Biochemistry 2 Flashcards
Which four elements do amino acids contain?
NOCH
Carbon, hydrogen, oxygen and nitrogen
From this, there are 20 different variations
What are amino acids made up of?
Every amino acid has a Carboxylate group/acid at one end and an amino group at the other… Hence amino acid
They also have an R group which is a sidechain that determines its characteristics
What is an amino acid and how many types are there in the body?
Amino acids of the building blocks for proteins.
The body needs 20 different amino acids to create the proteins needed to function.
What is the bond between two amino acids and between three amino acids called. Give examples of each.
A dipeptide is when two amino acids are joined together and an example is aspartame. This example does not occur in nature however and is manufactured.
It is also a neurotoxin.
Tripeptide is when three amino is joined together and an example is glutathione which is a powerful antioxidant.
Why are pH levels so important when it comes to amino acids?
The pH of the fluid the protein will affect its 3-D structure. If the pH level that the enzyme requires to work is not available, it will unravel and its shape will change. It will become denatured.
The shape of the protein works like a lock and key, and if they unravel they weren’t fit the lock and won’t function properly.
Describe what drives the 3-D structure of proteins
Nonpolar amino acids are hydrophobic and when a protein folds up in a water environment they like to be on the inside.
Conversely, polar amino acids are hydrophilic and they like to be on the outside of the protein structure in a water environment.
It is the combination of the polar and nonpolar amino acids that ultimately determine the 3-D shape of the protein
List at least five functions of proteins
- Structure of body tissues
- Movement.
- Carrying molecules for substances (haemoglobinh
- Storage molecules (ferritin)
- Fluid balance in the blood (Albumin)
- Enzymes
- Immune function
- Clotting Mechanisms
What is denaturation and how can it happen?
Proteins have unreeled and lost their shape and therefore no longer functional properly because they cannot fit their lock.
It can happen from
- heat - think about egg whites
- Heavy metals
- Wrong pH
Talk me through protein digestion
- Proteins mechanically broken down in the mouth to increase the surface area for enzymes to work on.
- Chemical digestion starts in the stomach where the enzyme pepsin breaks down protein chains.
(Pepin is released by gastric chief cells in the inactive form of pepsinogen. It is the presence of hydrochloric acid with pH of approximately 2 that converts pepsinogen into pepsin. - As protein in chyme enters the small intestine the hormone CCK is released which triggers the pancreas to release pancreatic juices.
- Pancreatic juices contain protein enzymes the continue to work on the polypeptide chain breaking it down to di and tripeptides.
- Enzymes in Villi brush border of the small intestine continue this work breaking tri and di peptides into single peptides in amino acids.
- Amino acids and small peptides are then absorbed into the blood.
What are the 2 most common nucleic acids and how are they different structurally?
They are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).
RNA is a single strand of nucleotides which contain the sugar ribose.
DNA is a double-stranded structure and instead has the sugar deoxyribose.
It is a molecule of mRNA that copies specific subsections of DNA (genes) from DNA
What are nucleic acids?
They are the largest molecules in the body and they are used to store our genetic information.
DNA and RNA are the most common nucleic acids. Every living cell in the body contains at least one DNA molecule. They are huge and could be extracted to 2 m long.
What are the building blocks of nucleic acids?
Building blocks of nucleic acids are called nucleotides.
Nucleotides consist of
- a phosphate group
- Sugar
- nitrogenous base
There are four possible nucleotide bases in different patterns, giving us all the information we need to make all of our human proteins.
Adeline always pairs with thymine. Guanine always pairs with cytosine
How is the DNA recipe made available for a protein to produce?
- DNA is unzipped at the relevant section and the gene exposed?
- mRNA takes a copy of the recipe matching the bases of the DNA. TRANSCRIPTION
- mRNA leaves the nucleus of the cell and goes to ribosome where it is translated into a protein. Ribosomes are like the chefs that read the recipe to make a protein.
TRANSLATION - The protein chain will be released and fold up into its 3-D shape.
What is the end section of a chromosome called? What might affect their length?
They are called telomeres and they are ike the shoelaces tips at the end of DNA.
The shorten as cells and tissues age and this can be accelerated through things like stress, poor nutrition, poor sleep, chemical agents, a lack of exercise and even negative thoughts
What is a mutation?
A change in the sequence of amino acids in the protein which will likely change it 3-D shape and ultimately its function
What do you mean by gene expression?
We can’t change our genes but there are many different things that can change - our gene expression – which is whether we copy the gene and make the protein or not.
Our body is really flexible with this. An example might be someone who hasn’t drunk alcohol for six months and then goes out for a birthday celebration. The enzymes in their liver the breakdown alcohol have diminished because they haven’t been needed They will therefore be more affected by the alcohol but if they continue to drink over the next month more liver enzymes will be produced and tolerance for alcohol will get higher.
What affects gene expression?
There are many things that send signals to ourselves telling them whether or not to copy a particular gene. If we copy a gene we are making it. If we don’t copy it we are expressing less of it.
Gene expression is affected by:
- Acidic, anaerobic, toxic, stressful and glucose rich environments bathe our genes in a negative way and influence gene expression
- the metabolites vitamin A, vitamin D, essential fatty acids and zinc.
- Components of fibre can also have an effect on gene expression by affecting hormone levels and intestinal Flora
Give an example of how gene mutations can affect enzyme activity
MTHFR is an enzyme whose job it is to methylate folate. Methylation is used to control gene expressions and get rid of certain toxins like homocysteine and heavy metals. It is a very important process.
Some people have a genetic mutation in this enzyme which makes it about 50% efficient compared to a healthy version.
If they have this mutation then they will likely have a build up of homocysteine which is part of the methylation cycle and is involved in excess in diseases such as dementia and cardiovascular disease. When someone is methylating healthily homocysteine levels are low.
Someone with this mutation could have high homocysteine levels but if they are bathing themselves in the right nutrients, the environment it can compensate for the genetic difference.
Explain what is meant by an enzyme
Enzymes of biological catalysts made from protein the speed up reactions.
Enzymes are vital for life. They participate in every single chemical reaction in the body. Without them everything in our body would stop.
They are not themselves changed in the process so they can be used over and over again.
In enzyme reactions the molecules at the beginning of the process are called substrates and the enzyme converts them into a molecule known as a product..
The substrate sits in the enzyme active site which slightly stresses the chemical bond making it easier to break the bond or an enzyme allows two things to come closer together to make it easier to bond
How do enzymes work?
They are proteins that are folded into a very specific 3-D shape. It is this shape that is the key to how they work.
Each enzyme has an active site which has a unique shape that is complementary to the shape of the substrate molecule.
This is known as the lock and key.
Explain what is meant by an enzyme cofactor and give one example
Factor is a vitamin or mineral that the enzyme requires in order to function correctly.
A lack of cofactor can lead to a reduction in enzyme activity.
This is relevant for us because if we have a deficiency of a co-factor it will affect the enzymes reaction.
For example, zinc is required for the enzyme that breaks down alcohol – alcohol dehydrogenase.
Selenium is required for the antioxidant enzyme glutathione peroxidase. A lack of selenium compromises the livers ability to produce this.
What might affect enzyme function?
- If an enzyme is denatured and therefore not the right shape due to high temperature or conditions that are too acidic or too basic
- Enzymes co- factor is not available
- if there is too much substrate the enzyme can reach saturation point and cannot go any faster
List the digestive enzymes and where we find them
Mouth: salivary amylase to breakdown starch
Stomach:
- Pepsin working on protein in the stomach
- gastric lipase working on fats in the stomach
Small intestine: pancreatic enzymes.
- Pancreatic amylase works on the starches,
- pancreatic lipase works on the fat and
- pancreatic proteases work on proteins.
Small intestine:
brush enzymes - sucrase, Maltese and lactates do the final breakdown of disaccharides to allow transport into the blood.
What can influence a persons ability to produce digestive enzymes?
- Modern dietary habits overtax digestive enzymes when we eat large portions and when we eat continuously.
- There is too much substrate and not enough enzymes to efficiently convert that substrate into a digested form. The result is fermentation and putrification of food further down in the intestines.
- although enzymes are reusable, once they’ve gone into the intestinal track they will end up in the toilet and new ones and needed to be produced and digest the next meal. If we’re constantly snacking, we are constantly releasing enzymes into the digestive system and we don’t give our body enough time to build up enzyme supplies.
- Drinking whilst eating also interferes with enzyme function because it interferes with the correct pH in the stomach
- Prolonged stress turns off digestion
- Nutritional deficiencies meaning co factors are not available
How do humans and plant enzymes differ?
Plants of subject to wide range of conditions and therefore have a higher tolerance range of pH. They are therefore less likely to be denatured by pH.
However, as with human enzymes, they are denatured by heat, for example microwaving food
What happens to human enzyme activity at temperatures above 40°C?
Enzymes start to be destroyed when food is heated above 40°C.
The longer the exposure high the heat, the great the loss
????Why might me we eat raw food, overcooked food or vice versa?
Raw foods contain more micro nutrients than cooked food.
Cooking often decreases vitamins, minerals, probiotics, antioxidants and water soluble compounds such as vitamin C can be lost with boiling, leaching into the water.
However…
- Some compound in plant-based food such as like a peanut and beta keratin become more available when heated
- In some cases raw is not favourable such as Sebo where it can cause bloating
- when someone runs cold, they might be better off with warming foods
-
At what pH does salivary amylase work best?
PH of 7
Which enzymes are involved in creating inflammation in the body and are typically targeted by anti-inflammatory medication?
Given an example of one of these drugs
How else could we inhibit those enzymes with natural agents?
COX 1 Cox2 and 5-Lox
NSAIDS
Aspirin
Ibuprofen
Celebrex - Cox 2 only which meant to be less damaging to the GIT
Natural agents such as Boswellia, Curcumin and Ginger also inhibit these enzymes
Describe two specific effects of serrapeptase
Enzymes can be therapeutic..
Serrapeptase is a proteolytic ( breaks down protein ) enzyme that has potent anti-inflammatory effects on body tissues.
- It reduces pain and swelling without inhibiting prostaglandins and unlike NSAID has no gastrointestinal adverse effect
- Alleviates pain by inhibiting the release of Bradykinin which is involved in activating pain receptors from inflamed tissues
Examples of other enzymes used for therapy are bromelaine and pancreatic enzymes.
What are nucleotides?
Nucleotides are the basic building blocks of nucleic acids, such as DNA and RNA. Each nucleotide is composed of three components:
- A nitrogenous base (adenine and Thymine, cytosine and guanine.
- A five-carbon sugar (deoxyribose in DNA or ribose in RNA).
- A phosphate group.
Nucleotides are crucial for various biological processes, including the storage and transfer of genetic information and energy transfer within cells.
What does ATP stand for and what is its role?
Adenosine triphosphate and it is the energy currency of the body
It is how the body traps energy from reactions so that it can be used.
Which mineral exists in a complex with ATP?
Why would insufficiency in this mineral lead to low energy?
How do you acquire this mineral in the diet?
Magnesium.
If binds to ATP and holds the molecule in a slightly curved shape that sits in the enzyme to release energy. without magnesium energy releases compromised
Magnesium is essential component of chlorophyll so essentially anything green particularly green vegetables
What are the functions of ATP?
Capture the energy created when we burn fuel like glucose.
Examples of how these are used are:
- Drive body reactions such as building proteins
- Fuel movement
- Transport substances across membranes (active transport)
- Cell division
What nutrients are needed and what stage in order for energy production to function correctly?
Glycolysis – Mg + B3
Acetyl coA formation - B1 + B3 + B5 + lipoic acid
Krebs cycle - Mg + Mn + Fe + B1+ B2+ B3
electron transport chain - FE + S + CU + CoQ10
What is the main vitamin that the main intermediate energy characters are derived from?
B vitamins
1.2,3 and 5
What are the four stages involved in cellular respiration where carbohydrates are broken down into glucose by the digestive process?
Cellular respiration is the process where carbohydrates are broken down into glucose by the digestive system. There are four stages
- Glycolysis
2 Formation of acetyl CoA
3 Krebs Cycle.
- Electron transport chain
Where do the four stages of cellular respiration occur?
What is produced at the end of each stage?
In the cytosine
1. Glycolysis
In the mitochondria
- Formation of acetyl CoA
- Krebs Cycle.
- Electronic transport chain
What goes into and what energy comes out of each stage of cellular respiration
stages
- Glycolysis
In: 2 ATP, Mg, B3
Trapped: 4 ATP, 2 NADH
Pyruvate is made for the formation of acetyl CoA
2 Formation of acetyl CoA
In: B1, B5, lipoic acid
Trapped: 2 NADH
3 Krebs Cycle.
In: Mg, Mn, B1, B2, B3, Fe
Trapped: 6 NADH, 2FADH2, 2ATP
- Electron transport chain
In: Fe, S (sulphur), Cu (copper), CoQ10
Trapped: 10 NADH (30 ATP) and 2 FADH2 (4 ATP)
Which stage of cellular respiration can occur without oxygen?
Only stage one. Glycolysis.
This is known as anaerobic respiration and is used for short bursts of activity where you get a buildup of lactic acid which is what causes muscle pain when we exert ourselves.
Unfortunately, anaerobic respiration is not always only used for short bursts as many individuals are chronically hypoxic leading to accumulation of lactic acid and the creation of an acidic environment
Describe two functions of CoQ10
CoEnzyme Q10 is a key component of the electron transport chain and a very important antioxidant.
What causes mitochondrial damage and why are we concerned about this?
Free radicals
Things that lead to free radicals such as medical drugs, alcohol, and environmental toxins.
This can compromise the electron transport chain which will affect the abilities generate energy.
Poor mitochondrial functioning is linked to fibromyalgia, type 2 diabetes, chronic fatigue syndrome and the pathogenesis of cancer
????! What can we do to support mitochondria?
- Reduce toxic load from heavy metals, free radicals, junk Food etc
- provide nutrients to support cellular respiration
- Increase nutrient co- factors that are involved in the cellular respiration cycle
- the production of glutathione and glutathione peroxide by increasing sulphur and selenium rich foods
- CoQ10
*Increase antioxidants
- Introduce herbs that support mitochondrial functions and cleans the blood
- adaptogenic herbs such as ginseng and rodiola
- Antioxidant herbs like ginko and rosemary
- Support detoxification and elimination
How and when do we get energy from fats?
It is not the first port of call because although it has more energy per gram at 9 cal compared to 4 in carbs accessing that energy is a little more convoluted.
- First we split triglycerides from adipose tissue into glycerol and fatty acids and put them in the bloodstream.
- They are then transported to the liver where they undergo beta-oxidation – a series of chemical steps that allows us to take a long carbon chain of fat and chop it into acetyl CoA units that can go into the Kreb cycle
What molecule is needed to help ferry fatty acids into mitochondria?
L-Carnitine
What is needed in terms of cofactors and enzymes in order to get fatty acid into the mitochondria to be used for energy
- Fatty acids must combine with a co enzyme which comes from vitamin B5.
- This process requires ATP and therefore we need magnesium
- L Carnitine is needed to ferry the fatty acid into the mitochondria
- Once there beta oxidation takes place to gradually chop the fatty acid chain into acetyl co-A’s. Vitamin B2 and B3 and sulphur is required for this process.
What are ketone bodies?
Ketones are produced in the liver when it breaks down fats
Ketogenesis is neither a good thing or a bad thing. It is just a process of creating ketones.
Most body tissues can use fatty acids for energy when carbs are in short supply but the brain cannot. Ketones can cross the blood barrier and used as an energy source by the brain.
When are ketone bodies and ketogenesis good?
When are they problematic?
Positives:
The brain gets its energy from ketone bodies when sufficient glucose is not available
Ketosis can be highly beneficial to the body and is never harmful from diet alone
- It is sometimes recommended to children with refractory epilepsy because it increases gather in the brain
- Enhance mitochondrial function and be a benefit in neuro degenerative diseases such as Alzheimer’s and Parkinson’s
- Cancerous cells cannot adapt to ketones because they rely on glucose for their metabolism so it prevents the feeding of cancer
Negatives
When ketone bodies become excessive and lead to keto acidosis- acid can reach dangerous pH point .
This is more of a danger for people with diabetes and alcoholism
Can the body gain energy from protein?
It is not the preferred way of getting energy, but it is possible as a last resort. It is not ideal because we don’t want to metabolise our structural tissues like muscles.
In a fed state, the body uses very little protein for energy, only when the body is starving.
When we do gain energy from protein, we need to remove nitrogen which we don’t find in carbohydrates or fats. This must be removed before we enter the Kreb cycle. It requires B3 and B6 and produces ammonia which has to be disposed of through the urea cycle .
Which two vitamins are needed for the removal of nitrogen from amino acids?
B3 and B6
What is gluconeogenesis?
Glucose – new – formation
The formation of new glucose from other non-carbohydrate sources?
It takes place in the liver and to a lesser extent in the kidneys during periods of fasting, starvation or intense exercise.
Examples of non-carbohydrate sources are they used for gluconeogenesis…
- pyruvate
- Lactic acid
- Glycerol
- Some amino acids such as glutamine
Fill the gaps in this sentence
Match the enzyme with the food it is found in
??!?? What is the energy carrier NAD made with
FAD - B2
What nutrient is needed at what stage I. The electron transport change
What is coenzyme A synthesised from
B5
What is the name of the process that chops up fatty acids into acetyl CoA’s in the Kreb cycle?
Beta-oxidation
Match the protein function with the Protein structure
List at least five functions of proteins
I
NAD plus is an intermediate energy carrier molecule. What can it be synthesised from?
Aspartic acid
Tryptophan
Vitamin B3
What amino acids does the antioxidant glutathione contain and which is the limiting one?
L- Cysteine most commonly limits glutathione production. Legumes, sunflower seeds and eggs will optimise production.
L-Glutamate
Glycine
How does the body digest proteins to breakdown the peptide bonds between amino acids?
Proteins are mechanically broken down in the mouth to increase the surface area for enzymes to work
Chemical digestion begins in the stomach where the enzyme pepsin breaks down long protein chains.
Pepsin needs to be the pH 2 in order to function correctly so adequate stomach acid is critical for good protein digestion
