ib biology joni rogan escuela de lancaster a.c.. course outline - theory 1: the chemistry of life ...

IB BiologyIB Biology

Joni Rogan

Escuela de Lancaster A.C.

Course outline - Theory1: The chemistry of lifeStatistical analysis2: Cells 3: Genetics4: 5: Ecology and evolution 6: Human health and physiology

Theory AssessmentMakes up 76% of final grade3 exam papers:

Paper 1- 30 MCQ Paper 2- data based Qs, Extended

response Paper 3- short answer questions

Course Outline- PracticalPracticals make up 24% of final grade.The marks are in 2 parts:

Investigations Group 4 projects

InvestigationsThroughout course as fits with theory

You are assessed on 2 examples of each of the following: Design Data collection Concluding Evaluating

Group 4 ProjectsCross-curricular Science project in

small groups (with Chemistry and Physics)

You design and carry out an investigation on a theme

You are marked on: Manipulative skills Personal skills

To do well in IB Biology.....Work hard and learn at home

throughout the year

Use the rubrics

Learn the command terms

Take the practical work seriously

Biological MoleculesTopic 1

What are living things made of?4 most commonly occuring elements?Other elements?

Element Role served in living things

Sulfur Component of amino acids

Phosphorus Component of nucleotides in DNA and RNA

Iron Role in oxygen transport in animal blood.Component of cytochrome proteins involve in electron transport in plants, animals and prokaryotes

Sodium Role in nerve impulse in animals.Essential for maintaining metabolic activities in some bacteria.

Calcuim Component in strengthening bones and teeth.

What are elements are made of?Chemistry revision!

What are we made of?

Richmond upon Thames College

Introduction For each of the following you should be able to:

Describe the properties Know the general formulae & structure Understand the role in animals & plants

•Water

•Carbohydrates

•Lipids

•Proteins

•Nucleic acids

Water

What is it made of?

How is it chemically arranged and held together?

What does this mean for how it behaves?

How is this useful for life?

WaterWater is a polar molecule It forms weak hydrogen bonds It remains a liquid over a wide

temperature rangeWater molecules stick to one another =

cohesion (surface tension)Water molecules stick to other

substances = adhesion (capillarity)

O

H

H

+

+-

Water It has a high specific heat capacity – so

water can maintain a reasonably constant temperature (homeostasis)

It has a high latent heat of vaporisation – so animals use water to cool themselves

It is less dense as a solid (ice)…… and ice is a poor conductorWater is a good solvent

Property Chemistry Use in living organism

Cohesion Water molecules stick to each other because of Hydrogen bonds

Water is used as a transport medium in the xylem of plants, it can be pulled up tall plants.

Solvent Waters’ polartiy means it can dissolve particles with positive or negative charges or other polar molecules.

Water is the medium for metabolic reactions. It also can be used as a transport medium.

Thermal Water has a large heat capacity, high energy is needed to break the Hydrogen bonds.

Blood (mainly water) can carry heat from warmer parts of body to cooler parts.Water is most useful as a liquid, and is a liquid in most parts of the earth.When water evaporates, energy to break Hydrogen bonds comes from the liquid water, which cools it down. So water can be used as a coolant.

Carbohydrates Contain the elements Carbon

Hydrogen & Oxygen There are 3 types:

Monosaccharides Disaccharides Polysaccharides

Monosacharides

(CH2O)n

If n=3, triose (glyceraldehyde) If n=5, pentose (fructose, ribose) If n=6, hexose (glucose, galactose)Monosaccharides are used for

Energy Building blocks O

C C

C C

C

C

IsomerismThey can exist as isomers:

& glucose OH

OH

DisaccharidesFormed from two monosaccharidesJoined by a glycosidic bondA condensation reaction:

glucose + glucose maltose glucose + galactose lactose glucose + fructose sucrose

Condensation reaction

O

C C

C C

C

CO

C C

C C

C

C

OH OH

Condensation reaction

O

C C

C C

C

CO

C C

C C

C

C

OH OH

Condensation reaction

O

C C

C C

C

CO

C C

C C

C

C

O

H2O

Condensation reaction

O

C C

C C

C

CO

C C

C C

C

C

O

A disaccharide1,4 glycosidic bond

41

PolysaccharidesPolymers formed from many

monosaccharidesThree important examples:

Starch Glycogen Cellulose

Starch Insoluble store of glucose in plantsformed from two glucose polymers:

Amylose

-glucose

1,4 glycosidic bonds

Spiral structure

Amylopectin

-glucose

1,4 and some 1,6 glycosidic bonds

Branched structure

Glycogen

Insoluble compact store of glucose in animals

-glucose units1,4 and 1,6

glycosidic bondsBranched structure

CelluloseStructural polysaccharide

in plants-glucose1,4 glycosidic bondsH-bonds link adjacent

chains

O

O

O

O

O

LipidsMade up of C, H and OCan exist as fats, oils and waxesThey are insoluble in waterThey are a good source of energy

(38kJ/g)They are poor conductors of heatMost fats & oils are triglycerides

TriglyceridesFormed by esterification……a condensation reaction between 3

fatty acids and glycerol:

Glycerol

H

C

H C

C

H

H

H

H

O

O

O

Fatty acidsCarboxyl group (-COOH) attached to a long non-polar

hydrocarbon chain (hydrophobic):

H

H

C

HH

C

H

H

C

HC

O

O

H

C

HH

C

H

H

C

H

H

C

H

H

A saturated fatty acid (no double bonds)

HH

C

O

O

H

C

HH

C C

C C H

C

H

H

C

H

HA polyunsaturated fatty acid

C

O

O

H

C

HH

C

H

H

C

H

H

C

H

C

HH

C

H

H

C

H

H

A monounsaturated fatty acid

H H

Esterification

H

C

H C

C

H

H

H

H

O

O

OC

O

O

H

C

HH

C

H

H

C

H

H

C

H

H

Glycerol Fatty acid

Esterification

H

C

H C

C

H

H

H

H

O

O

OC

O

O

H

C

HH

C

H

H

C

H

H

C

H

H

Glycerol Fatty acid

Esterification

H

C

H C

C

H

H

H

H

O

O

OC

O

O

H

C

HH

C

H

H

C

H

H

C

H

HGlycerol Fatty acid

Esterification

H

C

H C

C

H

H

H

H

O

O

OC

O

O

H

C

HH

C

H

H

C

H

H

C

H

H

Ester bond

water

EsterificationThis happens three times to form a

triglyceride:

glycerol fatty acids

PhospholipidsOne fatty acid can be replaced

by a polar phosphate group:

glycerol Hydrophobic fatty acids

hydrophilicphosphate

Functions of lipidsProtection of vital organsTo prevent evaporation in plants &

animalsTo insulate the bodyThey form the myelin sheath around

some neuronesAs a water source (respiration of lipids)As a component of cell membranes

Research Topics1) Hydrogenated fats

What are they? What foods are they in? How do your bodies deal with them? Why do some people want them banned?

2) Atkins Diet

Why does the diet get people to lose weight? What is the difference between how carbohydrates and fats are stored and metabolised? Why are Doctors worried about people on the diet?

Proteins Made from C H O N & sometimes SLong chains of amino acidsProperties determined by the aa

sequence

Amino acids

H

CH

N C

HH

O

O

R

~20 aaGlycine R=HAlanine R=CH3

aminecarboxyl

Peptide bonding

HC

HN C

HH

O

O

R

HC

HN C

HH

O

O

R

Peptide bonding

HC

HN C

HH

O

O

R

HC

HN C

HH

O

O

R

Peptide bonding

H

CH

N C

HH

O

O

R

HC

HN C

HH

O

O

R

Peptide bonding

CH

N C

HH

OR

HC

HN C

H

HO

H

O

O

R

water

Peptide bond

A condensation reaction

Peptide bonding

CH

N C

HH

OR

HC

HN C

H

O

O

R

A dipeptide

Primary structureThe sequence of aas is known as the

primary structureThe aa chain is a polypeptide

Secondary structureH-bonding forms between adjacent aa

R groupsThis results in the chains folding:

Secondary structure

-helix -pleated sheet

Tertiary structureBonding between R-groups

gives rise to a 3D shapeH-bonds =O HN-

Ionic bonds –NH3-COO-

Disulphide bridge

--CH2S-SCH2-

affected by temp & pH

affected by pH

affected by reducing agents

Quaternary structureSome proteins have

more than one polypeptide chain

Each chain is held together in a precise structure

eg Haemoglobin

Types of proteinsFibrous proteins

e.g. collagen Insoluble structural

Globular proteins e.g.enzymes Soluble 3D shape

Functions of proteins Enzymes – Transport – Movement – Cell recognition – Channels – Structure – Hormones – Protection –

Amylase

Haemoglobin

Actin & myosin

Antigens

Membrane proteins

Collagen & keratin

Insulin

Antibodies

Nucleic acidsDNA & RNAMade up of nucleotides:

phosphate

pentose sugar

base

Nucleotides2 types of base:

Pyrimidines - Cytosine C Thymine T

Purines Adenine A Guanine G

Complimentary base pairingAdenine will only bind with ThymineCytosine will only bind with Guanine

T C GA

DNA structure

nucleotide

Condensation polymerisation of the deoxyribose nucleotides

Questions What things must DNA be able to do to allow an

organism to survive?

How is it possible that DNA can control all of the chemical reactions occurring inside a cell?

What type of protein molecules control DNA replication (can you name any specific ones)?

Why is DNA replication called “semi-conservative”?

Replication During cell division the DNA must replicate The DNA double helix unwinds (helicase

enzyme does this) at the replication fork The exposed bases bind to free floating

nucleotides in the nucleoplasm The enzyme DNA polymerase binds the

complimentary nucleotides Replication is

semiconservative

ReplicationDNA polymerase can only work in one

directionTherefore on one DNA strand

replication occurs in small sections called okazaki fragments

The okazaki fragments are then joined together by an enzyme called DNA ligase

Questions Briefly explain the purpose of DNA replication Summarise the steps involved in DNA

replication (3) Explain the jobs of the following enzymes:

Helicase DNA polymerase

How long do you think it would take for one bacterial cell to replicate all of its DNA?

The genetic codeThe sequence of nucleotide bases

forms a codeEach ‘code word’ has three letter – a

triplet codeEach codon codes for a specific amino

acid e.g: GGG = proline CGG = glycine ATG = tyrosine ACT = stop (no amino acid)

Protein synthesisThe DNA codes for

proteinsA copy of DNA

(mRNA) is made in the nucleus (transcription)

The mRNA is used to make a protein (translation) in the cytoplasm

Transcription The DNA unwinds Only one DNA strand will

be transcribed (the sense strand)

Free nucleotides join onto complimentary bases

RNA polymerase links adjacent nucleotides

The completed mRNA moves out of the nucleus

In RNA there is no thymine (T). Instead, another base, uracil (U) takes its place. U forms hydrogen bonds with A

Transcription

Amino acid activation transferRNA:

tRNA binds onto a specific amino acid

TranslationmRNA binds to a ribosome tRNA carries an amino acid to the

ribosome

TranslationA second tRNA brings another aaThe two aa’s bindThe process repeats

TranslationA polypeptide chain formsEventually a stop codon is reached

The Human Genome Project A multinational project aimed at sequencing

the entire human genome Visit the Human Genome Web site:

www.ornl.gov/hgmis/project/about.html www.sanger.ac.uk

Acknowledgements Animated cell models used by kind

permission of The Virtual Cell website:

Feel free to use this presentation for educational non-profit making purposes.

Quiz 1. Which of the following is not an

important property of water

a) Its polar nature

b) Its low specific heat capacity

c) Its high latent heat of vaporisation

d) Its low density in solid form

Quiz 2. The general formula for a

monosaccharide is:

a) (CH2O)n

b) (CHO)n

c) C(H2O)n

d) CnH2On

Quiz 3. Sucrose is made up of

a) glucose + fructose

b) glucose + galactose

c) glucose + glucose

d) galactose + fructose

Quiz 4. Amylopectin is made up of:

a) -1,4 glycosidic ondsb) -1,4 & -1,4 glycosidic ondsc) -1,4 & 1,6 glycosidic ondsd) -1,4 & 1,6 glycosidic onds

Quiz 5. Formation of a triglyceride does

NOT involve:

a) A condensation reaction

b) Esterification

c) Polymerisation

d) A reaction between 3 fatty acids & glycerol

Quiz 6. The general formula of a saturated

fatty acid is:

a) CnH2nO2

b) Cn(H2O)n

c) (CH2O)n

d) (CH2)nO

Quiz 7. Which of the following is not

responsible for a proteins tertiary structure

a) ionic bonding

b) covalent bonding

c) hydrogen bonding

d) disulphide bonding

Quiz 8. Which of these is not an amino

acid:

a) alanine

b) cysteine

c) glycine

d) cytosine

Quiz 9. Which process involves tRNA:

a) transciption

b) translation

c) DNA replication

d) gene mutation

Quiz 10. The formation of RNA does not

involve:

a) ribose sugar

b) thymine

c) removal of water

d) phosphate