Chapter 1_Introductiodftyn-What Do Life Sciences Study_20150115

Chapter 1 Introduction: What do life sciences study?

Fundamentals in Biology (2014-2015)

Dr. Ibis KC Cheng

1

Textbook:

Lehninger Principles of Biochemistry; DL Nelson (Sixth Edition) Chapter 1: The Foundations of Biochemistry

Overview

Five Kingdoms

The Cell Concept

Prokaryotic Cells

Eukaryotic cells

Functions of Organelles

Bioenergetics

2

Life Science

Life Science (Biology) is devoted to the study of living organisms.

3

Anatomy

(gross structure) Physiology

(gross function)

Histology

(tissue)

Cell biology

(cells)

Biochemistry and Molecular Biology

(molecules)

Genetics

(inheritance)

Zoology

(animals)

Botany

(plants)

Microbiology

Virology (viruses)

Bacteriology (bacteria)

Mycology (fungi)

Branches of Biology

Five Kingdoms

All cellular organisms fall into two natural groups, known as prokaryotes and eukaryotes.

The terms prokaryote and eukaryotes refer to differences in the location of the DNA (the genetic material).

Prokaryotes

The DNA is not enclosed by nuclear membranes and lies free in the cytoplasm.

The cells therefore lack of true nuclei.

Eukaryotes

Do contain true nuclei.

Evolved from prokaryotes.

4

Five Kingdoms

Five kingdoms include the prokaryotae and four eukaryotae kingdoms.

5

Living organism

Prokaryotae

e.g. Bacteria

Eukaryotae

Protocitista Fungi Plantae Animalia

Viruses

not cellular

Five kingdoms

One group of “organisms” that does not fit neatly into any classification scheme is the viruses.

Viruses are extremely small particles consisting only of a piece of genetic material (DNA or RNA) in a protective coat of protein.

They do not have a cellular structure.

They can only reproduce by invading living cells.

6 Influenza virus Human immunodeficiency virus

(HIV)

Bacteriophage Human Papilloma virus

(HPV)

Hepatitis C virus

(HCV)

Hepatitis B virus

(HBV)

The Cell concept One of the most important concepts in biology is that the basic unit of structure and function in living organisms is the cell.

Cells as seen with the light microscope.

7

The Cell Concept

The size of the cells bears no relationship to the size of the organism.

An elephant and a flea have cells of about the same size

The elephant just has more cells than the flea

Why is such uniformity in cell size maintained?

8

The Cell Concept

9

The surface area to volume ratio for an object of a given shape depends on its size.

The Cell Concept

The complex chemical processes in a cell and the large molecules that participate in them require a significant volume.

The cell must also exchange substances with its surroundings to support the active metabolism within the cell that require a significant surface area.

Too large a cell will not have enough surface for this exchange to occur.

10

The Cell concept

A cell can be thought of as a bag of chemicals which is capable of surviving and replicating itself.

Without a barrier between the bag and the environment, the chemicals would mix freely and the differences could not be maintained. Life could not exist.

The barrier which surrounds all living cells is known as a cell membrane.

11

The Cell concept

Cell membrane

It is made by phospholipid bilayer.

It allows the cell to maintain a constant internal environment.

12

The Cell concept

Cell membrane (con’t)

It is selectively permeable controlling exchange between the cell and its environment.

It can communicate with adjacent cells and receive extracellular signaling.

13

The Cell concept

14

Cytoplasm

The living material between the nucleus and the cell surface membrane is known as cytoplasm.

This contains a variety of organelles.

An organelle is a distinct part of a cell which has a particular structure and function.

Prokaryotic Cells

They are the most ancient group of organisms, having appeared about 3500 million years ago.

The smallest organisms with a cellular structure.

Typical example: Escherichia coli (E. coli) - Rod-shaped bacterium

15

Prokaryotic Cells

Surrounded by a plasma membrane and usually by a strong and rigid cell wall which is made up of polysaccharide chains.

The cytoplasm is not divided into compartments. Flagella

Nucleoid region

Ribosomes

Cytosol

Plasma membrane

Periplasmic space

Outer membrane

Pili

~~

Cell wall

E. coli cell

~ 0.5µm, diameter

~ 1.5 µm long

16

The genetic information is in form of one or more DNA molecules that freely exist in the cytosol.

The total DNA is much less than that of a eukaryotic cell.

The surface of a prokaryotic cell may carry pili (for attaching to other cells) and flagella (for swimming).

Eukaryotic Cells

Most eukaryotic cells are larger than prokaryotic ones.

They are compartmentalized.

Specialized functions are carried out in organelles.

Animal Cells

Plant Cells

17

Animal cell

18

Eukaryotic Cells

19

Plant cell

Eukaryotic Cells

Comparison of Prokaryotic and Eukaryotic Cells

Prokaryotes and Eukaryotes

20

Chloroplast

Mitochondria

Evolution of Eukaryotes

21

Organelles in Eukaryotic cells

22

Nucleus

Surrounded by nuclear envelop of two membranes that is perforated by nuclear pores.

Nuclear pores allow exchange of substances between the nucleus and the cytoplasm. E.g. messenger RNA (mRNA)

The nucleolus appears as a rounded, darkly stained structure in nucleus. Its function is to make ribosomes for protein synthesis.

Chromatins

Nuclear pores

Nuclear

envelop

Nucleolus

Chromosome

Organelles in Eukaryotic cells

23

Nucleus (con’t)

Deeply staining material known as chromatin is the loosely coiled form of chromosomes.

Chromosomes contain DNA associated with basic protein called histone.

Chromatin and condensed chromosome

DNA is wound around the histones which from bead-like structures called nucleosomes.

Chromosomes appear as thread-like structures just before nuclear division.

Organelles in Eukaryotic cells

Nucleus (con’t)

DNA is the genetic material for controlling the cell’s activities.

Nuclear division is the basis of cell replication (DNA can replicate itself), and hence reproduction (new cells can form).

24

Cell division (mitosis)

Organelles in Eukaryotic cells

25

Mitochondrion

Surrounded by an envelop of two membranes.

The inner membrane being folded to from cristae.

Contains a matrix with a few ribosomes, a circular DNA molecule.

It is the powerhouse of cells providing energy in the form of ATP from oxidative respiration.

Organelles in Eukaryotic cells

Endoplasmic reticulum (ER)

A system of flattened, folded membrane-bound structure.

It is continuous with the outer membrane of the nuclear envelope.

If ribosomes are found on its surface it is called rough ER and transports proteins made by the ribosomes through the sac.

Smooth ER (no ribosomes) is a site of lipid and steroid synthesis.

26

Organelles in Eukaryotic cells

Ribosomes

Attached to the surface ER or free in cytoplasm.

Inside the mitochondria and chloroplasts.

Consist of a large and a small subunit.

They are made of roughly equal parts of protein and RNA (ribosomal RNA, rRNA).

They are used in protein synthesis.

27

Organelles in Eukaryotic cells

Ribosomes (con’t)

28

Protein synthesis (Translation)

Organelles in Eukaryotic cells

29

Golgi apparatus

Flattened membrane-bound chambers.

It is continuously formed at one end of the stack and budded off as vesicles at the other.

Internal processing system

Modifies proteins from ER

Internal transport system

Transport the materials to other parts of the cell or to the cell surface membrane for secretion.

Organelles in Eukaryotic cells

Golgi apparatus (con’t)

Makes lysosomes.

Lysosomes contain many digestive enzymes to get rid of old organelles, digest bacteria, autolysis (self-digestion).

30

Organelles in Eukaryotic cells

31

Pieces of the ER bud off around proteins, form vesicles and deliver these proteins to the Golgi

Organelles in Eukaryotic cells

32

Microfilaments and microtubules

They are cytoskeleton providing the cell with shape, strength, and movement (cell motility).

Organelles in Eukaryotic cells (Plant)

33

Cell wall

Outside the cell membrane.

It is rigid because it consists of cellulose microfibrils.

It provides mechanical support and protection.

It prevents osmotic bursting of the cell.

Cell wall

Organelles in Eukaryotic cells (Plant)

34

Cell wall (con’t)

It contains pores containing fine threads known as plasmodesmata which link the cytoplasm of neighboring cells through the cell walls.

Plasmodesmata

Organelles in Eukaryotic cells (Plant)

35

Chloroplast

Present in photosynthetic eukaryotes.

It is surrounded by an envelop of two membranes.

Contains a gel-like stroma through which runs a system of stacked membranes called grana where starch is stored.

The stroma also contains ribosomes, a circular DNA molecule.

Photosynthesis takes place there, producing sugars from carbon dioxide and water using light energy trapped by chlorophyll.

Biological Molecules

Biochemistry is the study of the chemicals of living organisms.

Living creatures are composed mainly of a very few elements, principally carbon (C), hydrogen (H), oxygen (O) and nitrogen (N).

These elements are important to life because of their strong tendencies to form covalent bonds.

A “second tier” of essential elements includes sulphur (S) and phosphorus (P).

Sulphur: constituent of proteins.

Phosphorus: energy metabolism (ATP) and the structure of nucleic acids (DNA and RNA).

36

Bioenergetics

A living cell is a dynamic structure.

It GROWS, MOVES, SYNTHESIZES complex macromolecules (Proteins, Carbohydrates, Lipids and Nucleic acids) and SHUTTLES substances in and out between compartments.

All of these activities requires ENERGY.

Energy has an ability to do work or bring about change.

Plants gather energy from sunlight while animals use the energy stored in plants or other animals.

Bioenergetics is a quantitative analysis of how organisms gain and use energy.

37

Bioenergetics

First law of Thermodynamics

Energy cannot be created nor can it be destroyed.

The quantity of energy remains the same.

It can be transformed from one form into another, but the total amount of energy in the universe remains constant.

38

Bioenergetics Second law of Thermodynamics

Systems of molecules have a natural tendency to randomization.

The degree of randomness or disorder of a system is called entropy (S).

The entropy of an isolated system will tend to increase to a maximum value.

39

Bioenergetics

Every biological system is open to exchange energy and matter with its environment.

40

Both energy and entropy changes will take place in many reactions.

Both are important in determining the direction of thermodynamically favorable processes.

Bioenergetics

The total (internal) energy is called enthalpy (H).

The useable energy is called Gibbs free energy (G).

The unusable energy is entropy (S), a measure of the disorder of the system.

The Gibbs free energy is defined as:

41

For favorable reaction: DG < 0 (Spontaneous, exergonic)

Decrease in DH (-ve) Increase in DS (+ve)

For unfavorable reaction: DG > 0 (Not spontaneous, endergonic)

Bioenergetics - Metabolism

Exergonic reaction

G products < G reactants

Reaction will proceed. spontaneously

Free energy is released.

Endergonic reaction

G product > G reactants

Free energy is required or consumed.

42

Bioenergetics - Examples

?ΔG? ?ΔG?

?ΔG?

43

44

Functions of ATP

Provision of energy in macromolecules synthesis.

Transporting substances across the plasma membrane.

Motility, muscle contraction, beating flagella.

Bioenergetics - Metabolism

Structure of ATP

Bioenergetics - Metabolism

45

ATP

Bioenergetics - Metabolism

46

Bioenergetics - Metabolism

(Exergonic)

(Endergonic)

Coupled reactions

The free energy released by the exergonic reaction can be used to drive the endergonic reaction.

47