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Bio > Chapter 3 - Biological Molecules > Flashcards

Chapter 3 - Biological Molecules Flashcards

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Biology 101 flashcards
1
Q

What determines bonding?

A

Bonding is determined by the number of unpaired electrons present in the outer orbitals of different elements:

  • carbon atoms can form 4 bonds with other atoms.
  • nitrogen atoms= 3 bonds.
  • oxygen atoms= 2 bonds
  • hydrogen atoms = 1 bond
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2
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.

Cation= +ion
Anion= -ion

Electrolytes = ions in a solution

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3
Q

Explain ionic bonding.

A

One atom in the pair donates an electron and the other receives it. This forms positive and negative ions held together by the attraction of opposite charges.

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4
Q

What are the 5 main cations and their roles?

A
  • calcium ions (Ca2+): nerve impulse transmission. Muscle contraction.
  • sodium ions (Na+): nerve impulse transmission. Kidney function.
  • potassium ions (K+): nerve impulse transmission. Stomatal opening.
  • hydrogen ions (H+): catalysis of reactions. pH determination.
  • ammonium ions (NH4+): production of nitrate ions by bacteria.
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5
Q

What are the 5 main anions and their roles?

A
  • nitrate ions (NO3-): nitrogen supply to plants for amino acid and protein formation.
  • hydrogen carbonate ions (HCO3-): maintenance of blood pH.
  • chloride ions (Cl-): balance +charges of sodium and potassium ions in cells.
  • phosphate ions (PO4*3-): cell membrane formation. Nucleic acid & ATP formation. Bone formation.
  • hydroxide ions (OH-): catalysis of reactions. pH determination.
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6
Q

What are the elements present in each of the 4 main biological molecules?

A
  • carbohydrates: carbon, hydrogen, oxygen.
  • Lipids: carbon, hydrogen, oxygen.
  • Proteins: carbon, hydrogen, oxygen, nitrogen, sulfur.
  • Nucleic acids: carbon, hydrogen, oxygen, nitrogen, phosphorus.
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7
Q

What are polymers and monomers?

A

Polymers are long chains made up by the linking of multiple individual molecules (monomers) in a repeating pattern.

Monomers that are sugars= saccharides

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8
Q

What monomers and polymers make up carbohydrates, proteins and nucleic acids?

A

Carbohydrates:

  • monomer = monosaccharides (eg. Glucose)
  • polymer= polysaccharides.

Proteins:

  • monomer= amino acids (eg. Histidine)
  • polymer= polypeptide, protein, enzyme.

Nucleic acids:

  • monomer= nucleotides ( eg. Guanine)
  • polymer= DNA, RNA.
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9
Q

Explain what is meant when a molecule is polar.

A

Covalent bonds occur when atoms share electrons, however, electrons are not always shared equally, so they spend more time closer to one of the atoms.
The atoms with the greater share of electrons will be slightly more negative (delta-), and the other slightly more positive (delta+).

Molecules in which this happens = polar
(They have regions of positivity and negativity)

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10
Q

Explain the bonding in water molecules.

A

Water is a polar molecule: oxygen= delta- Hydrogen= delta+

Hydrogen bonds are relatively weak interactions, which break and reform between the constantly moving water molecules.
Although they are weak, hydrogen bonds occur in high numbers. Hydrogen bonds are what gives water its unique characteristics.

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11
Q

What are the characteristics of water?

A
  • high boiling point (100*C)
  • liquid at room temperature (due to hydrogen bonds)
  • high specific heat capacity.
  • liquid water is less dense than ice.
  • cohesive ( moves as one mass because molecules are attracted to each other).
  • adhesive ( attracted to other molecules)
  • high surface tension (molecules are more cohesive to each other than to the air).
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12
Q

What are the metabolic functions of water?

A
  • reactant in photosynthesis.
  • hydrolysis in digestion.
  • medium for biochemical reactions.
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13
Q

Explain water as a solvent.

A
  • Because water is polar, it acts as a solvent in which many of the solutes in an organism can be dissolved.
  • The cytosol of prokaryotes/ eukaryotes is mainly water.
  • water acts as a medium for chemical reactions and also helps transport dissolved compounds into and out of cells.
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14
Q

Water as a transport medium.

A
  • cohesion between water molecules means the molecules will stick together when transported through the body.
  • adhesion occurs between water molecules and other polar molecules.
    Therefore water exhibits capillary action.
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15
Q

What is meant by capillary action?

A

It is the process by which water can rise up a narrow tube against the force of gravity.

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16
Q

Water as a coolant.

A

Acts as a coolant- helps buffer temperature changes during a chemical reaction in cells as a large amount of energy is needed to overcome the hydrogen bonds.
-maintaining constant temperatures in cellular environments is important due to enzyme activity.

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17
Q

Water as a habitat.

A

-provides a constant environment as it doesn’t change temperature or become a gas easily.
- ice floats on the surface of ponds and lakes, forming an insulating layer.
Aquatic organisms wouldn’t be able to survive freezing temperatures.
- some organisms inhibit the surface of the water, surface tension is strong enough to support small insects such as pond skaters.

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18
Q

What are carbohydrates?

A
  • molecules that only contain carbon, hydrogen and oxygen.
  • general formula = Cn(H2O)n
  • also known as saccharides.
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19
Q

What are mono, di and poly saccharides (with examples)?

A
  • Monosaccharides= single sugar unit. Eg. Glucose, fructose, ribose.
  • Disaccharides = 2 monosaccharides linked together. Eg. Lactose, sucrose.
  • Polysaccharides= more than 2 monosaccharides linked together. Eg. Glycogen, cellulose, starch.
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20
Q

Glucose.

A

Chemical formula = C6H12O6
- composed of six carbons = hexose monosaccharide.

Two structural variations:

  • alpha glucose (OH down)
  • beta glucose (OH up)
  • glucose molecules are polar and soluble in water, due to hydrogen bonds that form between the hydroxyl group and water molecules.
    Solubility in water is important as it means glucose is dissolved un the cytosol of cells.
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21
Q

Explain the condensation reaction of two alpha glucose molecules.

A

When two alpha glucose molecules are side by side, two hydroxyl groups react. -Bonds are broken and are reformed in different places.

  • two hydrogen atoms and an oxygen atom are removed from the glucose monomers and join to form a water molecule (hence condensation).
  • a bond forms between carbons 1 and 4 on the glucose molecules = 1,4 glycosidic bond.
  • maltose is formed (disaccharide)
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22
Q

What makes up sucrose and lactose?

A

Fructose + glucose = sucrose (sugar)

Galactose + glucose = lactose (milk)

Fructose and galactose = hexose monosaccharides.

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23
Q

What are the two main pentose monosaccharides?

A
  1. Ribose (the sugar present in RNA nucleotides)

2. Deoxyribose ( the sugar present in DNA nucleotides)

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24
Q

Amylose.

A
  • one of the polysaccharides in starch.
  • formed by alpha glucose molecules joined together by only 1,4 glycosidic bonds.
  • this long chain of glucose forms a helix which is stabilised by hydrogen bonding. This makes the polysaccharide more compact and less soluble than the glucose molecules used to make it.
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25
Q

Amylopectin.

A
  • another type of starch polysaccharide.
  • formed when glycosidic bonds form in condensation reactions between carbon 1 and 6 on two glucose molecules.
  • contains both 1,4 and 1,6 glycosidic bonds.
  • therefore has a branched structure:
    the 1,6 branching point occur approximately once every 25 glucose subunits.
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26
Q

Glycogen.

A
  • is the energy store molecule in animals and fungi.
  • more branched than amylopectin so it is more compact and less space is needed for it to be stored.
  • the branching means that there are many free ends where glucose molecules can be added/removed which speeds up the process of releasing/storing glucose molecules.
27
Q

How are glucose stores released?

A

Glucose is stored as starch by plants and glycogen by animals and fungi until it is needed for respiration.
To release glucose a hydrolysis reaction takes place. It requires the additional of water and bonds are broken.
The reaction is catalysed by enzymes.

28
Q

Cellulose.

A
  • beta glucose molecules are unable to join together in the same way as alpha glucose molecules.
  • due to this every second beta glucose monomer is flipped upside down.
  • this forms 1,4 glycosidic bonds.
  • when a polysaccharide is formed in this way it is unable to coil or form branches.

Instead cellulose is formed which is a straight chain molecule. (Unbranched)

29
Q

Explain the formation of cellulose fibres.

A
  • cellulose molecules make hydrogen bonds with eachother forming microfibrils.
  • these microfibrils join together forming macro-fibrils which then combine to form fibres
  • these fibres are strong and insoluble and are used to make cell walls.
  • cellulose is an important part of our diet as fibres are hard to break down and are necessary for a healthy digestive system
30
Q

What is meant by reducing sugars?

A

All monosaccharides and some disaccharides are reducing sugars. This means that they can donate electrons to (or reduce) another molecule/chemical.

31
Q

Benedict’s test for reducing sugars.

A
  1. Place sample in a boiling tube in liquid form.
  2. Add an equal volume of Benedict’s reagent.
  3. Heat the mixture gently in a water bath for 5mins.
  • reducing sugars react with copper ions in Benedict’s reagent. Results in the addition of electrons to the blue Cu2+ ions, reducing them to brick red Cu+ ions.
  • brick red precipitate represents positive result.
  • the more reducing sugar present, the more precipitate formed so colour depends on conc of reducing sugars present = qualitative test.
32
Q

Benedict’s test for non-reducing sugars.

A

Non-reducing sugars don’t react with Benedict’s so solution stays blue.
Sucrose is the most common non reducing sugar.

  1. Boil with dilute HCL.
    (will get hydrolysed by the acid to form 2 monosaccharides.)
  2. Do Benedict’s test. Will give a positive result.
33
Q

Test for starch.

A

Iodine test:

  1. A few drops of iodine dissolved in potassium iodide solution are mixed with the sample.
  2. Yellow/brown to purple/black indicates presence of starch.
34
Q

What is the use if reagent strips?

A

Can be used to test for reducing sugars, most commonly glucose.

advantage: with the use of a colour coded chart, concentration of the sugar can be determined.

35
Q

What are the 2 quantitative methods to find concentration?

A
  1. Colorimetry

2. Biosensors

36
Q

Explain colorimetry.

A

Allows you to estimate glucose present in a solution.
It quantitatively measures the absorbance/transmission of light by a coloured solution.
More concentrated solution= higher absorbance & less transmission.

  1. Place filter in colorimeter.
  2. Calibrate using distilled water.
  3. Benedict’s test done on a range if conc.
  4. Solutions filtered to remove precipitate.
  5. % transmission of solution measured.
  6. Calibration curve plotted then used to calculate concentration in unknown sample.
37
Q

Explain biosensors.

A

They use biological components to find the presence and concentrations of molecules.
Analyte= compound under investigation.j

  1. Molecular recognition= a protein/ single DNA strand is immobilised to a surface which will interact/ bind to the specific molecule under investigation.
  2. Transduction = transducer detects changes (eg. pH) and produces a response (such as a dye or electric current being released).
  3. Display= produces visible (quantitative or qualitative) signal.
38
Q

What are lipids?

A

Made up of carbon, hydrogen and oxygen.

  • non polar molecules as electrons on the outer orbitals are evenly distributed. Therefore lipids are not soluble in water.
  • fats = solid at room temp. Oils= liquid at room temp.

Lipids are large molecules known as macromolecules. They are not built from repeating units or monomers.

39
Q

Triglycerides.

A

A triglyceride is made by combining one glycerol molecule with three fatty acids.
- glycerol = alcohol
- fatty acids = carboxylic acids (-COOH)
Esterification:
Hydroxyl groups from both elements interact to form 3 water molecules (condensation reaction).
Ester bonds are formed.

To break down triglycerides 3 water molecules are needed to reverse the reaction= hydrolysis.

40
Q

What are the differences between saturated and unsaturated fatty acids?

A

Saturated:

  • no double bonds
  • can pack closely together.
Unsaturated:
-double bonds present;
      > 1= monounsaturated 
      > 2+ = polyunsaturated
- double bonds cause the chain to bend so they can’t pack together.
-liquids at room temp.(oils)
41
Q

Phospholipids.

A

Modified triglycerides- one fatty acid chain is replaced with a phosphate group.
Contain CHO and phosphorus.

  • phosphate ions are negatively charged so are soluble.
  • have a hydrophilic head (polar) and a hydrophobic tail (non-polar).
  • called surfactants: form layer on the surface of water with phosphate head in water and fatty acid tail sticking out.
  • play a key role in forming cell membranes due to their bilayer arrangement.
42
Q

Sterols.

A

Also known as steroid alcohols.
Type of lipid found in cells- neither fats or oil.
-complex alcohol molecules based on 4 carbon ring structure with OH group at one end.
Hydroxyl group= hydrophilic (polar)
Rest of molecule= hydrophobic (non-polar)

43
Q

Cholesterol

A

Is a sterol.
Has a role in the formation of cell membranes.
-made in the liver and intestines.
- stabilises cell membranes and regulates fluidity by keeping membranes fluid at low temps and stopping them becoming too fluid at high temperatures.

Vit D, steroid hormones and bile manufactured using cholesterol.

44
Q

What are the roles of lipids?

A
  • membrane formation + creation of hydrophobic barriers.
  • hormone production.
  • electrical insulation (necessary for impulse transmission)
  • waterproofing (eg. Birds feathers)

Stored under the skin + around vital organs so also provide:

  • thermal insulation to stop heat loss.
  • cushioning to protect organs.
  • buoyancy for aquatic organisms.
45
Q

How are lipids identified?

A

Emulsion test:

  1. Mix the sample with ethanol.
  2. Mix solution with water + shake.
  3. If white emulsion forms as a layer on top= lipid present.
46
Q

Proteins

A

Peptides are polymers made up of amino acid molecules.
Proteins consist of one or more polypeptides arranged as complex macromolecules with specific biological functions.

Contain carbon, hydrogen, oxygen, nitrogen.

47
Q

Amino acids

A

All amino acids have the same basic structure- a carboxyl group (-COOH) and an amino group (-NH2) attached to a carbon atom.
The difference between different amino acids is the R-group (variable group).

48
Q

Explain the formation of peptide bonds.

A

Amino acids join when the hydroxyl in the carboxylic acid group of one amino acid reacts with a hydrogen in the amine group of another.
A peptide bond is formed between the amino acids and water is produced = condensation reaction.
Resulting compound = dipeptide.

49
Q

What is the importance of the R-group?

A
  • gives amino acids the ability to interact (form bonds) with other amino acids in specific ways.
  • results in complex structures as proteins fold in different ways.
50
Q

What are the first 2 levels of protein structure?

A
  1. Primary structure:
    - the sequence in which amino acids are joined.
    - directed by info carried within DNA.
    - the amino acids in the sequence will influence how it folds which therefore determines its function.
    - peptide bonds (only bond involved at thus stage)
  2. Secondary structure:
    - the O H and N atoms of the amino acids interact.
    - hydrogen bonds may form causing the chain to either coil into an alpha helix or fold into a beta pleated sheet.
51
Q

What is the third level of protein structure?

A
  1. Tertiary structure:
    -the folding of a protein into its final shape, often includes the secondary structure.
    -folding/coiling brings R-groups close enough to interact so further folding occurs.
    -following interactions happen:
    > hydrophilic/ hydrophobic interactions (weak interactions between polar + non-polar R-groups)
    > hydrogen bonds (weakest bonds formed)
    > ionic bonds ( form between oppositely charged R-groups)
    > disulfide bonds ( covalent and form between R-groups containing sulfur atoms)
52
Q

What is the final level of protein structure?

A
  1. Quaternary structure:
    - results from the association of 2 or more individual proteins (subunits).
    - the interactions between subunits are the same as in the tertiary structure except that they are between different protein molecules rather than within one molecule.
53
Q

How does the breakdown of peptides take place?

A

Hydrolysis reaction- reforms the amine and carboxylic acid groups.
Proteases catalyse the reverse reaction.

54
Q

How are proteins identified?

A

Biuret test:

  1. Mix liquid sample with equal volume of 10% NaOH.
  2. Add drops of 1% copper sulfate until it turns blue.
  3. Leave to stand for 5 mins.

Peptide bonds form violet coloured complexes with copper ions in alkaline solutions.
Biuret reagent= mixture of alkali + copper sulfate

55
Q

What are globular proteins?

A
  • compact
  • water soluble
  • roughly spherical in shape.

Formed when proteins fold into their tertiary structures in such a way that the hydrophobic R-groups on the amino acids are kept away from the aqueous environment.
Solubility is important because they regulate many necessary processes such as chemical reactions, immunity, muscle contraction.

56
Q

Insulin

A
  • globular protein
  • hormone that regulates blood glucose concentration.
  • transported in blood so has to be soluble.
  • have precise shapes as they need to fit into specific receptors on cell surface membranes.
57
Q

What are conjugated proteins?

A
  • globular proteins that contain a prosthetic group (non-protein component).
  • Haem groups are examples of prosthetic groups, they contain an iron ion (Fe2+).
58
Q

Haemoglobin

A

Conjugated protein.

  • quaternary protein made from 4 peptides: two alpha +two beta.
  • each subunit has a prosthetic haem group.
  • the iron ions present in haem groups can combine reversibly with an oxygen molecule = allows transportation.
59
Q

Catalase

A
  • an enzyme.
  • quaternary protein with 4 prosthetic haem groups.
  • iron ions allow it to interact with hydrogen peroxide and speed up its breakdown.
  • hydrogen peroxide= byproduct of metabolism which damages cells if allowed to accumulate however catalase stops this.
60
Q

What are fibrous proteins?

A
  • formed from long insoluble molecules.
  • insoluble due to the presence of a high proportion of amino acids with hydrophobic R-groups in their primary structures.
  • amino acid sequence is usually quite repetitive so leads to very organised structures.
  • make strong, long molecules which are not folded into complex 3D shapes like globular proteins.
61
Q

Keratin

A
  • present in hair, skin, nails.
  • large proportion of cysteine so results in many strong disulfide bonds.
  • strong, inflexible and insoluble.
  • degree of disulfide bonds determines flexibility
  • unpleasant smell when burnt is due to the large quantities of sulfur present.
62
Q

Elastin

A
  • fibrous protein found in elastic fibres which are present in the walls of blood vessels and alveoli in lungs; give these structures the flexibility to expand and return to normal size.
  • quaternary protein. Made by linking many soluble molecules called tropoelastin. This makes a large, insoluble, stable and cross-linked structure.
63
Q

Collagen

A
  • connective tissue found in skin, tendons, ligaments and the nervous system.
  • made up of 3 polypeptides wound in a long and strong rope like structure.
  • has flexibility.
64
Q

What are essential and non- essential amino acids?

A

20 different amino acids are commonly found in cells.

  • 5 of these are considered non-essential as the body is able to make them from other amino acids.
  • 9 are essential and can only be obtained from what we eat.
  • a further 6 are considered conditionally essential as they are only needed by infants and growing children.

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