Bio & Chem - Test 1

Front 1

Macromolecules

Back 1

All macromolecules are polymers – built up from smaller units (mers)

Poly means “many” thus poly–mer = many units In science we use the terms: MONO = 1 BI/DI = 2 TRI = 3 POLY = MANY

In the case of carbohydrates, each unit (mer) is called a saccharide

– so a single sugar molecule would be called a monosaccharide

Front 2

Carbohydrates

Back 2

CARBOHYDRATES contain C, H and OCARBON WATER The H and O are

in the ratio 2:1 as in water (H2O)

Carbohydrates are generally SUGARS or STARCHES.

Thus we have a simple sugar (monosaccharide)

GLUCOSE = C6H12O6 or [6 X ( C1 : H2 : O1 )]

Front 3

Carbohydrates (Continued)

Back 3

Monosaccharides may exist as units with different numbers of carbon atoms.Thus we can have Triose (3C) sugarsWe can have Pentose (5C)

sugarsWe can have Hexose (6C) sugarsNotice that ALL sugars are

given names ending in – OSE e.g fructose, glucose, maltose, ribose.

They may also exist as ALDOSES (aldehydes) or KETOSES (ketones) - depending where the C=O bond is in the sugar.

Front 4

Disaccharides

Back 4

If we have TWO monosaccharide units joined together, by a glycosidic

linkage,the sugar is called a DISACCHARIDE. Examples: maltose,

sucrose

The formation of a disaccharide from two monosaccharides is a

DEHYDRATION reaction - since a water molecule is released as the two sugars are linked together.Since it usually involves synthesis of a larger molecule - it is often called a Dehydration Synthesis reaction.

Front 5

Hydrolysis

Back 5

Conversely - to split a disaccharide into two monosaccharides

- a WATER molecule must be re-inserted between them.

This is called a Hydrolysis reaction.

Front 6

Polysaccharides

Back 6

When many sugar units are joined together - this is called a

Polysaccharide.

4 Examples: Starch, Glycogen, Cellulose, Chitin

There is a significant difference in the way different polysaccharides are built up.

The C1-C4 linkages are different in starch and cellulose.

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Humans/carbon linkage

Back 7

Human enzymes are unable to break the 1-4 β link - which is why we

cannot digest cellulose - but we can break the 1-4 α link - and so can

easily break down starch - into its many sugar units.

Sugars are stored in the human liver as another polysaccharide

macromolecule - Glycogen - again with 1-4 α links

Front 8

Storage Polysaccharides

Back 8

Starch and Glycogen are examples of storage polysaccharides -

used to store energy.

Front 9

Chitin/Cellulose

Back 9

Cellulose and Chitin are examples of structural polysaccharides

- used to form rigid structures for protection. Chitin forms the

exoskeleton of insects

Front 10

Lipids

Back 10

LIPIDS – also called FATS – all contain C and H with O – but contain lots

of Hydrogen Lipids are HYDROPHOBIC – soluble in (mix with) oils/fats

but not waterLipids are all made of TWO basic PARTS

1. A FATTY ACID C – C – C – COO(H)

2. An ORGANIC ALCOHOL C – C - OH

Front 11

Lipids (Continued)

Back 11

Just as in carbohydrates - the alcohol and fatty acid are linked together

by dehydration reactions - one water molecule being removed for

each fatty acid that is linked to the alcohol In the case of triglycerides

- a fat molecule is formed with THREE identical fatty acids linked to the glycerol. Once the water has been removed - the resulting bonds

between alcohol and fatty acid - are called ester linkages.

Front 12

Lipid Structure

Back 12

1.SINGLE BONDS = (SATURATED)

Each carbon atom holds the MOST (2)

hydrogens

happens once = "monounsaturated"

2. DOUBLE BONDS = (UNSATURATED)Carbon atom each side of double bond holds ONE

hydrogen

solid at RT : fat liquid at RT: oil

Front 13

Nucleic Acid

Back 13

NUCLEIC ACIDS are important macromolecules - called polynucleotides - made up of basic units (mers) called NUCLEOTIDES A nucleotide itself is formed of THREE parts:

1. A nitrogenous base

2. A pentose (5C) sugar

3. A phosphate group

Front 14

Nitrogenous Bases

Back 14

There are FIVE main nitrogenous bases that are found commonly in nucleotides (There are others but not common)A. Pyrimidines (single ring structure) 1. Cytosine (C) 2. Thymine (T) 3. Uracil (U)B. Purines (double ring structure) 4. Adenine (A) 5. Guanine (G)

Front 15

Nucleotides

Back 15

The pentose sugars involved are of TWO kinds

1. Deoxyribose (in DNA)2. Ribose ( in RNA)

Front 16

Phosphates

Back 16

If the phosphate is removed from a nucleotide – the remaining base-sugar unit is called a

NUCLEOSIDE.

Purines and Pyrimidines may occur as the free base, the nucleoside or the nucleotide. A nucleotide may therefore be considered as a

nucleoside monophosphate

Front 17

Nucleosides

Back 17

The nucleoside Adenosine (A+R) can have ONE, TWO or THREE phosphate groups attached.

+1 Phosphate = Adenosine Monophosphate (AMP)

+ 2 Phosphates = Adenosine Diphosphate(ADP)+3 Phosphates = Adenosine Triphosphate(ATP)

Front 18

Nucleotides

Back 18

TWO important nucleotides in living cells are:

1. ADP (ADENOSINE DI PHOSPHATE)

2. ATP (ADENOSINE TRI PHOSPHATE)

Front 19

DNA/RNA

Back 19

Deoxyribo Nucleic Acid (DNA) and Ribo Nucleic Acid (RNA) DNA is found in the cell nucleus and also in the mitochondria. Nuclear DNA is formed of two pairs of outer chains, each formed of alternating 5C sugars and phosphate groups – running in opposite directions. Each is thus described as an antiparallel double helix.

DNA Structure: Rosalind Franklin (Watson/Crick)

Front 20

DNA Linkage

Back 20

Thus bases are linked across the space as

either:

Adenine – Thymine (A – T) by 2 hydrogen bondsCytosine - Guanine (C – G) by 3 hydrogen bonds

Distance between outer strands accommodate for one pyrimidine and one purine.

Front 21

Semi Conservative Replication

Back 21

These weak bonds allow the two halves of DNA to be pulled apart.This process is called semi-conservative replication – since one part of the original DNA remains in each of the new

strands.

Front 22

Mitochondrial DNA

Back 22

Mitochondrial DNA is different from that in the cell nucleus – since it is thought to have a different evolutionary origin.

According to the concept of endosymbiosis

(Biol 124), mitochondria are considered to have originated from bacteria engulfed into early eukaryotic cells.

Front 23

Mt DNA

Back 23

Bacterial DNA is a circular double helix which

explains why Mt DNA is similar – circular in nature.Human mtDNA can be considered a

“Chromosome” being the smallest – coding for 37 genes – and containing roughly 16,600 base pairs. In most species, including humans,

mtDNA is inherited only from the mother.

Front 24

Proteins

Back 24

Proteins are probably the most important

macromolecules - since they comprise a large percentage of cellular components. Enzymes are usually proteins and are required in almost every metabolic process known. Enzymes are

required for the building of themselves and for virtually all other proteins.

Proteins are made of AMINO ACIDS - AKA peptide bonds therefore, proteins are also called polypeptides

Front 25

Protein Structures

Back 25

Proteins are made of AMINO ACIDS - AKA peptide bonds therefore, proteins are also called polypeptides

Front 26

Protein Levels

Back 26

Proteins have FOUR LEVELS of structure

The basic sequence of amino acids

= polypeptide chains

2. These fold into an α helix or β pleated sheet.

3. These chains folded into mass

= tertiary structure

4. Several tertiary units joined

= quaternary structure

Front 27

Primary Protein Structure

Back 27

There are 20+ amino acids that are normally used to make proteins. Each one contains an amino group (NH2), a carboxyl group and an R group of differing sizes.

Front 28

Polypeptide Chain

Back 28

Amino acids are joined together by peptide bonds to form long chains - called polypeptide chains. The peptide bond forms between the

carboxyl (-C=O) group end and the amino

(-NH2) end of the monomer (amino acid).

Because of the R group, some are polar and some are non polar

Front 29

Dimer Formation

Back 29

Again, the joining of two monomers (amino acids) to form a dimer - is a dehydration

reaction and a water molecule comes out for every two amino acids joined together.

Front 30

Secondary Protein Structure

Back 30

Secondary structure The polypeptide chain is further folded - often by self-assembly (it forms itself into these folds) - by hydrogen bonding between adjacent parts of the chain - into TWO distinct forms:

1. Alpha (α) helices 2 Beta (β) pleated sheets

Front 31

Beta Sheets

Back 31

Each alpha helix is a twisting (corkscrew) shape into which the polypeptide chains forms. Beta sheets are flattened kinked shapes that the polypeptide chain has formed. A protein may contain BOTH α helices and β sheets in its chain.

Front 32

Alpha Helix

Back 32

Alpha Helix The α helix forms a coil held together by hydrogen bonding between every fourth amino acid. This allows for a spiral coil with a rotational structure of 4 amino acids per turn. Beta Pleated Sheets In this structure, two or more regions of the polypeptide chain lie side by side and are joined by hydrogen bonds that span across between the two parallel parts of the chain. Pleated β sheets make up the core of many globular proteins.

Front 33

Tertiary Structures

Back 33

Tertiary Structure Further bonding occurs between side chains (R groups) of the polypeptide chain - to cause further twisting and kinking - to form it into the tertiary structure.

These include:

1. Hydrogen bonds

2. Disulphide bonds

3. Ionic Bonds

4.Hydrophobic bonds (Van der Waals)

Front 34

pH calculations

Back 34

pH = -log [ H+]

pOH = -log [OH-]

H+ = 10^(pH)

OH-=10^(-pOH)

Front 35

Metabolism

Back 35

Metabolism represents the total chemical

reactions within an organism - and involves

the transfer of matter and energy within that

organisms.

Metabolism proceeds in a definite direction as molecules are altered through a series of processes that is called a Metabolic Pathway.

Front 36

Two Metabolic Paths

Back 36

Large complex molecules are broken down to

release energy - in a process called Catabolism Small molecules may be built up into larger

ones, requiring energy input - in a process

called Anabolism.

Front 37

Energy

Back 37

ENERGY is defined as the capacity to bring about movement against an opposing force. Energy exists in TWO basic forms:

1. POTENTIAL energy – By POSITION

2. KINETIC energy – BY MOTION

Front 38

Pathway (enzymes)

Back 38

An enzyme is needed at every step of the pathway

Front 39

Kinetic/Potential

Back 39

Kinetic energy is usually due to the movement and heat of an orgasm's movements

Chemical energy is potential due to the potential stored in chemical bonds

The study of energy is called THERMODYNAMICS

Energy in living things: BIOENERGETICS

Front 40

Laws of thermodynamics

Back 40

1. Energy is neither created or destroyed but transformed from one kind to another (The Principle of Conservation of Energy)

2. Energy will only flow spontaneously from high to low order (disorder=entropy)

Front 41

Free Energy and Metabolism

Back 41

Downhill - where free energy is RELEASED – are called EXERGONIC reactions.

Uphill reactions – where energy must be SUPPLIED – are called ENDERGONIC reactions.

Front 42

Work (3 ways)

Back 42

1. PHYSICAL (mechanical) work

2. SYNTHETIC work (making large molecules)

3. TRANSPORT work (moving molecules)

Front 43

ENERGY USE Step 1

Back 43

Adenosine Triphosphate (ATP) is hydrolysed and in the process the third phosphate comes off - with the release of energy!

Front 44

ENERGY USE Step 2

Back 44

In cells, the receipt of this released phosphate causes a process called phosphorylation - which is the energy supply that often activates enzymes

Front 45

ENERGY USE Step 3

Back 45

Adenosine Diphosphate (ADP) is left. This has no energy and must be converted back to ATP by the addition of the third phosphate group and a dehydration reaction.

Front 46

Exergonic vs endergonic

Back 46

Converting ADP to ATP requires energy input and is therefore an Endergonic reaction.

The release of energy from ATP as it is converted back to ADP is an Exergonic reaction

Front 47

Equilibrium

Back 47

Reactions in isolated systems will reach equilibrium where the reaction stops. This means the cell dies. No living cell has reached metabolic equilibrium – there is always still some reactions going on.

In isolated vs closed systems, isolated reaches equilibrium quickly

Front 48

Concentration Gradient

Back 48

If there is a difference in concentration of a substance across a membrane - we say that a concentration gradient exists across that membrane.

Substances will normally always try to flow from the higher concentration to the lower concentration - in other words - they will flow down the concentration gradient

Front 49

Passive Movement

Back 49

From higher to lower = PASSIVE

1. Simple diffusion

2. Osmosis

3. Facilitated diffusion

Front 50

Simple Diffusion

Back 50

as the name implies – is the simple spreading out of particles from a high concentration to a lower concentration – and applies to solids, liquids and gases

Front 51

Osmosis

Back 51

Osmosis is also diffusion but diffusion of water through a semipermeable membrane – such as the cell’s plasma membrane (PM) This membrane only allows water to pass but not dissolved solutes such as sugars or salts. Fats can also pass through the tails of the phospholipids that make up the PM.

Front 52

Facilitated Diffusion

Back 52

Facilitated diffusion is again simple diffusion but carried through special protein cells that lie embedded in the PM. Since they pass right through the PM they allow substances into or out of the cell.

Front 53

Active Vs Passive

Back 53

1. Simple diffusion ….. passive

2. Osmosis …. passive

3. Facilitated diffusion …. passive

4. Active transport …. active (requires ATP)

Front 54

Enzymes

Back 54

An ENZYME can be defined as a BIOLOGICAL CATALYST

A Catalyst is any substance that speeds up a chemical reaction without taking part in that reaction

Substance that enzyme works on = substrate

initial substances = reactants

final = products place it bids to = active site

Enzymes are usually proteins and are required in almost every metabolic process known. Enzymes arerequired for the building of themselves and for virtually all other proteins.Proteins are made of AMINO ACIDS - AKA peptide bonds therefore, proteins are also called polypeptides

Front 55

Activation Energy

Back 55

Activation energy is often supplied to a reaction in the form of heat - which is why many reactions happen much faster when heated. The heat energy is used to break bonds holding the reactant molecules together and this allows them to reach a Transition state - from which the reaction can occur. However, the activation energy can be lowered by the presence of an enzyme - so that enzymes lower the activation energy barrier and thus make it easier for the reaction to occur.

sucrose + sucrase = breaks into = fructose and glucose

Front 56

Enzymes

Back 56

Substrate + enzyme = Enzyme-Substrate Complex

The substrate is usually held in the active site by hydrogen bonds

Front 57

Enzyme Action

Back 57

Firstly, 2+ substrates, active site may form a "Template" for the two reactants to link together.

Secondly, as active site clutches the substrates it may stretch the molecules - moving them towards their transition state, bending them bonds that need to break.

Thirdly - the active site may also produce a micro-climate of different pH

attracting acid/basic ions

Front 58

Enzyme Environment

Back 58

pH and temperature changes - also to specific chemicals. All enzymes have optimal conditions.

human enzymes an optimum temp of 35-40 degrees celsius and pH range of 6 - 8 - but there are exceptions.

If these are not optimal, the enzyme may denature

Cofactor/coenzyme= help the enzyme (may be inorganic ions)

Front 59

Inhibitors

Back 59

Covalent bonding = irreversible inhibition

Hydrogen bonding = reversible inhibition

Some inhibitors mimic substrate and bind at active sites, called competitive inhibitors

Non-competitive inhibitors bind to other parts of the enzyme molecule

Front 60

Enzyme Regulation

Back 60

Allosteric regulation of an enzyme is caused by the binding of a protein to it at a site other than the active site. It is a form of non competitive inhibition but alters the stability of the enzyme. It may inhibit or activate the enzyme

Front 61

Allosteric Activation

Back 61

Allosteric ActivationIn this case, when the allosteric activator links to the allosteric site this locks the enzyme in its active form with the active sites ready to accept substrate.Such activation is called allosteric activation.

Front 62

Allosteric Inhibition

Back 62

Allosteric InhibitionIn the case of allosteric inhibition, the allosteric inhibitor locks the enzyme by stabilizing it in the inactive form where all the active sites are nonfunctional.

ie: Caspases

Front 63

Location of Enzymes

Back 63

Since the mitochondria are the “powerhouses” of the cell – it is not surprising that many enzymes are located in mitochondria.

Front 64

Catabolic Pathway

Back 64

Metabolism is an example of a catabolic pathway.

Catabolic pathways yield energy by oxidizing organic fuels.

Catabolic processes are essentially process of breaking down large molecules into smaller molecules. In so doing - they produce energy – and are thus exergonic.

Front 65

Anabolic Pathway

Back 65

anabolic pathways are processes of building up larger molecules – often proteins from amino acids (e.g. anabolic steroids). Anabolic processes require energy input and are therefore endergonic.

Front 66

Fermentation

Back 66

Fermentation is a partial degradation of sugars or other organic fuels that takes place in the absence of oxygen. It is thus an anaerobic process

Front 67

Metabolism

Back 67

in contrast to the complete metabolism of sugars - that require oxygen and is therefore an aerobic process.

The terms: metabolism, aerobic – and cellular respiration are essentially interchangeable.

Front 68

Oxidation

Back 68

Since oxygen is required for full metabolism, energy is released from organic fuel by a process called oxidation.

Similarly, when things are heated in the absence of oxygen (reacted with pure hydrogen) – or when oxygen is removed from them – they change the other way – and this is called REDUCTION.

Front 69

Oxidation Vs Reduction

Back 69

We now know that oxidation and reduction are all to do with electrons - either receiving them or losing them. Oxidation = losing one or more electrons Reduction = gaining one or more electrons

Front 70

Combustion

Back 70

A simpler way to look at the equation is to note that CH4 has lost hydrogen and gained oxygen to become CO2 (thus oxidized) whereas oxygen itself has gained hydrogen (thus reduced).

Front 71

Oxidizing/Reducing Agent

Back 71

Oxidizing agent Any substance that is able to pull electrons away

Reducing agent This is the opposite of the above - any substance that will donate electrons to another substance

Front 72

Electron Transport Chain

Back 72

These electrons are part of the process of making ATP - and are used up in the last part of cellular respiration - called the Electron Transport Chain (ETC) An important electron shuttle - used in cellular respiration - is the coenzyme molecule Nicotinamide Adenine Dinucleotide (NAD)

Front 73

Cellular Respiration

Back 73

Food → NADH → ETC → Oxygen

oxygen is the final electron acceptor.

The first part of this process takes place in the cytoplasm of the cell - but the latter part takes place in the mitochondria of the cell (where most ATP is produced)

most of the ATP is produced during ETC

Front 74

Cellular Respiration

Back 74

1. Glycolysis (splitting of sugar)

2. The Krebs Cycle (citric acid cycle)

3. Electron Transport Chain (ETC) - also called

Oxidative Phosphorylation

Front 75

Glycolysis

Back 75

Takes place in the cytoplasm of the cell. Glyco (sugar) lysis (splitting).

ONE molecule of GLUCOSE - a 6-carbon molecule - that is split onto TWO 3-carbon sugars - and ultimately TWO molecules of 3-carbon Pyruvic Acid It is this final product of TWO molecules of PYRUVIC ACID – which goes into the Krebs Cycle.

Front 76

Glycolysis (continued)

Back 76

Remember that the last part of Glycolysis is Double - everything after Glyceraldehyde-3-phosphate is produced in double. Since each of these will go into the next stage - the Krebs Cycle - we will get TWO revolutions of the Krebs Cycle for each molecule of glucose at the beginning of Glycolysis

Front 77

Pyruvate Conversion

Back 77

before the pyruvate goes into the Krebs Cycle (Citric Acid cycle) it has to be converted into a coenzyme molecule - Acetyl Coenzyme A (Acetyl CoA) This happens inside each mitochondrion

happens twice per molecule of glucose

Front 78

Pyruvate Conversion (continued)

Back 78

The pyruvate is carried from the cytoplasm into each mitochondrion - by Active Transport - using a transport protein - and there in the mitochondrion - it is converted to Acetyl CoA - by a multi- enzyme complex The Acetyl CoA is a 2-carbon molecule and the other carbon atom comes off as CO2 - which is the first step in the production of carbon dioxide in respiration

Front 79

Krebs Cycle

Back 79

The citric acid cycle completes the energy-yielding oxidation of organic molecules.

only 1 molecule ATP for each cycle) BUT where it is much more efficient is in the production of electrons - in the form of the electron shuttles.

For every turn of the Krebs cycle - THREE NAD shuttles become filled with electrons (3NAD+ → 3NADH) and ONE FAD shuttle also becomes filled with electrons (FAD → FADH2 )

Front 80

Starting with ONE molecule of glucose at the beginning of glycolysis - How many NAD shuttles are filled in the Krebs cycle? How many FADH shuttles are filled?

Back 80

Starting with ONE molecule of glucose at the beginning of glycolysis - How many NAD shuttles are filled in the Krebs cycle? 3 x 2 = 6 How many FADH shuttles are filled? 1 X 2 = 2

Front 81

Role of Electrons

Back 81

The energy derived from the electrons cascading down the ECT is used to maintain a gradient of protons (H+ ions) across the mitochondrial membrane - with a higher concentration of protons outside the membrane - in the intermembrane space.

Front 82

Chemiosmosis

Back 82

This gradient is what provided the energy for ATP production and is called chemiosmosis - since it is not unlike osmosis - the flow of water across a gradient - although here it is the flow of H+ ions across a gradient.

Front 83

ATP Synthase

Back 83

ATP synthase is a multi-subunit complex with FOUR main parts - each made up of multiple polypeptide units.

ATP synthase works like an ion pump in reverse - using the energy from the inflowing hydrogen ions to carry out phosphorylation of ADP and so convert it into ATP. In the process - a small amount of ATP is used up

Front 84

ATP Production

Back 84

Glycolysis .......2

Pyruvate/acetyl coA......

Krebs.......2

conversion to ATP..... 30

2x2......4

used in chemiosmosis......-2

TOTAL 36

Front 85

Photosynthesis

Back 85

opposite of metabolism or cellular respiration. ← Photosynthesis

C6H12O6 + 6O2 + 6H2O ↔ 6CO2 +12H2O + Energy

plant cells take in CO2 and H2O- and by using the energy of sunlight - build those small molecules into sugars and in the process release the waste product O2

Since photosynthesis is an anabolic process - it will be endergonic

Energy comes from sun- absorbed by chlorophyll

Front 86

Photosynthesis and Autotroph

Back 86

Photo - synthesis means: (by light) - (building)

Troph- means "feeding" or "food" Hetero- means "different" Auto- means "self"

Front 87

Autotrophs

Back 87

Autotrophs = regular plants, multicellular protists (giant sea kelp and other seaweeds), diatoms and Dinoflagellates.

micro-organisms - such as Cyanobacteria (blue-green algae) and even unicellular protists like Euglena and Parameceum.

Front 88

Chlorophyll

Back 88

CHLOROPHYLL is found in special organelles inside plant leaves and other tissues. These organelles are a kind of plastid, called Chloroplasts.

below the surface epidermal layers (top and bottom) there are larger cells surrounded by many air spaces. These are MESOPHYLL cells

Inside these mesophyll cells there are many chloroplasts

Front 89

Light Stages

Back 89

1. A LIGHT - DEPENDENT Stage

2. A LIGHT - INDEPENDENT Stage

The first stage is just called the Light Stage. The second stage is called the Calvin Cycle

Front 90

Photosynthesis

Back 90

Photosynthesis is a REDOX reaction - with the transfer of electrons - and some reagents being oxidized, others reduced.

Front 91

(Own)

The Light Stage (first stage)

Back 91

Light-dependent reactions, which take place in the thylakoid membrane, use light energy to make ATP and NADPH.

The light-dependent reactions use light energy to make two molecules needed for the next stage of photosynthesis: the energy storage molecule ATP and the reduced electron carrier NADPH. In plants, the light reactions take place in the thylakoid membranes of organelles called chloroplasts.

Front 92

Photosystems

Back 92

Photosystems, large complexes of proteins and pigments (light-absorbing molecules) that are optimized to harvest light, play a key role in the light reactions. There are two types of photosystems: photosystem I (PSI) and photosystem II (PSII).

photosystem I is called P700, while the special pair of photosystem II is called P680.

Front 93

The Calvin Cycle

Back 93

CO2 enters the interior of a leaf via pores called stomata and diffuses into the stroma of the chloroplast—the site of the Calvin cycle reactions, where sugar is synthesized. These reactions are also called the light-independent reactions because they are not directly driven by light.In the Calvin cycle, carbon atoms from 2CO​2​​ C, O, start subscript, 2, end subscript are fixed (incorporated into organic molecules) and used to build three-carbon sugars. Powered by ATP and NADPH from light stage. The Calvin cycle take place in the stroma (the inner space of chloroplasts).

Front 94

C3, C4

Back 94

Photorespiration is a wasteful pathway that occurs when the Calvin cycle enzyme rubisco acts on oxygen rather than carbon dioxide.

The majority of plants are 3C​3​​ C, start subscript, 3, end subscript plants, which have no special features to combat photorespiration.

C​4​​ C, start subscript, 4, end subscript plants minimize photorespiration by separating initial 2CO​2​​ C, O, start subscript, 2, end subscript fixation and the Calvin cycle in space, performing these steps in different cell types.

Front 95

Cam Plants

Back 95

Some plants that are adapted to dry environments, such as cacti and pineapples, use the crassulacean acid metabolism (CAM) pathway to minimize photorespiration.

Front 96

C3 Plants

Back 96

About 85%85%85, percent of the plant species on the planet are 3C​3​​ C, start subscript, 3, end subscript plants, including rice, wheat, soybeans and all trees.

A "normal" plant—one that doesn't have photosynthetic adaptations to reduce photorespiration—is called a C3 plant. The first step of the Calvin cycle is the fixation of carbon dioxide by rubisco, and plants that use only this "standard" mechanism of carbon fixation are called C3 plants

Front 97

C4 Plants

Back 97

The C4 pathway is used in about 3% of all vascular plants; some examples are crabgrass, sugarcane and corn. In hot conditions, the benefits of reduced photorespiration likely exceed the ATP cost of moving CO2

Front 98

Lactic Acid Fermentation

Back 98

NADHN, A, D, H transfers its electrons directly to pyruvate, generating lactate as a byproduct. Lactate, which is just the deprotonated form of lactic acid, gives the process its name.

Muscle cells also carry out lactic acid fermentation, though only when they have too little oxygen for aerobic respiration to continue

Lactic acid produced in muscle cells is transported through the bloodstream to the liver, where it’s converted back to pyruvate and processed normally in the remaining reactions of cellular respiration.

Front 99

Alcohol Fermentation

Back 99

Another familiar fermentation process is alcohol fermentation, in whichNADHN, A, D, H donates its electrons to a derivative of pyruvate, producing ethanol.

n the first step, a carboxyl group is removed from pyruvate and released in as carbon dioxide, producing a two-carbon molecule called acetaldehyde. In the second step,NADHN, A, D, H passes its electrons to acetaldehyde, regenerating NAD​+​​ N, A, D, start superscript, plus, end superscript and forming ethanol.

Front 100

NAD

FAD

Back 100

Full Names

NAD = nicotinamide adenine dinucleotide

FAD = flavin adenine dinucleotide

Front 101

ETC

Back 101

The electron transport chain is the stepwise process of cellular respiration that is responsible for producing: Water (with the help of oxygen we breathe) up to 34 ATP (thanks to the proton gradient) NAD and FAD (which are recycled to be used again in the Citric acid cycle and glycolysis)

Front 102

ETC continued

Back 102

This energy is derived from the oxidation of NADH and FADH2 by the four protein complexes of the electron transport chain (ETC). The ten NADH that enter the electron transport originate from each of the earlier processes of respiration: two from glycolysis, two from the transformation of pyruvate into acetyl-CoA, and six from the citric acid cycle. The two FADH2 originate in the citric acid cycle.

Takes place in membranes of mitochondria

Front 103

Krebs

Back 103

the citric acid cycle, refers to the first molecule that forms during the cycle's reactions—citrate, or, in its protonated form, citric acid.

-

Front 104

Krebs Cycle Step 1&2

Back 104

STEP 1 Citric acid (citrate) is the first product produced from the Acetyl CoA as it goes into the cycle - which is why the Krebs cycle is also called the citric acid cycle.

STEP 2Citrate is converted to isocitrate and then to α ketoglutarate - and loses another CO2 molecule. In this process another NAD electron carrier is filled.

Front 105

Krebs Cycle Step 3 & 4

Back 105

Another CO2 molecule is lost as this is converted to Succinyl CoA andanother NAD carrieris filled(NAD+ → NADH)

Succinyl Co A is then converted to succinate with the formation of another ATP molecule.

Front 106

Krebs Cycle Step 5 & 6

Back 106

Succinate is then converted to fumarate and an FADH electron carrier is filled in the process

Fumarate is then converted to malate – which in turn is oxidized to oxaloacetate and in turn fills another NAD carrier.Oxaloacetate then starts the cycle again, when converted to citrate.

Front 107

Krebs Cycle Products

Back 107

Notice - that in going around the Krebs Cycle - we create THREE full NAD shuttles - and also ONE full FADH2 shuttles Thus - with respect to this citric acid cycle

Front 108

Enzymes - Structure/how they are modified

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An ENZYME can be defined as a BIOLOGICAL CATALYST. A Catalyst is any substance that speeds up a chemical reaction without taking part in that reaction. Substance that enzyme works on = substrateinitial substances = reactantsfinal = products place it bids to = active site Enzymes are usually proteins and are required in almost every metabolic process known. Enzymes are required for the building of themselves and for virtually all other proteins. Proteins are made of AMINO ACIDS - AKA peptide bonds therefore, proteins are also called polypeptides

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Inhibition/Activation Metabolism

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Glycolysis- Initial/End products

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Takes place in the cytoplasm of the cell. Glyco (sugar) lysis (splitting).ONE molecule of GLUCOSE - a 6-carbon molecule - that is split onto TWO 3-carbon sugars - and ultimately TWO molecules of 3-carbon Pyruvic Acid It is this final product of TWO molecules of PYRUVIC ACID – which goes into the Krebs Cycle.

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Laws of Thermodynamics

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1. Energy is neither created or destroyed but transformed from one kind to another (The Principle of Conservation of Energy)

2. Energy will only flow spontaneously from high to low order

(disorder=entropy)

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Exergonic/Endergonic Reactions

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Downhill - where free energy is RELEASED – are called EXERGONIC reactions. (photosynthesis) (ATP back to ADP is exergonic)

Uphill reactions – where energy must be SUPPLIED – are called ENDERGONIC reactions. (converting ADP to ATP require energy, cellular respiration) (anabolic pathways)

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Four Levels of Protein Structure

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Proteins have FOUR LEVELS of structure

1. The basic sequence of amino acids= polypeptide chains

2. These fold into an α helix or β pleated sheet.

3. These chains folded into mass= tertiary structure

4. Several tertiary units joined= quaternary structure

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Carbon Links in Fatty Acids

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Human enzymes are unable to break the 1-4 β link - which is why wecannot digest cellulose - but we can break the 1-4 α link - and so caneasily break down starch - into its many sugar units.Sugars are stored in the human liver as another polysaccharidemacromolecule - Glycogen - again with 1-4 α links

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Saturated/Unsaturated Fats

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1.SINGLE BONDS = (SATURATED)Each carbon atom holds the MOST (2)hydrogenshappens once = "monounsaturated"

2. DOUBLE BONDS = (UNSATURATED)Carbon atom each side of double bond holds ONEhydrogensolid at RT : fat liquid at RT: oil

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DNA

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Deoxyribo Nucleic Acid (DNA) and Ribo Nucleic Acid (RNA) DNA is found in the cell nucleus and also in the mitochondria. Nuclear DNA is formed of two pairs of outer chains, each formed of alternating 5C sugars and phosphate groups – running in opposite directions. Each is thus described as an antiparallel double helix.DNA Structure: Rosalind Franklin (Watson/Crick)

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DNA/RNA Bases

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There are FIVE main nitrogenous bases that are found commonly in nucleotides (There are others but not common)A. Pyrimidines (single ring structure)

1. Cytosine (C)

2. Thymine (T)

3. Uracil (U)B. Purines (double ring structure)

4. Adenine (A)

5. Guanine (G)

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Macromolecules

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All macromolecules are polymers – built up from smaller units (mers)Poly means “many” thus poly–mer = many units In science we use the terms: MONO = 1 BI/DI = 2 TRI = 3 POLY = MANYIn the case of carbohydrates, each unit (mer) is called a saccharide– so a single sugar molecule would be called a monosaccharide

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Linking Monomers to make Polymers

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Again, the joining of two monomers (amino acids) to form a dimer - is a dehydrationreaction and a water molecule comes out for every two amino acids joined together.

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Solutes/Solvents/Solutions

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a solution is a homogeneous mixture composed of two or more substances. In such a mixture, a solute is a substance dissolved in another substance, known as a solvent.

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Calculate pH from H+ and OH- concentration

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pH = -log [ H+]

pOH = -log [OH-]

H+ = 10^(pH)

OH-=10^(-pOH)

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Water Molecule

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The water molecule maintains a bent shape (bent at 107.5 degrees actually) because of two considerations. First the tetrahedral arrangment around the oxygen and Second the presence of lone pair electrons on the oxygen.

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Water Properties

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A Water with its six properties is essential for life on Earth. Three of the important properties are:

1) water has a high heat capacity;

2) water has a high heat of vaporization;

3) water is cohesive and adhesive.

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Electron Ring Capacity

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Maximum number per ring

The first shell can hold up to two electrons, the second shell can hold up to eight (2 + 6) electrons, the third shell can hold up to 18 (2 + 6 + 10)

Valency

The valency of an atom is equal to the number of electrons in the outer shell if that number is four or less. Otherwise, the valency is equal to eight minus the number of electrons in the outer shell.

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Isotopes

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One of two or more atoms that have the same atomic number (the same number of protons) but a different number of neutrons.

Carbon 12, the most common form of carbon, has six protons and six neutrons, whereas carbon 14 has six protons and eight neutrons.

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Diffusion

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Simple Diffusion - as the name implies – is the simple spreading out of particles from a high concentration to a lower concentration – and applies to solids, liquids and gases

Facilitated - Facilitated diffusion is again simple diffusion but carried through special protein cells that lie embedded in the PM. Since they pass right through the PM they allow substances into or out of the cell.

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Atomic Number/Mass Number

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Atomic # - All the atoms of a particular element have the same atomic number (number of protons).

Atomic mass - The mass number of an atom is the total number of protons and neutrons it contains.

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Bondings

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Covalent, Ionic, Hydrogen

ionic - complete transfer of electrons

covalent - shared electrons

hydrogen - bonds between polar molecules containing H O N F

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Basic Chemistry

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Hydrogen, carbon, oxygen, nitrogen

How they link:

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Nitrogenous Bases

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Deoxyribo Nucleic Acid (DNA) and Ribo Nucleic Acid (RNA) DNA is found in the cell nucleus and also in the mitochondria. Nuclear DNA is formed of two pairs of outer chains, each formed of alternating 5C sugars and phosphate groups – running in opposite directions. Each is thus described as an antiparallel double helix.DNA Structure: Rosalind Franklin (Watson/Crick)

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Lipids

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LIPIDS – also called FATS – all contain C and H with O – but contain lotsof Hydrogen Lipids are HYDROPHOBIC – soluble in (mix with) oils/fatsbut not waterLipids are all made of TWO basic PARTS1. A FATTY ACID C – C – C – COO(H)2. An ORGANIC ALCOHOL C – C - OH

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Carbohydrates

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CARBOHYDRATES contain C, H and OCARBON WATER The H and O arein the ratio 2:1 as in water (H2O)Carbohydrates are generally SUGARS or STARCHES.Thus we have a simple sugar (monosaccharide)GLUCOSE = C6H12O6 or [6 X ( C1 : H2 : O1 )]

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Proteins

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Proteins are probably the most importantmacromolecules - since they comprise a large percentage of cellular components. Enzymesare usually proteins and are required in almost every metabolic process known. Enzymes arerequired for the building of themselves and for virtually all other proteins.Proteins are made of AMINO ACIDS - AKA peptide bonds therefore, proteins are also called polypeptides

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Nucleic Acids

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NUCLEIC ACIDS are important macromolecules - called polynucleotides - made up of basic units (mers) called NUCLEOTIDES A nucleotide itself is formed of THREE parts:1. A nitrogenous base2. A pentose (5C) sugar3. A phosphate group

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Monosaccharides

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Monosaccharides may exist as units with different numbers of carbon atoms. Thus we can have Triose (3C) sugarsWe can have Pentose (5C)sugars

We can have Hexose (6C) sugarsNotice that ALL sugars aregiven names ending in – OSE e.g fructose, glucose, maltose, ribose.They may also exist as ALDOSES (aldehydes) or KETOSES (ketones) - depending where the C=O bond is in the sugar.

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Disaccharides

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If we have TWO monosaccharide units joined together, by a glycosidiclinkage, the sugar is called a DISACCHARIDE. Examples: maltose,sucroseThe formation of a disaccharide from two monosaccharides is aDEHYDRATION reaction - since a water molecule is released as the two sugars are linked together.Since it usually involves synthesis of a larger molecule - it is often called a Dehydration Synthesis reaction.

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Allosteric Activation

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Allosteric Activation

In this case, when the allosteric activator links to the allosteric site this locks the enzyme in its active form with the active sites ready to accept substrate. Such activation is called allosteric activation.

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Allosteric Inhibition

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Allosteric Inhibition

In the case of allosteric inhibition, the allosteric inhibitor locks the enzyme by stabilizing it in the inactive form where all the active sites are nonfunctional.ie: Caspases

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Osmosis

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Osmosis is also diffusion but diffusion of water through a semipermeable membrane – such as the cell’s plasma membrane (PM) This membrane only allows water to pass but not dissolved solutes such as sugars or salts. Fats can also pass through the tails of the phospholipids that make up the PM.

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Passive Movement

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From higher to lower = PASSIVE

1. Simple diffusion

2. Osmosis

3. Facilitated diffusion

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Energy Transfer