure Tertiary structure R groups attract similar R groups. This causes the polypeptide chains to become folded, coiled or twisted into the protein’s functional shape or conformation. Protein molecules with the same sequence of amino acids will fold into the same shape. A change to just one amino acid will alter the shape of the protein molecule and it may not function properly.

59 12 BIOLOGY, CH 1

Proteins - structure

60 12 BIOLOGY, CH 1

Proteins - structure Quaternary structure Many large, complex protein molecules consist of two or more polypeptide chains. Haemoglobin, for example, which carries oxygen in the blood, consists of four polypeptide chains. A variety of bonds holds the polypeptide chains together and gives the overall shape to the molecule.

Run Cn3D

Program


Jac

aran

da B

iolo

gy 3

&4

62 12 BIOLOGY, CH 1

Protein binding site

63 12 BIOLOGY, CH 1

Proteins - structure

The function of protein molecules may change as a result of a number of factors:

misreading the DNA code for proteins high temperatures strong salty solutions or very acidic or alkaline conditions (pH).

These conditions can denature or change the shape of the protein molecules.

64 12 BIOLOGY, CH 1


65 12 BIOLOGY, CH 1

Review Questions – set 9

Presenter

Presentation Notes

33. Each protein is a chain of amino acids in a particular order. There are 20 different amino acids, so the number of possible combinations on the chain is very large. 34. The structure of a protein (eg. an enzyme) will determine its active site and therefore the type of reaction it can catalyse. 36. Hydrophilic a.a.s are found on the outside of the protein because they interact with water quite easily. Some a.a.s are hydrophilic because they are polar or can form ions. 38. Tertiary structure for single strand (polypeptide chain) proteins; quaternary structure for proteins with more than one polypeptide chain.

66 12 BIOLOGY, CH 1

Nucleic Acids

Nucleic acids store information in a chemical code that directs the machinery of the cell to produce proteins. Nucleic acids DNA (deoxyribonucleic acid) and RNA (ribonucleic acid), are large, linear polymers. A molecule of DNA is composed of two long strands of subunits called nucleotides, wound around each other to form the familiar double helix. RNA is usually composed of a single chain of nucleotides and forms a single strand.

67 12 BIOLOGY, CH 1

Nucleic Acids - Nucleotides A nucleotide has three chemical parts: a five carbon sugar (ribose in RNA and deoxyribose

in DNA) a negatively charged phosphate group an organic nitrogen-containing compound called a

base

68 12 BIOLOGY, CH 1

Nucleic Acids - Bases

There are four kinds of nitrogenous bases in DNA: adenine (A) thymine (T) guanine (G) cytosine (C).

69 12 BIOLOGY, CH 1

Nucleic Acids - Nucleotides In each nucleotide strand, the sugar molecule of one nucleotide binds to the phosphate group of the next nucleotide, leaving the nitrogenous base sticking out from each sugar and opposite the nitrogenous base of the second strand. Hydrogen bonds between the opposing pairs of nitrogenous bases hold the double helix together, much like the rungs of a twisted ladder or a spiral staircase.

70 12 BIOLOGY, CH 1

Nucleic Acids - Nucleotides The bonding of the nitrogen bases does not happen by chance: A bonds with T and C bonds with G,

giving rise to the base-pairing rule.

• also refer to SRAM on Nucleic Acids

71 12 BIOLOGY, CH 1

Nucleic Acids – DNA vs RNA

The difference between the deoxyribose sugar of the DNA and the ribose sugar of RNA is that ribose has one more oxygen atom. The nitrogenous base thymine is replaced by the base uracil (U) in RNA.

72 12 BIOLOGY, CH 1

Nucleic Acids – DNA code The code carried by the DNA is organised in triplets (three nucleotides) that determine the order in which the amino acids are sequenced and this determines which protein is formed. Each cell of our body has over a metre in length of DNA, twisted and coiled into 46 chromosomes that have more than three billion base pairs (bp). The parts of the DNA that code for proteins are called genes. The total set of genes that each cell of an organism has is called its genome. The study of these sets of genes and the way they interact with each other is called genomics.

73 12 BIOLOGY, CH 1

Nucleic Acids – function of RNA RNA has many functions in producing proteins. The information on genes in the DNA that codes for making proteins is transferred to messenger RNA (mRNA). The mRNA molecule carries the code out of the nucleus and into the cytoplasm. This is where the protein-making factories (ribosomes) are located. The ribosomes read the mRNA code three nucleotides at a time (in codons). The ribosomes are composed of ribosomal RNA (rRNA) and protein. The incoming amino acids are attached to transfer RNA (tRNA) molecules. Each tRNA molecule has an anticodon that will bind with a complementary codon on mRNA. This is how the ribosomes know the correct amino acid to add to a growing protein chain.

74 12 BIOLOGY, CH 1

DNA Interactive

View and discuss some of the sections within “THEMES – DNA Molecule”

75 12 BIOLOGY, CH 1

Molecular Specificity DNA and PROTEIN molecules

have specific

structure There is interaction between

molecules The shape of a

molecule determines its function

Binding sites have specificity

Presenter

Presentation Notes

The specificity of binding sites is seen in: Enzyme – substrate binding at the active site. DNA and RNA base pairing during replication, transcription to RNA, codon/anticodon matching Antibody – antigen binding Recognition proteins on cell membranes And many more

76 12 BIOLOGY, CH 1

Review questions – set 10

77 12 BIOLOGY, CH 1

Challenge question 1

78 12 BIOLOGY, CH 1

Challenge question 2

Presenter

Presentation Notes

This is a very good summary and review question.

79 12 BIOLOGY, CH 1 From Jacaranda Biology 3&4

Presenter

Presentation Notes

This is a very good summary and review question.

GTAC Summary Slides covering all biomolecules.

http://www.gtac.edu.au/site/teacher_access/teacher_access_resources/Making%20Biomacromolecules/index.html

80 12 BIOLOGY, CH 1

81 12 BIOLOGY, CH 1

Visual Summary

82 12 BIOLOGY, CH 1

At the end of the chapter do the following activities:

Matchup (on text CD) Self-test (on text CD) Biotech Game

83 12 BIOLOGY, CH 1

What is this?

Clue: Parrot’s name is Polly POLYUNSATURATED

84 12 BIOLOGY, CH 1

What is this?

Clue: Parrot’s name is Polly POLYSACCHARIDE

85 12 BIOLOGY, CH 1

What is this?

Clue: Parrot’s name is Polly POLYNOMIAL

86 12 BIOLOGY, CH 1

What is this?

Clue: Parrot’s name is Polly POLYGON

Date post:	21-May-2018
Category:	Documents
Upload:	tranque
View:	219 times
Download:	2 times

12 BIOLOGY, CH 1 1melba12biology.weebly.com/uploads/1/0/9/9/10997732/biol_3_ch_1... · 12 BIOLOGY,...

Documents