Biochemistry Summaries Flashcards
What is an element?
How many are there in the human body?
A substance made up of just one type of atom so it cannot be split up into simpler substances.
There are 26 different elements; the major 4 are C, H, O, N = 96% of the human body.
What is an isotope?
Are atoms of the same element but with different number of neutrons in the nucleus. This does not affect the chemical activity but changes the mass.
Describe what happens and types of radio active decay
Some isotopes have such an imbalance of protons and neutrons that is can cause the atom to become unstable leading to radioactivity.
I.e. the unstable atom needs to get rid of energy to become stable again and does this by:
- alpha decay - ejecting protons and neutrons from the nucleus
- beta decay - splitting neutrons into protons and electrons that can be ejected
- gamma decay - emitting energy as gamma rays
Describe uses of radiation in medicine
Radiotherapy uses gamma rays to target rapidly dividing cancer cells
Radioactive glucose uptake to evaluate cancer treatment
Breath test for H Pylori - the detection isotope labelled carbon dioxide in exhaled breath indicates that the urea was split and that urease is present in the stomach.
Name the four most electronegative elements?
Fluorine, Chlorine, Oxygen and Nitrogen
CL, F, O, N
What is an electrolyte and what do they do?
An ionic compound i.e. salt when dissolved in water is an electrolyte
- conduct electricity essential for nerve and muscle function
- exert osmotic pressure important for water balance allowing fluid to travel inside and outside of the cell (sodium potassium pump)
- play an important role in the acid-base balance
Main ones: Na+, Cl-, K+ (pace maker of the heart) and Mg+
Difference between an acid and a base
An acid is a substance that releases a high amount of H+ when dissolved in water, whereas a base binds hydrogen ions in solutions increasing lots of OH- (hydroxide)
What is the energy of activation?
Minimum energy that is required for a chemical reaction to occur. Can be lowered by catalysts or stopped by an inhibitor.
(Example of inhibitors are Botox or antibiotics)
What is a chemical reaction and what is is reliant on?
It’s the breaking or formation of chemical bonds. for this to occur there needs to be an opportunity for two molecules to collide.
Starting materials are reactants, end molecules are products.
Written in a formula that must balance balance in electrons on both sides i.e. A + B = AB.
Reliant on: the correct temperature, high enough concentration of reactants;
Increasing pressure can speed up reactions.
Difference between endothermic and exothermic reactions and examples
Endothermic take in heat and tend to be anabolic i.e. body building or freezing water
Exothermic release heat or energy - catabolic i.e. fire, melting ice
What’s a buffer system ? Give an example and how does it work?
Substances that maintain the H+ (pH) concentration in the body within normal limits. The most important one in the blood stream is the bicarbonate buffer.
COs (from cellular respiration) reacts with H2O in the blood = carbonic acid (H2CO3) = bicarbonate ion (HCO3-) and H+.
These reactions are reversible.Lungs and kidneys key players.
What’s a free radical?
Molecules or compounds that have an unpaired electron in its outer shell. They become destructive and steal electrons = oxidation, causing a chain reaction.
Results from normal aerobic respiration, metabolism and information; from within the body or from environment (pollution, sunlights, strenuous exercise, X-rays, smoking, alcohol.
What are antioxidants?
Group of vitamins, minerals, photo chemicals and enzymes that donate electrons without becoming unstable themselves.
ACE, Glutathione (naturally produced in our body)
Work best as a collection, so they can recycle each other.
Functional Groups
Attached to carbon skeleton contributing to structure and function
Hydroxyl: R-O-H (polar and hydrophilic)
Sulfhydryl: R-S-H (polar and hydrophilic; in some proteins)
Carboxyl: R-COOH (hydrophilic, weak acid, found in amino acids)
Esters: R-OOR’ (predominant in triglycerides)
Phosphates: C-POOOO (in ATP, very hydrophilic)
Amine: -NH2 (weak base found in amino acids)
Metabolism of fat for energy production is stimulated or inhibited by what hormones?
Stimulated by Adrenalin/epinephrine
Inhibited by insulin
What are two types of complementary bases that form nucleotides?
Purines and pyrimidines
What is the structure of an amino acid?
Formed from elements C, H, O and N (some have Sulphur)
There are 20 AAs in humans;
Everyone has a carboxyl (-COOH) and an amino (-NH2) group with different R- side chain
What are the essential amino acids? (9)
Histidine. Valine
Isoleucine. Phenylalanine
Leucine. Threonine
Lysine. Tryptophan
Methionine
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What are non-essential amino acids? (5)
Alanine Aspartic Acid Glutamic acid Serine Asparagine
My friend Alan was a spartan who ate asparagus and seriously developed an ass personality.
What are conditionally essential amino acids? (6)
Arginine Cysteine (depends on Methionine) Glutamine Glycine Proline Tyrosine
I get tired of arguing with mean ass cysts, they glide into the scene and act like pro lean body builders.
Give an example of a di-peptide?
Aspartame is made up of aspartic acid and phenylalanine
Give an example of a tri-peptide
The body’s own glutathione is made up of L-cysteine, L-glutamate and glycine.
Different protein structures
Primary structure - linear sequence held by peptide bonds
Secondary - nearby side chains interacts to cause twists and folds - alpha helix or beta pleated sheet
Tertiary - further interactions to create 3D structure via hydrogen bonds, salt bridges, disulphide bonds or non-polar hydrophobic interactions
Quaternary - larger structures made up of individual protein chains
What is an example of a quaternary structure?
Haemoglobin which is made up of 4 x protein chains.
Why are disulphide bonds in tertiary protein structures important?
A disulphide bond is the only proper covalent bond in tertiary protein structure so very important for stabilisation
What is desaturation? And what can it caused by? (6)
Shape = function; denaturation is the unfolding of protein chains (breaking interactions) leading to inability to function.
Denaturing agents include heat (fried egg), solvents, mechanical mixing, strong acids or bases, detergents and ions of heavy metals like lead or mercury.
Function of Proteins (12)
Structure of body tissues i.e. collagen Movement i.e. actin and myosin fibres Carrier molecules i.e. haemoglobin Storage molecule i.e. ferritin Fluid balance in the blood i.e. albumin Enzymes Hormones i.e. insulin Immune function i.e. antibodies Clotting mechanism Alternative energy source (not ideal) Control of gene expression Cell membrane receptors
What is hydrolysis and what is the opposite?
Hydrolysis is when water is the medium that breaks down the molecule into smaller pieces.
when water is formed as a waste produce, it’s dehydration synthesis or condensation reaction.
What are isomers?
Molecules that have the same chemical formula but different structures like fructose, glucose, galactose and mannose.
How are disaccharides formed?
glycosidic bond via dehydration synthesis (condensation reaction)
Structure of carbs
Monosacs - fructose, glucose, galactose, ribose and deoxyribose
Disaccs - sucrose, lactose, maltose
polysaccs - glycogen (made and stored in liver and muscles)
starch - 25% Amylose (resistant starch) and 75% amylopectin (branched)
Cellulose - flat ribbon,lacking enzyme, fibre
Function of carbs (3)
Fuel for energy production
stored energy (glycogen)
Fibre
Function of fibre and how much is needed? (6)
needed for proper bowel function protects against CV disease (14g per 1000 kcal) protects against diabetes (15g per day) increase satiety (14 - 24g per day) aids weight loss (14g per day) protects against colorectal cancer
current intake 3 - 5g per day; optimal 30g
Functions of glucose in particular (4)
ATP production
glycogen synthesis
triglycerides synthesis
amino acid synthesis
Functions of triglycerides (4)
energy source (but less efficient than carbs)
storage of excess calorific intake
insulation
protection of body parts (kidneys)
What are essential fatty acids?
polyunsaturated acids that the body cannot made and therefore must be supplied by the diet i.e. Omega 3 and Omega 6’s.
examples of Omega 3’s (anti-inflam)
ALA - alpha linolenic acid (green leafy veg, flaxseed, walnuts, brazil nuts
EPA - Eicosapentaenoic acid (fish oil)
DHA - docosahexaenoic acid (fish oil)
examples of Omega 6’s (anti and pro inflam)
LA - Linoleic acid (veg oils, nuts, seeds)
GLA - Gamma linoleic acid (primrose, borage oil)
AA - Arachidonic acid (meat)
Functions of EFAs (what they do 7, what they make 5)
What is does?
- regulates energy production
- fluidity and chemical activity of cell membranes
- proper nerve transmissions especially in the brain and - generates electrical currents keeping heart rate regular
- helps balance immune system and prevent allergies
- helps transport cholesterol in the blood
- bone formation and repair
What is makes?
- synthesis of prostaglandins (hormone like substances involved in functions at cellular level and regulation of body processes)
- helps to form haemoglobin
- support production of digestive enzymes
- needed by tissues of the brain, adrenals, testes and retina
- helps to make lubricants in the joints
What are eicosanoids?
term for a family of hormone like substances derived from 20 carbon polyunsaturated fatty acid, comprising of prostanoids (prostacyclin, prostaglandin, thromboxanes), leukotrienes (WBCs) and Lipoxins.
What are lipoproteins and give examples
Lipoproteins are fat molecules bonded with proteins to allow lipids to be transported in the blood.
Chylomicrons - transports triglycerides from intestines to body cells in liver, skeletal muscles and adipose tissue
VLDL - newly synthesised fat from liver to adipose tissue; sign of overeating i.e. excess glucose
LDL - cholesterol from liver to cells used for repair or making hormones
HDL - excess cholesterol from cells to liver
What are phospholipids and its property?
similar to triglycerides, glycerol plus 2 x FAs plus phopshate head; makes up the cell membrane; is amphiphatic (hydrophillic and phobic)
What are steroids?
Lipid based on the cholesterol 4-ring structure; involved in hormone production.
What is the structure of proteins?
made up of amino acids; formed from C, H, O, N and sometimes Sulphur; contain a carboxyl group (-COOH) and an amino group (-NH3) and an individual side chain; there are 20 amino acids in the human body.
What are the classifications of Amino Acids?
non polar (hydrophobic), polar(hydrophilic) , acidic or basic
What are the essential amino acids? (9)
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Tryptophan, Threonine, Histidine, Valine, Isoleucine, Phenylalanine, Methionine, Leucine and Lysine
What are the non-essential amino acids? (5)
AGASA
Alanine (from Phenylalanine), Glutamic acid, aspartic acid, serine, asparagine
What are the conditionally essential amino acids and one example? (6)
CG GAPT
Cysteine (needs methionine), Glutamine, Glycine, Arginine, Proline and Tyrosine.
How do amino acids bond and 2 x examples?
via condensation/dehydration synthesis; 2= amino acids joined together via a peptide bond ie. di-peptide or tri-peptide.
Give an example of a di-peptide bond
aspartame = aspartic acid and phenylalanine
give an example of a tri-peptide bond
gluthathione = L-cysteine, L-glutamine and glycine
what is glutathione ?
a tri-peptide that is the body’s own antioxidant
Examples of secondary structure
sequence of amino acids in a primary structure is such that the nearby side chains interact, causing twists and folds in the chain. the two types are alpha helix or a beta pleated sheet.
what causes the twists and folds in secondary chain?
caused by imbalances in electrical charges
What interactions lead to a tertiary structure? (4)
hydrogen bonds (polar) salt bridges formed between positively and negatively charges side chains disulphide bonds non-polar hydrophobic interaction
Why is the disulphide bond the most important interaction in a tertiary protein structure?
form between sulphur containing amino acids; it is the only proper covalent bond so important for stabilisation.
give an example of a sulphur containing amino acid
cysteine
what is quaternary structure and give an example
the term quaternary structure describes a situation where individual protein changes join together to make a larger structure e.g. haemoglobin which is made up of 4 x protein chains.
what is denaturation?
the unfolding of proteins due to breaking of bonds that inactivates the protein. denaturing agents include include heat, solvents, mechanical mixing, strong acid or bases, detergents or heavy metal ions (lead/mercury).
Is denaturing good or bad for digestion?
it is good as it will help digestion; hence put vinegar in salad dressing;
Functions of proteins (12)
building materials for growth and maintainance for muscles, blood, skins, and most body structures
Movement - actin and myosin fibres
carrier molecule - haemoglobin, lipoprotein, albumin
storage molecule - ferritin,
regulator of fluid balance
enzymes i.e. pepsin, and hormones - tryptophan - melatonin, tyrosine and iodine = thyroid hormone;
immune function - antibodies (immunoglobulins)
clotting mechanism (coagulants)
cell membrane receptors (glycoproteins)
control of gene expression (folate binding protein)
least preferred energy source
What is structure of a nucleotide?
Nucleotides are the building blocks of nucleic acids and consist of
- a five carbon sugar ring
- a base
- one of more phosphate group
what type of bases form nucleotides?
purines = double ring structure (adenine, guanine) pyrimidine = single ringed structure (cytosine and thymine) (they all have ''y's''
How do bases pair up in DNA and RNA and why?
DNA: A with T and C with G
RNA: A with Uracil and C with G
to keep an even backbone, so they can twist.
What bonds are there in a double helix?
two strands wound together like a twisted ladder. the sides of the ladder are covalent bonds (P of one, and sugar of the other). the strands in between the bases are hydrogen bonds, so easily unzipped for transcription.
How is RNA different from DNA?
Ribonucleic acid contains a single strand of nucleotides which contain the sugar ribose instead of deoxyribose. the prescence of the extra OH group stops the RNA being able to pair up and form a double helix. the base thymine is uracil.
What are the functions of nucleic acids?
DNA stores genetic info; every cell has at least one DNA molecule; DNA acts as a template for protein synthesis;
what is the difference between the sense strand and the anti-sense strand?
The sense strand codes for the sequences of amino acids in a protein and will be copied by RNA in the transcription process; the anti-sense strand carries the complementary bases to balance the molecule so it can twist.
what is a codon?
The code to copy DNA is read in sets of 3 which is also called a codon i.e. GAG, GGT, GCA etc.
what are enzymes? and how do they work?
biological catalysts made from proteins, that speed up a reaction by lowering the activation energy but do not change themselves. Enzyme has a specific area called the active site where the substrate (molecule at the beginning of the reaction) binds via lock and key. they are highly specific and need optimum conditions (temperature and pH and substrate concentration) to work properly.
what do oxidases do?
enzymes that add oxygen
what do dehydrogenases do?
enzymes that remove hydrogen
what do kinases or phosphotransferases) do?
enzymes that add phospate from ATP or another compound
what do ATPases do?
enzymes that split ATP
what do Anhydrases do?
enzymes that remove water
what do proteases do?
enzymes that split proteins
what do lipases do?
enzymes that split triglycerides
what do isomerases do
enzymes that lead to an isomerisation reaction where one molecule is transformed to another which has the same atoms but the atoms are in a different arrangement from A-B-C to B-A-C.
why do we need protein to build bones?
cells first lay a matrix from the protein collagen, which will then get filled in with mineral crystals
How do proteins regulate fluid balance in the body?
proteins (albumin) attracts water; if plasma proteins leak out of the capillary walls faster than they can be reabsorbed, fluid accumulates in the tissues leading to swelling and edema.
How is Carnitine synthesised?
Carnitine is synthesised from methionine and lysine using cofactors Fe, Vit C and Vit B6.
what role does glycine play in detoxification?
glycine binds to a toxic substance forming a less toxic substance that can be excreted from the body.
what can phenylalanine be converted to?
to tyrosine which can in turn be used to make dopamine, epinephrine, norepinephrine, melanin and thyroid hormones.
What can help to fight or prevent a herpes outbreak?
Lysine supplementation plus Vitamin C
what amino acid produces a calming effect in the brain ? How and where can it be found?
theanine by increasing levels of serotonin and dopamine; found in green tea.
How does Vitamin C help tissue recovery?
Vit C is a cofactor in collagen formation. collagen lays down a matrix from which bones and cartilage is formed. with injuries, collagen glues the separated tissues together.
What food is excellent for promoting the healing of peptic ulcers?
Cabbage Juice as it contains glutamine. studies suggest glutamine stimulates intestinal mucosal grown and protects from mucosal atrophy.
Give examples of zinc based metalloenzymes
superoxide dismutase (SOD) - cell antioxidant defences alcohol dehydrogenase - important in the conversion of alcohols to aldehydes corboxypeptidase - secreted by the pancreas needed for the digestion of protein.
What is the transcription?
the process of mRNA copying the sense strand in the DNA
what is translation?
the creation of a protein in the ribosome, by reading the codon and matching up to tRNA with the appropriate amino acid.
Give two examples of enzyme co factors
zinc is required for alcohol dehydrogenase and selenium is needed for glutathione peroxidase.
Describe how a competitive enzyme inhibitor works
Competitive inhibitors compete with the substrate for a position in the active site and therefore slow down the conversion of substrate to product (bald person in hairdressers chair); this is different to non competitive inhibitors that will bind to a different site (allosteric site) and change the shape. (can be reversible or irreversible)
Give an example of a genetic mutation formed by misfolding of protein
MTHFR (Methyl tetra hydro folate reductase); this enzyme converts folate and folic acid to an active form the body can use to break down homocysteine). the genetic mutation (due to one nucleotide) causes misfolding and the different shape struggles to stay attached to its riboflavin cofactor and therefore only works 50% of the time.
