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Biological Molecules Flashcards

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1
Q

How does hydrogen bonding occur

A

1) A molecule of water is one atom of oxygen covalently bonded with two atoms of hydrogen by shared electrons.

2) The shared negative hydrogen electrons are pulled towards the positive oxygen atom, each hydrogen is left with a slightly positive charge.

3) The unshared negative electrons on the oxgen atom give it a slightly negative charge

4) This creates a polar molecule (partial negative on one side and partial positive on the other)

5) The slightly negative charged oxygen atoms attract the slightly positively charged hydrogen atoms of other water molecule. This attraction is called hydrogen bonding.

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2
Q

What is the unit of ‘delta positive’ and ‘delta negative’

A

δ+ delta positive

δ- delta negative

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3
Q

Explain the function of water

A

Water is a reactant in many chemical reactions e.g hydrolysis reactions

Water is a solvent, many substances dissolve in it e.g ions in water in the bloodstream. Most biological reactions require a solution.

Water transport substances e.g glucose, mineral ions, oxygen gas

Water is involved in temperature control because it has a high specific heat capacity and large latent heat of evaporation

Water is a habitat. Nutrients can be dissolved in water . Contains oxygen gas which is essential for life. Forms an insulating layer for organisms when formed into ice

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4
Q

How does the structure of water relates to its function

A

• Hydrogen bonds give water a high specific heat capacity

• Hydrogen bonds also give water a high latent heat of evaporation

• Water’s polarity makes it very cohesive

• Water’s polarity also makes it a good solvent

• Water is less dense when it’s solid - makes a good habitat

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5
Q

Explain how hydrogen bonds gives water a high specific heat capacity

A

Specific heat capacity (SHC) is the energy needed to raise the temperature of 1 gram of a substances 1c

The hydrogen bonds between water molecule absorb a lot of energy so water has a high SHC- requires a lot of energy to heat up.

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6
Q

How can the SHC of water contribute for the survival of organism

A

Water doesn’t experience rapid temperature change due to having a high SHC.

This property makes water a buffer against rapid temperature change thus a good habitat- the temperature under water is more stable than on land.

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7
Q

Explain how hydrogen bonds gives water a large latent heat of evaporation

A

It takes a lot of (heat) energy to break the bonds between water molecules.

As a result water has a high latent heat of evaporation- a lot of energy is used when water evaporate

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8
Q

How can the large latent heat of evaporation of water contribute for the survival of organism

A

Large latent heat of evaporation is useful for living organisms because it means water great for cooling things:

This is why some mammals like u sweat when they’re too hot. When sweat evaporates they cool the surface of the skin

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9
Q

Explain how water polarity makes it very cohesive

A

Cohesion is the attraction between molecules of the same type .

Water molecules are very cohesive because they’re polar

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10
Q

How can the cohesion of water contribute for the survival of organism

A

Cohesion of water helps water to flow making it great for transporting substances.

It helps columns of water to be transported up by plant stems in the transpiration stream

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11
Q

Explain how water polarity makes it a good solvent

A

Many biological molecules are ionic. This means they’re made from one positively charged atom or molecule and one negatively charged atom or molecule.

Water is polar, the slightly positive end of the water molecule will be attracted to the negative ion and the slightly negative end of a water molecule will be attracted to the positive ion.

Thus , Ions will get surrounded by water molecules (dissolve)

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12
Q

How can the water being a good solvent contribute for the survival of organism

A

Water’s polarity makes it useful as a solvent in living organism - water is an excellent transport medium

E.g in humans, important ions can dissolve in the water in blood and then be transported around the body (blood plasma- transport carbon dioxide, mineral acid and amino acids).

Water is used to transport substances in xylem vessels of plants. Water in the xylem contains dissolved mineral ions such as magnesium ion.

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13
Q

Explain how water is less dense when solid

A

At low temperature water freezes and turn from liquid to solid.

Water molecules are held further apart in ice than they are in liquid water because each water molecule forms four hydrogen bonds to other water molecules, making a lattice.

This makes ice less dense and float

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14
Q

How can the density of water when solid contribute for the survival of organism

A

This is useful for living organisms because, in freezing temperatures, ice forms an insulating layer on top of water- the water below doesn’t freeze. So organisms that live in the water, like fish, don’t freeze and can still move around,

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15
Q

What is the element composition of carbohydrates

A

C , H , O

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16
Q

What is the element composition of lipids

A

C, , H , O

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17
Q

What is the element composition of proteins

A

C , H , O , N , S

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18
Q

What is the element composition of Nuclei acids (DNA and RNA)

A

C , H , O , N , P

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19
Q

Explain what a monomer is

A

Monomers are small units which are the components of larger molecules

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20
Q

What are examples of a polymer

A

Starch and cellulose

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21
Q

Explain what a polymer is

A

Polymers are molecules made from many monomers joined together

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22
Q

Explain what is the condensation reaction

A

A reaction with two molecules joined together by a chemical bond with the release of a water molecule.

E.g when two glucose molecules bond together

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23
Q

Explain what is the Hydrolysis reaction

A

Hydrolysis is the opposite of a condensation reaction.

It is when water is added to break a chemical bond within a molecule.

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24
Q

Draw a diagram of a condensation and Hydrolysis reaction

A
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25
Q

What are single, paired and large chain of monomers called

A

Monosaccharide

Disaccharide

Polysaccharide

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26
Q

What are the bonds in carbohydrates called

A

Glycosidic bonds

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27
Q

Examples of monosaccharides

A

Glucose (hexose monosaccharide)

Ribose (Pentose monosaccharide)

Galactose

Fructose

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28
Q

What are the different forms of glucose

A

Alpha-glucose

Beta- glucose

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29
Q

What are the similarities differences between a-glucose and b-glucose

A

They have the same chemical formula but have slightly different structures.

If the carbon 1 hydroxyl pointes above the ring we call this isomer beta glucose

If the carbon 1 hydroxyl points below the ring we call this isomer alpha glucose

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30
Q

Draw the structure of a Glucose and Ribose

A
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31
Q

Draw the structure of Alpha glucose and Beta Glucose

A
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32
Q

What is an isomer

A

Isomers are molecules with the same chemical formula but have different structures.

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33
Q

Explain the structure of glucose

A

Glucose is a hexose sugar- a monosaccharide with six carbon atoms in each molecule

There are two types of glucose, glucose A and B which have the same chemical formula but have different structures

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34
Q

What are examples of Disaccharides

A

Maltose

Sucrose

Lactose

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35
Q

How is maltose , sucrose and lactose formed

A

Maltose is a disaccharide formed by condensation of two glucose molecules

Sucrose is a disaccharide formed by condensation of glucose and fructose

Lactose is a disaccharide formed by condensation of glucose and galactose

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36
Q

Explain a polysaccharide

A

A polysaccharide is a macromolecule consisting of more than 2 sugars - often a long chain of polymers joined together by glycosidic bonds

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37
Q

What are example of Polysaccharides

A

Glycogen

Starch

cellulose

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38
Q

How is Glycogen , starch and Cellulose formed

A
  • Glycogen is formed by the condensation of alpha glucose molecules.
  • Starch is formed by the condensation of alpha glucose molecules.
  • Cellulose is formed by the condensation of beta glucose molecules.
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39
Q

Polysaccharide chains may be:

A

• These chains may be:

• Branched or unbranched.

• Folded (making the molecule compact which is ideal for storage eg. starch and glycogen).

• Straight (making the molecules suitable to construct cellular structures e.g. cellulose) or coiled.

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40
Q

Explain what glycogen is

A

The glucose storage molecule is glycogen and the major stores of glycogen are found in the liver and in the muscle cells

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41
Q

Explain the structure of Glycogen

A
  • It is a multi-branched alpha glucose polymer joined together by 1, 4 and 1, 6 glycosidic bonds.

-stored within the muscles and in the liver

  • It has a large number of side branches meaning that energy can be released quickly as enzymes can act simultaneously on these branches.

-Glycogen is more branched than amylopectin which makes glycogen a very compact molecule .

-Glycogen has large number of branches thus a lot of free ends. This means that enzymes can convert glycogen back to glucose very rapidly

-Glycogen is insoluble in water. Glycogen does not draw water into the cell by osmosis . Additionally, being a a large molecule glycogen cannot diffuse out of the cell

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42
Q

Explain the function of Glycogen

A
  • Glycogen is the main energy storage molecule in animals.
  • Glycogen is stored in the muscles and in the liver.
  • In times of high energy usage, these organs hydrolyse the glycogen stored and break it down into glucose molecules which can be used in respiration
  • It is a relatively large but compact molecule thus maximising the amount of energy it can store. Makes it optimal for an energy storage molecule.
  • Finally being insoluble means it will not affect the water potential of cells and cannot diffuse out of cells being a large molecule .

Glycogen has a a large number of branches + free ends thus enzymes can convert glucose very rapidly

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43
Q

What is starch made from

A

• Starch is constructed from two different polysaccharides:

  • Amylose (10 - 30% of starch)
    • Unbranched helix-shaped chain with 1,4 glycosidic bonds between α-glucose molecules
    • The helix shape enables it to be more compact and thus it is more resistant to digestion
  • Amylopectin (70 - 90% of starch)
    • 1,4 glycosidic bonds between α-glucose molecules but also 1,6 glycosidic bonds form between
    glucose molecules creating a branched molecule
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44
Q

How does the structure of starch relate to its function

A

Amylose forms a tight helix which make style starch compact.. Thus the starch can store a large amount of glucose molecule for its size.

Amylopectin and amylose are polymers which are too large to diffuse through the cell membrane and pass out of the cell. Thus starch is insoluble in water and does not cause water to enter the cell by osmosis.

As amylopectin has a large number of branches it has a large number of ends thus the enzymes can break down starch rapidly by breaking the glycosidic bonds at the end of molecules.

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45
Q

Explain the structure of Amylose

A

Amylose is a polymer of alpha glucose molecules.

The amylose molecule twists into a compact helix with hydrogen bonds forming between glucose molecules along the chain.

Amylose contain hundreds or thousands of alpha glucose molecules which are joined together by 1,4 glycosidic bonds.

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46
Q

Explain the structure of Amylopectin

A

Amylopectin is a polymer of alpha glucose joined together by 1,4 glycosidic bonds However, amylopectin chains have a branch every 25-30 glucose molecules.

The brach is connected to the main chain by a glycosidic bond which is connected to carbon 1 of one glucose molecule and carbon 6 of another (1,6 glycosidic bond).

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47
Q

What is the structure of cellulose

A

Cellulose is a polymer of beta glucose

The structure of beta glucose is similar to alpha glucose. However, the hydroxyl on carbon 1 points above the plane of the ring.

Glycosidic bonds cannot form between carbon 1 and 4 as the hydroxyl groups point in different directions. As a result when a molecule of cellulose is formed every second beat glucose molecule flips. Thus a 1,4 glycosidic bond is formed

Cellulose is an unbranched polysaccharide joined by glycosidic bonds in a condensation reaction

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48
Q

What is the function of cellulose

A

Cellulose forms a straight chain without any branches. This allows cellulose molecules to get close together.

Hydrogen bonds can now form between neighbouring chains. As a result a large number of hydrogen bonds are formed which makes cellulose extremely strong.

Cellulose cell wall is permeable to molecules

The contents of the plant cell push against the turgid cell of the cellulose cell wall. The strength of the cell wall resists the outwards pressure due to the cells contents, This prevents plants cell from bursting.

Plant called filled with water become rigid. These turgid cells give the plant an upright structure.

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49
Q

What are some examples of monomers

A

Monosaccharides such as glucose, amino acids and nucleotides

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50
Q

What is the structure of oxygen

A

Molecule of water contains one atom of oxygen chemically bonded to two atoms of hydrogen.

The bonds between atoms are covalent bonds

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51
Q

What is the structure of oxygen

A

Molecule of water contains one atom of oxygen chemically bonded to two atoms of hydrogen.

The bonds between atoms are covalent bonds

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52
Q

Explain how waters polarity make it useful for metabolic reactions

A

Water’s polarity makes it a very good polar solvent for many biological molecules.

E.g: in ionic calcium chloride, the positive Ca2+ will be attracted to the negative pole of a water molecule, and Cl- will be attracted to the positive pole.

Many metabolic reactions occur in water.

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53
Q

Explain how water being a good metabolic reactant can ensure the survival of an organism

A

water is a reactant in many different reactions such as hydrolysis reactions and photosynthesis

Water is also produced in certain metabolic reactions. These include condensation reactions and aerobic respiration

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54
Q

Explain the key features of monosaccharides

A

They are soluble in water. This is because they contain a large number for OH groups within their structure (hydroxyl groups).

As a result the hydroxyl group will form hydrogen bonds with water molecules which cause the molecule to be soluble (hydrophilic)

Hydrophilic= water loving (hydrophilic molecules dissolve in water)

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55
Q

What is the word equation of glucose

A

C6H12O6

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56
Q

What product are made when creating a disaccharide

A

A molecule of water is produced which is formed from hydrogen atom from one of the monosaccharides and a hydroxyl group from the other

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57
Q

What alternative products are created when a disaccharide is formed

A

A molecule of water is produced which is formed from hydrogen atom from one of the monosaccharides and a hydroxyl group from the other

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58
Q

How can a disaccharide be formed into a monosaccharide

A

If water is added to a disaccharide we can break the glycosidic bond. This converts the disaccharide back to the original monosaccharides This is called hydrolysis reaction.

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59
Q

Explain why glucose is soluble and why this is a problem

A

Glucose is extremely soluble in water. It contains a large number of hydroxyl groups which are polar. As a result hydroxyl groups can form hydrogen bonds with water molecules. This makes glucose soluble in water.

However,if a cell contains a large amount of dissolved glucose this can cause water to move into the cell through osmosis. As a result plant store glucose as starch.

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60
Q

What is a microfibril

A

Polymer of 10,000 beta glucose molecules in a long unbranched chain is called a microfibril (long cellulose chains)

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61
Q

What is a macrofibril

A

Microfibrils group together to form a larger structures called macofibrils

62
Q

What is a microfibril

A

Polymer of 10,000 beta glucose molecules in a long unbranched chain is called a microfibril (long cellulose chains)

63
Q

What is a cellulose fibre

A

Macrofibrils grouped together form a cellulose fibre

64
Q

What is a cellulose fibre

A

Macrofibrils grouped together form a cellulose fibre

65
Q

What four elements are primarily found in living organisms

A

Carbon-C

Hydrogen-H

oxygen-O

Nitrogen-N

66
Q

Describe a covalent bond

A

A covalent bond is the sharing of two or more electrons between two atoms

The electrons can be shared equally forming a nonpolar covalent bond or unequally (where an atom can be more electronegative δ-) to form a polar covalent bond

67
Q

How are covalent bond formed

A

Covalent bonding occurs when pairs of electrons are shared by atoms. Atoms will covalently bond with other atoms in order to gain more stability, which is gained by forming a full electron shell (valence shell is formed)

68
Q

What is an ion

A

An atom or molecule in which the total number of electrons is not equal to the total number of protons is called an ion.

69
Q

What are cation and anions

A

Cations are ions with a positive charge, meaning they have lost electrons.

Anions are ions with a negative charge, meaning they have gained electrons.

70
Q

Describe an ionic bond

A

Ionic bonds form between a positively charge atom and a negatively charged atom

71
Q

How are ionic bonds formed

A

Ionic bonds are formed between two or more atoms by the transfer of one or more electrons between atoms. Electron transfer produces negative ions called anions and positive ions called cations

72
Q

What is an organic and inorganic substance

A

Organic substances contain carbon covalently bonded to a hydrogen atom. (CH4)

Inorganic substances lack C-H bonds. (NH4)

73
Q

What are lipids

A

Lipids are macromolecules that contains carbon, hydrogen and oxygen atoms.

Unlike carbohydrate, lipids contain a lower proportion of oxygen

74
Q

What are the groups of lipids

A

Triglycerides (main components of fats and oils)

Phospholipid

75
Q

Explain the Properties of lipids

A

They contain carbon, hydrogen and oxygen- lots of of energy can be released

The proportion of carbon to oxygen and hydrogen is smaller than in carbohydrates

They are insoluble in water

They are soluble in organic solvents such as alcohol and acetone

76
Q

Explain the function of lipids

A

Storage of energy for long term use (e.g triglycerides) or adipose tissue in humans.

Hormonal roles (e.g steroid such as oestrogen and testosterone)

Insulation- both thermal (triglycerides) and electrical (sphingolipids). Furthermore, adipose tissue in humans help to insulate the body, reducing heat loss to the environment.

Protection of internal organs (triglycerides and waxes). Furthermore, adipose tissue is found around organs to protect it from injury

Structural components of cells (phospholipids , cholesterol, mitochondria, )

Lipids are used for water proofing- oils which coat the feathers of aquatic birds

77
Q

Explain how are triglycerides formed

A

Triglycerides form when a condensation reaction occurs between one glycerol and three fatty acid chains

-the 3 hydroxyl group of the glycerol molecule combine with a carboxylic group of 3 fatty acid molecules to form an ester linkage (esterfication)

This condensation reaction results in the formation of three water molecules

78
Q

Explain how triglycerides are used in animals compared to plants

A

Animals tend to store triglycerides as fat (solids)

plants tend to store triglycerides as oils (liquids)

79
Q

Explain the structure of saturated fatty acids

A

Fatty acids are long hydrocarbon chains that are found in certain types of lipids (triglycerides and phospholipids)

They differ in length (2-24 carbons) and in the number of double bonds

Contains a carboxylic group on one end

Fatty acids with no double bonds are saturated

80
Q

Explain the properties of saturated fatty acids

A

This generates fats that are usually solid at room temp

Saturated fats are usually linear in structure, originate from animal sources (I.e fats)

81
Q

Explain the structure of unsaturated fatty acids

A

Fatty acids with double bonds are unsaturated- either mono saturated (1 double bonds) or polyunsaturated (> 1 double bond)

Contains a carboxylic group on one end

82
Q

Explain the properties of unsaturated fatty acids

A

Unsaturated fatty aids are bent in structure, originate from plant sources (I.e oils)

Unsaturated fatty acids are usually liquid at room temperature and are called oils

83
Q

what are example of real life items which contain trans fats

A

Hydrogenated veritable oils

Fast foods

Cakes/pastries

Chocolate

Deep fried food

84
Q

what are example of real life items which contain saturated fats

A

Vegetable fats:

Coconut

Palm oil

Condensed milk

Animal dats:

Poultry skin

Fatty meat

Butter

Ghee

85
Q

what are example of real life items which contain unsaturated fats

A

Polyunsaturated:

Com oil

Soybean oil

Sunflower oil

Seeds

Monounsaturated:

Olive oil

Cannoli oil

Peanut oil

86
Q

Explain the structure for phospholipids

A

Structure similar to triglyceride, but one Fatty acid chain is replace with a Phosphate group (PO4)3- group

87
Q

Explain the properties of phospholipids

A

Phospholipids are amphipathic (hydrophobic and hydrophilic)- the phosphate head is negatively charged and thus is polar (hydrophilic) whereas the fatty acids tails are non-polar (hydrophobic)

Phospholipids have both mono layers and bilayers

88
Q

Explain the function of phospholipids

A

Phospholipids play a crucial role in forming the plasma membrane of cells:

• In an aqueous environment being polar means a bilayer can be formed.

• They form a bilayer with the FA tails facing into each other, and the polar heads facing outwards and dissolving in the aqueous intra- and extracellular fluids.

• The hydrophilic heads of the phospholipids can be used to hold at the surface of the cell surface membrane.

• Their structure allows them to form glycolipids with carbohydrates which are important on the cell surface membrane for cell recognition.

• They are ideal for forming cell surface membranes as they enable integration of other molecules into the ‘mosaic’ and help to regulate the movement of molecules in and out of
the cell.

89
Q

Compare phospholipids with triglycerides

A

No. Fatty acids tails: 2 / 3

Presence of phosphate: yes / no

Polar / non-polar: polar phosphate head / non-polar

No,water molecules released when formed :

3 / 3

Function:

Cell membrane components / energy storage

90
Q

What is cholesterol

A
91
Q

Explain the structure of cholesterol

A

Has a 4 carbon ring structure with a hydroxyl (OH) group at one end

92
Q

Explain the function of cholesterol

A

• Cholesterol is important in the formation and
fluidity of cell surface membranes and in the
production of certain hormones e.g.
testosterone and oestrogen .

Hormones are able to pass through cell membranes and interact with receptors inside the cell as they are based on cholesterol

Cholesterol creates vitamin D in the skin in response to UV light (development of bones)

Cholesterol is used in the liver to create bile which increase the rate of digestion of lipids by the enzyme lipase

Forms a small, thin molecule that fits into a lipid bilayer giving strength and stability

Cholesterol can insert into cell membranes by using its hydrophilic hydroxyl group to interact with the head groups of phospholipids. While the rest of it interacts with the hydrophobic fatty acids tails

93
Q

Explain the properties of cholesterol

A

Not soluble in water . ( has a hydroxyl group which is hydrophilic). However, the rest of the molecule is hydrophobic.

94
Q

What are the two different major lipoproteins

A

Low-density lipoproteins (LDL)

High-density lipoproteins (HDL)

95
Q

Draw the structure of a triglyceride

A
96
Q

Draw the structure of a phospholipids

A
97
Q

Explain the function of LDLs

A

• Low density lipoproteins (LDL) carry cholesterol from the liver to the rest of the body

• LDLs bind to receptors on cell surface membranes before being taken up by the cells where the cholesterol is involved in the synthesis and maintenance of cell membranes.

98
Q

Explain how LDLs form

A

• Triglycerides (from fats in our diet) combine with cholesterol and proteins to form LDLs
which transport the cholesterol to our body cells.

99
Q

Explain the problem with LDLS

A

Excess LDL overload on these membrane receptors, results in high blood cholesterol levels, which may be deposited in the artery walls forming atheromas.

Therefore it is desirable to maintain a higher HDL:LDL ratio in the blood. As HDLs reduce blood cholesterol deposition

100
Q

Explain how HDLs form

A

HDLs are made when triglycerides (from fats in diet) combine with cholesterol and proteins.

101
Q

Explain the function of HDLs

A

High density lipoproteins (HDL) scavenge excess cholesterol in the body tissues and carry it back to the liver where it is broken down.

• This lowers blood cholesterol levels, and helps to remove the fatty plaques of atherosclerosis.

102
Q

Dietary factors that increase cholesterol levels

A

High intake of certain types of fast will differentials affect cholesterol levels in the blood:

• Saturated fats increase LDL levels within the body, raising blood cholesterol levels

• Trans fats increase LDL levels and decrease HDL levels within the body, significantly raising blood cholesterol levels

• Unsaturated (cis) fats increase HDL levels within the body, lowering blood cholesterol
levels

103
Q

How do Saturated/mono-saturated and polyunsaturated fats contribute to cholesterol levels

A

Saturated fats: studies have shown they increase LDL and HDL cholesterol, however increase in LDL cholesterol is greater.

Monounsaturated fats:Help the removal of LDLs from the blood

Polyunsaturated fats: Increase the activity of the LDL receptor sites so the LDLs are actively removed from the blood

104
Q

Describe the general structure of amino acids

A

Amino aids are formed from an amine group and a carboxyl group attached to a single carbon atom.

The R group attached to the carbon is different for each of the 20 amino acids

105
Q

What are the general elements within a amino acid

A

Carbon,hydrogen, nitrogen and oxygen

Some contain sulfur

106
Q

Explain how amino acids can bond together

A

Two amino aids can react together and form a chemical bond. This is known as a ** peptide bond **.

A molecule of water is produced from this reactor (condensation reaction)

The molecule form is called a dipeptide as it contains two amino acids which are bonded together

107
Q

If three or more amino acids bond together what is formed

A

If three or more amino acids bond together a polypeptide is formed

(Consist of hundred of amino acids formed together)

108
Q

Explain how we can reverse a peptide bond

A

A peptide bond is formed through a condensation reaction where water is produced.

The peptide bond can be broken by adding a molecule of water (hydrolysis reaction)

This reaction is carried out by protease enzymes in the digestive system

109
Q

Explain the difference between a polypeptide and a protein

A

In order to be classed as a protein a polypeptide has to fold into a complex, 3-dimensional shape

Once a polypeptide has folded into the correct shape it carries out its function e.g as an enzyme or hormone. It is then considered to be a protein molecule.

Protein consist of several different polypeptides forming a large and complex molecule. It also contains other molecules to support its function (eg haemoglobin)

110
Q

Explain the primary structure of proteins

A

The primary structure is simply the specific order of amino acids in a polypeptide

It helps to determine the final 3 dimensional shape of the protein molecule which is critical for its function

111
Q

Explain how the primary structure of a polypeptide is determined

A

The primary structure for a polypeptide is determined by the DNA sequence of the gene which encodes the polypeptide

112
Q

Explain how the secondary structure of a protein is formed

A

Within a polypeptide chain there are C=O groups and N-H groups

The oxygen atoms in C=+O groups have a small negative charge and the hydrogen atoms in teh N-H groups have a small positive charge.

This means they attract to each other and a hydrogen bonds form between amino acids all along the polypeptide chain

The polypeptide chain will twist and fold into shapes and scientists call this the secondary structure

113
Q

What are examples of secondary structures

A

Alpha-helix

Beta-pleated sheet

114
Q

Describe the structure of Alpha-helix

A

The polypeptide chain is twisted into a helical shape held in place by hydrogen bonds

115
Q

Describe the structure of the Beta-pleated sheet

A

The polypeptide chain folds into a flatter, sheet-like structure. The hydrogen bonds between the amino acids hold the shape into place.

116
Q

What is the secondary structure determined by

A

The type of secondary structure formed depends on the primary structure in that region

117
Q

How do amino acid sequences influence the formation of alpha helices and beta pleated sheets in protein structures?

A

Many proteins have regions with alpha helices and regions with beta pleated sheets.

Certain amino acid tend to be found in alpha helices and other in beta-pleated sheets

118
Q

Explain how the tertiary structure of a protein is formed

A

The regions of secondary structure form,the chain now continues folding forming the final tertiary structure

119
Q

Explain what is the tertiary structure of a protein

A

It is the overall 3-dimensional shape of a polypeptide chain

120
Q

Explain what is the tertiary structure of a protein

A

It is the overall 3-dimensional shape of a polypeptide chain

It is critical for how a protein function e.g the active site of an enzyme depends on the protein forming a very specific tertiary structure

If the tertiary structure of an enzyme is changed (e.g by heating) the shape of the active site changes. Thus the enzyme no longer function effectively (denatured)

121
Q

Explain why the tertiary structure important

A

It is critical for how a protein function e.g the active site of an enzyme depends on the protein forming a very specific tertiary structure

If the tertiary structure of an enzyme is changed (e.g by heating) the shape of the active site changes. Thus the enzyme no longer function effectively (denatured)

122
Q

Explain why the tertiary structure important

A

It is critical for how a protein function e.g the active site of an enzyme depends on the protein forming a very specific tertiary structure

If the tertiary structure of an enzyme is changed (e.g by heating) the shape of the active site changes. Thus the enzyme no longer function effectively (denatured)

123
Q

Explain the quaternary structure of a protein

A

The quaternary structure shows how the individual subunits are arranged to form a larger three dimensional structure

It only applies to proteins with at least two subunits

Some protein contain other non-protein molecules forming part of the structure. These are called prosthetic groups and they help the protein to carry out its role

Protein with a prosthetic group are called conjugated proteins.

They show the arrangement of subunits and the position of any prosthetic group

124
Q

Explain what prosthetic group support RBCs

A

Haemoglobin contains the prosthetic group haemoglobin which binds to oxygen

125
Q

Explain hydrogen bonding in proteins

A

A polypeptide chain will have two amino acids with R groups containing a hydroxyl

Due to the slight positive and negative changes present on the hydroxyl a hydrogen bond can form these two R groups and this contributes to the 3 dimensional shape of the polypeptide chain

Hydrogen bonds are weak and are easily broken by high temperature or by pH changes

126
Q

Explain hydrophobic and hydrophilic interaction within bonding proteins

A

Several amino acids have uncharged R groups we call these non-polar amino acids which aren’t attracted to want (hydrophobic). These cluster which work to exclude water molecules (hydrophobic interactions). These tend to be in the centre of proteins away from water molecules

Hydrophilic amino acids tend to be found on the surface of proteins where they can interact with water molecules.

Both hydrophobic and hydrophilic interactions are relatively weak bonds

127
Q

Explain ionic bonding during bonding of proteins

A

Ionic bonding occurss between amino acids with charged R groups

An amino acid will be a positively charged R group and the other will be a negatively charged R group

These opposite charges attract each other and form an ionic bond. This holds different parts of the polypeptide chain together and contributes to protein structure

Ionic bonds are broken by pH. This is why enzymes can denature under acidic or alkaline conditions

128
Q

Explain disulfide bonds in the bonding of proteins

A

A polypeptide contains two molecules of an amino acid called cysteine. The R group of cysteine contains a sulfur atom.

The sulfur atom in the two cysteine molecule form a covalent bond. This is called a disulfide bond.

Disulfide bonds are relatively strong and are not broken by high temperatures or pH changes

129
Q

Explain what happens when these bonds form between amino acids on the same polypeptide chain

A

They’ll be involved in tertiary structure

130
Q

Explain what happens when these bonds form between amino acids on the same polypeptide chain and different subunits

A

They’ll be involved in quaternary structure

131
Q

Why is the structure of a protein significant

A

The structure of a protein is critical to its function

132
Q

What 2 different protein groups are there based on a proteins structure

A

Globular proteins

fibrous proteins

133
Q

Explain the structure of a globular protein

A

They have an approximately spherical shape

They are surrounded by hydrophilic amino acids

There are hydrophobic amino acids deep in the centre of the protein away from water molecules

134
Q

Explain the key features of globular proteins

A

They are soluble in water - This is due to hydrophilic amino acids surrounding the surface. This means that hydrophilic R groups can interact with water molecules. Therefore, globular proteins are soluble in water

Contains hydrophobic amino acids within the centre of the protein away from water molecules.

135
Q

Describe how the structure of haemoglobin link to its function

A

Each haem group contains a fe2+ ion where the oxygen binds. Thus one haemoglobin molecule can bind to four oxygen molecules. This supports the function of haemoglobin in the RBC as it role is to bind reversibly to oxygen in the lungs to release oxygen in the body tissue.

Furthermore, as oxygen attaches to the haemoglobin, the quaternary structure of the protein changes slightly. This makes it easier for more oxygen to attach. Thus more oxygen traveling across the body to muscle tissue

136
Q

Explain the structure of haemoglobin

A

Haemoglobin is a polypeptide with four polypeptide subunits.

Two are called the alpha submit and the other two are called the beta subunit .

Each subunit contains a prosthetic group haem. Therefore, haemoglobin is a conjugated protein.

Each haem group contains a fe2+ ion where the oxygen binds.

137
Q

Explain the structure of insulin

A

Insulin consist of two polypetide chains. The chains are linked by a disulfide bonds.

138
Q

Describe how the structure of insulin link to its function

A

The hormones like insulin carry out their function by binding to specific receptor molecules. These receptor are proteins found on the cell membrane of target cells

The shape of the insulin molecule mean that it fits perfectly within its receptor even slight changes to the shape of the molecule could prevent it from binding effectively .

The shape of protein hormones such as insulin are critical for how they bind to receptor and carry out their effects.

Insulin can support blood glucose concentration

139
Q

Explain the structure of lysozyme

A

Lysozyme consist of a single polypeptide chain. The chain folds to form a groove along the surface. This groove is called the active site. The shape of active site fits perfectly to substrate molecule in the bacterial cell wall.

140
Q

Describe how the structure of lysozyme link to its function

A

Found in Saliva and tears

Enzymes (lysozyme) can only react with a specific substrate molecule. This specificity is due to the structure of the enzyme.

Lysozyme consist of a single polypeptide chain. The chain folds to form a groove along the surface (active site). The shape of active site fits perfectly to substrate molecule in the bacterial cell wall.

As a result the lysozyme and the active site work together to catalyse the breakdown of a molecule in the bacterial cell wall. This helps defend the body against bacteria

Surrounding the substrate are amino acids which work to hold the substrate in place.

Lysozymes contain regions where amino acids catalyse reaction.

141
Q

What role do fibrous protein mainly play

A

They play a structural role e.g bones, tendons or wall of blood vessels

142
Q

Explain the structure of fibrous proteins

A

Forms long, rope like molecules e.g collagen

143
Q

Explain the properties of fibrous proteins

A

Fibrous proteins are insoluble in water

144
Q

Where is collagen found

A

Collagen is found in tendon, which connects muscle to bones and ligaments which connects bones to each other

It is also found in skin

145
Q

Explain the key features in collagen

A

It is a strong molecule due to its structure. The polypeptide chains in collagen wrap tightly together to form a triple helix.

146
Q

Explain the structure of collagen and how it relates to its strength

A

The polypeptide chains in collagen wrap tightly together to form a triple helix.

In collagen polypeptides every third amino acid is glycine. The R group of glycerin is a hydrogen atom. Thus glycine has the smallest R group of any amino acid.

This allows collagen polypeptides to wrap tightly around each other

As it wraps around each other a large number of hydrogen bonds form between the polypeptide chains. This helps to stabilise the quaternary structure of the proteins. They are also joined to each other by strong crosslinks.

A large number of these triple helical molecules join together to form large structures called microfibrils and fibrils. The molecules are staggered thus have no weak spots

Cross linking between different triple helical molecules further strengthens collagen

147
Q

Where is keratin found

A

It is found in hair, fingernails and the outer surface of skin

148
Q

Explain the key features in keratin

A

Keratin is extremely strong and insoluble in water

149
Q

Explain the structure of keratin and how it relates to its strength

A

keratin consists of long stranded molecules with a high proportion of the amino acid cysteine. This is used to form disulfide bonds which are strong covalent bonds.

Due to the high proportion of cysteine keratin molecules contains a large number of disulfide bonds which contributes to the strength of keratin molecules

150
Q

Where is elastin found

A

The skin and walls of arteries

151
Q

Explain the key features in elastin

A

Elastin fibers stretch when blood passes through the artery and then recoil in between pulses, helping the artery to return to its original shape.

152
Q

Explain the structure of elastin and how it relates to its elasticity

A

Elastin molecules are long strands, containing hydrophobic regions. These strands are cross linked to each other.

The hydrophobic regions on different strands associated causing the elastin molecules to group together. However, when stretched the strands move apart but remain attached at the cross link.

After stretching, the elastin molecules reassociate, springing back together.

This makes elastin a very elastic molecule

Biology A-level (29 decks)

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