Lesson 4 Biochemistry 2 Flashcards
(64 cards)
Proteins
-AAs have TWO distinctive functional groups: amino -NH3 and carboxyl (acid) -COOH group.
-20 different AAs in the body.
-each aa has a side chain (R) that determines its characteristics.
-formed by aas joined together using dehydration synthesis (by removing H2O) to create ‘peptide bonds’.
Creating dipeptides, tripeptides. Eg. glutathione=glutamate, cysteine, glycine.
Aspartame
Toxic dipeptide. It’s manufactured. Doesn’t exist in nature and it’s a neurotoxin.
Glutathione
Powerful antioxidant.
It’s a tripeptide containing the AAs L-cysteine, L-glutamate and glycine.
Cysteine is normally a limiting aa (the least abundant). Contained in legumes, sunflower seeds and eggs). Increasing the intake of these foods will optimise glutathione production.
Amino Acid Types
-AAs with acidic side chains release Hydrogen ions (H+). Whether they do or not depends on surrounding pH.
-AAs with basic side chains can bind to H+, whether they do or don’t depends on surrounding fluid pH.
-Meaning, the pH of the fluid protein is in, will affect its 3D structure and therefore its function.
-eg. Ceviche- when you squeeze lemon juice (citric acid) on raw fish, protein get debatu red and changes its structure. From soft and translucent to firm and more opaque. Doesn’t kill all the potentially harmful organisms, including the parasites.
Denaturation
The Protein unfolding and unraveling.
Polar and non-polar AAs
Determination of the 3D shape
-Non-polar AAs are hydrophobic.
When proteins folds up in watery environment, they like to be on the inside of the protein structure, away from water. Eg tryptophan (used to produce serotonin which stimulates gut motility and digestive juices).
-Polar AAs are hydrophilic.
When proteins folds up in watery environment they like to be on the outside of the protein structure. Eg. Tyrosine (which is also used to create adrenaline and thyroxine).
It’s the combinations of polar and non-polar AAs that ultimately determine the 3D shape of the protein.
Functions of proteins
-structure of body tissues eg. collagen
-movement eg. actin and myosin fibres in muscles
-carrier molecules eg. Haemoglobin
-storage molecules eg. ferritin (iron)m-fluid balance in the blood eg. albumin
-enzymes (for reactions in the body)
-hormones eg. insulin
-immune function eg. antibodies
-clotting mechanisms eg. clotting factors
-cell membrane proteins eg. receptors
-alternative E source-much less efficient than CH-te or fat so only used during dietary deficiency
Denaturation of proteins
-Proteins work like lock and key. If a 3D protein structure changes or ‘unfolds’ (it unravels) we say it’s denatured. Denatured proteins no longer function correctly.
-Proteins can be denatured by:
-HEAT: eg. Cooking (egg whites become white-easier to digest) and pH CHANGES.
-HEAVY METALS:eg. mercury and lead (can damage hormones, antibodies and enzymes). Exposure must be minimised.
Natural chelating agents: Corriander, and chlorella remove heavy metals from the body. Try steeping 2 tsp of corriander in 1 cup of boiling water, with mint for flavour. (Made in pesto/salad and mix when eating tuna-high in Hg)
Protein digestion
Enzymes used to break down peptide bonds by hydrolysis reaction (using water).
-1stly mechanically broken in the mouth by chewing to increase the surface area for enzymes to work on.
-Chemical digestion begins in the stomach where enzyme PEPSIN breaks down long proteins chains.
-pepsinogen (inactive form), is released in the stomach from gastric chief cells, and gets converted to pepsin in the presence of HCl. Pepsin needs to be at pH 2 in order to function correctly.
-Adequate stomach acid is crucial for good protein digestion.
-As protein-rich chyme enters the small intestine, the hormone CCK is released, which triggers pancreas to release PANCREATIC JUICES, which contain PROTEASES called TRYPSIN and CHYMOTRYPSIN.
-In the SI, these shorter protein chains are further broken down into tripeptides, dipeptides and single amino acids by pancreatic enzymes and villi brush border enzymes.
-AAs and small peptides are then absorbed into the blood.
NUCLEIC ACIDS
Largest molecules in the body and are used to store our genetic information.
The most common nucleic acids are:
-DNA- deoxyribonucleic acid &
-RNA- ribonucleic acid.
-Building blocks of nucleic acids are called NUCLEOTIDES.
Nucleotides consist of: PHOSPHATE GROUP, SUGAR and a NITROGENOUS BASE.
Functions of nucleic acids
Store genetic information and acts like a recipe book.
DNA is very long -2m unraveled.
DNA is a template for protein synthesis.
RNA is used to copy specific sub-sections of DNA called GENES, and translate it into proteins.
20,000-25,000 genes in human genome (complete set of DNA)
DNA and nucleotide bases
Deoxyribonucleic acid.
Contains 5C sugar: deoxyribose.
4 possible nucleotide bases:
A- Adenine (purine base)
T- Thymine (pyrimidine base)
G- Guanine (purine) pairs with
C- Cytosine (pyrimidine)
A-T
C-G
Purine-rich foods contain lots of cellular material (lots of A and G), and form iris acid when metabolised. In excess can crystallise and cause gout.
Structure of DNA
Two strands wound together like a twisted ladder. A DOUBLE HELIX.
Two strands are held together by HYDROGEN BONDS (weak) and sugar-phosphate bonds are COVALENT BONDS.
Hydrogen bonds being much weaker unzip easily during protein synthesis.
Adenine always pairs with thymine.
Guanine always pairs with cytosine. These pairs will code for creating protein chains.
RNA
-Single strand of nucleotides which contain sugar ribose.
-mRNA- RNA goes into the nucleus and copies the DNA in the process of TRANSCRIPTION, creating mRNA.
-The mRNA then travels to a ribosome where it is read. The ribosome then produces the protein coded for eg. an enzyme. This is called TRANSLATION.
A-U uracil
G-C
At the end of this process a new protein is released which folds into its unique shape.
Genetics/ Telomeres
DNA is a manual for making all the proteins in the body, everything from muscle tissue to enzymes.
DNA is condensed to form chromosomes. (Genetic material).
Temhe end sections of DNA are called TELOMERES.
-the length of T shortens as cells and tissues age.
-the process at ageing can be accelerated from:
Stress, poor sleep, poor nutrition, chemical agents, a lack of exercise and even negative thoughts.
-GOTU KOLA (Centella asiatica) has been shown to reduce telomere shortening and hence support healthy ageing.
Mutation
A mutation is an abnormal change in the DNA sequence, hence can cause a change in the sequence of amino acids in the protein.
It can be something person’s born with or it occurs during lifetime.
This can cause the protein to be a slightly different shape, which may affect the functionality of the protein.
Eg sickle-cell anaemia- mutation of the gene that codes for the production of haemoglobin proteins, hence making blood cells defective.
Eg. Haemophilia mutation of the genes associated with production of blood clotting factor 8 (Haem. A) or clotting factor 9 (Haem.B). Hence individuals have problems clotting and stopping bleeding.
Cancer mutations
Occur due to factors such as radiation, sunlight, poor nutrition, chronic inflammation, medications, chronic stress and carcinogenic chemicals.
These mutations affect genes that code for proteins involved in regulating cell division.
Gene Expression
We can’t change our genes, but there are many things that can change gene expression-whether the genes associated is copied and the protein is made or not.
Eg. Liver makes many different enzymes involved in breaking down toxins. The more of a particular toxin is present in the body, the more enzyme that metabolising that toxin the liver will make. This might also affect how quickly liver metabolises other herbs and drugs also metabolised by the same enzyme. This is why some herbs can interact with some medications.
-Can be influenced by certain nutrients:
-metabolites of Vit A, vit D, essential fatty acids and Zn.
-fibre: by affecting hormone levels and through the metabolites created when intestinal flora feed on the fibre.
Pathological gene expression
It is essential to consider the environment we bathe our genes in, as such environment would promote negative health outcomes.
Ie. Cancerous cells thrive in acidic, anaerobic and glucose-rich environment. This environment would promote pathological gene expression promoting excessive cell growth.
Other factors:
Lack of oxygen, chronic stress, radiation, vaccine and drug toxins, junk food, etc…
Enzymes
Are biological catalysts made from proteins.
They speed up reactions but are not themselves changed in the process.
End is suffix -ase.
Substrates binds to enzyme and are converted into products.
They bind temporarily to substrate providing an alternative pathway to get to the end result much quicker. They lower the activation energy point, hence using less E for the reaction.
How Enzymes Work?
Enzymes have a very specific 3D shape.
Each enzyme has an active site- where substrate binds and it’s specific for that particular substrate. Referred to as ‘A lock and key’.
-Enzymes are highly specific and require optimum conditions; temperature and pH.
-they create a lower energy way for reactions to occur
Enzyme Co-factors
Enzymes need co-factors for activity and without these they are inactive. These are usually vitamins and minerals.
-Zn is required for the enzyme alcohol dehydrogenase
-Se is required for glutathione peroxidase
Enzymes : Substrate Concentration
Substrate concentration can affect the speed of enzyme reaction.
-⬆️ in the substrate concentration means more enzyme molecules are utilised
-hence the rate of reaction ⬆️.
-eventually all the enzymes are being involved in reactions, and substrates have to wait for available enzymes, so reaction can’t go any faster. It’s at its maximum already.
Eg. Very relevant with Omega-3s and Omega-6s. Way more Omega-6 in diet through vegetable oils, meat and dairy. Both use enzyme desaturases. Hence a lot of Omega-6s will overwhelm the enzymes and conversion of Omega-3s to EPA and DHA will be very slow or halted-compromised. Less abundant Omega-3s will not be converted.
-Hence it is vital to have a good balance of Omega-3 and -6.
Enzymes pH
Changes of pH can cause the protein structure to change. Changing the 3D structure and causing them to denature.
-in acidic conditions AA side chain can bind to H+
-in basic(alkaline) conditions, the side chains can lose H+
This changes can affect whether or not these side chains can form the bonds and interactions which are essential for the 3D structure of the enzyme.
So for every enzyme there is a specific pH at which it will work best.
