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BIO1011 > Building Life: Macromolecules > Flashcards

Building Life: Macromolecules Flashcards

1
Q

organic molecules

A

carbon-containing molecules.
Carbon makes up 47% of human cells
Oxygen, Hydrogen and Nitrogen make up the rest

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2
Q

four covalent bonds in carbon

A

Can form 4 covalent bonds in a tetrahedron
Each bond can rotate freely
Structural diversity

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3
Q

structurally and functionally diverse carbon

A

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

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4
Q

isomers

A

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

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5
Q

proteins and their polymers

A

provide structural support and catalyse reactions.

Polymers of amino acids

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6
Q

nucleic acids and their polymers

A

provide structural support and catalyse reactions.

Polymers of amino acids

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7
Q

carbohydrates and their units

A

provide a source of energy and make up cell walls in bacteria, plants and algae.
Polymers of simple sugars

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8
Q

lipids and their components

A

make up cell membranes, store energy and act as signalling molecules.
Lipid membranes are made of fatty acids

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9
Q

polymer

A

complex molecules made up of repeated simpler units connected by covalent bonds

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10
Q

functional groups and some examples

A 
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
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11
Q

nitrogen, oxygen, phosphorus and sulfur

A

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

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12
Q

functions of proteins, what are they made of? what determines function?

A

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

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13
Q

amino acid structure

A

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

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14
Q

amino acids at pH 7.4

A

pH commonly found within cells
Amino acid and carboxyl groups are ionised
NH3+
COOH-

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15
Q

peptide bond

A

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

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16
Q

primary structure

A

polypeptide chain

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17
Q

secondary structure

A

coils and folds (alpha helix) and pleated sheets (beta pleated sheets)
Held together by hydrogen bonds
Interactions between R groups

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18
Q

tertiary structure

A

globular 3D structure determined by more folding.

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19
Q

quaternary structure

A

multiple polypeptide structures joined together.

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20
Q

enzymes and their models

A

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

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21
Q

what do nucleic acids do?

A

Carry information in the sequence of nucleotides that make them

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22
Q

DNA - what is it, what does it do, what is it made of?

A

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

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23
Q

RNA - what does it do? structure?

A

Protein synthesis
Regulation of gene expression
Ribose sugar (OH)
A, U, G, C (connected by covalent bonds)

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24
Q

nucleotide components

A

5 carbon sugar (pentose) - carbons are numbered 1’, 2’ etc.
Nitrogen containing base - carbons are numbered 1,2
One or more phosphate groups

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25
bases
Made of nitrogen containing rings Pyrimidine bases - single ring; cytosine, thymine and uracil Purine bases - double ring; guanine and adenine
26
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
27
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)
28
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
29
saccharides
simplest sugars. Linear or cyclic molecules 5 or 6 carbons All six sugar carbons are C6H12O6 isomers
30
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
31
disaccharide
two simple sugars linked together eg. Sucrose (one glucose and one fructose)
32
oligosaccharide
3-10 sugars | Glycoproteins
33
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
34
complex carbohydrates
long, branched chains of monosaccharides. Made of one type or multiple types of sugars Great variety
35
hydrolysis
breaking sugars by adding a water molecule
36
condensation/dehydration reaction
lose a water to break molecules apart.
37
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. ```
38
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)
39
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)
40
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)
41
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
42
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
43
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
44
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
45
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)
46
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)
47
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)
48
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
49
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) ```
50
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 ```
51
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
52
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 ```
53
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)
54
how do we overcome activation energy?
Heat - biological systems don’t deal well with large increases Enzymes (catalysts of biological reactions)
55
catalysts
assist in a reaction but are not themselves changed (can be reused)
56
types of enzymes
``` Protein enzymes RNA enzymes (ribozymes) ```
57
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
58
substrate
the things the enzyme acts on
59
active site (highly specific)
where the substrate binds to the enzyme Specific for shape Specific for what it does (function)
60
induced fit
enzyme changes shape to hold the substrate more closely
61
substrate enzyme complex
substrate and enzyme bound together | Covalent bonds or hydrogen bonds
62
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)
63
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
64
gene regulation
Making the enzyme as needed
65
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!

BIO1011 (12 decks)

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