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Biology AS > 3.1 Biological Molecules > Flashcards

3.1 Biological Molecules Flashcards

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1
Q

what is a biological molecule?

A

a molecule that is really important in biology

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2
Q

give examples of biological molecules

A
  • carbohydrates
  • enzymes
  • lipids
  • proteins
  • nucleic acids
  • water
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3
Q

give examples of proteins

A
  • insulin
  • amylase
  • lipase
  • protaze
  • maltase
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4
Q

give examples of carbohydrates

A
  • cellulose
  • starch
  • sucrose
  • fructose
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5
Q

give an examples of nucleic acids

A
  • ATP
  • DNA
  • Water
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6
Q

what are monomers?

A

they are smaller units from which larger molecules are made

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7
Q

what are polymers?

A

polymers are molecules made from large (complex)numbers of monomers joined together

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8
Q

give examples of monomers

A
  • monosaccharides
  • amino acids
  • nucleotides
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9
Q

what is a condensation reaction?

A

it is a reaction where two molecules are joined together with the formation of a chemical bond, and a water molecule is made

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10
Q

what is a hydrolysis reaction?

A

it is a reaction where a molecule of water is added to split a substance

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11
Q

what is the function of a water molecule?

A

makes up 80% of a cells content and is used in many chemical reactions

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12
Q

what is the function of a protein molecule?

A

used for growth and repair of tissues and also used for a transport structure

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13
Q

what is the function of a DNA molecule?

A

-long term storage information on a cell, contains instructions to construct other components of the cell such as RNA and protein molecules

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14
Q

what is the function of a cellulose molecule?

A

for plant cell walls

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15
Q

what is the function for a starch molecule?

A

storage compound in plants

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16
Q

what is the function of an enzyme molecule?

A

biological catalyst made from proteins

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17
Q

what is the function of lipid and fat molecules?

A

an energy source, insulation and protection to make some of the molecules we study

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18
Q

explain an ionic bond?

A
  • an ionic bond occurs between a metal and non metal.
  • bonds occur between two oppositely charged ions
  • this is an electrostatic force of attraction
  • ionic bonds are weaker than covalent bonds
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19
Q

explain a hydrogen bond

A
  • the electrons within a molecule are evenly distributed and is known as polar molecule
  • This is where a slightly positively charged part of a molecule meets a slightly negatively charged part of another molecule
  • a weak electrostatic force is formed
  • this is a hydrogen bond
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20
Q

what is a macromolecule?

A

a molecule that is large and complex e.g proteins

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21
Q

what is polymerisation?

A

the process of making polymers from monomers

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22
Q

for the monomer, amino acid, give the polymer and an example

A

polymer= protein (polypeptide)

example= haemoglobin

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23
Q

for the monomer, monosaccharide, give the polymer and an example

A

polymer= carbohydrate (poly-saccharide)

example= starch

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24
Q

for the monomer, Nucleotide, give the polymer and an example

A

polymer= nucleic acid

example= DNA

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25
Q

give examples of a condensation reaction

A

amino acids to proteins

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26
Q

give examples of a hydrolysis reaction

A
  • DNA to nucleotide
  • starch to glucose
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27
Q

what is a monosaccharide? and what are the common monosaccharides?

A
  • monosaccharides are the simplest sugars and are the building blocks of carbohydrates;
  • glucose
  • galactose
  • fructose
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28
Q

what are the properties of monosaccharides?

A
  • simplest sugars
  • white crystalline solids
  • dissolves in water to form sweet tasting solutions
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29
Q

in a condensation reaction a bond is formed between two monosaccharides, what is this bond called?

A

glycosidic bond

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30
Q

what is the difference between an alpha glucose and beta glucose

A

a beta glucose is the isomer of a alpha glucose, this means that it has the same molecular formula but a different structural formula.

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31
Q

when are disaccharides formed?

A

they are formed by the condensation of two monosaccharides

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32
Q

give examples of disaccharides and state what monosaccharides they are made from

A
  • sucrose= fructose + glucose
  • lactose= galactose + glucose
  • maltose= glucose + glucose
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33
Q

what enzyme is required to break down sucrose to glucose and fructose?

A

sucrase

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34
Q

what enzyme is required to break down lactose to galactose and fructose?

A

lactase

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35
Q

what enzyme is required to break down maltose into glucose and glucose?

A

maltase

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36
Q

describe the test for reducing sugars

A
  • to test for reducing sugars we use the benedict’s solution
  • add a couple of drops of blue benedict’s solution to the sample -place the solution at 70 degrees Celsius for 15 minutes so that the solution is heated
  • observe any colour changes
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37
Q

if a test for a reducing sugar is positive what colour will the solution be and what does this mean?

A

the blue benedict’s solution will form a brick red/orange to green precipitate to show that a reducing sugar is present.

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38
Q

if a test for a reducing sugar is negative what colour will the solution be and what does this mean?

A

the solution will remain blue showing that a reducing sugar is not present.

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39
Q

if you have done a test for a reducing sugar and the result is negative what further experiments can you do? for each outcome explain why

A
  • if a test for a reducing sugar is negative this means that there is no reducing sugar present
  • you will have to heat a new sample with dilute hydrochloric acid and then neutralise the sample by adding sodium hydrogen carbonate.
  • then you can heat the sample with Benedict’s solution
  • if the sample remains blue then a non-reducing or a reducing sugar is not present
  • if the sample forms a green to a brick red precipitate then a non-reducing sugar is present
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40
Q

draw the simple structure of alpha glucose

A

-

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41
Q

draw the simple structure of beta glucose

A

-

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42
Q

this is the structure for galactose. draw the structure for lactose

A

-

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43
Q

what are polysaccharides?

A

polymers containing many monomers (monosaccharaides)

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44
Q

what bond links polysaccharides?

A

glycosidic bonds

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45
Q

in which reaction are polysaccharides formed?

A

condensation reaction

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46
Q

what are polysaccharides used for?

A

they are mainly used as a energy store and a structural component of cells

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47
Q

give examples of polysaccharides

A

-starch -cellulose -glycogen

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48
Q

draw the structure of a polysaccharide made up of 3 a glucose molecules, what molecule could this be?

A

-Amylose

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49
Q

where can starch be found in plants?

A

-chloroplasts -underground storage tubers e.g potato

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50
Q

why cant plants not store glucose? how is stored instead/

A

because it is soluble and has an osmotic effect on the cell, plants therefore store glucose as starch

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51
Q

what is starch made up of?

A

two polysaccharides: amylose and amylopectin

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52
Q

what sort of glucose molecule is amylose and amylopectin made from?

A

a long chain of alpha glucose

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53
Q

what are the properties of amylose?

A
  • long and un-branched
  • coiled structure held in place by a hydrogen bond
  • compact
  • good for storage because you can fit more in a small space
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54
Q

what are the properties of amylopectin?

A
  • long branched
  • side branches allow the enzymes that break this molecule down to get the glycosidic bond easily
  • alpha glucose is released very quickly
  • good for storage because you can fit more in small space
  • compact
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55
Q

what is amylose?

A

a long chain of alpha glucose molecules coiled into a spiral and held together by a hydrogen bond

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56
Q

what is amylopectin

A

-a long branched chain of alpha glucose molecules

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57
Q

why is starch a good energy storage molecule?

A
  • it allows you to fit more into a small space
  • starch is insoluble and has no does not affect the water potential so it does not have a osmotic effect
  • it is large so it does not leave a cell
  • it is hydrolysed to form alpha glucose which is easily transported and is readily used in respiration
  • glucose is quickly and easily released because of the many branched ends where enzymes can act quickly
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58
Q

what is celullose made up of?

A
  • long straight unbranched chains of beta glucose
  • each of the chains are linked togther by lots of hydrogen bonds to form strong fibres called microfibrils which in turn are arranged in paralell groups called fibres
  • These strong fibres means that cellulose provides structural support for plant cells
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59
Q

what does cellulose provide plant cells with?

A

structural support

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60
Q

what is the function of the cellulose wall?

A
  • provides rigidty to the plant cell
  • prevents the cell bursting when water enters osmosis
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61
Q

which organisms store glucose in the form of glycogen?

A

animal and bacterial organsims

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62
Q

compare the structure of glycogen to amylopectin, explain why

A

Glycogen has more side braches. This means that Glucose can be released quickly as animals have a higher metabolic rate and therefore a higher respiratory rate than plants.

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63
Q

what are the different types of lipids?

A

triglycerides and phospholipids

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64
Q

what is the basic structure of trigylceride

A
  • glycerol
  • fatty acid which contains its variable group (‘R group’ chain) and carboxyl group (HO-C-OO)
  • The ester bond that joins up the glycerol and the fatty acid
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65
Q

what is an ester bond?

A

covalent bond between the carboxyl group and hydroxyl group

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66
Q

what do you call the reaction where a triglyceride is formed from glycerol and fatty acids. What is the product?

A

condesation reaction

a water molecule is produced

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67
Q

what is a saturated fatty acid?

A

a saturated fatty acid is a fatty acid that has no double covalent bonds between its carbon to carbon atoms

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68
Q

what is an unsaturated fatty acid?

A

an unsaturated fatty acid is one that does contain double covalent bonds between their carbon to carbon atoms

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69
Q

in what state is an unsaturated fatty acid at room temperature? what are they known as?

A

unsaturated fatty acids tend to be a liquid at room temp and are known as oils

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70
Q

in what state is a saturated fatty acid at room temp? What can it be know as?

A

saturated fatty acids are solid at room temperature and are called fats and waxes.

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71
Q

relate the structure of a triglyceride to their function

A
  • triglycerides have a high ratio of energy storing carbon-hydrogen bonds to carbon atoms… and therefore are a high source of energy
  • they have a low mass to energy ratio… making them goof storage molecules as lots of energy can be stored in small volume
  • are large non-polar molecules and therefore insolube in water so… storing them does not have an osmotic effect
  • have a ratio of Oxygen atoms to Hydrogen atoms and release water when oxidised providing an important source of water especially in organisms living in dry climates e.g camels
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72
Q

where do you find phosolipids?

A

in cell membranes

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73
Q

what is a phospholipid made up of?

A

a phosopholipid is made up of two sections

  • hydrophobic tail; made up of fatty acid molecuels which repel water but readily mixes with fat
  • hydrophillic head; made up phospate that molecules attract water but not fat
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74
Q

what is the difference between a phospholipid and a triglyceride?

A

a phospholipid only has 2 fatty acid chains, whlist a triglycerid has 3. instead of a 3rd chain a phospholipid has a phosphate group

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75
Q

on a cell membrane phospolipids combine with a molecule. what are these molecules called?

A

-they combine with glycoproteins which are involved in cell recognition

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76
Q

how is the test of phospholipids realated to their structure?

A

-*phospholipids are polar moelcules

they have a hydrophillic head and a hydrophobic tail of two fatty acids

this means in aqueous environment, phospholipids molecules form a bilayer within cell-surface membrane.

As a result a hydrophobic barrier is formed between the inside and outside of the cell.*

  • *the hydrophillic phosphate ‘heads’ of phospholipids molecules help to hold the surface of the cell surface membrane together*
  • *The phospholipid structure allows them to form glycoproteins by combining with carbohydrates within the cell-surface membrane.

These glycolipids are involved with cell recognition*

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77
Q

what are glycolipids?

A

lipids with carbohydrates attached

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78
Q

what is the test for lipids?

A
  1. add lipid sample to test tube
  2. add 2cm cubed of ethanol and shake
  3. add 2cm cubed of water and shake
  4. if the test is positive you will see a white emulsion.
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79
Q

what are the parts of an amino acid?

A
  • the amino group (H-N-H) (basic group from which the amino part of the name amino acid is derived)
  • the R group (carbon containing chain) (variety of different chemical groups)
  • carboxyl group (OH-C=O) (acidic group which gives the amino acids part of its name)
  • Hydrogen atom
80
Q

what elements make up an amino acid?

A
  • hydrogen
  • oxygen
  • nitrogen
81
Q

what determines the sequence of amino acids? and if the sequence was changed what would happen?

A
  • your genetics determine the sequence of amino acids
  • if the sequence was changed a different protein would be made with a different function
82
Q

what is it called when two amino acids join together and what is the name of the bond formed?

A
  • a dipeptide molecule is created
  • a peptide bond is formed
83
Q

what is it called when more amino acids are added to dipeptide molecule?

A

a polypeptide chain

84
Q

how are proteins formed?

A
  • when three amino acids are joined together
  • in a condensation reaction with the removal of a water molecule to form a polypeptide
  • where the amino acids are joined by a peptide bond between the carbon atom of one amino acid and the nitrogen atom of another amino acid
85
Q

how is water produced in the reaction where peptides and polypeptides are formed?

A

-the water molecule is made by combining an -OH from the carboxyl group of one amino acid with an -H from the amino group of another amino acid

86
Q

what is the reverse process of the formation of a protein and what is the reaction called?

A

this process involves a hydrolysis reaction where the addition reaction of water breaks the peptide bond forming two amino acids

87
Q

what is the test for proteins?

A
  • add biuret reagent to the sample (this is a mixture of Sodium hydroxide solution- this makes sure the solution is alkaline and copper (II) sulphate solution)
  • if the test is positive the blue solution turns purple which shows a protein is present.
  • if the test is negative it will remain blue
88
Q

what is the primary structure of a protein?

A

the unique sequence of amino acid

89
Q

what determines the shape and function of a protein?

A

the primary structure of the protein- the sequence of amino aicds

  • a change in just a single amino acid in the primary structure can lead to a change in shape of the protein hence it may stop carrying out its function
  • a protein shapes is very specific to its function
90
Q

what is the sencondary structure of a protein?

A

this structure refers to the way in which the polypeptide chain is either coiled into a alpha helix or folded into a beta pleated sheet.

hydrogen bonds form between the amino acids (hydrogen and oxygen atoms) holding the structure together

91
Q

what is the tertiary structure of a protein?

A
  • the coiled or folded chain of amino acids is often folded further
  • more bonds form between teh different parts of the polypeptide chain;

hydrogen bonds

ionic bonds (formed between the carboxyl an amino groups that are not involved in forming peptide bonds.

Disulphide bridges (form when two molecules of the amino acid cysteine come close together, the sulphur in one molecule joins the the sulphur in the other)

for a protein made from one polypeptide chain the tertiary structure forms their final 3D structure.

92
Q

what is the qauternary structure of a an enzyme?

A
  • this where you have proteins that have more than one polypeptide chain held together by hydrogen chains e.g collagen has 3 polypeptide chains and haemoglobin has 4 poly peptidechain
  • sometimes non proteins are associated with the quaternary structure. These are called prosthetic proteins e.g Iron in heamoglobin
93
Q

sometimes non proteins are associated with the quaternary structure. what are these called? give an example

A

prosthetic proteins, iron in heamoglobin

94
Q

give the properties of fibrous proteins adn examples

A
  • formed by parallel polypeptide chains and held together by cross links
  • have high tensil strenght
  • insoluble in water
  • e.g collagen (in the ligament), keratin (use ind your hair) and silk (forms the spider’s webs)
95
Q

give the properties of globular proteins and examples

A
  • usually have a spherical shape caused by tightly folded polypeptide chains
  • they are soluble in water
  • e.g transport proteins (haemoglobin), enzymes (lipase), hormones (insulin)
96
Q

what are the different types of proteins and what do they do?

A
  • enzymes;
    • roughly spherical in shape due to the tight folding of the polypeptide chains
    • soluble
    • often have roles in metabolism, help synthesise large molecules
  • antibodies;
    • involved in immune response
    • made up of four polypeptide chains (2 long and 2 short) bonded together
  • transport proteins;
    • channel proteins are present in the cell membrane
    • contain hydrophobic and hyrdophillic amino acids which cause the protein to fold up and form a channel
    • the proteismn transport ions across membranes
  • structural proteins
    • physically strong
    • consist of a long polypeptide chains lyring parallel to each other with cross links between them
    • e.g keratin and collagen
97
Q

what are enzymes?

A

biological catalyst

98
Q

what is a catalyst?

A

a substance that speeds up a chemical reaction without being used up in the reaction itself

99
Q

which metabolic reactions will you find enzymes in?

A
  • respiration
  • digestion
100
Q

what does intracellular mean?

A

within the cell

101
Q

what does extracellular mean?

A

outside the cell

102
Q

what is the active site of an enzyme?

A

where the substrate molecule can bind to on the enzyme

103
Q

what is formed when a substrate fits into the active site of an enzyme?

A

a enzyme substrate complex is created

104
Q

what do enzymes do?

A

lower the activation energy of a reaction which allows reactions to happen at a relatively low temperature found inside a living cell (37 degrees)

105
Q
A
106
Q

explain the lock and key model

A

the lock and key model suggested there was a substrate with a complementary shape to the shape of the enzyme’s acitve site so that when drawn to the active site it fit perfectly into the active site like a key in a lock

107
Q

explain how the induced fit model is different from lock and key

A

in the lock and key model the enzyme acitve site stays rigid

the induced fit model shows that the enzyme is flexible because when then substrate is binding to the active site it can change and mould it self tightly around the substrate to create the enzyme substrate complex

once the product is released the enzyme retains its former shape

108
Q

how do ezymes lower the acitvation energy of reaction?

A

they do this by

  • oreinting the substrate
  • adding charges
  • inducing strain so that bonds are destabilised and the substrate is more reactive
109
Q

enzymes are very specific and usually only catalyse one reaction. for each enzyme state which substrate they would break down.

sucrase

lipase

amylase

A
  • sucrase will break down sucrose
  • lipase will break down lipids
  • amylose will break down amylase
110
Q

what is the enzyme’s active site determined by?

A

-it is determined by its tertiary structure which is its 3D shape which is determined by the primary structure which is the sequence of amino acids

111
Q

what happens if the tertiary structure of an enzyme is altered

A
  • the shape of the active site will change
  • this means the substrate will not fit into the active site
  • an enzyme substrate complex wont be formed
  • the enzyme will no longer be able to carry out is function
112
Q

what happens if the worng enzyme is put with the wrong substrate?

A

the enzyme is specific to the substrate’s and requires a complementary shape to the substrate

-if the substrate shape doesnt match the enzyme’s active site, then a enzyme substrate complex will not be formed and the enzyme will no onger be able to carry out its function.

113
Q

how could a mutation affect an enzyme

A
  • the primary structure of a protein (sequence of amino acids) is determined by a gene
  • this means that if a mutation occurs then the primary structure will change therefore the tertiary structure (its 3D shape will be changed).
114
Q

what is the;

independant variable

dependant variable

controlled variable

A
  • independant= one that is changed
  • dependant variable= the one that you measure
  • controlled variable= things you keep the same
115
Q

what factors affect enzyme acivity?

A
  • temperaure
  • ph
  • enzyme concentration
  • substrate concentration
116
Q

how does temperature affect enzyme acitivity?

A
  • increasing the temperature gives enzymes more kinectic energy
  • this increases the chance of substrate molecules colliding with the active site of the enzyme
  • however at very high temperatures excessive vibrations break some of the bonds holding the enzyme’s 3D shape
  • the high temps cause the 3D shape of the active site to change hence the substrate can nor fit
  • the enzyme is now denatured
117
Q

explain why the graph on a rate of activity vs temperature graph slow down?

A
  • it slows down because the active site is only starting to change
  • so the substrate can fit but less easily which slows down the rate of reaction
  • at some point the active site is so disrupted because the bonds are broken and the substrate can not fit
118
Q

what is the optimum temperature?

A

a temperature at which the enzyme catalyses the reaction best at

119
Q

how can you controlt the temperature in a investigation?

A

-you would need a thermometer and a water bath

120
Q

how does ph affect enzyme activity?

A
  • the ph solution is the measure of of its H+ concentration
  • most metabolic enzymes have a an optimum close to alkaline (6-8) but there are some that have extreme optimums e.g pepsin
  • if the ph is on the extreme ends of the ph spectrum they cause hydrogen and ionic bonds in rhe enzyme to be disrupted
  • the 3D shape of the active site changes and the substrate can no longer fit
  • the enzyme is denatured
121
Q

how can you control the ph in a investigation?

A

-use a buffer solution

122
Q

how does substrate concentration affect enzyme activity?

A
  • higher the subtrate concentration the faster the rate of reaction as there is more chance of collision
  • this only holds up to the saturation point
  • beyond this adding more substrate will not increase the rate of reaction as all the active sites are occupied
  • now the concentration of enzyme has now become the limiting factor
123
Q

what is the saturation point?

A

-the point at which all enzyme active site are occupied at any one time

124
Q

explain the shape of the substrate concentration affecting enzyme activity graph

A
  • the graph is steep at the start because the there are more substrate molecules available
  • then it plateaus off because it has reached satutration point where all the active sites of the enzymes are occupied
  • the rate of reaction does not go any faster
125
Q

what is the effect of enzyme concentration on enzyme activity?

A
  • increasing the enzyme concentration increases the rate of reaction
  • the more enzyme molecules there are in a solution, the more likely a substrate molecule is to collide with one and form an enzyme substrate complex
  • but if the amount of substrate is limited there comes a point when there is more than enough enzyme molecules to deal with the available substrate so adding more enzyme substrate has no effect
126
Q

complete the sentence:

the rate of reaction is ____________ proportional to ___________ concentration when there is an ________ of _________

A

the rate of reaction is directly proportional to the concentration of enzymes when there is an excess of substrate

127
Q

graph on substrate concentration

A
128
Q

how to calculate initial rate of reaction

A

-

129
Q

what are inhibitors?

A

substances that slow down the rate of enzyme controlled reactions

130
Q

what is an competitive inhibitor molecule and what does it do?

A
  • these molecules have a simlar shape to the substrate molecules
  • the compete with the substrate molecule to bind with the acitve site but no reaction takes place
  • instead they block the active site so no substrate molecule can fit
131
Q

how can the effect of a competitive inhibitor be reduced?

A

-by increasing the amount of susbtrate concentration

132
Q

explain the competitiv inhibition graph

A
  • without the inhibitor there is a faster rate of reaction becasue the there are no competitive inhibitors blocking the active site to substrate molecules
  • with the inhibitor there is a slower rate of reaction. This is because the competitive inhibitor will compete with the substrate molecules and sometimes block the active site to the substrate molecules so no reaction take place
  • it increases tho because as you increase substrate concentration you increase the chances of substrate molecules getting to the active site, incresing the rate of reaction
133
Q

what are non competitive inhibitors and what do they do?

A
  • these bind to another part of the enzyme away from the active site
  • this produces a change in shape of the active site so no substrate molecules can no longer bind to it
  • this change is irreversible
134
Q

what would happed if you were to increase the substrate concentration in the presence of a non competitive inhibitor?

A

nothing would happen as non of the substrate molecules can bind to the active site to form a enyme substrate complex and release a product.

135
Q

explain the graph with a non competitive inhibitor

A

-the graph for the non competitive inhibitor does not reach a high rate of rate of reaction and plateaus of quickly because the substrate may have binded with the acitve site before the inhibitor but once the non competitive inhibitor is on there the rate of reaction does not increase

136
Q

What are the two types of nucleic acis?

A

ribonucleic acid (RNA) and deoxyribonucleic acid (DNA)

137
Q

what does DNA stand for and what does it do?

A

DNA stands for deoxyribonucleic acid.

-it used to store genetic information

138
Q

What does RNA stand for and what does it do?

A

RNA stands for ribonucleic acid.

it’s main function is to transfer genetic information from DNA to the ribosomes.

139
Q

what are the 3 components that make up an individual nucleotide?

A
  • a pentose sugar
  • a phospate group
  • a nitrogen-containing organic base
140
Q

if DNA or RNA are polymers, what is their monomer?

A

a nucleotide

141
Q

what bond forms between two nucleotides and in which reaction will this happen?

A

a phoshodiester bond forms between the nucleotides and this happens in a condensation reaction.

142
Q

on which part of nucleotides does the phosphodiester bond form?

A

between the phosphate group of one nucleotide and the sugar of another

143
Q

what do you call two nucleotides joined together by a phosphodiester bond?

A

a dinucleotide

144
Q

what do you call a molecule that is made up of more than two nucleotides?

A

a polynucleotide

145
Q

what 3 components make up DNA?

A
  • the pentose sugar; deoxyribose
  • phosphate group
  • nitrogen containg organic base (A, T, C, G)
146
Q

what 3 coponents make up RNA?

A
  • the pentose sugar; ribose
  • phosphate group
  • nitrogen containg organic base (A, U, C, G)
147
Q

who were the scientist to work out the structure of DNA?

A

Watson and Crick

following the work by Rosalind Franklin on the X-ray diffraction patterns of DNA

148
Q

what is the name given to the structure of DNA and what is it made up of?

A

a DNA molecule is a double helix with two polynucleotide chains held together by hydrogen bonds between specific complementary base pairs

149
Q

what is complementary base pairing?

A

where each base in DNA can only join with one particular base

150
Q

finish of the sentence: in dna adenine (A) always pairs with…

A

in dna adenine (A) always pairs with thymine (T)

151
Q

finish off the sentence: in dna guanine always pairs with…

A

in dna guanine always pairs cytosine

152
Q

how many hydrogen bonds form between adenine and thymine?

A

two hydrogen bonds

153
Q

how many hydrogen bonds form betwen cytosine and guanine?

A

3 hydrogen bonds

154
Q

what is the DNA double helix made up off?

A

two antiparrallel (running in opposite directions) polynucleotide strands twist to form the DNA double-helix

155
Q

why is DNA a stable molecule?

A

because;

  • the phosphodiester backbone protects the more chemically reactive organic bases inside the double helix
  • hydrogen bonds link the organic base pairs forming bridges (rungs) between the phospodiester uprights. As there are three hydrogen bonds between cystine and guanine, the higher the proportion of C-G pairings, the more the stable the DNA molecule.
156
Q

how is the dna molecule adapted to carry out it’s functions?

A
  • it is a very stable structure which normally passes from generation to generation without chnage. Only rarely does it mutate
  • its two seperate strands are joined only with hydrogen bonds, which allow them to seperate during DNA replication and protein synthesis
  • it is an extremely large molecule and therefore carries an immense amount of genetic information
  • by having the base pairs within the helical cylinder of the deoxyribose-phosphate backbone, the genetic information is protected from being curropted by outsde chemical and physical forces
  • base pairing leads to DNA being able to replicate and to transfer information as mRNA
157
Q

before cell division what does DNA do?

A

DNA copies itself

158
Q

why must chromosomes copy themselves perfectly?

A

to make sure their daughter cells recieve the correct genetic information

159
Q

what is meant by when DNA replicates by a semi-conservative method?

A

this means that half of the strands in each new DNA molecule are from the original DNA molecule

which means that there’s a genetic continuity between the generations of cells

160
Q

describe what happens when DNA replicates by the semi-conservative method

A
  1. )-dna unwinds
    - hydrogen bonds are broken between the base pairs on the two polynucleotide chains using the enzyme helicase
    - sometimes this is known as unzipping
  2. )-the two polynucleotide chains seperate to form single strands
    - each polynucleotide chain acts as a template to make 2 new complementary strands

3 .)-unzipped polynucleotide strands have their bases exposed

  • ‘free floating’ nucleotides in the cytoplasm move into the nucleus and attach to their complementary bases following specific base pairing
    4. ) -the enzyme dna polymerase joins the nucleotides together forming a nerw sugar phosphate backbone in a condensation reaction
  • phosphodiester bonds form between the phosphate group of one nucleotide and the sugar on another nucleotide in the sugar phosphate backbone
161
Q

what is the name of the different ends on a DNA molecule?

A

3’ (prime) and 5’ (prime)

162
Q

on which end of DNA is the active site of DNA polymerase only complementary?

A

the active site of dna polymerase is only complementary to the 3’ end of the newly forming dna strand - so the enzyme can only add nucleotides to the new strand at the 3’ end.

163
Q

if an inhibitor of dna polymerase were introduced into a cell explain what the effect would be on dna replication

A
  • the linking together of the new nucleotides could not take place
  • while the nucelotides would match up with their complementary nucleotides on the origanl dna strand, they would join together to form a new strand.
164
Q

even after watson and crick’s model of the dna people were still not sure if dna replication was semi-conservative or conservative.

who were the scientists that validated watson and cricks’s model?

A

Meselson and stahl

165
Q

describe how meselson and stahl showed dna replicated using the semi-conservative method

A
  1. )-two samples of bacteria were grown (E. coli) for many generations one in a nutrient broth containing light nitrogen and one in a broth with heavy nitrogen.
    - as the bacteria replicated they took up nitrogen from the broth to make nucleotides for new dna, so the nitrogen gradually became part of the bacter’s dna
  2. )-a sample was taken from each batch of bacteria, and spun in a centrifuge.
    - the dna from the heavy nitrogen bacteria settled lower down the centrifuge tube than the DNA from the light nitrogen bacteria because its heavier
  3. ) -then the bacteria grown in heavy nitrogen broth was taken out and put in a broth containing only light nitrogen.
    - the bacteria were left for one rounf of dna replication, and then another dna sample was taken ouyt and spun in the centrifuge
  4. ) if replication was conservative, the original heavy dna, which would still be together would settle at the bottom and the new light dna would settle at the top
  5. ) if replication was semi-conservative, the new bacterial dna molecule would contain one strand of the old dna containing heavy nitrogen and one strand of new dna containing light nitrogen.
    - so the dna would settle out between where the light nitrogen dna settle out and where the heavy nitrogen and dna settled out.
  6. ) -as it turned out, the dna settle out in the middle, showing that the dna moelcules contained a mixture of heavy and light nitrogen.
    - the bacteria had replicated semi-conservatively in the light nitrogen.
166
Q

what did the conservative model of dna replication suggest?

A

-it suggested that the original dna molecule remained intact and that a seperate daughter dna copy was built up from new molecules of deoxyribose, phosphate and organic bases.

of the two molecules produced, one would be made of entirely new material while the other would be entirely original material.

167
Q

what are the main parts in the structure of atp?

A
  • adenine: a nitrogen containing organic base
  • ribose: a pentose sugar that acts as the backbone to which the other parts are attached
  • phosphates: a chain of three phosphates group
168
Q

note

A

you should not say ‘make’ or ‘produces’ when talking about energy but ‘realeased’ or ‘transfered’

169
Q

what is respiration?

A

the release of energy from glucose in a cell

170
Q

what does ATP stand for?

A

adenosine triphosphate q

171
Q

why is ATP known as a nuclear derivative?

A

because it has a simlar shape of nucleotide e.g it has base, a ribose sugar and a phosphate group

172
Q

how is energy transferred into a cell from the use of ATP?

A
  • A cell can’t get its energy directly from glucose
  • so in respiration, the energy released from glucose is used to make ATP
  • once made, ATP diffuses to the part of the cell that needs energy
  • the energy in ATP is stored in high energy bonds between the phosphate group
  • its released via hydrolysis reactions
173
Q

in the hydrolysis of ATP what is produced?

A

ATP + H2O –> ADP + P1 + E

adenosine triphosphate + water –> adenosine diphosphate + inorganic phosphate + energy

174
Q

in what ways is the hydrolysis of ATP an efficient recation?

A
  • ATP hydrolysis can be coupled to other energy requiring reactions in the cell, this means that energy can be directly used to make the coupled reactions rather than being lost as heat
  • the released inorganic phosphate can also be put to use; it can be added to another compound (this is known as phoshorylation) which often makes the compound more reactive
175
Q

what happens when ATP is resynthesised and what type of reaction is this?

which bond is formed?

what enzyme catalyses this reaction?

A

when in ATP is re-synthesised this happens:

ADP + P1 –> ATP

this happens in a condesation reaction

a phosphate bond is formed

the enzyme ATP synthase catalyses this reaction

176
Q

what are the three ways in which the synthesis of ATP from ADP occurs (in plant and animal cells)?

A
  • in chlorophyll-containing plant cells during photosynthesis (photophosphorylation)
  • in plant and animal cells during respiration (oxidative phosphorylation)
  • in plant and animal cells when phosphate groups are transferred from donor molecules to ADP (substrate-level phoshorylation)
177
Q

why is ATP a good energy donor?

A

it is an immediate energy source of a cell as it does not have to be stored in large quantities because it is very quickly synthesised from ADP + P1

178
Q

why is ATP not a good energy donor?

A
  • it is not a long-term energy store because the phospate bonds are unstable
  • it can not be stored and therefor has be continously made wthin the mitochondria of cells that need it
179
Q

why is ATP a better immediate energy source than glucose?

A
  • each ATP molecule releases less energy than each glucose molecule so the energy for reactions is therefore released in smalle, more manageable quantities.
  • the hydrolysis of ATP to ADP is a singl recation that releases immediate energy, whlist the break down of glucose is a long series of reacations and therefore the energy release takes longer
180
Q

give examples of energy requiring processes where ATP is used

A
  • metabolic processes: ATP provides the energy needed to build up macromolecules from their basic units e.g making starch from glucose or polypeptides from amino acids
  • movement: ATP provides energy for muscle contraction e.g enrgy for the filamwents of muscle to slide past one another and therefore shorten the overall length of a muscle fibre
  • active transport: ATP provides energy to change the shape of the carrier proteins in plasma membranes which allows molecules or ions to be moved against the concentration gradient
  • secretion: ATP is needed to form the lysosomes necessary for the secretion of cell products
  • activation of molecules: inorganic phosphates during the hydrolysis of ATP can be used to phosphorylate other compounds in ordeer to make them more reactive thus lowerng the activation energy in enzyme-catalysed reactions e.g the addition of glucose molecules at the start of glycolysis
181
Q

the movement of calcium ions across a cell memebrane can occur via the energy requiring process of active transport. This movement of calcium ions is coupled with the breakdown of ATP. suggest why (2m)

A

the break down of ATP in hydrolysis releases energy so when this reaction is coupled to the process of active transport it provides the energy for this process directly q

182
Q

ATP can be reformed by the addition of an inorganic phosphate to ADP.

what type of reaction is this?

give an example of a proces during which this reaction takes place

A
  • this is condensation reaction
  • this takes place in respiration
183
Q

talk about the importance of water in metabolsim

A

a metabolic reaction is a chemical reaction that happens in a living organism to keep the organism alive

  • a hydrolysis reaction requires a molecule of water to break a bond
  • a condensation reaction releases a molecule of water so a new bond is formed
  • chemical reactions takes place in an aqueous medium
  • water is a major raw material in photosynthesis
184
Q

talk about water as a solvent

A
  • water’s polarity makes it a useful solvent it readily dissolves substances such as:
  • gases e.g oxygen and CO2
  • wastes e.g ammonia and urea
  • inorganic ions and small hydrophyllic molecules e.g amino acids, monosaccharides and ATP
  • enzymes whose reactions take place in solution
185
Q

discuss water and its relatively high specific heat capacity and its buffering changes in temperature

A
  • because some water moelcules stick together (by hydrogen bonding) it takes more energy to separate them than would be needed if they did not bond to one another
  • for this reason the boiling point of water is higher then expected and without its hydrogen bonding water would be gas at temperatures commonly found on earth and life as we know it would not exist
  • for the same reason it takes more energy to heat a given mass of water (aka its high specific heat capacity)
  • water therfore acts as a buffer against sudeden temperature variations, making th aquatic environment a temperature-stable one and as organisms are mostly water, it also buffers them against sudden temperature
186
Q

discuss water’s large latent heat of vapourisation

A
  • the hydrogen bonding between water molecule means that it requires a lot of energy to evaporate 1 gram of water (aka the latent heat fo vapourisation)
  • this is useful for living organisms because it meands they can use water loss through evaporation to cool down e.g humans sweat to cool down, without losing too much water
187
Q

discusss the cohesive property of water

A

cohesion is the tendancy of molecules to sticke together

  • with its hydrogen bonding water has a large cohesive forces and these allow it to be pulled up througha tube, such as xylem vessel in plants
  • strong cohesions means water also has a high surface tension when the molecules meet air, (they tend to be pulled back into the body of water rather than escaping from it)
    e. g sweat froms droplets, which evaporate from the skin to cool an organism down or the surface of the water is strong enough to support small organisms such as pond skaters
188
Q

discuss water and its transparency

A

-water is transparent and therefore aqauitc plants can photosyntesise and also light rays can penertrate the jelly-like fluid that fills the eye and so reach the retina.

189
Q

why is that large bodies of water rarely freeze over entirely at colder temperatures?

A
  • at colder temperatures the cooler water (ice) becomes less dense than warmer water.
  • ice floates on warmer water, forming a layer that insulates the water beneath with the result that large bodies of water rarely freeze over entirely
190
Q

In hot temperatures, elephants commonly spray themselves with water. With reference to the strucure and properties if water, explain:

a. ) why this behaviour acts as a cooling mechanism for the elephant
b. ) why water forms droplets when the elephant sprays it from its trunk

A

a. ) as the water evaporates from the surface of the elephant’s body, some of the elephants heat energy is used to break the hydrogen bond which hold the water molecules together. This cools the surface of the elephants body
b. ) there is strong cohesions between the water molecules. this results in water having a high surface tension when in contact with air causing it to form droplets

191
Q

what the symbol for a Iron Ion? and what is it its role?

A

Fe2+

  • it is a component of haemoglobin
  • haemoglobin is made up of four different polypeptide chains, each with an Fe2+ ion
  • it is the Fe2+ ion that binds to the oxygen in haemoglobin and temporarily becomes and Fe3+ ion until oxygen is released
192
Q

what is the symbol for a hydrogen ion and what is its role?

A

H+

they determine pH

  • pH is calculated based on the concentration of hydrogen ions in the environment
  • the more H+ ions present the lower the pH (and the more acidic the environment)
  • enzyme-controlled reactions are all effected by pH
193
Q

what is the symbol for a sodium ion and what is its role?

A

Na+

they help transport glucose and amino acids across membranes

  • a molecule of gluocse or an amino acids can be transported into a cell alongside sodium ions. This is known as co-transport
194
Q

what is the symbol for a phosphate ion and what is its role?

A

PO4^3-

essential component of ATP and DNA

  • when a phosphate ion is attached to another molecule its know asa phosphate group
  • DNA, RNA and ATP all contain phosphate groups
  • its the bonds between phosphate groups that store energy in ATP
  • the phosphate groups in DNA and RNA allow nucleotides to join to up to form the polynucleotides
195
Q

End of Topic

A
196
Q

EQ: The concentration of glucose in the blood rises after eating a meal containing carbohydrates. The rise is slower if the carbohydrate is starch rather than sucrose. Explain why

3 marks

A
  1. Starch digested to maltose/by amylase;
  2. Maltose digested to glucose/by maltase;
  3. Digestion of sucrose is a single step/only one enzyme/sucrase
197
Q
A

Biology AS (5 decks)

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