Full notes for Botany BIOL251 PDF

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All the notes from the basic botany concepts used for the course. Including some accessory concepts that aren't mentioned but are really important....

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Full notes for Botany BIOL251 Chapter 1 This course is a freshman course, that will introduce you to some of the main topics that are important in Botany. The course has no prerequisites, and assumes that you have had little, or no, previous experience of Biology. Botany is the study of plants. The main subject matter in this course is: A) Life : the characteristics of living things B) Biochemistry : the important biological chemicals, like proteins and sugars C) Cell structure : what plant cells contain D) Chemical reactions : respiration and photosynthesis E) Cell division : including meiosis F) Plant ancestors and relatives : bacteria, protists and fungi G) The plant kingdom : spore plants, seed plants H) The applications of botany: crops, plant breeding and ecology Why study Botany? Plants are the source of many important products such as:      

Food (including grass for animals) Cotton and other fabrics Paper Wood Coal and oil Antibiotics and other medicines

Botany as a Science Sciences, such as Biology, Chemistry and Physics, use a series of steps, called the scientific method, to try to understand the world around us. Some of the main steps are: 1. Make an observation (for example: plants in one part of my yard grow faster). 2. Come up with a hypothesis : an idea that can be tested. (eg. part of the yard gets more sunlight) 3. Make a prediction : a logical consequence of a hypothesis. (if slow growing plants are given more sunlight they will grow faster) 4. Test the prediction by conducting an experiment. Experiments are often designed to disprove the hypothesis. It is easy to disprove a hypothesis, but

virtually impossible to prove that a hypothesis is correct in all possible situations. The experimental group differs from the control group usually in one variable eg amount of sunlight. Experiments should be repeatable. Sample size : the larger the sample, the more accurate the results. It is better to do an experiment with 200 plants than with 2 plants. Theory : a scientific theory has been supported by many experiments eg atomic theory, the theory of evolution. The main areas of Botany Plant anatomy: the structure of plants Plant physiology: the function of parts of the plant Plant taxonomy: the classification of plants Plant ecology: the interactions of plants and other species Genetics: the study of inheritance Economic botany: the practical uses of plants and plant products. Biological Classification Organisms are classified (put into groups) using this system devised by the Swedish biologist Linnaeus, around 1750. The example below is the classification of corn: Kingdom Plant Phylum ( Phyla ) Magnoliophyta Class Monocots (Liliopsida) Order Commelinales Family Poaceae (grasses) Genus ( Genera ) Zea Species mays

The scientific name is the Genus name followed by the species name eg Zea mays. Members of the same species can interbreed to produce fertile offspring. Members of the same genus are similar, but do not interbreed in the wild. Example: wild perennial maize (Zeaperennis ) is in the same genus as corn, but they do not interbreed.

Chapter 2. Chemicals

Attributes of Living things 1. They are composed of cells. Cells consist of a membrane around the outside, a nucleus containing DNA, and the cytoplasm. 2. Growth 3. Reproduction Sexual reproduction: the offspring vary from the parents Asexual reproduction: the offspring are identical clones 4. Respond to stimuli: for example plants respond to light, water, gravity, touch. 5. Metabolism: all the chemical reactions in an organism. The most critical reactions are respiration and photosynthesis. 6. Movement: for example sperm can swim, whole plants grow in particular directions, or there is cyclosis in cells. 7. Complexity: they are made of molecules and organelles. 8. Adaptation and evolution: populations evolve to become better adapted to their environment.

Atoms & Bonds Element : a substance that cannot be broken down by chemical reaction eg carbon, gold. Everything in the universe is made of 92 different elements. Living things contain a maximum of 25 elements. Important biological elements : Carbon Hydrogen

C

Calcium Potassium

Ca K

H

Oxygen Nitrogen

O N

Phosphorus P Sulfur S

Compound - two or more elements joined by chemical bonds eg salt, water, plastic. Atom - the smallest unit of an element. Particle Proton Neutron Electron

Location Nucleus Nucleus Shells

Weight Charge 1 dalton (amu) +1 1 dalton (amu) 0 1/2000 dalton (amu) - 1

Atomic number = Number of Protons per atom. Atomic number also equals the number of electrons. Example : Carbon has 6 protons and 6 electrons (Table 2.1).

Atomic mass = Number of Protons + Neutrons. Example: carbon 14 has 8 neutrons (14 minus 6 ). Isotopes : atoms of the same element that differ in the number of neutrons. Radioactive atoms : large isotopes that break apart, releasing energy. The energy is either: Alpha particles : weak, cannot penetrate paper. Beta particles : stronger, can penetrate paper but not metal. Gamma rays : very strong, can penetrate metal and harm living things. Radioactive atoms can be used to: a) Track chemicals in the body b) Work out the age of fossils. Accuracy of fossil dating methods c) Track the movement of individual animals (eg butterflies). Isotopes and murder

Chemical bonds Chemical bonds only involve electrons. Valence electrons - electrons in the outer shell ( the valence shell ) of an atom. All atoms try to fill their valence shell of electrons. Maximum number of electrons per shell : First shell 2 Second shell 8 Third shell 8

So, for example, oxygen has a total of 8 electrons. Two go in the first shell, and 6 go in the second shell. Molecule: two or more atoms joined by chemical bonds. A) Covalent bonds are very strong. The atoms share electrons. Examples: hydrogen gas H2 , water H2O B) Ionic bonds are also strong. One atom gives electrons to another. Eg. NaCl or Na+ClC) Hydrogen bonds are weak. A hydrogen atom is attracted to a slight negative charge on a different molecule. Hydrogen bonds are important in holding together proteins.

Macromolecules : very large molecules, made of hundreds, or thousands, of atoms. Many are polymers : large molecules made of similar, small monomers joined together. Hydrolysis : a chemical reaction that breaks polymers into monomers eg digestion Condensation synthesis : a chemical reaction that joins monomers together by removing water. There are 4 types of macromolecule in living things : carbohydrates, lipids, proteins and nucleic acids. 1). Carbohydrates Carbohydrates contain C , H and O. They are made of simple sugars called monosaccharides, such as glucose (C6H12O6), fructose (C6H12O6) and glyceraldehyde (C3H6O3). Monosaccharides dissolve in water. Disaccharides consist of 2 monosaccharides joined by condensation synthesis such as maltose or brewing sugar ( 2 glucose ) and sucrose or table sugar ( glucose + fructose ). Polysaccharides are made of many monosaccharides such as: starch ( energy storage in plants ) and cellulose ( cell walls in plants ). 2). Lipids Lipids contain C , H , and O. Lipids do not dissolve in water. Lipids can be fats, phospholipids , waxes or steroids. A) Fats (triglycerides). Fats are made of glycerol and 3 fatty acids. They are used for energy storage. Saturated fats : no double bonds (only single bonds); straight molecules ; solids ; found in animals ; eg butter Unsaturated fats : have 1 or more double bonds ; bent molecules ; liquids; in plants ; eg corn oil Trans fats are produced during cooking, and are common in cookies, snacks and fried food. Only unsaturated fat in the diet is healthy. You should try to cut back on the saturated and trans fat, as they increase the risk of heart attack.

B) Phospholipids. Phospholipids are made of glycerol, 2 fatty acids and phosphate. Part of the molecule is hydrophobic, part is hydrophilic. Phospholipids make up most of the cell membrane. C) Waxes. Waxes consist of a fatty acid joined to an alcohol. They are used for waterproofing in plants ( and some animals ). 3). Proteins Proteins contain C , H , O and N. They are made of amino acids joined together. There are 20 different amino acids. The order of amino acids in a protein is important. Proteins are found in cell membranes, seeds and as enzymes. Primary structure : the order of amino acids. Secondary structure : the protein folds, and is held by hydrogen bonds. Tertiary structure : covalent or ionic bonds between different side chains of the protein. 4). Nucleic acids Nucleic acids contain C , H , O , N and P. They are made of nucleotides, ( phosphate, sugar and base ) DNA ( Deoxyribonucleic acid ) DNA has deoxyribose as the sugar. It has 4 bases : Adenine Guanine

Thymine Cytosine

Bases pair up and join with hydrogen bonds to form a double helix (Adenine opposite thymine and guanine opposite cytosine). The code on DNA carries information the cell needs to make proteins ( the primary structure). Closely related species have similar DNA. Humans and primates. Similarly, DNA studies can show if what looks like one species is really two different species. RNA ( ribonucleic acid ) RNA has ribose as the sugar. RNA has 4 bases : with Uracil instead of Thymine. RNA is a single strand. RNA moves from the nucleus of the cell to the cytoplasm to allow the cell to make proteins ( mRNA : messenger RNA ). New RNA drugs could be very useful, for example to prevent blood clots or treat cancer.

Chapter 3: Cells All living things are made of cells. Cells are microscopic; cells were first identified in 1665.

Microscopes 1) Light microscopes - focus light on the specimen. - advantages : you can see living cells in color, microscopes are portable and cheap. - disadvantage : magnification only up to 1000 times. 2) Electron microscopes - focus a beam of electrons on the specimen. - advantage : high magnification ( up to 1 million times ). - disadvantages : you can only see dead cells in black/white, not portable and expensive. Prokaryotic cells are in bacteria. They are small, and have no nucleus or organelles. Eukaryotic cells are in plants, fungi, animals. They are larger, and have specialized organelles. The Cell Cells consist of : membrane, nucleus and cytoplasm. Membrane The plasma membrane separates cells from their surroundings. Membranes are made of phospholipid and protein, arranged in a fluid mosaic. Membranes are selectively permeable : they only let some chemicals through (generally small moelcules). Nucleus: The nucleus contains DNA arranged in chromosomes. It is surrounded by nuclear membrane which has pores to let chemicals in and out. The nucleolus, which is inside the nucleus, produces ribosomes. Cytoplasm : the area outside the nucleus. It contains many organelles, listed below: 1). Ribosomes : contain RNA. They use this RNA to produce proteins. 2). ER (Endoplasmic reticulum) is in two types: Rough ER : a series of membranes with ribosomes. It produces new membrane and proteins. Smooth ER : is membranes without ribosomes. Smooth ER produces lipids.

3). Dictyosomes (called Golgi body in animals) : packages and ships off chemicals around the cell. 4). Vacuoles : typically found in plants. Storage vacuoles hold water, minerals, & poison (to deter herbivores). 5). Mitochondria : have a smooth outer membrane, and a folded inner membrane. They break down food to produce ATP (energy). 6). Plastids such as Chloroplasts : only found in plants. They contain chlorophyll. Chloroplasts consist of grana (membranes) and stroma (liquid). They carry out photosynthesis to produce carbohydrate. 7). Cytoskeleton : controls the shape, and movement, of the cell. It consists of microtubules and microfilaments ; Microtubules : are made of the protein tubulin . They move cellulose to the cell wall. Microfilaments : made of the protein actin. They cause acytoplasmic streaming or cyclosis in plants.

Chapter 4 : Cell reproduction Mitosis (Chapter 3 in the textbook) Cell division is needed for growth, asexual reproduction and to replace dead cells. Cell cycle Fig 3.16.: Interphase (where the cell grows and DNA replicates) is followed by Mitosis ( where the cell divides into two ). Stages of Mitosis

Prophase : the spindle (made of microtubules) forms. The spindle will control the movement of the chromosomes. The chromosomes are visible scattered at random. Metaphase : the chromosomes line up in the center of the cell. Anaphase : the centromeres divide. The chromosomes move to opposite ends of the cell ( many chromosomes form a V shape ). Telophase : two nuclei form. The cytoplasm divides ( cytokinesis ). Animal cells divide from the outside towards the center, plant cells divide from the center outwards.

Reproduction and Meiosis Diploid cells - have two sets of chromosomes ( 2n ). Fig 12.6. Examples leaf, root, stem. Haploid cells - have one set of chromosomes ( n ). Examples sperm (or pollen) and egg.

Comparison of Mitosis and Meiosis Mitosis Meiosis One cell division Two cell divisions One cell produces 2 cells One cell produces 4 cells

No pairing Chromosomes pair up in Prophase I No crossing over Crossing over occurs Chromosome number unchanged Chromsome number halved in Anaphase I Produces diploid cells Produces haploid cells eg leaf eg sperm or egg

Alternation of generations The sporophyte is a diploid plant which produces spores by meiosis. Each spore is haploid and will grow into a haploid gametophyte. The gametophyte produces sex cells (gametes) by mitosis. Once the sperm fertilizes the egg you have a diploid zygote (fertilized egg), which will grow into a diploid sporophyte again. Chapter 5 : Metabolism Producers and consumers

: a chemical process that uses light energy and produces carbohydrates. Photosynthesis is carried out by plants, algae and some bacteria. Anything which carries out photosynthesis is called a producer. Photosynthesis

Consumers, like animals (including humans) and fungi, get their

food by eating plants. They cannot make organic molecules from scratch, like producers. Photosynthesis is a series of reactions that form glucose and other carbohydrates.

Photosynthesis

6 CO2 + 12 H2O ----------> C6H12O6 + 6 H2O + 6 O2 Leaf structure

Water comes into the leaf through veins from the roots. CO2 enters the leaf through small holes called stomata. Chloroplasts are mainly on the top surface of the leaf. There are two stages of photosynthesis : 1) Light reactions : use light energy to form chemical energy (ATP and NADPH). 2) Calvin cycle (light-independent reactions) : uses NADPH and ATP to form carbohydrate from carbon dioxide. Chlorophyll reflects ( does not use ) green light; it absorbs ( uses )

red and blue light. Fig 10.7. Electron acceptor molecules hold high energy electrons, to stop them from wasting the energy as heat. A photosystem is a chlorophyll molecule, electron acceptor and other light gathering molecules like carotene. Fig 10.5 Light reactions

The light reactions take place in the grana of the chloroplast. The light reactions produce ATP and NADPH, and also split water molecules. Fig 10.8

Calvin cycle

This takes place in the stroma of the chloroplast. It takes in CO2 and produces carbohydrate ( glyceraldehyde phosphate or GA3P ). Fig 10.10. The Calvin cycle uses the ATP and NADPH that were produced in the light reactions. Three different types of plants: Fig 10.12

: typical plants that open their stomata during the day, and close their stomata at night. Common plants in cool areas eg Canada.

1) C3 plants

: open their stomata only briefly during the day. They store CO2 as a 4 carbon sugar. Mainly tropical plants eg sugarcane.

2) C4 plants

: only open their stomata at night. These are desert plants like cactus. 3) CAM plants

Respiration Cellular respiration is a chemical reaction that releases energy

from

food. Animals, plants and fungi all carry out respiration. In respiration, oxygen is used to break apart food molecules. The energy released by this reaction is stored as the chemical ATP. When the cell needs energy, it breaks down ATP (adenosine tri-phosphate) to ADP (adenosine di-phosphate). respiration : uses oxygen. does not use oxygen. Aerobic

Aerobic respiration

Anaerobic

respiration :

Glucose + Oxygen produces Carbon dioxide + Water + Energy C6H12O6 + 6 O2 produces 6 CO2 + 6 H2O. Energy is stored in the cell as ATP or NADH. Aerobic respiration is divided into three main stages: Glycolysis, Citric acid cycle and Electron transport chain. Fig 10.14 Glycolysis:

Glucose ( 6 carbon atoms) is split into 2 molecules of pyruvic acid (3 carbons each). This produces 2 ATP and 2 NADH. Glycolysis takes place in the cytoplasm. Citric acid cycle

This breaks down the pyruvic acid to carbon dioxide. This produces 2 ATP and 6 NADH , for every glucose molecule entering glycolysis. The citric acid cycle takes place inside the mitochondria. The citric acid cycle produces the CO2 that you breath out. Electron transport chain

This stage produces most of the energy ( 32 - 34 ATP molecules, compared to only 2 ATP for glycolysis and 2 ATP for Krebs cycle). Table 10.1. This stage converts the NADH into ATP. The electron transport chain works as a proton pump: it pumps hydrogen ions (protons) through the membrane, and only allows them back through a protein (ATP synthase) which makes ATP.

The electron transport chain uses oxygen to accept electrons at the end of the chain (the electrons combine with hydrogen ions and oxygen to produce water molecules). The electron transport chain takes place in the mitochondria. Anaerobic respiration ( or fermentation) Anaerobic respiration does not use oxygen. Only glycolysis can occur. Single celled organisms eg bacteria and yeast can survive anaerobically. Large animals (eg humans) build up an oxygen debt when anaerobic. During anaerobic respiration, pyruvate builds up and is converted to : lactic acid in animals. ethanol ( alcohol ) in plants. Chapter 6 : Biological classification (Review from chapter 1:) Linnaeus first used this system of classification in 1753 for his book "Species Plantarum" (Species of plants). Kingdom Phylum

Plant Anthophyta

Class

Monocotyledons

Order

Commelinales

Family

Poaceae

Genus

Zea

Species

mays

The "scientific name" is the genus and species name eg Zea mays, Homo sapiens, Alligator mississipiensis. Classification website

Originally, Linnaeus had only two Kingdoms: Plants and Animals. More recently, this has been expanded to six kingdoms: Archaea: ancient bacteria: prokaryotic cells, often anaerobic, cell walls lack muramic acid. Bacteria: more modern, prokaryotic, usually aerobic, cell walls have muramic acid. Protists: eukaryotic, very diverse group: unicellular and multicellular, some photosynthetic, some animal like, some slime molds. Basically, this group is a mess! Fungi: eukaryotic, cell walls have chitin, typically multicellular, heterotrophs, often decomposers. Plants: eukaryotic, photosynthetic, cell walls have cellulose. Animals: eukaryotic, heterotrophs, no cell wall. Taxonomists classify living organisms, and also produce dichotomous keys to help identify living things. Simple key Cladistics means comparing organisms, to try to find features in common that will indicate the natural, or evolutionary, relationship between the organisms.A cladogram shows the evolutionary relationships between species, so you can tell which animal is most closely related to another.

Chapter 7 : Kingdoms Bacteria and Archaea. Bacteria have prokaryotic cells, usually 1 - 5 micrometers wide. Many sp...