topic 2: molecular biology Flashcards
organic
contains carbon in living tissue
carbons which are not organic
carbon dioxide, carbon monoxide, carbonates and hydrogen carbonates
examples of organic molecules
lipids, carbohydrates, nucleic acids and proteins
macromolecules contain…
carbon, hydrogen and oxygen- nitrogen appears in proteins and nucleic acids, phosphorous sometimes appears in lipids
macromolecules
build living cells and take part in chemical reactions
ratio of hydrogen and oxygen in carbohydrates
2:1
types of carbohydrates
monosaccharides, disaccharides, polysaccharides
types monosaccharides
glucose (blood sugar found in the plasma), fructose and galactose (part of lactose)
Disaccharides
two sugars that are joined together. examples: Sucrose (plant sugar), lactose (milk sugar), maltose (would in malt)
polysaccharides
many sugars. examples: cellulose, starch (stored in plants), glycogen (temporarily stored In liver to be broken down)
use of carbohydrates
short term energy, plant cell walls
subunit of carbohydrates
Monosaccharides
examples of proteins
muscles, enzymes, glycoproteins and hormones
use of proteins
defense, transport, contractile movement, catalytic
subunit of proteins
amino acids
examples of lipids
oils/fats, phospholipids, cholesterol and wax
use of lipids
long term energy, storage of glucose (stored in adipose tissue)
subunit of lipids
glycerol fatty acids (they are long chains of carbon and hydrogen)
examples of nucleic acids
RNA and DNA
uses of nucleic acids
RNA- brings the ribosome to build a polypeptide
DNA- turns genes into proteins
subunit of nucleic acids
nucleotides
metabolism
all the enzymatic reactions that take place in a living organism
anabolism
the synthesis of complex molecules from simpler molecules. requires an energy input. this includes the formation of macromolecules from monomers by condensation reactions
catabolism
the breakdown of complex molecules into simpler molecules, a process which releases energy. This includes the hydrolysis of macromolecules into monomers.
hydrolysis reaction
takes polymer molecules and synthesises them into monomer molecules. This requires water
condensation reaction
two monomer molecules join to make a polymer molecule, which produces water
glucose bonds
glycosidic bonds
amino acid bonds
peptide bonds
glycerol bonds
ester
vitalism
organic compounds were thought to have a non physical element which inorganic molecules lacked. Vitalism was falsified because organic molecules can be synthesised artificially
urea
used by the body to excreted oxygen, is high soluble. the artificial synthesis of urea shows that organic molecules are not essentially different from inorganic molecules
water
metabolism takes place in water, water is polar. Water is attracted to other water molecules as a result of its positive and negative infinities
polar molecules
slightly charged regions and different distribution of charge
thermal properties of water
- boiling point
- high specific heat capacity
- high latent heat of vaporisation
cohesion
gives the water surface tension, allowing organisms to move across the surface. Surface tension transmits vibrations. without cohesion, there will be a difficulty in transport of water
surface tension
caused by the cohesive hydrogen bonding resisting an object trying to penetrate the surface.
adhesion
Adhesion is the ability of water molecules to form hydrogen bonds. A large number of hydrogen bonds gives adhesive forces a lot of strength.
adhesion and cohesion
help the transpiration of water
solvent
Water can dissolve many organic and inorganic substances that have charged or polar regions. Water is a good solvent for a lot of different substances; however it is not universal. It is a good transportation medium
solvent and thermal properties of water
- water has a high specific heat capacity, therefore water changes in density based on temperature.
- water has a high heat of vaporisation
hydrophilic
substances are chemically attracted to water. All substances which dissolve in water are hydrophilic. These substances are polar molecules or substances with positive or negative charges.
hydrophobic
substances that are insoluble in water. These substances don’t have a negative or positive charge and are nonpolar. All lipids are hydrophobic.
three types of carbohydrates
- monosaccarides
- disaccharides
- polysaccharides
monosaccharides
used for an immediate energy source. are recurring monomers and linked together via a condensation reaction. two monosaccharides can be joined together by a glycosidic bond, forming a disaccharide
examples of monosaccharides
glucose
galactose
fructose
three types of disaccharides
- lactose
- sucrose
- maltose
disaccharides
held together by a glycosidic bond, are formed when two monosaccharides are joined together by a condensation reaction.
three examples of polysaccharides
cellulose
glycogen
starch
polysaccharides
are large molecules
cellulose
present in plant cell walls, gives the walls extra strength and protects the cell from over-expanding and bursting, as well as storing enough energy to be a source for biofuels. Cellulose is a beta glucose with 1-4 linkages, held together by hydrogen bonds.
glucose/glycogen
can be converted to glycogen in the liver and changed back for aerobic respiration. Glycogen is a polymer made out of alpha glucose, and 1-4 and 1-6 linkages. not soluble
sucrose
Sucrose can be converted to starch, starch is insoluble and can be converted back to sucrose for plants to use
polysaccharide linkages
1-4 linkage is linear
1-6 linkage creates bends- this creates branched polysaccharides
amylose and amylopectin
forms of starch and made from repeating glucose units. They are both consist of alpha glucose (the subunit).
amylopectin
branched chain with 1-6 linkages as well as 1-4 linkages
amylose
unbranched and can be stored y itself
lipids
are hydrophobic and can be stored by itself
three types of lipids
triglycerides
phospholipids
sterols
lipid bond
lipids are held together by ester bonds
saturated lipids
no double bonds, all single bonds, all lipids are saturated with hydrogen, because there is potential space for hydrogen to fill
monounsaturated
one double bond
polyunsaturated
more than one double bond, therefore it doesn’t have all potential hydrogen that it could have
cis isomers
hydrogen on the same side, therefore there can be a bend or kink in the chain. Cis isomers are liquid at room temp . Cis isomers are naturally occurring and are healthy.
trans isomers
hydrogen is on opposite sides, there are double bonds therefore are linear. Trans isomers are solid at room temp. trans isomers are rare in nature and made artificially
high density lipids
are good- they purify fats and remove it in the liver
low density lipids
bad- take lipids from liver and take and store it around the body. These can be stored around organs.
proteins/polypeptides
are a number of linked peptides. subunit is an amino acid.
amino acids binding
bind during a condensation reaction, held together by a covalent bond, peptides. This forms a dipeptide. Long chains of covalently bonded amino acids are called polypeptides. polypeptides can be broken down by a hydrolysis reaction
amino acids binding
bind during a condensation reaction, held together by a covalent bond, peptides. This forms a dipeptide. Long chains of covalently bonded amino acids are called polypeptides. polypeptides can be broken down by a hydrolysis reaction
primary structure
the sequence of amino acids
secondary structure
involves the folding of chains to themselves to form pleated sheets (beta) or alpha helixes.
tertiary structure
the polypeptide folds and coils (alpha or beta) in a 3D structure. This is an R group interaction. Tertiary structure includes disulphide bridges, ionic interactions, polar associations etc.
quaternary
only occurs in proteins that are made of two or more polypeptide chains.
denaturation
changes the shape of the active site, resulting in a. loss of biological properties
temperature and denaturation
High levels of thermal energy break the hydrogen bonds that hold the protein together, this causes denaturation
pH and denaturation
changes the protein, altering the protein solubility and shape. All proteins have an optimum pH, but varies on environment and function. pH alters bonds causing confrontational change
gene
a section of DNA that contains the instructions for polypeptides of an organisms. genes usually only code for one polypeptide.
ribose
a pentose sugar and nucleic acid. ribose forms the backbone of RNA
genome
all the genes of an organism, genes are coded for in DNA
proteome
all the proteins of an organism, at a particular time- proteins are always changing
there are more proteome than genomes, proteome is larger
Rubisco
the catalysing reaction with enzymes, carbon is fixed in the atmosphere. Rubisco is found in anything that involves photosynthesis
Insulin
a hormone secreted by the pancreas. Absorbs glucose and reduces glucose concentration in blood. Corrects blood sugar concentration
Immunoglobulins
antibodies- they respond to a range of pathogens and acts as a marker to phagocytes. There are two antigen binding sites
Rhodopsin
absorbs light and is found in the eyes. A protein in the rod of the retina, consists of the opsin polypeptide
collagen
rope like proteins made of polypeptides wound together. Forms a mesh of fibres in skin and blood vessel walls, collagen gives strength to resist tearing. Prevents cracks in bones.
spider silk
very strong beta pleated sheets. Is interlocked strands. Stronger than steel. When stretched the polypeptide extends, stopping it from breaking.
enzymes
are a globular protein that increases rate of biochemical reactions by lowering the activation energy threshold. Enzymes are catalysts and therefore can be reused.
the active site
where the surface of the enzyme binds to the substrate. Enzymes are specific, therefore only bind to a specific substrate, determined by the shape and chemical properties. The shape and chemical properties are dependent on the tertiary structure of the enzyme.
enzyme structure changes
Enzyme structure can be changed as a result of the environment. Examples include high temperature and pH changes. These changes disrupt the chemical bonds, which are required to maintain the tertiary structure.
low temperatures and enzyme activity
result in insufficient thermal energy for the activation of an enzyme catalysed reaction to proceed
increase in temperature and enzyme activity
increases the speed and motion of the enzyme and the substrate. This results in more activity of the enzyme. High kinetic energy results in more frequent collisions.
optimum temperature and enzyme activity
enzyme activity is at its peak
higher temperature and enzyme activity
thermal energy breaks the hydrogen bonds in the enzyme. This means the enzyme shape will change, and there will be less activity because of denaturation.
changing pH and enzyme activity
change the charge of the enzyme, changing the shape of the enzyme
optimum pH
enzyme activity will be at its peak.
enzyme catalysis
Enzyme reactions usually occur in aqueous solutions. Therefore the substrate and the enzyme move randomly withing the aqueous solution.
immobilised enzymes
enzymes used in industry. Taking enzyme, attached to material to restrict movement, improving the efficiency of catalysed reactions.
The enzyme can be used again and again (reusable). The enzymes can also be entrapped in beads. They can be used in biofuels, medicine, biotechnology, food production, textiles and paper
lock and key model
extremely specific - the active site and substrate are the exact same. However this model is falsified
the induced fit model
-enzymes are not an a exact fit for the active site of the substrate, the active site undergoes a confrontational change, to improve binding.
This model explains how enzymes can show a range of specificity and explains how catalysis may occur.
nucleotides
the genetic materials of a cell and are made up of nucleotides (building blocks of DNA)
DNA bases
adenine, cytosine, thymine, guanine
RNA bases
adenine, cytosine, uracil, guanine
purines
double ring
pyrimidines
single ring
