Building Life: Macromolecules Flashcards
organic molecules
carbon-containing molecules.
Carbon makes up 47% of human cells
Oxygen, Hydrogen and Nitrogen make up the rest
four covalent bonds in carbon
Can form 4 covalent bonds in a tetrahedron
Each bond can rotate freely
Structural diversity
structurally and functionally diverse carbon
Can link covalently to form long chains - can be branched, straight or form a ring etc.
Can form double bonds by sharing two pairs of electrons between carbons
Not as free to rotate
Shorter
Found in chains or rings
isomers
molecules with the same chemical formula but different structures.
Millions of carbon-based molecules
Some think that silicon could be a backbone of life on different planets but it is often found bound to oxygen and does not have as many different forms as carbon so this is unlikely
proteins and their polymers
provide structural support and catalyse reactions.
Polymers of amino acids
nucleic acids and their polymers
provide structural support and catalyse reactions.
Polymers of amino acids
carbohydrates and their units
provide a source of energy and make up cell walls in bacteria, plants and algae.
Polymers of simple sugars
lipids and their components
make up cell membranes, store energy and act as signalling molecules.
Lipid membranes are made of fatty acids
polymer
complex molecules made up of repeated simpler units connected by covalent bonds
functional groups and some examples
roups of one or more atoms that have particular chemical properties (can be attached to the non polar carbon chains). Often reactive. Amine Amino Carboxyl Hydroxyl Ketone Phosphate Sulfhydryl Methyl
nitrogen, oxygen, phosphorus and sulfur
more electronegative than the carbon
Functional groups containing these atoms are polar
Non polar molecules containing these, become polar and are soluble in the cell’s aqueous environment
functions of proteins, what are they made of? what determines function?
Function as catalysts that speed up reactions (enzymes)
Structure for shape and movement (collagen etc.)
Receptors
Growth factors
Made of a chain or amino acids
20 different amino acids, each with a different R group
The order or amino acids, determines how the protein folds
The 3D structure determines how the protein functions
amino acid structure
Central carbon, linked to four groups - alpha carbon
Amino group (NH2)
Carboxyl group (COOH)
R (residue) group or side chain - differs between amino acids
Hydrophilic, hydrophobic, positive, negative
Non polar = hydrophobic
Polar = hydrophilic
amino acids at pH 7.4
pH commonly found within cells
Amino acid and carboxyl groups are ionised
NH3+
COOH-
peptide bond
Carbon in carboxyl group is joined with the nitrogen in the amino group
A water molecule (condensation or polymerisation or dehydration) is produced
A type of covalent bond
primary structure
polypeptide chain
secondary structure
coils and folds (alpha helix) and pleated sheets (beta pleated sheets)
Held together by hydrogen bonds
Interactions between R groups
tertiary structure
globular 3D structure determined by more folding.
quaternary structure
multiple polypeptide structures joined together.
enzymes and their models
Highly specific catalysts (specificity determined by protein structure)
Lock and key model - active site locks to the substrate (key); outdated model
Induced-fit model - active site can change shape so it holds the substrate tight
what do nucleic acids do?
Carry information in the sequence of nucleotides that make them
DNA - what is it, what does it do, what is it made of?
Genetic material in all organisms
Transmitted from parents to offspring
Contains info needed to specify the amino acid sequence of all proteins synthesised by the organism
Deoxyribose sugar (only H)
A, T, G and C
Double helix - two strands twisted around each other
Complementary base pairs
RNA - what does it do? structure?
Protein synthesis
Regulation of gene expression
Ribose sugar (OH)
A, U, G, C (connected by covalent bonds)
nucleotide components
5 carbon sugar (pentose) - carbons are numbered 1’, 2’ etc.
Nitrogen containing base - carbons are numbered 1,2
One or more phosphate groups
bases
Made of nitrogen containing rings
Pyrimidine bases - single ring; cytosine, thymine and uracil
Purine bases - double ring; guanine and adenine
nucleotides in RNa and DNA
DNA and RNA are made of nucleotides, covalently bonded
Sequence of nucleotides determines information in DNA and RNA
Each adjacent nucleotide is connected by a phosphodiester bond
phosphodiester bond
phosphate group in one nucleotide is covalently bonded to the sugar unit in another nucleotide
Formation by a condensation reaction (loss of water molecule)
carbohydrates - empirical formula, uses, broken down
CHO usually in 1:2:1 (empirical formula the same)
Source of energy for metabolism (used in respiration)
Structure
Larger sugars may need to be broken down by enzymes
Programmed to desire sugar to get fruit and vegetables
saccharides
simplest sugars.
Linear or cyclic molecules
5 or 6 carbons
All six sugar carbons are C6H12O6 isomers
monosaccharides
simple sugar with one unit. eg. Glucose
Unbranched carbon chains with aldehyde or ketone groups
Aldehydes from aldoses
Ketones form ketoses
Other carbons each have an OH and H
Linear sugars are numbered from the functional group to the end
Nearly all are cyclic in cells (often hexagonal)
Functional group forms a covalent bond with the oxygen of an OH group
Polar hydroxyl groups make these sugars highly soluble in water
Especially 6 carbon monosaccharides are building blocks of complex carbohydrates
Attached to each other by glycosidic bonds (loss of water and bond forms between carbon 1 and a hydroxyl group on another sugar)
Can readily be moved into the blood stream from the gastrointestinal tract
disaccharide
two simple sugars linked together eg. Sucrose (one glucose and one fructose)
oligosaccharide
3-10 sugars
Glycoproteins
polysaccharide
many (hundreds and thousands) simple sugars. eg. Starch and glycogen (store energy) and cellulose (structural support in plants).
Store glycogen in the liver for when we need it
We don’t have enzymes to break down cellulose
complex carbohydrates
long, branched chains of monosaccharides.
Made of one type or multiple types of sugars
Great variety
hydrolysis
breaking sugars by adding a water molecule
condensation/dehydration reaction
lose a water to break molecules apart.
lipids - uses and what are they?
Hydrophobic molecules (share property and not structure so are chemically diverse) Fats, cell membrane components and signalling molecules etc.
triacylglycerol
lipid that stores energy (fat storage)
Major component of animal fat and vegetable oil
Three fatty acids connected to a glycerol
Fatty acid - long chain of carbon atoms attached to a COOH
Glycerol is a three carbon molecule with an OH on each carbon
The COOH and OH attach, releasing water (condensation reaction)
Can have different types of fatty acids attached to the glycerol backbone
Hydrocarbon chains are non-polar
Their electrons are evenly distributed so they are uncharged
Hydrophobic and form oil droplets in cells
By excluding water, they are compactly packaged (efficient energy storage)
van der Waals forces
Constant movement of electrons results in slight negative and slight positive charges, allowing weak binding (van der walls forces). Can help stabilise molecules
Longer the chain, the more forces and therefore the higher melting point
Kinks (double bonds) reduce closeness and therefore these forces, lowering melting point
Saturated fats have higher melting points
Unsaturated fats are healthier (can’t pack as many in)
cis and trans fatty acids
Cis - double has hydrogens on same side (extra repulsion and extra kink)
Trans - double bonds have hydrogens on opposite sides (more linear shape) - harder for enzymes to recognise and act on (most have been made artificially and are in fast food)
fatty acids
Differ in length of hydrocarbon chain
Saturated - do not have double bonds, max number of hydrogens attached to each carbon, straight
Unsaturated - have double bonds, have a kink
steroids
Cholesterol etc.
Cores composed of 20 carbon atoms bonded into four rings
Hydrophobic
Cholesterol acts in membranes and as a precursor for synthesis for steroid hormones
phospholipids
Major component of cell membranes
Hydrophilic head
Hydrophobic fatty acid tails
Amphipathic - combination of water loving and water fearing
Commonly found in bilayers in cellular membranes
energy and types
capacity to do work
Kinetic - energy that is in motion (water flowing)
Potential - an example is energy stored as chemical energy in the bonds of atoms
strong and weak bonds
Strong bonds contain less energy = less energy required to keep bonds together
Weak bonds = great sources of energy (lots of energy keeping them together)
ATP
Storage of energy (potential energy)
Often seen as a currency of energy
Phosphate, a ribose group and an adenine
Bonds in phosphate are weak (negative charges on O) repel each other (lots of energy)
Cells use to carry out tasks
If you add water, you get ADP and Pi (inorganic phosphate)
two laws of thermodynamics and what this means
Energy is neither created nor destroyed
Systems tend toward disorder (entropy) - some energy will be lost (often as heat)
Energy cannot be created
Energy is lost in every energy transformation
Constant input of energy to maintain living things (chemical source/light source)
chemical reactions
breaking and reforming of bonds in molecules
Reactants to products
Arrows indicate direction
Most biological reactions are reversible (concentration affects direction)
No matter is being created or destroyed
Gibbs free energy
Energy is not equal in the bonds on both sides of the reaction (Gibbs free energy or G)
G = enthalpy (H) - [absolute temp (T) x entropy (S)]
Usually higher temperature = more energy lost to entropy Will not be asked to calculate it ** Delta G (change)
endergonic
Gibbs free energy has increased Products are at a higher energy state Reactants were in a more stable arrangement than products Delta G is polistive Requires an input of energy
energetic coupling
Cells struggle with endergonic reactions because of the input of energy
Take the energy from an exergonic reaction and feed in into an endergonic one
Intermediate between each reaction such as ATP (hydrolyse ATP into ADP + Pi to supply energy)
Net energy in emblematic of an exergonic reaction
exergonic
Gibbs free energy has decreased Delta G is negative Products are at a lower energy state Products are not more stable than reactants Energy is released
activation energy
energy input that is required to start the reaction
Exergonic reactions need this
Need to be able to stretch and break bonds which requires energy (transition state)
how do we overcome activation energy?
Heat - biological systems don’t deal well with large increases
Enzymes (catalysts of biological reactions)
catalysts
assist in a reaction but are not themselves changed (can be reused)
types of enzymes
Protein enzymes RNA enzymes (ribozymes)
what is the effect of enzymes?
Gibbs free energy remains the same (amount of energy released overall)
Activation energy is lowered by positioning and interacting with reactants
substrate
the things the enzyme acts on
active site (highly specific)
where the substrate binds to the enzyme
Specific for shape
Specific for what it does (function)
induced fit
enzyme changes shape to hold the substrate more closely
substrate enzyme complex
substrate and enzyme bound together
Covalent bonds or hydrogen bonds
negative regulation (via inhibitors)
Inhibitors bind to enzymes to prevent them from binding to substrate
Permanent or reversible
Permanent covalent bonds that stop the enzyme from every binding again
Inhibitor can bind and then unbind (reversible)
Competitive - binds to active site, competing for active site with substrate
Non-competitive: binds elsewhere on the enzyme, so that active site changes shape and substrate can no longer bind (a form of allosteric inhibition)
positive regulation (via activators)
Allosteric regulation
Activator binds to allosteric site, causing a change in shape of active site that makes it ready to bind to substrate
gene regulation
Making the enzyme as needed
what roles do enzymes play?
Lactase: breaks down lactose into glucose and galactose
Lipase: break down lipids
DNA polymerase: synthesises DNA by catalysing the addition of deoxyribonucleotides to a growing strand of DNA
Pepsin: breaks proteins down into short polypeptide chains in the stomach
“-ase” often denotes an enzyme!
