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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
Q

bases

A

Made of nitrogen containing rings
Pyrimidine bases - single ring; cytosine, thymine and uracil
Purine bases - double ring; guanine and adenine

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26
Q

nucleotides in RNa and DNA

A

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

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27
Q

phosphodiester bond

A

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
Q

carbohydrates - empirical formula, uses, broken down

A

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
Q

saccharides

A

simplest sugars.
Linear or cyclic molecules
5 or 6 carbons
All six sugar carbons are C6H12O6 isomers

30
Q

monosaccharides

A

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
Q

disaccharide

A

two simple sugars linked together eg. Sucrose (one glucose and one fructose)

32
Q

oligosaccharide

A

3-10 sugars

Glycoproteins

33
Q

polysaccharide

A

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
Q

complex carbohydrates

A

long, branched chains of monosaccharides.
Made of one type or multiple types of sugars
Great variety

35
Q

hydrolysis

A

breaking sugars by adding a water molecule

36
Q

condensation/dehydration reaction

A

lose a water to break molecules apart.

37
Q

lipids - uses and what are they?

A 
Hydrophobic molecules (share property and not structure so are chemically diverse)
Fats, cell membrane components and signalling molecules etc.
38
Q

triacylglycerol

A

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
Q

van der Waals forces

A

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
Q

cis and trans fatty acids

A

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
Q

fatty acids

A

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
Q

steroids

A

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
Q

phospholipids

A

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
Q

energy and types

A

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
Q

strong and weak bonds

A

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
Q

ATP

A

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
Q

two laws of thermodynamics and what this means

A

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
Q

chemical reactions

A

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
Q

Gibbs free energy

A

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
Q

endergonic

A 
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
Q

energetic coupling

A

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
Q

exergonic

A 
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
Q

activation energy

A

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
Q

how do we overcome activation energy?

A

Heat - biological systems don’t deal well with large increases
Enzymes (catalysts of biological reactions)

55
Q

catalysts

A

assist in a reaction but are not themselves changed (can be reused)

56
Q

types of enzymes

A 
Protein enzymes 
RNA enzymes (ribozymes)
57
Q

what is the effect of enzymes?

A

Gibbs free energy remains the same (amount of energy released overall)
Activation energy is lowered by positioning and interacting with reactants

58
Q

substrate

A

the things the enzyme acts on

59
Q

active site (highly specific)

A

where the substrate binds to the enzyme
Specific for shape
Specific for what it does (function)

60
Q

induced fit

A

enzyme changes shape to hold the substrate more closely

61
Q

substrate enzyme complex

A

substrate and enzyme bound together

Covalent bonds or hydrogen bonds

62
Q

negative regulation (via inhibitors)

A

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
Q

positive regulation (via activators)

A

Allosteric regulation

Activator binds to allosteric site, causing a change in shape of active site that makes it ready to bind to substrate

64
Q

gene regulation

A

Making the enzyme as needed

65
Q

what roles do enzymes play?

A

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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