IB Biology Topics 3 Chemistry of Life, Nucleic Acids, Cell Respiration & Photosynthesis

3.1 Chemical Elements & Water

3.1.1
The most frequently occurring chemical elements in living things are carbon, hydrogen, nitrogen and oxygen. A variety of other elements are needed by living organisms including sulfur, calcium, phosphorus, iron and sodium.
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3.1.3
Element Sulfur Calcium Co-factor in some enzymes Role in plants Role in animals In some amino acids Co-factor in some enzymes and component of bones Co-factor in some enzymes Role in prokaryotes

Phosphorous Iron In cytochromes (enzyme that contains iron)

Phosphate groups in ATP In cytochromes In cytochromes and in hemoglobin (protein responsible for transporting oxygen) In membrane function and sending nerve impulses In membrane function

Sodium

In membrane function

3.1.3
Nitrogen is a major element of proteins and nucleic acid (for DNA and RNA). Calcium is neccesary for bone and tooth formation, blood clotting, and nerve impulse transmission. Phosphorus is also used for bone and tooth formation, and to balance acid and base concetrations in the body. Iron is a part of hemoglobin, a molecule needed to carry oxygen in the blood. Sodium balances both water in the body and acid/base concentration. It also functions in nerve function.
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3.1.4
H and O in a single water molecule are held together by a polar covalent bond. Single O atom is bonded to 2 different H atoms. Each O-H bond is a polar covalent bond and results in (-) charge at O end and (+) charge a the H end.

3.1.4

3.1.5
Properties of Water
Thermal Properties: Cohesive Properties: Solvent Properties: Thermal Properties:
High specific heat: water can absorb or give off a great deal of heat without changing temp. quickly
In living things water acts as a temp. stabilizer High heat of vaporization: absorbs a lot of heat when it evaporate

Cooling mechanism internal body that result in perspiration. Perspiration then evaporates. Heat that turned the water from liquid to vapor came from the body and thus sweating makes you feel cooler and lowers body temp.
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3.1.5
Properties of Water
Cohesive Properties:
Result of polar covalent bonding Cohesion results in
Water forms droplets Surface tension Water able to move as a column in vascular tissues of plants High heat capacity and high heat of vaporization

 Properties of Water
Solvent Properties:
Carbohydrates Proteins Nucleic acids (RNA and DNA)

3.1.5

Water is an excellent solvent of other polar molecules

Non-polar molecules
Lipids body has special strategies to deal with transport and biochemistry

Aqueous solution (fluid that is primarily water)

Aqueous solution Cytoplasm

Location Fluid inside cell but outside organelles

Common reaction Glycolysis/protein synthesis reactions

Nucleoplasm
Stroma

Fluid inside nuclear membrane

Fluid inside chloroplast membrane Fluid in arties, veins, and capillaries

DNA replication/transcription
Light-independent reactions of photosynthesis Loading and unloading of respiratory gases/clotting

Blood plasma

3.1.5
Water is transparent which allows light to filter into the oceans. This allows for aquatic plants to absorb light and perform photosynthesis. Since the ancestor of all plants originated in the ocean, the transparency of water has had a immeasurable influence on life as we know it. Water is also cohesive, that is it binds to itself, due to the polarity of the water molecule. The positive, hydrogen side of the molecule binds to the negative, oxygen side of another water molecule. This bond is called a hydrogen bond Thus, a glass of water could be considered one giant molecule, because all of the water molecules inside of it are bonded to one another. This property allows for transport of water against gravity in plants.

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3.1.5 (Continued)
Water is the universal solvent because it is capable of dissolving many organic and inorganic particles. All the reactions in cells must take place in aqueous solution. Water's polarity also inhibits movement of its molecules. Since all the molecules are connected, they cannot freely move about as other, nonpolar molecules do. Heat, the kinetic energy of molecules, is thus restricted and so water has a high specific heat (it must absorb large amounts of energy in order to change states). This means that water can serve as a temperature insulator, and does so in organisms of all kinds.

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3.1.6
Water's high specific heat allows it to absorb large amounts of energy and act as an insulator for all living things. For example, our bodies use water in the for of sweat to lower body temperature. The sweat absorbs a large amount of heat, and then evaporates carryiing that heat away from the body.
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IB Biology Topics 3 Chemistry of Life, Nucleic Acids, Cell Respiration & Photosynthesis
3.2 Carbohydrates, Lipids & Proteins

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3.2.1
Compounds containing carbon that are found in living organisms, except hydrogencarbonates, carbonates and oxides, are organic. Compounds that do not contain carbon are inorganic.

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3.2.2: Identify amino acids, glucose, ribose, and fatty acids from diagrams showing their structure.

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Amino Acids

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 Glucose

3.2.2 (Continued)

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3.2.2 (Still)
Ribose

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3.2.2 ()
Fatty Acids

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3.2.3
Three examples of monosaccharides are glucose, fructose, and galactose. Three examples of disaccharides are maltose, lactose, and sucrose. Three examples of polysaccharides are starch, cellulose, and glycogen.

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Animals:

3.2.4
Monosacchari Chemical fuel de for cell respiration Disaccharide Makes up some of the solutes in milk Polysaccharide Stores glucose in liver and muscle 22

Glucose

Lactose

Glycogen

3.2.4 (continued)
Plants:
Fructose Monosaccharide Found in many fruits (makes them sweet)
Often transported from leaves of plants by vascular tissue One of the primary components of plant cell walls
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Sucrose

Disaccharide

Cellulose

Polysaccharide

3.2.5:
For monosaccharides, fatty acids, and amino acids to become disaccharides, glycerol, and didpeptides, a condensation reaction needs to occur. When these monomers covalently bond, a water molecule is released; this is a condesation reaction. When many monomers join together through condensation reactions, polymers result. In a hydrolysis reaction, the addition of a water molecule breaks down the covalent bonds and polymers break down into monomers.

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Hydrolysis Reaction
When animals eat foods, the food is digested (or hydrolysed) into building blocks. After these building blocks are transported to body cells, they are bonded together to form larger molecules once again.
Foods are chemcially digested in your alimentary canal. Digestive enzymes = hydrolysing enzymes. Hydrolysis reaction requires a molecule of water as a reactant.

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Hydrolysis Reaction
Hydrolysis of a disaccharide to 2 monosaccharides
Lactose + water glucose + galactose Hydrolysis of a polysaccharide to many monosaccharides
Strach + many (water) many glucose

Hydrolysis of a triglyceride lipid to gylcerol & fatty acids

Triglyceride + 3 water glycerol + 3 fatty acids

Hydrolysis of a polypepetide (protein) to amino acids

Protein + (many) water (many) amino acids

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Condensation Reactions
Reverse of hydrolysis reactions. Re-form the larger biochemically important molecules. Water molecule(s) are produced. Require a different type of enzyme, one that is capable of catalysing reactions in which covalent bonds are created not broken. Condensation of amino acids to form a polypepeide.
(many) amino acids protein + (many) water

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3.2.6: Role of Lipids

Triglyceride lipids solid form, referred to as fat Triglyceride lipids liquid form, referred to a oil Important roles: Energy storage Adipose cells gets larger or smaller depending on how much lipid is being stored. Stores ~2x more chemical energy as carbs Thermal insulation blubber (fat) Cell membrane special category of lipids called phospholipid Also, some lipids function as hormones.

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3.2.7: Compare the use of carb and lipids in energy storage

The use of carbohydrates in energy storage is through its sugar polymers, glycogen in animals and starch in plants.
These sugars are released when the demand for sugar increases.

Animals use lipids, mainly fats, for longterm energy storage. Lipids store ~approximately 2x chemical energy as the carbs
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3.2.7 Compare the use of carbohydrates and lipids in energy storage

Similarities: Complex carbohydrates (e.g. polysaccharides) and lipids both contain a lot of chemical energy and can be used for energy storage Complex carbohydrates and lipids are both insoluble in water - they are not easily transported Carbohydrates and lipids both burn cleaner than proteins (they do not yield nitrogenous wastes) Differences: Lipid molecules contain more energy per gram than carbohydrates (about twice as much) Carbohydrates are more readily digested than lipids and release their energy more rapidly Monosaccharides and disaccharides are water soluble and easier to transport to and from storage sites than lipids Animals tend to use carbohydrates primarily for short-term energy storage, while lipids are used more for long-term energy storage Carbohydrates are stored as glycogen in animals while lipids are stored as fats (in plants carbohydrates are stored as cellulose and lipids as oils) 30 Lipids have less effect on osmotic pressure within a cell than complex carbohydrates

IB Biology Topics 3 Chemistry of Life, Nucleic Acids, Cell Respiration & Photosynthesis
3.3 DNA Structure

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 Subcomponents of DNA
Nucleotide

3.3.1 & 3.3.2

Made of a phosphate group, deoxyribose and nitrogenous base.

Four bases in DNA Adenine, Thymine, Guanine, Cytosine

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3.3.3
DNA is shaped like a spiral staircase. There are two strands. The sides are made of deoxyribose sugars and phosphates. Rungs are made of nitrogenous bases.
Two nitrogenous bases make up each rung. The bases are held together by hydrogen bonds. A T bonded together by two hydrogen bonds G C bonded together by three hydrogen bonds

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3.3.5
Diagram of the molecular structure of DNA.

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IB Biology Topics 3: Chemistry of Life, Nucleic Acids & Cell Respiration and Photosynthesis
3.4 DNA Replication

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 Cells prepare for cell division by doubling the DNA content of the cell, and this ensures that there is an exact copy of the DNA molecule.

Two types of molecules are very important in DNA replication.

Enzymes: Helicase and a group of enzymes called DNA polymerase. Free nucleotides: found floating freely in the nucleuoplasm and they contain adenine, thymine, cytosine, or guanine. Helicase initiates the separation of the of the double helix into two strands. It starts in or at the end of a DNA molecule and moves up one complementary base pair, breaking the hydrogen bonds.

Unpaired nucleotides on the single strands can be used as a template to create two new double-stranded DNA molecules that are identical to the original.
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 The free-floating nucleotides in the nucleoplasm locate an opened strand at the end of the unzipped DNA strand. Once this happens, a second nucleotide joins the first. This requires that the two nucleotides are covalently bonded together at the beginning of a new strand. The bonds between the two adjoining nucleotides are catalyzed by DNA ploymerase. A third nucleotide joins the first two, and this process continues repetitively. The other unzipped strand forms in the same manner as the first, but in the opposite direction.

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38

 Pattern of DNA replication makes sure that two identical copies of DNA are produced. Where the replication has occurred the two strands are identical to each other. The original double-stranded molecule had complementary pairs of nucleotides, and it was the complementary nucleotides that used the unzipped single-stranded areas as templates.

This means that no DNA molecule is ever totally new. Every DNA molecule after replication consists of an old strand and a new strand.
This process is considered to be a semiconservative process because half of the pre-existing DNA molecule is saved.

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State that DNA replication is semiconservative.

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IB Biology Topics 3: Chemistry of Life, Nucleic Acids & Cell Respiration and Photosynthesis
3.5 Transcription & Translation

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Protein, Protein, Protein, Protein

DNA controls the proteins produced in a cell.
Some proteins are enzymes Production (or lack of production) of a particular enzyme can have a dramatic effect on the biochemistry of the cell DNA indirectly controls the biochemistry of carbs, lipids, and nucleic acids by the production of enzymes

Protein synthesis has 2 sets of reactions

Translation and transcription
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3.5.1 (Venn Diagram)

DNA RNA contains a 5-carbon sugar contains ribose sugar Each nucleotide has one of four nitrogenous bases two strands forming a double helix contains deoxyribose sugar nucleotides Adenine, Cytosine, Guanine, Thymine contains one strand nucleotides Adenine, Cytosine, Guanine, Uracil

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Transcription Fun!!!
Sections of DNA that code for polypeptides are called genes A specific sequence of nitrogenous bases found in a specific location in DNA DNA is in nucleus but proteins are synthesized outside the nucleus in the cytoplasm mRNA intermediary molecule which carries the message of DNA to the cytoplasm where enzymes, ribosomes, and amino acids are found Nucleoplasm (fluid in nucleus) contains free nucleotides for DNA replication and RNA nucleotides
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3.5.2
Note: Transcription is the copying of the nucleotide base sequence of a gene found in DNA by making an RNA molecule matching nucleotide sequence. Area of DNA of one gene becomes unzipped (different from replication b/c only one small section is unzipped) 2 complementary strands created only one of the 2 strands of DNA will be used as a template An enzyme called RNA Polymerase attaches to promoter regions of a DNA strand
RNA polymerase will bind free RNA nucleotides to one of the strands of DNA to create messenger RNA (mRNA) correlate with the DNA strand.

The mRNA breaks away from the DNA strand and can be used for future needs. The DNA strands then recoil and reform into the original double helix shape.

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Transcription FACTS!
Only one of the 2 strands of DNA is copied, the other strand is not used; mRNA is always single-stranded and shorter than the DNA that it is copied from as it is a complementary copy of only one gene; Presence of thymine in a molecule identifies it as DNA Presence of uracil in a molecule identifies it as RNA 47

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3.5.3
Genetic code written in triplets The genetic code is a code that runs on the fact that three nucleotide bases can code for one particular amino acid. The collection of these three bases is called a codon. Every 3 bases codes for 1 of 20 amino acids mRNA produced by transcription represents a complementary copy of one gene of DNA
mRNA is typically enough info. To make one polypeptide (composed of a.a. covalently bonded) Message written into mRNA determines the order of the a.a.
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Types of RNA
mRNA each mRNA is a complementary copy of a DNA gene and is enough genetic info to code for a single polypepetide rRNA ribosomal RNA, each ribosome is composed of rRNA and ribosomal protein
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Types of RNA
tRNA transfer RNA, each type of tRNA transfers 1 of the 20 a.a. to the ribosome for polypeptide formation 3 bases in the middle loop are called anticodon bases and determine which of the 20 a.a. is attached to the tRNA
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Translation 3.5.4
Once mRNA is transcribed it detached from the template DNA and floats free in the nucleoplasm mRNA will float through one of the many holes in the nuclear membrane to the cytoplasm.

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Translation 3.5.4
-mRNA will locate a ribosome and align with it so that the 1st 2 codon triplets are within the boundaries of the ribosome. Specific tRNA molecules now floats in its tRNA anticodon must be complementary to the 1 codon of the mRNA Thus the 1st a.a. is brought into the translation process
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Translation 3.5.4
1st tRNA sits on the ribosome holding the 1st a.a., a 2nd tRNA floats in and brings a 2nd a.a. 2nd tRNA matches its anticodon bases with the 2nd codon triplet of mRNA 2 amino acids are being held side by side An enzyme now catalyses a condensation reaction between the 2 a.a. and the resulting covalent bond between them is a pepetide bond.
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3.5.4 d

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Translation 3.5.4
Next Step: Involves the breaking of the bond b/w the 1st tRNA and the a.a. it transferred This bond is not longer needed as the 2nd tRNA is currently bonded to its own a.a. and that a.a is covalently bonded to the 1st a.a.
1st tRNA floats away into the cytoplasm and reloads with another a.a.
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3.5.4 d

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Translation 3.5.4
Ribosome that has only one tRNA in it now moves one codon triplet down the mRNA molecule. This puts the 2nd tRNA in the ribosome position that the 1st tRNA occupied and creates room for a 3rd tRNA. Fianl codon triplet will be a triplet that doesnt code for an a.a. but signals STOP Entire polypeptide breaks away and floats 59 free in the cytoplasm

3.5.4 d

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Translation in more detail

Step one: A cap and tail are added to the mRNA strand to allow the mRNA strand out of the nucleus. There are intron and exon segments of the RNA strand. The introns are removed by the introduction of a splicesome.
The splicesome pushes out the introns and binds the exons together.

The mRNA then passes through the nuclear pore of the nucleus and travels into the cytoplasm. Step Two: a ribosome and its two subunits will attach onto the mRNA at the ribosome-binding site. Transfer RNA or tRNA are clover-leafed shaped molecules that have a specific amino acid attached.
Each tRNA molecule has three bases that make up the anticodon that binds to the mRNA. The anticodon determines which amino acid the tRNA carries.

The tRNA can only bind to the mRNA in the presence of a ribosome. In each ribosome there are two tRNA binding sites which are the Aminoacyl tRNA binding site or A site and the Peptidinal tRNA binding site or the P site
Each ribosome also has a tRNA exit site or an E site.
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Translation in more detail

The mRNA or the messenger RNA will divide into groups of three nucleotide bases or a single codon. The anticodon on the transfer RNA binds to the complementary codon on the messenger RNA. The mRNA is fed between the two subunits of the ribosome.
The first transfer RNA or codon with the attached start amino acid, methanine, attaches at the A site and is transferred to the P site. The next tRNA binds to the mRNA and contains an amino acid.

When two transfer RNA molecules are bound to the messenger RNA at the ribosome, a ribosomal enzyme forms a peptide bond between the two amino acids. The first transfer RNA molecule becomes detached from its amino acid and moves off from the ribosome after it slides into the exit site or E site.
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Translation in more detail

The ribosome moves a distance of one codon at a time and a new transfer RNA binds bringing in another amino acid to be made into polypeptide chain. The first codon that can be found first and that is translated first on any strand of messenger RNA is always AUG, which is known as the initiation codon. There are also three codons that signal the end of the strand of messenger RNA and stop the process of translation. They are known as stop codons, and some examples are UAG, UAA and UGA. The process of translation can be occurring in several different ribosomes but can be working on the same strand of messenger RNA. This occurrence is known as polysome.
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3.5.5 a
Polypeptides are long chains of amino acids held together by peptide bonds. Amino acids are the translated molecules, that in a certain order, compose a particular type of polypeptide. Genes store the nucleotide bases that are translated to form amino acids in DNA. The sequence of nucleotide bases found in DNA or in genes code for a particular sequence of amino acids in the manufactured polypeptide. The information of the DNA or gene is translated into a specific polypeptide during the process of translation. However, this entire process if accomplished through the actions of transcription and translation.
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3.5.5 b

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IB Biology Topics 3, 7, & 8: Chemistry of Life, Nucleic Acids & Cell Respiration and Photosynthesis
3.6 Enzymes

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3.6.1 Definition of enzyme and active site

Enzymes are proteins Globular shape: Complex and very specific Active site: area that is designed to match a specific molecule (enzyme substrate) Catalysts which speed up biological reactions Can not force reactions to occur that wouldnt otherwise occur Enzymes role: lower the energy needed to start the reaction (activation energy) Not reactants and not used up in a reaction
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3.6.2 Enzyme-substrate specificity

a) Large globular protein enzyme b) Active Site where the substrate combines to the enzyme c)Substrate which fits the active site d) Activated complex. The substrate is weakened to allow the reaction. e)Unchanged enzyme/re-used at low concentrations f) Product of the reaction Enzyme specificity is due to the complementary shape of the active site and the substrate.
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3.6.3 Factors affecting the enzyme reaction Effect of temperature on the rate of an enzyme catalysed reaction:

Reactions are dependent on molecular collisions Reactions with or without enzymes will increase as temp. increases Reactions with enzymes have limits Based on the temp at which the enzyme begins to lose its shape due to intramolecular bonds being stressed or broken. Denaturation permanent or temporary.

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3.6.3 Factors affecting the enzyme reaction Effect of temperature on the rate of an enzyme catalysed reaction:

(a) As temperature increases enzyme stability decreases. The kinetic energy of the constituent atoms increases causing hydrogen bonds to break and active site shape changes. (b) As the temperature increases the kinetic energy of the substrate and enzyme molecules increases. Therefore more collisions of the substrate with the active site and the formation of activated complex's and product. The rate of reaction is increasing. (c) The optimal temperature (X) is the highest rate of reaction. Compromise between enzyme stability and kinetic energy of the reactants. (d) Higher temperature increases the kinetic energy of the enzyme atoms so much that they break bonds, change shape of the active site.

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3.6.3 Factors affecting the enzyme reaction B: The effect of pH on the rate of an enzyme catalysed reaction:

Active site typically included many a.a. Amino acids have areas that are charged (+ or -) (+) and (-) areas of a substrate must match the opposite charge when the substrate is in the active site of an enzyme in order for the enzyme to have catalytic action Too acidic: H+ can bond with (-) charges of the enzyme or substrate Too basic: (OH-) bond with (+) charges Either will result in an enzyme becoming less efficient or inactive Numerous extra (+ or -) charges can result in the enzyme becoming denatured. 73

3.6.3 Factors affecting the enzyme reaction B: The effect of pH on the rate of an enzyme catalysed reaction:

- At the optimal pH (a) or (b) the maximum rate of reaction is achieved. - Above or below the optimal pH the rate decreases. - The change in rate is because bonds are made and broken which change the shape of the active site and therefore decrease the rate of reaction. - The two enzyme shown in the image illustrate the fact that different enzymes can have very different optimal pH. - e.g. Blue curve = pepsin (a)= pH3, Red curve =salivary amylase (b)= pH 7.2
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3.6.3 Factors affecting the enzyme reaction C:

(a) As the substate concentration is increased the rate of reaction increases. There are more collisions between the substrate and the enzyme such that more activated complex's are formed and therefore product per unit time. (b) Further increases in substrate also increase the rate but proportionately less than previously. The number of occupied active site is increasing and there is competition for the active site. (c) The rate is constant. The enzyme active site is fully saturated with substrate such that adding more substrate does not increase the rate of reaction. The enzymes molecules are fully occupied converting substrate to product and any substrate must await a free active site before conversion to product.

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3.6.4 Denaturation
Denaturation: -a structural change in a protein that results in the loss (usually permanent) of its biological properties. -irreversible changes to the structure of an enzyme or other protein so that it can no longer function.

Temperature:(see section 3.6.3) - Temperature rises cause the average kinetic energy of the enzyme atoms to increase. - This vibration breaks the weakest bonds first, which in the enzyme are the hydrogen bonds. - The breaking of bonds, changes the shape of the enzyme. - Change the shape of the enzyme changes the shape of the active site. - Change the shape of the active site prevents substrate from entering. -The rate of reaction reduces or stops.

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3.6.4 Denaturation B

pH: (see section 3.6.3) - At pH lower than the optimal pH the concentration of H+ in the solution will be higher than normal. - The hydrogens will tend to be attracted to electronegative regions of the enzyme protein. - Bonds are formed or changed as a consequence of the additional H+ which changes the shape of the enzyme molecule. - Changes in shape, change the active site shape. - Changes in active site shape reduces the ability of the substrate to bind with the active site. - This reduces the rate of reaction that changes substrate to product. - The rate of reaction reduces. - For pH values above the optimum breaks bonds in the same way and have the same reductions in the rate of reaction

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3.6.5 Lactose-free milk production

Enzyme Immobolisation:
It is possible to make the process more efficient by immobilising the lactose on a recoverable surface such as alginate. -Milk contains the sugar lactose, which is digested in the intestine by the enzyme lactase. -This produces glucose & galactose that can be absorbed by the body. -Lactase can be obtained from a yeast that grows in milk & the enzyme is used to produce lactose-free milk.
- First the Lactase is immobilised in alginate beads. - Next the beads are placed in a container over which milk can be passed. - The milk is collected and re-circulated (pump) to convert any remaining lactose to glucose and galactose. - The circulation is maintained until all lactose has been converted. - This model of an industrial process allow the lactase to be recovered and re-used (cheaper). - Efficient conversion of lactose to glucose and galactose. - Reduced purification of milk since enzyme is retained and a high % lactose conversion is achieved. - All these factors reduce cost particularly on the downstream processing and purification.
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IB Biology Topics 3: Chemistry of Life, Nucleic Acids & Cell Respiration and Photosynthesis
3.7 Cell Respiration

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Some exciting stuff.

Covalent bonds in glucose, a.a., or fatty acids represent stored chemical energy. Burning wood release of stored chemical energy in the from of heat and light.
Rapid oxidation: not controlled by enzymes & results in the breaking of may covalent bonds in a short period of time uncontrolled energy release Slow oxidation: how cells break down organic nutrients
Molecules (glucose) is acted on by a series of enzymes
Catalyse a sequential series of reactions that break covalent bonds (oxidized) one at a time.

Each time a bond is broken energy is released

Ultimate Goal of releasing energy in a controlled way is to trap the released energy in the form of ATP.

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3.7.1 & 3.7.2

Cell respiration: the controlled release of energy from organic compounds in cells to form ATP In cell respiration, glucose in the cytoplasm is broken down by glycolysis into pyruvate, with a small yield of ATP

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Glycolysis
If glucose is being metabolized Glucose enters a cell through the plasma membrane & floats in the cytoplasm 1. an enzyme modifies glucose slightly 2. 2nd enzyme modifies it even more 3. series of reactions which cleave the 6 carbon glucose into 2 3-carbon molecules (pyruvate)
Some covalent bonds in glucose were broken some energy that was released from breaking the bonds was used to form a small # of ATP
2 ATP needed to begin gylcolysis 4 ATP formed NET GAIN = 2 ATP
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3.7.4 Aerobic Respiration

Begins with glycolysis
Glycolysis generates 2 ATP molecules and 2 pyruvate.

The pyruvate enter the mitochondria.

Each pyruvate loses a carbon dioxide molecule and becomes acetyl-CoA.

Acetyl-CoA enters the Krebs Cycle.

From the Krebs Cycle, two more carbon dioxide molecules are produced from each original pyruvate that entered. Cycle because each time it returns to the molecule it reacts with there is another incoming acetyl-CoA

Some ATP is generated in the Krebs Cycle.

Because oxygen is present, aerobic cell respiration breaks down a glucose molecule.

The end products are carbon dioxide and water.

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Cellular Respiration: Step 1: Glycolysis Glycolysis is the process when 1 molecule of glucose(reactant) is broken down into:
2 molecules of pyruvic acid
3-carbon molecule Product of Glycolysis Reactant of Krebs Cycle

2 ATP molecules (Product)

Cellular Respiration: Step 1: Glycolysis 90% available energy is still locked inside the pyruvic acid molecules Takes place in the cytoplasm.

2 Pyruvic acid Glucose

To the electron transport chain

Cellular Respiration: Step 2: Krebs Cycle Overview

The Krebs Cycle is the process where pyruvic acid is broken down into:
carbon dioxide (PRODUCT- waste), ATP (PRODUCT- energy!), NADH (PRODUCT- can generate ATP), FADH2 (PRODUCT- can generate ATP)

Takes place in the mitochondria. ENERGY TALLY (PRODUCT) from 1 pyruvic acid molecule: 4 NADH, 1 FADH2, & 2 ATP

Cellular Respiration: Step 3: Electron Transport Chain

Electron carriers (carrier molecules) are compounds that can accept a pair of highly energized electrons and take them (electron transport chain) and most of their energy to another part of the cell In eukaryotes, it happens in the inner membrane of the mitochondria In prokaryotes, it happens in the cell membrane Produces most of the ATP in the process (32 ATP molecules)

3.7.3 Anaerobic Respiration

Gylcolysis is common to all organisms Fermentation breakdown of organic molecules for ATP production in an anaerobic way

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Cellular Respiration: Fermentation An anaerobic (no oxygen) reaction 1. Alcoholic Fermentation

Glycolysis then the 2 pyruvate molecules are converted into ethanol Pyruvic acid + NADH alcohol + CO2 + NAD+ + 2ATP Ethanol & carbon dioxide are waste Ethanol 2 carbon molecule, a carbon is lost & given off as carbon dioxide Examples- yeast and other microscopic organisms use, causes bread dough to rise

Cellular Respiration: Fermentation An anaerobic (no oxygen) reaction

2. Lactic Acid Fermentation
Exercise rate exceeds a persons capability of supplying oxygen, then some glucose entering cell resp. will follow the anaerobic pathway lactic acid fermentation Pyruvic acid + NADH lactic acid + NAD+ + 2ATP Excess pyruvate molecules are converted into lactic acid, a 3 carbon molecule so no carbon dioxide is produced Build up of lactic acid in muscle tissue causes cramping Allows glycolysis to continue with the small gain of ATP generated in addition to ATP already being generated through aerobic pathways

IB Biology Topics 3: Chemistry of Life, Nucleic Acids & Cell Respiration and Photosynthesis
3.8 Photosynthesis

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3.8.1-3 States
Photosynthesis involves the conversion of light energy into chemical energy. Light from the sun is composed of a range of wavelengths. Chlorophyll is the main photosynthetic pigment.

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3.8.4
Chlorophyll absorbs light for photosynthesis. Chlorophyll is a green pigment. This means that chlorophyll reflects green light and absorbs the other wavelengths of the visible light spectrum.

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Photosynthesis: An Overview
light 6CO2 + 6H2O C6H12O6 + 6O2
The process uses energy from the sun (non-usable energy) to convert water and carbon dioxide into high-energy sugars and starches (usable energy) and oxygen Light and Pigments Sequence of events: 1. Plants gather suns energy with light-absorbing molecules called pigments
Chlorophyll- primary pigment, but plants also contain red and orange pigments; does not absorb green well, which is why most plants are green!

2. Because light is a form of energy, any compound that absorbs light, also absorbs the energy. 3. When chlorophyll absorbs light, much of that energy is transferred directly to electrons in the chlorophyll molecule raising energy levels of those electrons. 4. These high-energy electrons make photosynthesis work!

The Reactions of Photosynthesis

Take place in the chloroplast 2 parts to the processlight dependent & light independent.

chloroplast Light dependent

Light independent phase

http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookPS.html

The Reactions of Photosynthesis Light Dependent Phase

The light dependent phase takes place within the chloroplasts thylakoids Thylakoid structure & function:
Saclike photosynthetic material Arranged in stacks known as grana (singular granum) Proteins in the thylakoid membrane make photosystems- organized chlorophyll & other pigments that collect light energy

Capturing Energy

What Goes In Must Come Out!

Light Dependent Phase: Reaction that traps light energy & convert it to chemical energy (ATP) Light energy also used in photolysis of water ( water is split into H & O), oxygen that is split is released as waste
Goes in: Light, Water, NADP+, and ADP + P Produced by the reaction but does not leave the chloroplast: NADPH and ATP (Goes to the Calvin cycle) Produced by the reaction but leaves the chloroplast: Oxygen gas

What Goes In Must Come Out!

Light Independent Phase:
AKA: Calvin Cycle Reactions in which ATP is used to help bond carbon dioxide & water together to create glucose. ATP & H are used as chemical energy to convert carbon dioxide and water into useful molecules
Goes in: Carbon dioxide, ATP, and NADPH Produced by the reaction but does not leave the chloroplast: NADP+ and ADP + P (Goes back to Light Dependent Cycle) Produced by the reaction but leaves the chloroplast: Sugar

3.8.5 State
Light energy is used to produce ATP, and to split water molecules to form oxygen and hydrogen. ATP and hydrogen are used to fix carbon dioxide to make organic molecules.

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3.8.7
Carbon dioxide molecules are reactants of photosynthesis and oxygen are products of photosynthesis. Why dont photosynthesis and cellular respiration cancel each other out?
Plants have a consistent rate of cell respiration. Its pretty slow (plants dont have muscles)

Biomass also serves as a way of measuring photosynthesis because it is an indirect reflection of photosynthetic rate. Measuring the rate of oxygen production or CO2 intake is a direct measurement of photosynthetic rate
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3.8.7
Ways to measure the rate of reaction 1) Aquatic plants release bubbles
Measure vol. of bubbles

2) Terrestrial plants
Measure the carbon dioxide up take and release

3) Determining biomass a different times

Indirect method Collected and measured @ different times Rate of increase calculated to determine rate 105 of reaction

3.8.8a effect of temperature

As temperature increases, photosynthetic rate increases.
Increased molecular collision

This continues until the temperature reaches the denaturization point. Once this temperature is reached, enzymes and other proteins become denaturized. This causes the rate of photosynthesis to drop suddenly. 106

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3.8.8b effect of light intensity

As light intensity increases, the rate of photosynthesis increases. This increase continues until a certain intensity is reached. Once a certain intensity is met and enzymes are working at their maximum rate, the rate of photosynthesis plateaus.

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3.8.8c effect of carbon dioxide concentration

As carbon dioxide concentration increases, the photosynthetic rate increases. This increase continues until carbon dioxide reaches a certain point and the rate of photosynthesis plateaus.

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