Biological Molecules

Front 1

What are the 4 main biologic molecules?

What elements do each of them contain?

Back 1

- Carbohydrates...C,H,O

- Lipids...C,H,O

- Proteins...C,H,O,N,S

- Nucleic acids...C,H,O,N,P

Front 2

Carbohydrates and proteins are known as polymers. What is a polymer? What are the basic monomer units for each of these polymers?

Back 2

Polymer is a long chain molecule made by the linking of multiple individual monomers in a repeating pattern.

Carbohydrates/polysaccharides have monomers called sugars/saccharides.

Proteins have monomers called amino acids.

Front 3

What is it about water that gives it anomalous properties?

Back 3

Ability to form hydrogen bonds between water molecules.

Front 4

What are water's main anomalous properties caused by hydrogen bonding?

Back 4

- High melting/boiling point

- Expansion on freezing

- Cohesive and adhesive properties

- Surface tension

Front 5

Explain the importance of water's solvent properties to biology.

Back 5

The cytosol of cells is mostly water. Many solutes are also polar and so interact with water molecules and dissolve. Water acts as a medium for chemical reactions and helps transport dissolved compounds into, around, and out of cells.

Front 6

Explain how water's cohesive and adhesive properties help make it an efficient transport medium.

Back 6

Cohesion means that as water moves through the body, water molecules will stick together. Adhesion means that water will stick to polar surfaces. These means that water exhibits capillary action (water moves up a narrow vessel against the force of gravity). This is demonstrated well in the xylem of plants.

Front 7

How does water act as a coolant?

Back 7

Water has a high SHC which means lots of energy is needed to heat it up. This helps to buffer temperature changes caused by chemical reactions. Maintaining a constant temperature in cells is vital as enzymes are often only active in a narrow temperature range.

Front 8

Water has a high SHC and expands on freezing. Why is this important to aquatic organisms?

Back 8

Water's high SHC means that the temperature remains fairly stable, providing a constant environment. As water expands on freezing, ice is less dense and therefore, floats. This means that ice forms from the top-down, not bottom-up. The ice provides an insulating layer over the water below, preventing the body of water from freezing solid.

Front 9

What is the general formula for carbohydrates?

Back 9

Cx(H2O)x

e.g. C6H12O6

Front 10

Give an example of a hexose and a pentose monosaccharide.

Back 10

Hexose...glucose

Pentose...ribose

Front 11

What is the difference between alpha and beta glucose?

Back 11

Alpha... The -OH group on C1 is on the opposite side of the pyranose ring as C6.

Beta... The -OH group on C1 is on the same side of the pyranose ring as C6

Front 12

What are the two main functions of carbohydrates?

Back 12

- Provide energy

- May be structural

Front 13

Relate glucose's structure to its function.

Back 13

- Small, polar molecule...dissolves in water and can travel through cell surface membranes.

- Lots of bonds...broken by hydrolysis to release lots of energy per molecule.

- Structure enables polymerization by condensation reactions to form larger storage molecules.

Front 14

Maltose, sucrose, and lactose all are disaccharides. What two monosaccharides do they contain?

Back 14

Glucose + Glucose --> Maltose

Glucose + Fructose --> Sucrose

Glucose + Galactose --> Lactose

Front 15

Monosaccharides are formed in a condensation reaction. Why is it called a condensation reaction and what type of bond is formed between the two monosaccharides?

Back 15

Condensation reaction as a water molecule is produced. A glycosidic bond forms between the molecules.

Front 16

What two polysaccharides is starch made of?

Back 16

Amylose and amylopectin.

Front 17

Describe the structures of amylose and amylopectin.

Back 17

Amylose...

alpha glucose

1,4 glycosidic bonds

the angle of bond makes a helical shape, further stabilised by H-bonds

compact and insoluble

Amylopectin...

alpha glucose

1,4 and 1,6 glycosidic bonds

1,6 bonds create branches every 25 subunits

Front 18

Where does starch comes from and why is it made?

Back 18

Starch is an energy storage molecule made by plants.

Front 19

Glycogen is used as an energy storage molecule in what type of organism?

Back 19

Animals and fungi

Front 20

Glycogen and amylopectin are similar, but what is the main structural difference?

Back 20

Glycogen is more branched than amylopectin, meaning it's more compact and can be stored more efficiently.

Front 21

Why are the many branches of glycogen important?

Back 21

Many branch ends create many points for metabolism of the molecule. Breaking up or building of glycogen is quick.

Front 22

What 2 things about cellulose make it unique compared to the other carbohydrates studied?

Back 22

Cellulose has a structural use.

Cellulose is made of beta glucose.

Front 23

Why, in cellulose, and beta glucose molecules alternate molecules the other way up? This arrangement results in cellulose being what shape?

Back 23

The hydroxy groups on C1 and C4 would otherwise be too far away to react and form a glycosidic bond. Cellulose ends up being a straight chain polysaccharide.

Front 24

Parallel chains of cellulose form microfibrils, macrofibrils, and then fibres. What type of bond joins the chains?

Back 24

Hydrogen bonds

Front 25

What test would you use to semi-qualitatively test for reducing sugars? How would you alter this test to test for non-reducing sugars?

Back 25

Benedict's test (alkaline solution of Copper II sulphate)

1. Sample to be tested in boiling tube

2. Add equal volume of Benedict's solution

3. Heat mixture in a water bath for 5 minutes.

4. R sugars will react with Cu2+ forming a brick red precipitate. The amount of precipitate suspended in blue solution alters the colour and generally indicated how R sugar was in solution.

NR sugars will not react with Benedict's so solution will remain. The most common NR sugar is sucrose (disaccharide). Sample is then heated with HCl to hydrolyze into reducing monosaccharides. Steps 1-4 repeated.

Front 26

Colorimetry is used to quantitatively test for reducing sugars. Outline the colorimetry process.

Back 26

1. Filter placed in colorimeter

2. Colorimeter calibrated with distilled water.

3. Benedict's test performed on a range of known concentrations of glucose.

4. Resulting solutions filtered to remove the precipitate.

5. Filtrate placed in the colorimeter.

6. % transmission or absorption is measured using colorimeter

7. This information is plotted on a graph and calibration curve is plotted.

8. Steps 3-6 performed using unknown concentration of glucose.

9. % transmission or absorption and the graph are used to estimate the concentration of glucose in solution.

Front 27

What are the building blocks of lipids?

Back 27

Glycerol and fatty acids

Front 28

What are the general functions of lipids?

Back 28

- Energy storage

- Cell surface membranes

- Waterproof surfaces

- Metabolic water source

- Electrical insulation

- Hormones

Front 29

There are 3 main types of lipids to know about...

Back 29

- Triglycerides

- Phospholipids

- Others (steroids, hormones, cholesterol, waxes)

Front 30

Describe the basic structure of a fatty acid and how being saturated or unsaturated affects its state at room temperature.

Back 30

Hydrocarbon chains with a carboxyl group at one end. Can be saturated or unsaturated. Double bonds create bends in the chain which create a fluid property. Most unsaturated fats are therefore oils at room temperature

Front 31

How would you test for lipids?

Back 31

1. Sample mixed with ethanol

2. Solution mixed with distilled water

3. White precipitate indicates presence of lipids

Front 32

What is the word equation for the formation of a triglyceride?

Back 32

Glycerol + 3 fatty acids --> triglyceride + 3H2O

Front 33

What type of bond is formed in a triglyceride between the glycerol and the fatty acids?

Back 33

Ester bond

Front 34

What are the general functions of triglycerides?

Back 34

- Energy source

- Metabolic water source

- Buoyancy aid

- Heat insulation

- Protecting vital organs

- Waterproofing

Front 35

How would you turn a triglyceride into a phospholipid?

Back 35

Replace a fatty acid with a phosphate group

Front 36

Phospholipids are amphipathic. Explain this.

Back 36

Hydrophilic and charged head, hydrophobic tail.

Front 37

Explain how phospholipids interact with water and relate this to function in cells.

HINT: bilayer, micelles.

Back 37

Bilayer...2 adjacent layers of phospholipid tails face inwards away from the aqueous environment with the hydrophilic tail towards it. This is the foundation for cell surface membranes.

Micelles...phospholipids arrange themselves in a spherical form in aqueous solution, with one layer of phospholipids (heads outwards, tails inwards).

Front 38

Sterols are steroid alcohols. How many carbon rings are there? Give an example.

Back 38

4

Cholesterol

Front 39

What do proteins consist of?

Back 39

One or more polypeptide chains made of amino acids.

Front 40

Amino acids all have the same general structure what is this structure?

Back 40

Front 41

When synthesizing polypeptides, amino acids are joined in a condensation reaction. Which groups/atoms are involved in this reaction? Which enzyme catalyses the reaction?

Back 41

The -OH of the carboxyl group of one AA reacts with an H from the amine group of the adjacent AA forming and H2O molecule. The C of one AA joins to the N of the other. Peptide bond forms.

Catalysed by peptidyl transferase.

Front 42

How many amino acids are there?

Back 42

20

Front 43

The primary structure of proteins refers to what?

Back 43

The sequence of amino acids in the polypeptide chain.

Front 44

In the secondary structure of proteins, the O, H, N of the basic AA structure interact. Hydrogen bonds may form to create one of a possible 2 structures. What are these structures?

Back 44

Alpha helix

Beta pleated sheet

Front 45

What 4 types of bond may be involved in determining the tertiary structure of proteins?

Back 45

- Ionic bond

- Hydrogen bond

- Hydrophilic/hydrophobic interactions

- Disulphide bridges

Front 46

Haemoglobin is an example of a quaternary protein. What is a quaternary protein?

Back 46

A protein made by more than one polypeptide chain. Each chain becomes known as a subunit.

Front 47

Globular proteins are often soluble in water.

Give an example of a globular protein that must be soluble given its function.

Back 47

Insulin is a hormone that is carried in the blood stream. It must be soluble in the blood in order to be transported.

Front 48

Conjugated proteins contain a prosthetic group. What is a prosthetic group?

Back 48

A non-protein component. e.g. a metal ion

4 Fe2+ ions per haemoglobin molecule.

These are called cofactors when they're essential in the functioning of a protein.

Front 49

Give some of the basic features of fibrous proteins.

Back 49

- long, strong

- not folded into complex shapes

- high proportion of hydrophobic R-groups

- primary structure is quite repetitive

Front 50

Fibrous protein example:

Describe the structure/function of elastin.

Back 50

- Present in blood vessel walls and alveoli

- Gives flexibility

- Returns to original size and shape

- Quaternary protein made from many cross-linked tropoelastin molecules

- Alternate hydrophobin lysine-rich areas

- Cross-linking covalent bonds between lysine stabilise the structure

Front 51

Fibrous protein example:

Describe the structure/function of elastin.

Back 51

- 3 peptide chains in a triple helix

- tough, rope-like structure

- every 3rd amino acid is glycine, a small amino acid which allows the chains to be very compact

- hydrogen bonds between chains

- long quaternary proteins with staggered ends which join end to end forming fibrils called tropocollagen.

- in the skin, collagen fibres form a mesh that's tear resistant

Front 52

How many types of RNA are there?

Back 52

2...DNA and RNA

Front 53

What is a nucleic acid?

Back 53

Long chain polymers formed from many nucleotides

Front 54

What are the 3 main components of a nucleotide?

Back 54

- pentose monosaccharide

- phosphate group

- nitrogenous base

Front 55

How are nucleotides joined?

Back 55

Phosphate group on C5 of one nucleotide forms a covlent bond with the hydroxyl group on C3 of the pentose monosaccharide on the adjacent nucleotide.

Front 56

What type of bond forms between nucleotides?

Back 56

Phosphodiester bonds. This forms a long, strong sugar-phosphate backbone with a base attached to each sugar.

Front 57

DNA is an initialism of what?

Back 57

Deoxyribonucelic acid

Front 58

In RNA the pentose sugar is ribose. In DNA, the pentose sugar is deoxyribose. What is the difference between ribose and deoxyribose?

Back 58

Deoxyribose has one fewer oxygen atoms than ribose.

Front 59

Nucleotides in both DNA and RNA have 4 possible bases. What are they?

Back 59

DNA...ATCG

RNA...AUCG

Front 60

What is the difference between pyramidine and purine bases?

Back 60

Pyramidines are smaller bases with only one carbon ring. Includes thymine (T) and cytosine (C).

Purines are larger with 2 carbon rings - adenine (A) and guanine (G).

Front 61

What shape is given to a molecule of DNA?

Back 61

Double helix

Front 62

The two strands of DNA are arranged so that they run in opposite directions. What phrase is given to this?

Back 62

Antiparallel

Front 63

How many hydrogen bonds form between adenine and thymine, and cytosine and guanine?

Back 63

A&T...2

C&G...3

Front 64

A gene refers to what?

Back 64

A section of DNA that codes for a specific protein

Front 65

Why is mRNA used in the coding for proteins?

Back 65

The DNA itself is too big to leave through a nuclear pore.

Front 66

What happens to RNA molecules after protein synthesis?

Back 66

They are degraded in the cytoplasm

Front 67

Outline the procedure for extracting DNA from plant material.

Back 67

1. Grind sample to break cell walls

2. Mix sample with detergent to break cell membrane

3. Add salt to break hydrogen bonds between DNA and water molecules

4. Add a layer of ethanol on top

5. Alcohol causes DNA to precipitate out of the solution seen as white strands.

Front 68

When a cell prepares to divide, DNA replicates. How is DNA said to replicate?

Back 68

Semiconservatively

Front 69

DNA replication is controlled by enzymes. Which two enzymes are involved?

Back 69

DNA helicase unwinds and unzips the two stands of DNA by travelling along the back bone and catalysing reactions that break the hydrogen bonds between bases.

DNA polymerase catalyses the formation of phosphodiester bonds between the nucleotides that have paired with the newly exposed bases.

Front 70

Errors made in the genetic code are known as what?

Back 70

Mutations

Front 71

What is a codon?

Back 71

A sequence of 3 bases that code for an amino acid

Front 72

There are 64 possible codons but only 20 amino acids. Some amino acids can be coded for by more than one codon, and some codon do not code for an amino acid. What do they do?

Back 72

Act as a 'start' or 'stop' codon at the beginning or end of a gene. There are 3 stop codons and one start codon. If it's in the middle of a gene, it codes for methionine.

Front 73

How do 'start' codons ensure the genetic code is read 'in-frame'?

Back 73

Start codons ensure the genetic code is read from base 1, not base 2 or 3 so the genetic code is non-overlapping

Front 74

The code for amino acids is known as degenerate. Why?

Back 74

More than one codon is able to code for a amino acid

Front 75

Transcription of DNA refers to what?

Back 75

The reading of the genetic code, resulting in the production of an mRNA molecule

Front 76

What is the sense strand and in which direction does it run?

Back 76

The strand of DNA that contains the code for the protein that is to be made. It runs 5'-3'.

Front 77

The anti-sense strand has another name. What is it? Why?

Back 77

The template strand. This is because this is strand on which the mRNA molecule is built. Complementary base pairing results in the mRNA molecule having the same code as the sense strand.

Front 78

Ribosomal RNA is abbrevatied to what?

Back 78

rRNA. It is important in maintaining the stability of the protein synthesis sequence.

Front 79

Ribosomes do what to mRNA?

Back 79

The translate them into a protein

Front 80

Which molecule of RNA is folded in such a way that 3 bases, the anticodon, are at one end of the molecule? What does the anticodon do in translation?

Back 80

Transfer RNA (tRNA). Molecules for RNA that carry amino acids to the ribosomes.

Anticodons bind to the complementary codons along the mRNA.

Front 81

ATPis the universal currency for energy. What 3 main activities do cells need ATP for?

Back 81

- Synthesis

- Transport

- Movement

Front 82

What does ATP stand for?

Back 82

Adenosine triphosphate

Front 83

What is the basic structure of an ATP molecule?

Back 83

Adenine base joined to a ribose sugar, followed by 3 phosphate groups

Front 84

How is ATP used to release energy?

Back 84

Last phosphate group is broken off ATP (requiring a small amount of energy), but the liberated phosphate group releases large amount of energy when involved in subsequent chemical reactions.

Front 85

Why is ATP a poor long term store of energy?

Back 85

Bonds between phosphate groups are unstable.

Front 86

How is ATP made?

Back 86

During respiration, a free phosphate group is reattached to ADP. This is phosphorylation. This is another example of a condensation reaction.

Front 87

Relate ATP's structure to it's function.

Back 87

- Small...moves into, out of, and around cells easily

- Water soluble...energy-requiring processes can occur is aqueous envrinoments

- Contains bonds between phosphates with immediate energy: large enough to be useful but not so large that energy is wasted as heat

- Easily regenerated...can be recharged with energy.