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B3 - Biological Molecules Flashcards

1
Q

How many bonds can Carbon, Nitrogen, Oxygen and Hydrogen form?

A
  • carbon = 4
  • nitrogen = 3
  • oxygen = 2
  • hydrogen = 1
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2
Q

What is the formula for Methane and Ammonia?

A
  • methane = CH4
  • ammonia = NH3
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3
Q

What are calcium ions (Ca^2+) necessary for?

A
  • nerve impulse transmission
  • muscle contraction
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4
Q

What are sodium ions (Na^+) necessary for?

A
  • nerve impulse transmission
  • kidney function
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5
Q

What are potassium ions (K^+) necessary for?

A
  • nerve impulse transmission
  • stomatal opening
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6
Q

What are hydrogen ions (H^+) necessary for?

A
  • catalysis of reactions
  • pH determination
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7
Q

What are ammonium ions (NH4^+) necessary for?

A
  • production of nitrate ions by bacteria
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8
Q

What are nitrate ions (NO3^-) necessary for?

A
  • nitrogen supply to plants for amino acid and protein formation
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9
Q

What are hydrogen carbonate ions (HCO3^-) necessary for?

A
  • maintenance of blood pH
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10
Q

What are chloride ions (Cl^-) necessary for?

A

-balance positive charge of sodium and potassium ions in cells

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11
Q

What are phosphate ions (PO4^3-) necessary for?

A
  • cell membrane formation
  • nucleus acid and ATP formation
  • bone formation
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12
Q

What are hydroxide ions (OH^-) necessary for?

A
  • catalysis of reactions
  • pH determination
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13
Q

What are the 4 biological molecules?

A
  • carbohydrates
  • lipids
  • proteins
  • nucleic acids
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14
Q

What do these 4 biological molecules consist of?

A
  • carbohydrates (C, H, O, Cx(H2O)x)
  • lipids (C, H, O)
  • proteins (C, H, O, N, S)
  • nucleic acids (C, H, O, N, P)
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15
Q

What is a monomer?

A
  • a single molecule that binds to other similar molecules to form a repeating chain molecule
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16
Q

What is a polymer?

A
  • a large molecule built up from a large number of similar units (monomers) bonded together
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17
Q

What are the three important groups of polymers (living organisms)?

A
  • nucleic acids (nucleotides)
  • polysaccharides (monosaccharides)
  • proteins (amino acids)
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18
Q

How many different amino acids are there?

A
  • 20 amino acids
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19
Q

What do nucleic acids consist of?

A
  • phosphate group
  • pentose sugar
  • organic base
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20
Q

What are the five different bases?

A
  • adenine (A)
  • cytosine (C)
  • guanine (G)
  • thymine (T)
  • uracil (U) = in RNA, replaces thymine
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21
Q

Water is a ______ _______

A
  • simple molecule
  • that can form hydrogen bonds
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22
Q

What are hydrogen bonds?

A
  • weak forces of attraction
  • form between water molecules/parts of a larger molecule
  • between oxygen of one molecule and hydrogen of another
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23
Q

Why does hydrogen bonding take place?

A
  • oxygen has a negative dipole (δ-) and hydrogen has a positive dipole (δ+) making water a polar molecule
  • the opposite charges attract the water molecules together
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24
Q

Between 0°C and 100 °C hydrogen bonds ____

A
  • hold water molecules together loosely
  • the molecules are able to move past one another
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25
Q

Water has a boiling point of ____

A
  • 100 °C
  • in order to evaporate hydrogen bonds must be broken (requires a lot of energy)
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26
Q

At 0°C (or less) water molecules form an _____ ______ _______

A
  • open lattice structure (further apart)
  • more hydrogen bonds form and they hold the water molecules in a stationary position
  • this makes ice less dense than water
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27
Q

Properties of water : thermal stability

A
  • water has a high specific heat capacity (lots of energy is required to overcome force of hydrogen bonds)
  • so a body of water maintains a fairly constant temperature
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28
Q

What are the benefits of thermal stability?

A
  • allows aquatic animals to use less energy to control temp.
  • body temp. remains fairly stable as water slowly changes the internal temp.
  • this reduces variations in metabolic rate
  • allows gases to remain soluble in water
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29
Q

Properties of water : Freezing

A
  • ice is less dense than water (open lattice structure)
  • forms an insulating layer on the water (prevents water below from freezing)
  • organisms below the ice do not freeze and nutrients can still circulate
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30
Q

Properties of water : Evaporation

A
  • water has high latent heat of evaporation (lots of energy is needed to go from liquid to gas)
  • efficient mechanism to cool surface of living things (molecules with highest K.E. are lost)
  • e.g. sweating
  • at most temps. water is a liquid (can flow/transport materials)
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31
Q

Properties of water : Cohesion

A
  • the attraction of water molecules to each other
  • produces surface tension (creates habitat on surface for invertebrates, e.g. pond skaters)
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32
Q

Properties of water : Adhesion

A
  • the attraction of water molecules to other polar molecules/surfaces
  • allows water to exhibit capillary action (upward motion against gravity, e.g. moving up glass tube)
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33
Q

What are the benefits of cohesion and adhesion?

A
  • makes water a very efficient transport medium within living things
  • e.g. columns of water pulled up the xylem, helps transport dissolved minerals
  • capillary action - cohesion (interaction between water molecules), adhesion (attraction between water molecules and glass walls of tube)
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34
Q

Properties of water : Transparent

A
  • allows aquatic plants to carry out underwater photosynthesis
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35
Q

Properties of water : High density

A
  • allows water to support organisms and allows for flotation
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36
Q

Properties of water : Solvent

A
  • water (polar) can dissolve a wide range of substances and can transport these substances around the body
  • cytosol is mainly water, many solutes (amino acids, proteins, nucleic acids) are polar molecules
  • it also acts as a medium for chemical reactions
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37
Q

Properties of water : Reactant

A
  • used in a wide range of metabolic reactions
  • hydrolysis, photosynthesis
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38
Q

Properties of water : Incompressibility

A
  • water cannot be compressed into a smaller volume
  • so it can be pressurised and pumped in transport systems
  • it can also be used in hydrostatic skeletons
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39
Q

In water questions include :

A
  • hydrogen bonds
  • cohesion/adhesion (transport)
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40
Q

Where else are hydrogen bonds found?

A
  • in alpha helices and beta pleated sheets (secondary protein structure)
  • protein tertiary structure
  • polypeptide chains (quaternary structures e.g. haemoglobin)
  • chains of cellulose
  • bases in DNA
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41
Q

What elements do carbohydrates contain?

A
  • carbon
  • hydrogen
  • oxygen
  • general formula (CH2O)x
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42
Q

What is a monosaccharide?

A
  • a single unit of sugar
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43
Q

What are examples of monosaccharides?

A
  • glucose
  • fructose
  • galactose
  • ribose
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44
Q

What is a disaccharide?

A
  • a carbohydrate made of 2 monosaccharides
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45
Q

How are disaccharides formed?

A
  • they are joined together by condensation reactions, and held together by (1,4) glycosidic bonds
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46
Q

What are examples of disaccharides?

A
  • sucrose
  • lactose
  • maltose
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47
Q

What is a polysaccharide?

A
  • a chain that is formed of multiple monosaccharide molecules joined together
  • they are large insoluble molecules
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48
Q

What are examples of polysaccharides?

A
  • glycogen
  • starch
  • cellulose
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49
Q

Why are monosaccharides reducing sugars?

A
  • they are able to donate electrons
  • can oxidise carbonyl groups (C=O)
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50
Q

What is the chemical formula of glucose?

51
Q

Examples of reducing sugars:

A
  • glucose
  • fructose
  • galactose
  • (different arrangement of atoms give slightly different properties)
52
Q

Example of non-reducing sugars:

A
  • sucrose
  • cannot donate electrons (not oxidised)
53
Q

What are the two types of glucose?

A
  • α-glucose (alpha)
    • OH group at the bottom
  • β-glucose (beta)
    • OH group at the top
54
Q

What are the functions of glucose?

A
  • used as a respiratory substrate (provides energy for ATP formation)
  • main energy source in plants and animals
  • it is soluble and so can be transported in water and is dissolved in cytosol of cell
55
Q

How is sucrose formed (disaccharide)?

A
  • α-glucose + fructose
56
Q

What reaction breaks down glycosidic bonds?

A
  • hydrolysis
  • reacts with water to break down the glycosidic bonds
57
Q

How is lactose formed (disaccharide)?

A
  • α-glucose/β-glucose + galactose
58
Q

Structure/properties of amylose (starch)

A
  • long unbranched chain of α-glucose molecules
  • joined by 1,4 glycosidic bonds (helix formed by hydrogen bonding)
    • causes OH to hide inside coil (less soluble)
    • prevents amylose from affecting water potential/osmosis
  • used for storage of glucose subunits
  • compact (takes up less space in cell)
59
Q

How is maltose formed (disaccharide)?

A
  • α-glucose + α-glucose
60
Q

What is a pentose monosaccharide?

A
  • a monosaccharide containing 5 carbons
  • e.g. ribose, deoxyribose
61
Q

What is a hexose monosaccharide?

A
  • a monosaccharide containing 6 carbons
  • e.g. glucose
62
Q

Structure/properties of glycogen:

A
  • long chain of α-glucose molecules
  • joined by 1,4 glycosidic bonds and 1,6 glycosidic bonds (branched, every 10 glucose subunits)
  • forms more branches than amylopectin (increases SA, can be hydrolysed easily)
    • insoluble so does not affect water potential of cell
    • compact (better for storage)
    • main storage polysaccharide in animals and fungi
63
Q

Structure/properties of amylopectin (starch)

A
  • long chain of α-glucose molecules
  • joined by 1,4 glycosidic bonds and 1,6 glycosidic bonds (branched, every 25 glucose subunits)
    • enzymes are able to get to the glycosidic bonds easily
    • allows glucose molecules to be released quickly
  • storage of glucose subunits/energy in plant cells
64
Q

Structure/properties of glucose

A
  • α-glucose and β-glucose have a ring structure
  • it has multiple polar hydroxyl (OH) groups which allows it to form hydrogen bonds with water molecules (soluble)
65
Q

Functions of carbohydrates

A
  • source of energy
  • energy store
  • structurally important
66
Q

What is starch used for/composed of?

A
  • main storage polysaccharide in plants
  • amylose
  • amylopectin
67
Q

Structure/properties of cellulose:

A
  • long chain of β-glucose molecules (1,4 glycosidic)
    • can only join if alternate β-glucose molecules are flipped
  • this creates a straight chain molecule (unbranched)
  • cellulose molecules can make hydrogen bonds and form microfibrils
  • microfibrils join together to form macrofibrils (which join to produce fibres)
    • insoluble and strong (suitable to form cell wall)
    • important for diet (‘fibre’/’roughage’ are necessary for healthy digestive system)
68
Q

Testing for non-reducing sugars:

A
  • sample must be hydrolysed first (boiled with dilute HCl) to break down disaccharide into monosaccharides
  • e.g. sucrose –> glucose + fructose
  • then follow Benedict’s test steps
69
Q

Testing for reducing sugars (Benedict’s + Reagent strips):

A
  • Benedict’s reagent (alkaline solution of copper (II) sulfate)
  • place sample in boiling tube
  • add equal volume of Benedict’s reagent
  • heat in water bath (5 mins)
  • reducing sugars react with copper ions (Cu2+ –> Cu+)
  • blue to brick red (qualitative test)
  • manufactured reagent strips can also be used
  • colour-coded chart can be used to determine conc. of sugar
70
Q

Iodine test for starch

A
  • add few drops of iodine (mixed with potassium iodide) to sample
  • colour change from yellow/brown to purple/black shows starch is ‎ present
71
Q

What are lipids?

A
  • they are fats and oils containing C, H, O
  • oils are lipids that are liquids at room temp. and fats are lipids that are solids at room temp.
  • non-polar molecules (electrons more evenly distributed)
  • large complex molecules (macromolecules)
72
Q

What are triglycerides?

A
  • consist of one glycerol (-OH) molecules and three fatty acids (-COOH)
    • hydroxyl groups interact and form water molecules
    • ester bonds are formed (esterification) which is a condensation reaction
  • to break them down, hydrolysis takes place
73
Q

What is a saturated fatty acid chain?

A
  • no double bonds present
  • all carbons form max. bonds with hydrogen
74
Q

What is an unsaturated fatty acid chain?

A
  • contains double bonds
    • one = monounsaturated
    • two = polyunsaturated
  • causes molecule to kink/bend making them harder to pack closely together (liquid at room temp.)
  • plants contain unsaturated triglycerides and are more healthy in the human diet
    • saturated fats can lead to coronary heart disease
75
Q

What are phospholipids?

A
  • (modified triglycerides) they contain phosphorus, carbon, hydrogen and oxygen
    • charged phosphate head (hydrophilic)
    • non-polar tails (hydrophobic)
76
Q

How do phospholipids interact with water?

A
  • form a layer on the surface of water with phosphate heads inside and tails sticking out
    • so they are surfactants
  • they can also form a bilayer which helps to form cell membranes
    • separates the aqueous environment where cells exists and their cytosol
77
Q

What are sterols?

A
  • complex alcohol molecules with hydrophobic/philic characteristics
  • hydroxyl is polar (hydrophilic) and the rest is hydrophobic
78
Q

What is the function of cholesterol?

A
  • manufactured in the liver and intestines
  • helps to form cell membranes (in between phospholipids)
    • adds stability to the membrane and regulates their fluidity
  • vitamin D, steroid hormones and bile are manufactured using cholesterol
79
Q

What are the roles of lipids?

A
  • membrane formation (hydrophobic barriers)
  • hormone production
  • electrical insulation (impulse transmission)
  • waterproofing
    ‎
  • thermal insulation to reduce heat loss
  • cushioning to protect vital organs
  • buoyancy for aquatic animals
80
Q

What is the test for lipids?

A
  • emulsion test
  • sample is mixed with ethanol and then with water
  • white emulsion = lipid is present
81
Q

What is the basic structure of an amino acid?

A
  • amine group (NH2)
  • carboxyl group (COOH)
  • R-group (different in each amino acid)
82
Q

What do amino acids form?

A
  • peptides (polymers)
  • polypeptides/proteins consist of long chains of amino acids
83
Q

What elements do proteins contain?

A
  • C, H, O, N
84
Q

How many amino acids are there?

A
  • 20 different amino acids
  • 5 = non-essential
  • 9 = essential
  • 6 = conditionally essential
85
Q

How is a peptide formed?

A
  • condensation reaction (peptide bond)
  • hydroxyl group of carboxylic acid (from one group) and hydrogen in amine group (of another) react
  • two amino acids form a dipeptide
86
Q

How is a polypeptide formed?

A
  • when many amino acids are joined together by peptide bonds
  • catalysed by peptidyl transferase, which is present in ribosomes
87
Q

How are peptides broken down?

A
  • hydrolysis reaction (water molecule is used to break the peptide bond)
  • proteases are enzymes that catalyse the reverse reaction
88
Q

What are the levels of protein structure?

A
  • primary
  • secondary
  • tertiary
  • quaternary
89
Q

What does the primary structure consist of?

A
  • the sequence of amino acids (influences the final shape of the protein)
  • peptide bonds
90
Q

What does the secondary structure consist of?

A
  • O, H, and N atoms interact
  • hydrogen bonds may form (alpha helix or beta pleated sheet)
91
Q

What does the tertiary structure consist of?

A
  • folding of protein into its final shape
  • brings R-groups together (interaction)
    • hydrophobic/philic
    • hydrogen bonds
    • ionic bonds
    • disulfide bonds (only between R-groups that contain sulfur)
  • produces complex-shaped proteins
92
Q

What does the quaternary structure consist of?

A
  • association of two/more individual proteins (subunits)
  • same as tertiary structure but is between different protein molecules
93
Q

What are the two main types of proteins?

A
  • globular (+ conjugated)
  • fibrous
94
Q

What are globular proteins?

A
  • compact
  • water soluble
  • spherical in shape
  • tertiary structure (hydrophobic R-groups are kept away from aqueous environment)
95
Q

Example of a globular protein

A
  • insulin:
  • hormone involved in regulation of blood glucose conc.
  • needs to be transported in the bloodstream so it is soluble
  • have to fit into specific receptors on cell-surface membranes (precise shapes)
96
Q

What is a conjugated protein?

A
  • globular proteins that contain a prosthetic group
  • without one it is a simple protein
  • lipids/carbohydrates can combine with proteins to form lipoproteins/glycoproteins
97
Q

Example of a conjugated protein

A
  • haemoglobin:
  • red, O2 carrying pigment in RBCs
  • quaternary protein made from 4 polypeptides
    • contains a prosthetic haem group
  • iron II ions can reversibly combine with O2 molecule
    ‎
  • catalase:
  • quaternary protein containing 4 haem groups
  • iron II ions allow for fast breakdown of hydrogen peroxide
    • damaging to cells/cell components
98
Q

What are fibrous proteins?

A
  • formed from long, insoluble molecules
    • high proportion of amino acids with hydrophobic R-groups
  • repetitive sequence leads to organised structures in fibrous proteins
  • fibrous proteins make strong, long molecules (not folded)
99
Q

Examples of fibrous proteins

A
  • keratin:
  • present in hair, skin, and nails
  • large proportion of sulfur-containing amino acid cysteine
    • forms strong disulfide bonds (inflexible, insoluble)
      ‎
  • elastin:
  • found in elastic fibres
  • present in walls of blood vessels/alveoli of the lungs
    • allows for them to stretch and return to original size
  • quaternary protein made from tropoelastin
    ‎
  • collagen:
  • connective tissue found in skin, tendons, ligaments, nervous system
    • formed from 3 polypeptides wound together
  • long and strong rope-like structure
100
Q

What are nucleic acids?

A
  • large molecules discovered in cell nuclei
  • made up of 30% C, 20% O, 20% N, 20% P, 10% H
101
Q

What are the 2 types of nucleic acids?

A
  • DNA (deoxyribonucleic acid)
  • RNA (ribonucleic acid)
102
Q

What is a nucleotide made up of?

A
  • pentose monosaccharide (sugar)
  • phosphate group (inorganic molecule - acidic and -ve charge)
  • nitrogenous base - complex organic molecule
    ‎
  • linked together by condensation reactions to form polynucleotide
  • phosphodiester bonds (covalent) are formed at 5’ and 3’ of an adjacent nucleotide
    • forms a long, strong sugar-phosphate backbone
    • they are broken down by hydrolysis
103
Q

What is DNA (deoxyribonucleic acid)?

A
  • contains one fewer O atom than ribose
  • nucleotides have four different bases:
    • adenine (+ T)
    • thymine (+ A)
    • cytosine (+ G)
    • guanine (+ C)
104
Q

What are pyrimidines?

A
  • smaller bases (single carbon ring structure)
  • thymine and cytosine
105
Q

What are purines?

A
  • larger bases (contain double ring structures)
  • adenine and guanine
106
Q

What is the structure of DNA?

A
  • double helix formed from 2 coiled strands of polynucleotides
  • they are held together by hydrogen bonds between the bases
  • two strands are antiparallel (run in opposite directions)
107
Q

What are the base pairing rules?

A
  • cytosine + guanine = three hydrogen bonds
  • adenine + thymine = two hydrogen bonds
    • (complementary base pairing)
108
Q

What is RNA (ribonucleic acid)?

A
  • plays important role in transferring genetic info from DNA to proteins making up enzymes/tissues
  • penrose sugar is ribose and contains uracil (U) instead of thymine
  • they can form polymers just like DNA (phosphodiester bonds)
109
Q

How does DNA leave the nucleus?

A
  • short section is transcribed into mRNA molecule
  • each individual is smaller than DNA chromosome so they are able to leave the nucleus and travel to ribosomes (site of protein synthesis)
  • after this they are degraded in the cytoplasm and the nucleotides are reused
110
Q

What is DNA replication?

A
  • when cell prepares to divide and two strands of double helix separate
  • each strand becomes a template for a new double-stranded DNA molecule
111
Q

What is semi-conservative replication?

A
  • hydrogen bonds between the complementary bases are broken
  • the free nucleotides pair with the exposed complementary bases and form hydrogen bonds
  • the new nucleotides then form phosphodiester bonds between them
    ‎
  • two new molecules of DNA are produced
  • each one contains a new/old strand of DNA
112
Q

What are the enzymes in replication?

A
  • DNA helicase:
    • carries out unwinding and separating of DNA double helix strands
    • travels along DNA backbone (catalyses reactions that break hydrogen bonds)
  • DNA polymerase:
    • catalyses formation of phosphodiester bonds between the new nucleotides
113
Q

What is a replication error?

A
  • where sequences of bases are not matched correctly
  • mutation = a random/spontaneous change in the sequence of a base
114
Q

What is the genetic code?

A
  • DNA codes for a sequence of amino acids which fold into complex structures
  • triplet code:
    • three bases (codon) code for an amino acid
    • section of DNA that has sequence of bases that code for an entire protein is a gene
    • genetic code is universal
  • degenerate code:
    • different codons can code for the same amino acid
    • there are only 20 amino acids and many more codons (64)
    • ** so some mutations may not have any effect on the organism **
  • non-overlapping:
    • codons do not overlap
    • so once a ribosome has read a codon, it moves onto a new one
115
Q

What is transcription?

A
  • the process of copying sections of DNA to produce smaller molecules of mRNA
  • this allows for them to be transported out of the nucleus via the nuclear pores (to site of protein synthesis)
116
Q

What happens in transcription?

A
  • sense strand (5’ to 3’) contains code for protein synthesis
  • other strand (complementary) runs from 3’ to 5’ and is the antisense strand as it does not code for a protein
    • acts as a template during transcription
    • so the complementary RNA strand has the same base sequence as the sense strand
      ‎
  • free nucleotides pair with the exposed antisense bases
    • uracil binds with adenine
  • RNA polymerase forms phosphodiester bonds between the RNA nucleotides
  • the short strand formed is mRNA
  • it then detaches from the DNA template and leaves the nucleus through a nuclear pore
117
Q

What do eukaryotic ribosomes consist of?

A
  • made of two subunits
  • equal amounts of protein and ribosomal (r)RNA
    • important in maintaining structural stability of protein synthesis sequence
    • plays biochemical role in catalysing reaction
118
Q

What is translation?

A
  • where the mRNA binds to a specific site on the ribosome subunit and is decoded into a sequence of amino acids
119
Q

What is tRNA?

A
  • transfer (t)RNA is necessary for translation of mRNA
  • composed of strand of RNA folded to form anticodon (3 bases) at one end of molecule
    • anticodon binds to complementary codon on mRNA
120
Q

What happens in translation?

A
  • mRNA binds to a specific site of the ribosome (middle)
  • tRNA with complementary anticodon will bind to the start codon of the mRNA
  • another tRNA will then bind to the next codon
  • first amino acid will transfer to the next by forming a peptide bond
    • catalysed by peptidyl transferase (RNA component)
      ‎
  • the first tRNA is then released to bind with another complementary codon along the mRNA
  • the ribosome will continue reading the rest of the mRNA
    ‎
  • when the chain is released, other bonds form which fold the amino acids into secondary/tertiary structures
    • e.g. there may be hydrophobic interactions causing this
121
Q

Why do cells need energy?

A
  • synthesis (of large molecules)
  • transport (pumping molecules/ions by active transport)
  • movement (protein fibres that cause muscle contraction
122
Q

What is ATP?

A
  • adenosine triphosphate
  • composed of nitrogenous base, pentose sugar and three phosphate groups (nucleotide)
    • base is always adenine
    • 3 phosphates instead of 1
    • ribose sugar (like RNA)
  • ** universal energy currency **
123
Q

How does ATP release energy?

A
  • bond breaking = energy needed
  • bond making = energy released
    • energy needed is less than energy released (30.6 kJ mol -1)
  • hydrolysis reaction takes place
    ATP + H2O –> ADP + Pi + energy
    • ADP = adenosine diphosphate
      ‎
  • instability of phosphate bonds in ATP means it is not a good long-term energy store (fats/carbohydrates are better)
  • ATP can be reformed by phosphorylation (condensation reaction)
124
Q

What are the properties of ATP?

A
  • small:
    • easily moves into/out of cells
  • water soluble:
    • energy-requiring process take place in aqueous environments
  • intermediate energy bonds between phosphates:
    • large enough for cellular reaction
    • energy is not wasted as heat
  • energy released in small quantities:
    • suitable to most cellular needs
  • easily regenerated:
    • can be recharged with energy

Biology (22 decks)

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