Chemistry & Biochemistry 2

Question 1

Proteins

Answer 1

Amino acids are building blocks for protein

Made from
Carbon
Oxygen
Hydrogen
Nitrogen (unique)

Body needs 20 different aa to create proteins needed to function

Every aa has a carboxyl group / acid (-COOH) and an aa group (-NH3)
Each aa has a side chain (labelled R) that determines its characteristics

Question 2

Peptides

Answer 2

Aa joined together using dehydration synthesis to create peptide bonds

Dipeptide: 2 aa joined together
Tripeptide: 3aa joined together

Glutathione, powerful antioxidant, is a tripeptide containing aa L-cysteine, l-glutamate and glycine

Question 3

Glutathione

Answer 3

Tripeptide

Powerful antioxidant

Contains
L-cysteine
L- glutamate
Glycine

Cysteine is commonly limiting glutathione production so ensuring good intake of cysteine (eg legumes, sunflower seeds, eggs) is optimal

Question 4

Amino acids

Answer 4

Combination of polar and non polar aa that ultimately determines the 3D shape of protein

Aa with acidic side chains can release H ions, whether they do or not depends on pH of surrounding fluid

Aa with basic side chains can bind to H ions. Depends on pH of surrounding fluid

PH of fluid the protein is in will affect its 3D structure

Question 5

Non polar aa

Answer 5

Hydrophobic

When protein folds up in a watery environment, they like to be on the inside of the protein structure away from water

Includes tryptophan (used for serotonin)

Question 6

Polar aa

Answer 6

Hydrophilic

When protein folds up in watery environment they like to be on the outside interacting with polar water molecules

Tyrosine (create adrenaline and thyroxine)

Question 7

Protein functions

Answer 7

Structure of body tissues
Movement
Carrier molecules
Storage molecules
Fluid balance in blood
Enzymes
Hormones
Immune functions
Clotting mechanisms
Alternative energy source
Cell membrane proteins

Question 8

Denaturation

Answer 8

3D structure of a protein is key to its function
Works like a lock and key
If structure changes they are denatured, no longer function correctly

Can be denatured by
Heat
Heavy metals

Question 9

Protein digestion

Answer 9

Body uses enzymes to help break down peptide bonds between aa

Broken by hydrolysis reaction (using water)
Mechanically broken down in mouth (increases surface area for enzymes)

Chemical digestion beginning in stomach, enzyme pepsin breaks down long protein chains

Pepsin released by gastric chief cells in active form pepsinogen (presence of HCl concerts it)
Pepsin needs to be at pH 2 in order to function correctly
(Parietal cells pump out HCI)

Question 10

Protein digestion and absorption

Answer 10

CCK released when protein rich chyme enters the small intestine, triggering pancreas to release pancreatic juices (contains proteases called trypsin and chymotrypsin)

In smaller intestine, the shorter protein chains that have renters from the stomach are further broken down by Tripeptide, dipeptites and single aa by pancreatic protease and brush border enzymes

Aa and small peptides are then absorbed into the blood

Question 11

Nucleic acid

Answer 11

Largest molecules in the body and used to store our genetic info

Most common:
Deoxynbonucleic acid (DNA)
Ribonucleic acid (RNA)

Building blocks of nucleic acid are nucleotides
Consists of
Phosphate group
Sugar
Nitrogenous base

Functions-
Holds genetic info and acts like a recipe book (DNA huge - 2m long)
Acts as template for protein synthesis (RNA used to copy specific sub sections of DNA called genes and translate into proteins)
20,000 - 25,000 genes in human genome

Question 12

DNA

Answer 12

5 nucleotides in DNA contain the 5 carbon sugar deoxyribose
DNA has 4 possible nucleotide bases:
Adenine
Cytosine (a purine)
Guanine
Thymine (a purine)

DNA has 2 strands that are wound together like a twisted ladder called double helix

Hydrogen bonds: 2 strands held together between the bases
Covalent bonds: by sugar-phosphate bonds
Hydrogen bonds are much weaker, why dna is able to unzip during protein synthesis

Adenine with thymine
Cytosine with guanine
Sequences of these pairs will ultimately code for the production of a certain product (eg hormone, insulin)

Question 13

RNA

Answer 13

Single strand of nucleotides which contains the sugar ribose
(DNA has sugar deoxyribose)

Transcription: A molecule of mRNA copies the recipe in dna.
mRNA travels to ribosome to be read
Translation: ribosome produces protein coded for, eg hormone

Question 14

Genetics

Answer 14

DNA also used as a manual for making all the proteins in the body, from muscle tissue to enzymes

DNA condensed form chromosomes.
Telomeres: End sections of dna (length of telomeres shortens as cells and tissues age. Accelerated aging due to stress, poor nutrition, poor sleep, chemical agents, lack of exercise)
Herb Gotu Kola helps

Question 15

Mutation

Answer 15

Describes abnormal change to the genetic sequence. Can be something born with, but commonly occurs during a persons lifespan

Change in dna sequence
Mutation can cause change in sequence of aa in the protein
Can cause protein to be a slightly different shape
Eg sickle cell anaemia

Question 16

Gene expression

Answer 16

Can’t change genes but many different ways we can change our gene expression (whether we copy the gene or not)

Eg liver makes many different enzymes involved in breaking chain toxins
More toxins exposed to, more enzymes needed for metabolising the toxin will be made
Will change livers ability to metabolise the toxin but also may affect how quickly the liver breaks down other substances that also require the enzyme
Therefore more enzymes are used. Less the other functions of those enzymes can be fulfilled

Question 17

Gene expression nutritional influences

Answer 17

Influenced by:
Metabolites of A, D, EFA and zinc can influence whether a gene is copied or not

Components of fibre also have an effect by affecting hormone levels and through metabolites created when intestinal flora feed on fibre

Essential to consider environment we bathe our genes in:
Pathological gene expression: acidic, anerobic, glucose rich, stress, radiation, vaccine

Question 18

MTHFR gene mutation.

Answer 18

Gene mutations affect enzyme activity

MTHFR is an enzyme necessary to convert folate into form used for methylation
Active form of folate (methylfolate) is involved in the metabolism of aa homocysteine - metabolite associated with heart disease and dementia
Mutation causes enzyme to fold up into and normal shape
People with MTHFR mutation may have higher homocysteine levels and may benefit from taking methylfolate

Methylation. Is a process also required to remove toxic metals such as mercury from body

Question 19

Other common mutations

Answer 19

Unable to convert beta carotene to VIT A

Some can’t co very D from skin

Question 20

Enzymes

Answer 20

Biological catalysts made from protein

Speed up reactions, but unchanged themselves so repeat use
Generally end in -ase

Substrates: molecules at beginning of enzymatic reaction process
Products: enzymes convert the substrates to this
Eg for pepsin:
Substrate = protein
Product = shorter protein chains

Vital for life and participate in every chemical reaction in the body
Many biological reactions v slow
Enzymes bind temporarily to substrate providing an alternative pathway to get to the end result

Allows biological reactions to occur in relatively mild conditions. Create low energy way for starting materials to meet and react which allows reactions to happen in mild conditions in the body

Each enzyme had specific region called active site
Unique shape completely complimentary to the shape of a substrate molecule: lock and key model

Enzymes highly specific and require optimum conditions: temp and pH

Question 21

Enzyme co factors

Answer 21

Without, inactive

Zinc: for enzyme alcohol dehydrogenase that breaks down alcohol

Selenium: for antioxidant enzyme glutathione peroxidase

A lack of cofactors can lead to reduction in enzyme activity

Question 22

Substrate concentration

Answer 22

Can affect speed of enzyme reaction (eg substrate could be starch, while enzyme is amalyse)

Increase in substrate concentration means more of the enzyme molecules can be utilised

As more enzymes become involved in reactions, the rate of reactions increase

Eventually, all enzymes are being involved in reactions. When this happens, some of the substrate must wait for enzymes to clear their active sites before the enzyme can fit with them so the reaction cannot become any faster
Eg investing a lot of omega 6 and small omega 3, as concerted using same enzyme omega 6 will occupy enzymes active site
Therefore less abundant omega 3 will be
Vital to have a balance

Question 23

Omega 3 and 6 conversion

Answer 23

Omega 6
ALA converts some into EPA which are then converted into DHA

Omega 3
Linoleic acid some concergs into GLA, then converts to AA

Question 24

Enzymes and pH

Answer 24

Changes in pH can affect properties of aa side chains

Acidic conditions: aa side chains bind to H+
Basic (Alkaline) conditions: side chains can lose H+

Changes can affect whether or not these side chains can form the bonds and interactions which are essential for 3D structure of enzyme

Can denature if in too acidic or basic conditions

Salivary amalyse: pH 7
Pepsin: pH 2

Question 25

Enzymes and temperature

Answer 25

High temps move faster
Leads to more collisions and a faster reaction rate

If atoms in enzyme vibrate too much, the weak bonds holding the 3D structure together can break and enzymes can denature
Enzyme then most

Fever speeds up immune reactions.

Imp not to go above 40 degrees as enzymes will denature and metabolic processes will break down

Question 26

Digestive enzymes

Answer 26

Saliva
Salivary amylase

Stomach
Gastric lipase
Pepsinogen (to pepsin)

Pancreas
Pancreatic amalyse
Pancreatic lipase
Pancreatic proteases

Villi
Sucrase
Maltese
Lactase

Modern diets mean problem often struggle to produce enough digestive enzymes
Constantly eating tires enzyme production
Drinking water diluted
Stress and nutritional deficiencies can reduce enzymes

Question 27

Enzymes in food

Answer 27

Plants contain enzymes

Bromelain = pineapple (protease)
Papain = in papaya (protease)

Tolerate wider pan range

Bromelain remains in tact in stomach
Denatured by high heat and microwave

Foods high in enzymes
Sprouts (100x more than fruit and veg)
Kiwi = actinidin (aids protein)
Avocado = lipase (fats)
Garlic = phytonutrient allin, enzyme alinase

Cooking can be damaging
Longer exposure to best, greater the loss

Enzymes that remain in damaged can support digestion, assisting with breakdown of macronutrients and reducing digestive burden

Question 28

Raw foods

Answer 28

Contain micronutrient
Cooking often lowers antioxidant
Water soluble compounds can be lost

Some compounds are more available when cooked as released from plant Walls:
Lycopene
Beta carotene

SIBo and raw food not good match

Brassica (goitrogenic food) is not good for thyroid issues in raw food. Hearing denatured

Yin conditions may be caused by excessive raw foods

Question 29

Enzymes and inflammation

Answer 29

COX (cyclooxygenase-1 & 2) and LOX (lipoxygenase-5) are enzymes involved in creation of key inflam mediators called prostaglandins and leukotrienes

Boswella, curculio and ginger inhibits these

Question 30

Enzyme inhibitors as drugs

Answer 30

Decrease rate of biological reaction

Antibiotics (penicillin) works by inactivating enzyme necessary for connection of aa in bacterial cell walls which is important for their structure

Statins inhibit HMG-CoA reductase - enzyme liver used to make cholesterol and CoQ10

Question 31

Enzyme therapy

Answer 31

Systemic enzyme therapy: taking large dose of proteolytic enzymes on an empty stomach so that some of the enzymes are able to reach the bloodstream in tact
Proteases thought to reduce inflam processes and aid in more efficient clearance of damaged tissue

Commonly used enzymes Bromelain, serrapeptase and pancreatic enzymes

Bromelain properties:
Anti inflam
Anti cancer
Anti clotting

Question 32

Serrapeptase

Answer 32

Proteolytic enzyme that has potent anti inflam effects on body tissues

Thought to reduce inflam by:
Thinning fluids formed from injury, facilitating fluid damage
Inhibiting release of pain mediating chemicals
Enhances cardiovascular health by breaking down the protein by product of blood coagulation called fibrin therefore can dissolve blood clots and artherosclorosis plaques

Reduces pain and swelling without inhibiting prostaglandins and has no GI effect (like NSAIDs)
Alleviates pain by inhibiting release of bradykinin from inflamed tissue

Therapeutic uses:
Inflam mediated pain; scar tissue, endometriosis, AI, excess music, resistant bacterial infections

Question 33

ATP: adenosine triphosphate

Answer 33

Energy currency of the body
Body has to synthesise it before can spend it
ATP used to capture the energy released by reactions in the body such as burning glucose (ATP is how the body traps energy from these reactions in a way the body can use it)

Nucleotide with 3 phosphate groups. Important as the bonds between the phosphate groups contain lots of energy

When water added to ATP, 1 phosphate group is removed releasing energy via hydrolysis action.

Question 34

ATP and magnesium

Answer 34

ATP always present as magnesium-ATP complex

Magnesium binds to phosphate groups in ATP, holding molecule in slightly curved / strained shape that aids the loss of phosphates, facilitating energy release

Without Mg, ATP isn’t biologically active as it’s difficult to release the energy from between the phosphate groups

Hence low energy is a symptom of Mg insufficiency

Question 35

ATP functions

Answer 35

Capture energy from oxidation reactions

Drive body reactions (eg building proteins)

Fuel movement

Transport substances across membranes (active transport)

Cell division

Question 36

Turning food into energy

Answer 36

Energy not always released in ATP sized packages
At certain points, energy has to use energy carriers to temporarily capture the energy released
Concerts trapped energy into ATP molecules later
Main intermediate energy carriers are derived from B vits

Question 37

Energy carriers

Answer 37

NAD
Made from B3 (niacin) or from aa tryptophan and aspartic acid
When traps energy, becomes NADH

FAD
Made from B2 (riboflavin)
When traps energy, becomes FADH2

NAD or FAD sweep in and steal electrons and a H from glucose (or fats)
Trap energy temporarily
Hence adequate intake levels of B VIT for optimum energy levels

Question 38

Cellular respiration

Answer 38

Carbs broken down into glucose via digestive process
Glucose than then be oxidised to form ATP (chemically burned inside the body)

Process known as cellular respiration and involves 4 steps:
1. Glycolysis (or anerobic cellular respiration) in cytosol
2. Formation of acetyl CoA
3. Kerbs cycle
4. Electron transport chain

Question 39

Glycolysis

Answer 39

Need magnesium and b3

In cytoplasm

Through 10 steps in glycolysis, glucose is transformed into 2 molecules of a substrate called pyruvate

Through this splitting of glucose, some energy is released but 2 are (ATP) used up

Glucose contains 6 carbon atoms, whilst pyruvate contains 3 = 2x 3 carbon structure

Energy is directly released and trapped as 4 ATP and 2 NADH. There is a net gain of 2 ATP and 2 NADH

Glycolysis can occur with or without O2
When O2 available, NADH can be recycled in electron transport chain and turned into ATP
When not available, cannot be recycled

In order to allow energy production to continue, NADH reacts with pyruvate to keep glycolysis going, turning into lactic acid
Ideally only used for short bursts of activity, but pollution, stress, lack of exercise, smoking and obesity can create chronically hypoxic individuals

Question 40

Acetyl CoA formation

Answer 40

Needs B1, B5 and lipoid acid

In mitochondrial matrix

If O2 plentiful, pyruvate will enter the mitochondria and be converted into acetyl CoA ready to enter the Kreb’s cycle. Allows us to get more energy out of glucose

Pyruvate will react with B5 carrier molecule, which then allows it to enter the mitochondria
B1 and lipoic acid enable pyruvate to lose 1 of its 3 carbon atoms (hence acetyl CoA had 2 carbons)

2 more packets of energy are trapped as NADH

Coenzyme A is naturally synthesised from B5

Question 41

The Krebs cycle

Answer 41

Needs magnesium, manganese, iron, B1, B2 & B3

Occurs in mitochondrial matrix

Series of reactions where acetyl CoA is modified by enzymes. Energy is released or trapped

Also known as citric acid cycle (refers to first molecule forms during cycles reaction)

Acetyl CoA enters the kreb cycle. For each glucose, enough energy is released to make:
2 x ATP
6 x NADH
2 x FADH

Many enzymes can be blocked by heavy metals such as aluminium and mercury

Question 42

Electron transport chain

Answer 42

Needs iron, sulphur, CoQ10, copper ions

In inter folds of mitochondria

Final step allows energy to be trapped in NADH and FADH2 to be formed into ATP with the help of 4 enzyme complexes which are embedded in the inner folds of the mitochondria
O2 essential for this step to occur

A hypoxic environment will reduce their ability to produce ATP
Without O2, NAD and FAD cannot be recycled

Each of 4 enzyme complexes in the electron transport chain requires certain nutrients as cofactors:
Complex 1: iron and sulphur
Complex 2: CoQ10
Complex 3: iron
Complex 4: copper ions

Question 43

CoQ10

Answer 43

Key component of electron transport chain and stored in mitochondria

Depleted by statin use (acts on pathway shared by cholesterol & CoQ10 synthesis in liver)

Antioxidant properties and helps recycle other antioxidants such as VIT C & E
Reduces free radical damage
Slows down aging changes and inhibits atrial LDL oxidisation

Sources: near, poultry, nuts, sesame seeds, broccoli

Question 44

Mitochondrial damage

Answer 44

Can occur by:
Free radicals
Medical drugs and alcohol
Environmental toxins

Damage may compromise electron transport chain, without generating energy

Poor functioning linked to
Fibromyalgia
Type 2 diabetes
Chronic fatigue syndrome
Pathogenisis of cancer

To support:
Reduce toxic load
Increase nutrient cofactors
Increase production of glutathione and glutathione perioxodase (sulphur and selenium rich foods)
Add mitochondrial antioxidants including CoQ10
Support detox and elimination process

Ginseng, rhodiola, Rosemary, curcumin

Question 45

Energy from fats

Answer 45

In a sense of carbs, fats can be used
Lipase split triglycerides from adipose tissue into fatty acids and glycerol

Beta- oxidation: Fatty acids transported to liver, where body uses process called beta - oxidation to convert them to molecules of acetyl CoA

Can then enter the krebs cycle just like carbs
Fats yield a lot more energy than carbs. So whilst burning carbs is easier, fats are more efficient

Question 46

Fats getting into the mitochondria

Answer 46

Needs to combine with co-enzyme A (from B5)
Process required ATP and Mg
A carnitine- dependent enzyme is then needed to ferry the fatty acid into the mitochondria
L-carnitine is therefore required to transport fatty acids into mitochondria
(Often found in weight loss formulas to help fatty acids to enter mitochondria and burn for energy)

Question 47

Fats and beta- oxidisation

Answer 47

Aim of beta- oxidisation is to gradually chop the fatty acid chain into a style CoA ready to go into Krebs cycle

Occurs in mitochondria

Requires B2, B3 and sulphur - produces energy

Process repeats until entire fatty acid chain is broken down into acetyl CoA units which can then enter the Krebs cycle

Amount of energy produced depends on length of fatty acid chain

Question 48

Ketone bodies

Answer 48

Brain can’t use fatty acids for energy
Gets energy from ketone bodies when sufficient glucose is not available

Mitochondria of liver cells can convert acetylene CoA into ketone bodies:
Acetone
Acetoacetic acid
B-hydroxybutyrate

These can cross BBB and used as source of energy

Ketone bodies can also be formed when protein is used for energy

Question 49

Ketosis and ketoacidosis

Answer 49

Ketogenesis: production of ketones

Ketosis: body state of forming ketones

Ketosis can occur during high fat and low carb diets whilst fasting
State is highly beneficial for the most

Ketosis is never harmful from diet alone (some pathological states ketone bodies form in excessively high quantities, creates a state of keroacidosis: can occur in diabetes mellitis and alcoholism)

If both acetoacetic acid and beta-hydroxybutyraye are high, both acidic and will drop blood pH

Smelt on persons breath = acetone like nail varnish

Being in ketosis has been shown to benefit in certain disease states:
Epilepsy (controls seizures)
Alzheimer’s and Parkinson’s = enhances mitochondrial function
Cancer: normal cells can adapt using ketones, cancer cells can’t

Question 50

Fasting

Answer 50

Presents body from expensing excess amounts of energy digesting food

Instead, focus on healing and regenerating

Question 51

Energy from protein

Answer 51

B3 and B6 important cofactors

Carbon parts of aa can be broken down to generate ATP or can be used to make gluconeogenesis (making glucose)

Degeneration of aa in idea loss of nitrogen

Must lose NH2 amine group first before entering Krebs cycle
Results in creation of ammonia (NH3). most then converted to urea in urea cycle

Question 52

Gluconeogenesis

Answer 52

Formation of new glucose from other non carb sources. Eg:
Lactic acid
Glycerol
Some aa
Pyruvate

Takes place in liver, and lesser extend kidneys during period of fasting, starving or intense exercise

Biotin is important co-factor for gluconeogenesis

Question 53

Energy from food

Answer 53

Major sources of energy for the body are:
Glucose
Fatty acids
Ketone bodies
Aa

Adults in their fed state will obtain energy roughly:
47% carbs
38% fat
15% protein

In fasting state; body will source its energy from glycogen then fat then available protein