Chemistry & Biochemistry 1 Flashcards
What is an element
Cannot split into a simpler form
Substance made up of 1 type of atom and cannot be split into simpler substances
How many elements in the human body
- 4 major ones are
Carbon
Hydrogen
Oxygen
Nitrogen
What makes an atom
Protons (+) and neutrons form nucleus = 1 atomic mass each
Electrons (-) outside of nucleus = virtually no mass at all
Atom will have an equal number of protons and electrons giving overall neutral charge to the atom
All chemical properties of an atom are down to its number of protons and electrons
Electrons
Move in groups along the nucleus known as electron shells
Electrons pair up within their shells
First pair in the ring is 2, then second ring is up to 8
Except hydrogen which is so small it only has 1 electron.
Atom becomes reactive if outer shell isn’t full or loses an electron.
More it loses, more reactive = free radical
Oxidation
Positive charged = volatile and creates tissue damage
Any atom with unfulfilled orbits of electrons are unhappy
Periodic table
Arranged in columns and rows to show which elements share reactivity and physical properties
The number assigned shows how many protons and therefore electrons each atom had
Large number is the mass (in atomic units).
To find out how many neutrons=
Mass number - atomic number
Halogens
In Row 17
Share very similar chemical properties
Thyroid issues: If chlorine and fluoride are present in body, they can enter the thyroid preventing formation of T3&T4 which insides hypothyroidism
Isotopes
Atoms of the same element which have different numbers of neutrons in the nucleus
Doesn’t affect chemical activity, only the mass
Isotopes and radiation
Some have imbalance of protons and neutrons in the nucleus which causes them to be unstable and therefore causes radioactivity. Unstable atom needs to get rid of energy to become stable
PET scan imaging technique, radioactive isotopes are introduced and often injected into the body
Radiotherapy uses gamma rays from radioactive isotopes to target rapidly dividing cells.
Breathe test for H.pylori uses urea labelled with either radioactive carbon or non-radioactive carbon
Electron shells
All of the reactions that happens in chemistry are driven by atoms trying to end up with a stable and full outer shell either by stealing or giving away or sharing a electrons
Inert elements
Atoms with outer shell filled with perfect number so rarely involved in chemical reactions
Bonding
Atoms trying to become stable by bonding with other atoms so they can get just the right number of electrons in their outer shell.
2 types; ionic and covalent
Ionic bonding
When one atom donates some of its electrons to another
Usually occurs when there are 1. 2 or occasionally 3 electrons to donate
Moving any more isn’t energetically favourable
Ions
If atom gives up or gains electrons to fill its outer shell, it becomes an ion
Ionisation: process of giving or gaining electrons
Gives an electron = positive charge
Takes an electron = negatively charged
Covalent bond
When 2 elements share electrons so that they both have the magic number they are looking for.
Tends to happen when 2 atoms are similar or when lots of space to be billed to reach a full outer shell
Polar bonds
Forms when electrons are shared unequally.
Happens as some atoms have a lot of electron pulling power
Electronegative: Some have lots of protons compared to number of electron shells (ie strong + centre) so they tend to pull shared electrons toward themselves
These electronegative atoms are able to pull electrons in a bond towards them, leading to uneven distribution of charge
Fluoride, chloride, oxygen and nitrogen are lost electronegative elements
Hydrogen and O2 making water most important example. 02 pulls electrons towards itself, resulting in - charge area over 02 and + over H
H are then attracted to the - charge
Loving interactions called H bonds and gives water its special properties:
Surface tension and ability to dissolve many things.
Hydrogen bonding
Hydrogen and O2 making water most important example. 02 pulls electrons towards itself, resulting in - charge area over 02 and + over H
H are then attracted to the - charge
Loving interactions called H bonds and gives water its special properties:
Surface tension and ability to dissolve many things
Water serves as medium for most chemical reactions
As water contains polar bonds, ideal docent for dissolving chemicals into their separate ions.
Hydrophilic molecules
Polar bonds.
Dissolve easily (eg alcohol)
Hydrophobic molecules
Non polar covalent bonds
Don’t dissolve easily
Electrolyte
Formed when ionic compound (eg salt) dissolves in water
Can conduct electricity
Key electrolytes in body
Potassium
Magnesium
Sodium
Chloride
Phosphate
Bicarbonate
Calcium
Electrolyte important body constitutions because
Conduction of electricity I’d essential for nerve/muscle function
Exert osmotic pressure important for water balance
Some play important role in acid base balance
pH balance
What is an acid
Substance that released a high amount of H+ ions when dissolved in water
What is a base
Substance which binds to H ions in solution.
Creates a lot of OH-
Water
Neutral solution
Because every H+ ion released and OH- is also created.
pH scale was developed using water as standard
pH is 7
(Blood is 7.35 - 7.45)
pH and digestive system facts
Fruit and veg contain organic acids. Low pH measured before consumption
- organic acids metabolised by body and intestinal bacteria make it alkaline
- foods high in alkaline minerals (potassium, magnesium, calcium) also contribute to net alkaline effect
Dairy not very acidic before consumption, high in calcium.
Yet more acidic due to high protein and sulphur content
The sulphur aa increases sulphuric acid formation, then disrupts blood ph drawing more calcium from bones and calcium loss in urine
Meat high in acid
Refined sugar and processed foods
Stress and sedentary acidic environment
Chemical reactions
Occurs when new bonds are formed or old bonds are broken between different molecules
Every reaction involves the transfer of energy to either potential (stored) energy, kinetic energy or heat
Starting molecules = reactants
End molecules = products
Reactions must always balance in electrons from one side to another
Collision theory (for chemical reaction to occur)
Needs to be an opportunity for 2 molecules to collide
- higher the energy of the molecule, the faster they move and the greater chance they have of reacting
- min energy that is required for a reaction is known as the energy of activation
- chemical reactions are reliant on the correct temp and enough reactants
- changes in pressure can also change the speed of reward on, with increased pressure forcing molecules closer together
Catalyst
Speeds up reactions by lowering the activation energy required
Means reaction is faster or can occur at lower temps
Body catalysts are enzymes
Inhibitors
Act antagonistically to catalysts
Stop catalysts from being so effective by making the activation energy higher and hence slow down the reaction time
Many drugs inhibitors - eg statins are HMG-CoA reductase inhibitors
Anabolic chemical reaction
Synthesis (building) reactions
Occurs when body is making new substances and building new bonds
Eg taking aa and building a protein. Requires energy
A+B = A - B
Catabolism chemical reaction
Reactions where breaking down occurs
Eg when breaking down food, releasing energy from them.
Trap energy as ATP
A - B = A+B
Hydrolysis reaction
When water is medium and breaks molecule into smaller pieces
Dehydration synthesis
When water formed as the waste product of a reaction
Normally when larger molecules are being made - eg making carbs
Reversible reactions
Products of the reaction can react together to produce the original reactions
A + B = AB / AB = A + B
These reactions establish equilibrium where are always some starting materials and some product present
Controlling direction of reversible reactions is very important in the body. Done using enzymes and having mechanisms in place that allow us to remove starting materials and products
Buffer system
Substances that maintain H+ concentration in the body within normal limits. They can bind to H+ ions and OH- to ensure the blood pH remains between 7.35 and 7.45
Most important is bicarbonate buffer system which mops up excess acidity. (HCO3)
Bicarbonate buffer system
Catalysed by carbonic anhydrase
CO2 from cellular respiration reacts with water in the blood to for. A carbonic acid which rapidly dissociates to form a bicarbonate and hydrogen ion
Reactions are reversible and any given time there is a balance of CO2, H2O carbonic acid, H+ and HC03 in the blood
Carbonic anhydrase
CO2 + H20 <-> H2CO3 <-> HCO3- + H+
When extra H ions accumulate in the blood, eg lactic acd, the reaction is able to adjust to mop up the excess H+ ions, making more CO2 and H20
Then accounted for by increased breathing rate and exhalation of C02 through lungs
Kidneys also play role in buffer system as they can produce HC03- buffer. Also can excrete H+ ions
Kidneys fairly slow in this system and their production of HC03- is fairly strenuous upon the organ, therefore important to avoid an acidic diet so as to reduce the stress on the system
Oxidation
Removal of electrons from an atom or molecule is oxidation
Reduces potential energy in a compound
Generally most oxidation occurs by removing electrons with the help of hydrogen.
As hydrogen is lost, often called dehydration reaction
When something is reduced, gains an electron resulting in the increased energy in that molecule
Free radical
Molecules or compounds that have impaired electron in outer shell
Wants to stabilise so tries to steal electrons from other stable molecules
Becomes destructive and causing oxidation
Leaves attacked molecule with impaired electron, so chain reaction of oxidative damage
Free radicals even take electrons from DNA which can ultimately result in cancerous changes
Oxidative damage
Free radicals can cause oxidative damage to tissues in the body
Linked to cancer, atherosclerosis, fibromyalgia, and neurodegenerative diseases
Need to reduce exposure to free radicals. Whilst optimising antioxidant status to help protect
Antioxidant
Work by donating electron to free radicals to covert them to harmless molecules, without being damaged themselves.
Consists of group of vitamins, photochemical and enzymes
Key to good antioxidant is must be stable once it has given away its electron
Types of antioxidant
Beta - carotene
Vitamin e
VIT c
Quercetin
Glutathione perioxodase
Alphahpoid acid (meat, eggs)
Biochemical molecules
Living things that are characterised by molecules made from carbon
Functional groups: any other groups of atoms attached to the carbon skeleton. Contributes to the structure and function of that molecule
Biochemical date important when considering the living nature of biochemistry
Functional groups
Hydroxyl group: alcohols. Polar and hydrophobic
Sulfhydryl group: common in some protein chains. Found in sulphur containing cysteine
Polar and hydrophilic
Carboxyl group: found in aa.
Hydrophilic and can interact as a weak acid or as negative particle
Amine group: found in as
-NH2 group can act as a weak base if necessary
Esters: predominant bond in triglycerides
Long term energy source
Phosphates: found in ATP
Very hydrophilic as they can form double negative charge
Can attract a lot of energy
Carbohydrates
Includes starches, cellulose (plants) and sugars
Carbon atoms normally arranged in a ring with 02 and H+ atoms attached
Have many OH- groups so they break for H bonds. Meaning smaller carbs such as simple sugars can dissolve easily in water
Monosaccharides
3-7 carbon atoms
Simple sugars, most have sweet taste
Grouped into families named after the number of carbon atoms
All end in -ose
Glucose
Fructose
Galactose
Deoxyribose
Ribose (in DNA)
Disaccharides
2 monosaccharides joined together as dehydration reaction to form a disaccharide
Removing water to form a glycosidic bond
If we’re to ingest a disaccharide we can break it down by putting water back into the bond
Sucrose (glucose and fructose)
Lactose (glucose and galactose)
Maltose (glucose and glucose)
Polysaccharides
10s to 100s of monos in glycosidic bonds - joined together by dehydration reaction
Normally insoluble in water (given up many OH molecules)
Do not taste sweet
Digestion begins in oral cavity
Glycogen (most common type)
Starch
Cellulose
(All glucose chains)
Starch: amylose and amylopectin
Starch is major dietary source of carbs
Digestion begins in oral cavity
Found in breads; rice, pasta, etc
Made up of 2 different polysaccharides:
25-25% amylose
76-80% amylopectin
Amylose: single chain of glucose units (limits surface area exposed for digestion)
Foods high in this referred to as resistant starch and digested more slowly
Ends up in large intestine and acts as good source for bacteria there
Amylopectin: branch like structure, also made by glucose (more surface area available for digestion: broken down quicker = blood sugar spike and higher rise in insulin)
Glycogen
Polysaccharides of glucose which functions as primary short term energy storage
Each molecule made up of 60,000 glucose molecules and even more branches than amylopectin
Made and stored primarily in liver and muscles
Glycogen in liver can be used to maintain blood sugar levels, whereas in muscle can only be used by that particular muscle
Cellulose
Structural material of plant cell walls
Glucose polymer but linked in a way to make flat ribbon like strand with overall rigid structure
Humans lack correct enzyme to break unique bond between glucose molecules so we cannot digest it
Cellulose acts as fibre assisting with bowel movement through intestines
Most abundant organic compound on earth
Carbohydrate functions
- Energy
- Fibre (proper bowel functions, prevents against cardiovascular disease, against diabetes, increase satiety, aids weight loss, protects against colorectal cancer)
- number of processes: ATP production, glucogen synthesis, aa synthesis
Carbohydrate digestion
Salivary amylase starts working on the end of the long glucose chains in starches (chew for long time tastes sweet)
Salivary analyse works well in fairly neutral pH but neutralised by stomach acid
In small intestine, pancreatic analyses continues carb digestion, goes into disaccharide units.
Brush border enzymes in small intestine do final stage (lactase, Maltase and sucrase)
Lipids
Contains elements - carbon, hydrogen and O2,
Like carbs but in different ratios
Few polar OH groups = hydrophobic
To move around body, often gets protein to make them more soluble (lipoproteins)
Triglycerides
Main form of dietary fats
Contains single glycerol molecule and 3 fatty acid chains (saturated or unsaturated)
Combination will determine if solid or liquid at room temp
Ester: Fatty acids attached to fully Erik by dehydration synthesis - bond known as ester (different from carbs)
Broken down by hydrolysis reaction
Triglyceride functions
Most efficient energy source, but process of energy released from fat is less efficient than when carbs are used
Provide convenient form to which to store excess calorie intake
Insulation
Protection of body parts and organs
Saturated fats
Form of triglycerides
Contain single covalent bond between each fatty acid atom
Each carbon atom Saturated with H atoms
Saturated fatty acids are very straight meaning they can line up close to each other and hence more likely to be solid
Eg coconut oil
Monounsaturated fats
Contains fatty acids with one double covalent bond between 2 carbons
Double bond forces molecule into bent configuration
Monounsaturated fats are generally liquids at room temp (,m can’t pack closely together)
Eg olive oil
Polyunsaturated fats
Contains more than 1 double bond in carbon chain
Molecules are kinked
Liquid at room temp
Eg sunflower, rapeseed, vegetable oil
Fatty acids
Omega 3 = double bond is 3 carbons up from end
Omega 6 = double bond is 6 carbons up from the end
Named according to the closest double bond to end of chain
End of chain is always the end without O2
Both essential in our diet
Cis and trans configurations
Presence of double bond means 2 different molecular configurations are possible
Cis = H atoms on same side of double bond
Trans = H atoms on separate sides of double bond
In nature, nearly all have cis bond.
Cis fats make cell membrane more flexible
Trans stiffens cell membranes and are prone to oxidative damage and making cell membranes leaky
Formed during high heat or hydro generation reactions
Omega 3
Alpha-linolenic acid (ALA) - essential in diet (flax seeds, walnuts, green leafy veg)
EPA & DHA - oily fish
Omega 6
Linoleic acid (LA) - essential in diet (veg oils, most nuts and seeds)
GLA - borage oil; evening primrose oil
AA - meat, dairy, eggs
Essential fatty acids
Polyunsaturated fatty acids that cannot be constructed within the body from other components and therefore must be obtained from diet
Conversion of ALA to EPA and DHA is only about 10% efficient, even lower for LA to GLA & AA
The conversion between them involves adding in double bonds. This involves desaturase enzymes
Same enzymes used; it will ultimately favour EFA
Fatty acid oxidisation
Polyunsaturated fats such as EFAs are v prone to becoming free radicals
When fats heated, electrons can be lost. Means that a fat is formed that becomes a free radical. (Further reacts with O2 in cooking pan which becomes even more damaging)
CH2 groups between double bond are especially vulnerable because radicals formed at these points in the molecule are very stable
Radical formation accelerated by:
Light, O2 and heat
Lipoproteins
Fat molecules that have been joined to a protein molecule, enabling lipid to move around the bloodstream
Contains triglycerides and cholesterol internally
Synthesised by the liver
TYPES:
Very low density lip (VLDL): carry newly synthesised triglycerides from the liver to adipose tissue
Low density lip (LDL): carry cholesterol from liver to cells of body. Needed to repair cells; support cell membranes and synthesise sex and adrenal hormones
High density lip (HDL): collect cholesterol from body’s tissues, bringing back to liver
Phospholipids
Contain glycerol part & 2 fatty acid chains
Phosphate head contains lots of -OH molecules which make it hydrophilic and therefore polar and water soluble
Fatty acid tails non polar and only interact with other lipids - hydrophobic and fat soluble
Fatty acid tails contain saturated and unsaturated fats (cells should contain a balance of these)
Amuphiphatic: soluble on one side, insoluble on other
Steroids
Lipid forms of cholesterol
Differ in shape than triglycerides where formed of 4 rings of carbon atoms joined together at their base
Sterols are steroid bases that contain -OH group
Used to create hormones, eg oestrogen and cortisol
We do not need to eat/ingest as liver produces it
