Biochemistry (optional unit B) Flashcards
What is metabolism
Chemical reactions that occur in living organisms
What are chemical reactions controlled by + where do they occur
Controlled by specific catalyst called enzyme + occurs in a controlled aqueous environment
What is catabolism
Breaking up of large molecules to form smaller molecules (energy is released)
Anabolism
Building up of small molecules to form larger molecules (energy is required)
How are catabolic and anabolic reactions connected
Energy released in catabolic reactions are used in anabolic reactions
Give an example of catabolism
The breakdown of glucose in respiration producing carbon dioxide and water + oxidation of fatty acids
what are reactants in anabolism known as
precursors
Example of anabolism
The synthesis of protein from amino acids, nucleic acids from nucleotides, photosynthesis which produces carbohydrates
What is photosynthesis
Plants undergo anabolism to build energy rich molecules such as carbohydrates (6CO2 + 6H2O –> (in the presence of sunlight) –> C6H12O6 + 6O2)
- this occurs in green plants in the presence of light absorbing pigments called chlorophyll
Is photosynthesis endo or exo?
endothermic - because its absorbing light energy
What is heat
a measure of the total energy in a given amount of a substance - therefore it depends on the amount of substance
what is temperature
the measure of the hotness of a substance - represents the average kinetic energy of the substance but is independent of the amount of the substance present
what is cellular respiration
energy rich molecules are broken down (catabolism) to produce carbon dioxide and water which the plant uses - releases energy in the process and is thus exothermic
What is a condensation reaction
Reaction where two smaller molecules come together to form one larger molecules, with the loss of a small molecule (usually water) and forming a covalent bond
- reactive functional groups on two molecules react together (such as OH and H)
What are biopolymers
A long chain molecule formed through condensation reactions, each molecule/monomer must have two reactive functional groups to form the chain
What is a hydrolysis reaction
reaction in which a larger molecule reacts with water, which breaks the covalent bond between the large molecule and forms two smaller molecules (the opposite of a condensation reaction)
Other than water what will hydrolysis occur in the presence of?
acids or an alkali (bases that dissolve in water e.g. NaOH)
Give an example of a structural protein and what it creates
Keratin - fingers and nails
What do proteins make up?
Enzymes and hemoglobins (molecules that carries oxygen in the blood)
Describe the structure of a 2-amino acid
H2N-CHR-COOH
R group is different for every amino acid
contains amine group and carboxyl group
what reaction bonds amino acids?
condensation reactions
what is a bond between two amino acids called?
peptide bond/amide link
Protein synonym
polypeptide
What is the ratio of peptide bonds to water?
1:1
What are zwitterions (zwitter ions)
Electrically neutral ions with both a positive and negative charge - these are formed by amino acids
- Hydrogen ion from carboxylic acid group bonds to nitrogen atom on amino group (in one amino acid) - creates negative charge on oxygen left from OH and a positive N which is now NH3
Amphiprotic
Can both accept protons and donate protons (both bronsted lowry acid and base)
Why are amino acids amphiprotic
As they form zwitterions, they can donate protons from the NH3 group and accept protons from the O group
What is the difference between amphiprotic and amphoteric
Amphiprotic means can accept and donate protons - amphiprotic is amphoteric however amphoteric is not always amphiprotic, amphoteric just means it acts like an acid or base (there are multiple versions)
What ion is formed at low pH
At low pH there is a high concentration of H+ ions, thus the amino acid gains an H+ and forms a cation
What ion is formed at high pH
At high pH there is a lower concentration of H+ ions and so the amino acid loses a proton to form an anion (is anion because theres the negative charge on oxygen still left there)
What does the charge of an amino acid depend on?
the pH - high pH anion - low pH cation
What is the isoelectric point
a point at which an amino acid is electrically neutral (has both positive and negative charges - is a zwitterion) (e.g. pH of the isoelectric point…)
What is the primary structure of a protein?
The sequence of amino acids in the polypeptide chain which make up the protein (a straight sequence)
What is the secondary structure of protein?
The folding of the polypeptide chain which resulted from the hydrogen bonds between the nitrogen and oxygen of the amino acids, creates two kinds: alpha helix or beta pleated sheet
tertiary structure of proteins
the twisting and folding of the secondary structure (which was helix and pleated sheets) to form specific 3D shape
- this is because of interactions between side chains (hydrogen bonding, hydrophobic interactions, ionic bonds, disulfide bridges and peptide bonds)
Hydrophobic interactions
London dispersion forces between nonpolar side chains
Hydrogen bonding in the polypeptide chain
bonding between polar sidechains
Ionic bonding in polypeptide chain
Bonds between charged side chaines
Disulfide bridges in polypeptide chains
Covalent bonds between side chains of cysteine which contain a sulfhydryl group (CH2-SH)
Peptide bonds
from carbon bonded to oxygen and nitrogen bonded to hydrogen (bond between carbon and nitrogen)
quaternary structure of proteins
same interactions as tertiary structure but between polypeptide chains
What are fibrous proteins
Elongated molecules in which the secondary structure is the most dominant (forms most of it), they form structural components of the human body and are insoluble in water. e.g. collagen, keratin
globular proteins
Spherical molecules soluble in water and most of tertiary structures some have quaternary. Used as catalysts and transport proteins. e.g. hemoglobins, insulin, catalase
what is the sequence of amino acids in fibrous vs globular proteins
fibrous proteins have a repetitive sequence, globular has an irregular sequence
Stability of fibrous vs globular proteins
Fibrous - less sensitive to changes in heat and pH
Globular - more sensitive to changes in heat and pH
Before proteins can be analyzed, what must happen?
They must be broken down into their component amino acids –> broken down through hydrolysis reactions
What is paper chromatography
a method of protein analysis - analyze what amino acids are in the protein (diff amino acids spread out as diff blobs on the chromatography filter paper)
What happens in chromatography (phase where the paper is put in solvent)
- sample of amino acid mixture spotted near the bottom of the filter paper (called origin)
- filter paper is suspended in a solvent - spot of amino acid mixture is above the solvent
- solvent rises up the filter paper through capillary action
- amino acids will distribute into two phases: stationary and the mobile phase
- mixture of amino acids will spread out and separate based on how strongly they adsorb to filter paper during stationary phase and how strongly they dissolve during mobile phase
Less travel up filter paper means amino acid is more adsorbent during stationary phase. More travel means more soluble during mobile phase
Paper chromatography after paper is removed
- paper removed
- sprayed with ninhydrous which is a locating reagent - organic dye
- amino acid mixture will show up mostly as purple spots on the paper
What is Rf and how to calculate it and why
Retention factor value
Rf = (distance moved by amino acid [amino acid])/(distance moved by solvent front)
Used to identify amino acids in mixture after being compared to known retention factor values. (Used to identify components of a mixture)
How to measure distance moved by solute/amino acid in paper chromatography
Halfway between the bottom and the top point of the circle
What is gel electrophoresis
Technique for separation and analysis of a mixture based on the movement of charged particles in an electric field.
Steps of gel electrophoresis
- Amino acids placed in a gel (usually polyacrylamide)
- potential difference is applied
- depending on pH of buffer solution amino acids will travel at different rates, positives attracted to the negative cathode and negatives towards the positive anode
- locating agent is sprayed on (ninhydrin - organic dye)
- compare distance travelled to known samples to identify
Analysis after measuring distance in gel electrophoresis
- by seeing weather the amino acid travelled to the cathode (negative) or anode (positive) we can determine what it is
- Depending on the pH level of the buffer solution, it may be higher, lower or equal to the isoelectric point of amino acids
- if lower, amino acid is positive and will attract to cathode (vice versa)
What are enzymes
Protein molecules that function as biological catalysts, they increase rate of reaction by providing an alternative pathway with a lower activation energy.
They are highly specific to the reaction they catalyze –> it depends on its 3D structure (conformation)
Substrate
Reactant molecule that reacts with enzyme
What is active site
The site that comes in contact with substrate - it changes shape to fit the substrate
Describe the process of an enzyme function
- substrate enters active site, which change shape to fit it
- substrate binds and forms enzyme-substrate complex
- catalyzed reaction takes place
- products leave the active site
- active site goes back to original shape
What is denaturation
The loss of the tertiary structure of an enzyme - irreversible
What are the factors affecting enzyme activity - detail them
Temperature:
- temperature past an optimal point will disrupt the tertiary structure and enzyme is no longer able to catalyze substrates –> rate of reaction decreases
- an increase in temperature will actually increase rate of reaction up until this optimal point due to an increased frequency of collisions and great proportion of molecules having enough energy (>Ea)
- decrease in temperature will only DEACTIVATE the enzyme and is reversible
- activity decreases but tertiary structure is not affected (e.g. putting things in the fridge)
pH:
- past optimal pH ror begins decreasing
- changes in pH affect charges on the acidic (COOH) and basic (NH2) groups of an amino acid
- disrupts tertiary structure
Heavy metal ions
- can react with sulfhydryl group on cysteine, replacing hydrogen atom with a heavy metal ion
- disrupts tertiary structure
What is the point of saturation of substrates
When there are more substrates than enzymes because the enzyme is fully staurated and the rate of reaction is constant
Lipids and what are the three types
organic molecules with long hydrocarbon chains, that are soluble in non-polar solvents
3 types:
- triglycerides
- phospholipids
- steroids
Function of triglycerides
- energy storage
- thermal insulation
function of phospholipids
components of cell membranes
electrical insulation of nerves
function of steroids
hormones
what are two negative health effects caused by excessive lipids in the diet
Atherosclerosis (narrowing of arteries) and obesity
What are carbs and lipids used for in the human body
used for energy storage in the human body
Why do lipids provide more energy than carbohydrates
In lipids they have a greater hydrogen to oxygen ratio which mean they are more reduced, when oxidized lipids release more energy
Compare the solubility of carbohydrates and lipids
Carbs: Glucose (a monosaccharide) is soluble in water b/c of its polar OH groups that form hydrogen bonds with water molecules
- more rapidly transported in the body and are used for short term energy supply
Fats are insoluble in water - non polar hydrocarbon chains
- more slowly transported in the body and used for long term energy storage
lipids provide overall more energy
How to form triglycerides
Condensation reaction between a glycerol (propane with 3 OH side groups) and 3 fatty acids
glycerol backbone and three fatty acids
Why do monounsaturated fatty acids have a lower bp
Contain carbon to carbon double bonds which has a kink in the chain which prevents close packing of molecules
Why do saturated fatty acids have higher mp
carbon to carbon single bonds - closer packing of molecules and stronger london dispersion forces
What are fatty acids
Carboxylic acids (COOH) with long hydrocarbon chain - carbon to carbon single bonds have a tetrahedral arrangement 109.5
monounsaturated fatty acid meaning
one carbon to carbon double bond - 120 bond angle trigonal planar (bc double bond creates kink in chain)
polyunsaturated fatty acid meaning
multiple carbon carbon double bonds (120 bond angle - trigonal planar arrangement)
Describe melting points of fatty acids
saturated (fats) fatty acids have carbon to carbon single bonds with 109.5 bond angles which allows for closer packing, stronger LDF and higher melting point
unsaturated (oils) fatty acids with c-c double bond has kink weaker LDF (liquid at room temperature)
Phospholipids
Glycerol backbone, have two fatty acids and a phosphate group
have a polar hydrophilic head (phosphate) and two non polar hydrophobic tails (fatty acids)
form phospholipid bilayer in cell membranes
Steroids
are lipids with a structure consisting of 4 fused hydrocarbon rings (steroidal backbone)
how to steroids differ?
by the functional groups attached to the steroidal backbone
Uses of steroids
female steroid hormones used in oral contraceptive pill and hormone replacement therapy
used to build up depleted muscle due to lack of activity and to assist in recuperation from an illness
abuse of steroids
anabolic steroids used by athletes to increase muscle and strength for unfair advantage in sport
health effects of steroids (f and m)
- infertility, breast development, shrinking of testicles, male patter baldness
- decrease in breast size and body fat
deepening of the voice
excessive growth of body hair - heart attacks and liver cancer
What is LDL?
low density lipoproteins, transports cholesterols around to the arteries leading to cardiovascular disease. Major sources of these low density lipoproteins is from saturated fats in particular those derived from lauric (C12), myristic (C14) and palmitic (C16) acids.
What is HDL
High density lipoproteins, remove cholesterols from the arteries and transport them back to the liver.
What is the iodine number
Number of grams of iodine that reacts with 100g of fat.
an addition of iodine to unsaturated fats to determine the number of double bonds in the fat
One mole of double bonds reacts with one mole of I2
what hydrolyses fats and oils in the human body?
the enzyme lipase
