Chemistry & Biochemistry 2 Flashcards
Proteins
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
Peptides
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
Glutathione
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
Amino acids
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
Non polar aa
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)
Polar aa
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)
Protein functions
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
Denaturation
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
Protein digestion
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)
Protein digestion and absorption
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
Nucleic acid
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
DNA
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)
RNA
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
Genetics
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
Mutation
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
Gene expression
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
Gene expression nutritional influences
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
MTHFR gene mutation.
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
Other common mutations
Unable to convert beta carotene to VIT A
Some can’t co very D from skin
Enzymes
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
Enzyme co factors
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
Substrate concentration
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
Omega 3 and 6 conversion
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
Enzymes and pH
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
Enzymes and temperature
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
Digestive enzymes
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
Enzymes in food
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
Raw foods
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
Enzymes and inflammation
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
Enzyme inhibitors as drugs
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
Enzyme therapy
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
Serrapeptase
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
ATP: adenosine triphosphate
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.
ATP and magnesium
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
ATP functions
Capture energy from oxidation reactions
Drive body reactions (eg building proteins)
Fuel movement
Transport substances across membranes (active transport)
Cell division
Turning food into energy
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
Energy carriers
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
Cellular respiration
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
Glycolysis
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
Acetyl CoA formation
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
The Krebs cycle
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
Electron transport chain
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
CoQ10
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
Mitochondrial damage
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
Energy from fats
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
Fats getting into the mitochondria
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)
Fats and beta- oxidisation
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
Ketone bodies
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
Ketosis and ketoacidosis
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
Fasting
Presents body from expensing excess amounts of energy digesting food
Instead, focus on healing and regenerating
Energy from protein
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
Gluconeogenesis
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
Energy from food
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
