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
2
Q
What is the formula for Methane and Ammonia?
A
- methane = CH4
- ammonia = NH3
3
Q
What are calcium ions (Ca^2+) necessary for?
A
- nerve impulse transmission
- muscle contraction
4
Q
What are sodium ions (Na^+) necessary for?
A
- nerve impulse transmission
- kidney function
5
Q
What are potassium ions (K^+) necessary for?
A
- nerve impulse transmission
- stomatal opening
6
Q
What are hydrogen ions (H^+) necessary for?
A
- catalysis of reactions
- pH determination
7
Q
What are ammonium ions (NH4^+) necessary for?
A
- production of nitrate ions by bacteria
8
Q
What are nitrate ions (NO3^-) necessary for?
A
- nitrogen supply to plants for amino acid and protein formation
9
Q
What are hydrogen carbonate ions (HCO3^-) necessary for?
A
- maintenance of blood pH
10
Q
What are chloride ions (Cl^-) necessary for?
A
-balance positive charge of sodium and potassium ions in cells
11
Q
What are phosphate ions (PO4^3-) necessary for?
A
- cell membrane formation
- nucleus acid and ATP formation
- bone formation
12
Q
What are hydroxide ions (OH^-) necessary for?
A
- catalysis of reactions
- pH determination
13
Q
What are the 4 biological molecules?
A
- carbohydrates
- lipids
- proteins
- nucleic acids
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)
15
Q
What is a monomer?
A
- a single molecule that binds to other similar molecules to form a repeating chain molecule
16
Q
What is a polymer?
A
- a large molecule built up from a large number of similar units (monomers) bonded together
17
Q
What are the three important groups of polymers (living organisms)?
A
- nucleic acids (nucleotides)
- polysaccharides (monosaccharides)
- proteins (amino acids)
18
Q
How many different amino acids are there?
A
- 20 amino acids
19
Q
What do nucleic acids consist of?
A
- phosphate group
- pentose sugar
- organic base
20
Q
What are the five different bases?
A
- adenine (A)
- cytosine (C)
- guanine (G)
- thymine (T)
- uracil (U) = in RNA, replaces thymine
21
Q
Water is a ______ _______
A
- simple molecule
- that can form hydrogen bonds
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
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
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
25
Water has a boiling point of ____
- 100 °C
- in order to evaporate hydrogen bonds must be broken (requires a lot of energy)
26
At 0°C (or less) water molecules form an _____ ______ _______
- 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
27
Properties of water : thermal stability
- 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
28
What are the benefits of thermal stability?
- 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
29
Properties of water : Freezing
- 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
30
Properties of water : Evaporation
- 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)
31
Properties of water : Cohesion
- the attraction of water molecules to each other
- produces surface tension (creates habitat on surface for invertebrates, e.g. pond skaters)
32
Properties of water : Adhesion
- 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)
33
What are the benefits of cohesion and adhesion?
- 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)
34
Properties of water : Transparent
- allows aquatic plants to carry out underwater photosynthesis
35
Properties of water : High density
- allows water to support organisms and allows for flotation
36
Properties of water : Solvent
- 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
37
Properties of water : Reactant
- used in a wide range of metabolic reactions
- hydrolysis, photosynthesis
38
Properties of water : Incompressibility
- 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
39
In water questions include :
- hydrogen bonds
- cohesion/adhesion (transport)
40
Where else are hydrogen bonds found?
- 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
41
What elements do carbohydrates contain?
- carbon
- hydrogen
- oxygen
- general formula (CH2O)x
42
What is a monosaccharide?
- a single unit of sugar
43
What are examples of monosaccharides?
- glucose
- fructose
- galactose
- ribose
44
What is a disaccharide?
- a carbohydrate made of 2 monosaccharides
45
How are disaccharides formed?
- they are joined together by condensation reactions, and held together by (1,4) glycosidic bonds
46
What are examples of disaccharides?
- sucrose
- lactose
- maltose
47
What is a polysaccharide?
- a chain that is formed of multiple monosaccharide molecules joined together
- they are large *insoluble* molecules
48
What are examples of polysaccharides?
- glycogen
- starch
- cellulose
49
Why are monosaccharides reducing sugars?
- they are able to donate electrons
- can oxidise carbonyl groups (C=O)
50
What is the chemical formula of glucose?
- C6H12O6
51
Examples of reducing sugars:
- glucose
- fructose
- galactose
- (different arrangement of atoms give slightly different properties)
52
Example of non-reducing sugars:
- sucrose
- cannot donate electrons (not oxidised)
53
What are the two types of glucose?
- α-glucose (alpha)
- OH group at the bottom
- β-glucose (beta)
- OH group at the top
54
What are the functions of glucose?
- 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
How is sucrose formed (disaccharide)?
- α-glucose + fructose
56
What reaction breaks down glycosidic bonds?
- hydrolysis
- reacts with water to break down the glycosidic bonds
57
How is lactose formed (disaccharide)?
- α-glucose/β-glucose + galactose
58
Structure/properties of amylose (starch)
- 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
How is maltose formed (disaccharide)?
- α-glucose + α-glucose
60
What is a pentose monosaccharide?
- a monosaccharide containing 5 carbons
- e.g. ribose, deoxyribose
61
What is a hexose monosaccharide?
- a monosaccharide containing 6 carbons
- e.g. glucose
62
Structure/properties of glycogen:
- 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
Structure/properties of amylopectin (starch)
- 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
Structure/properties of glucose
- 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
Functions of carbohydrates
- source of energy
- energy store
- structurally important
66
What is starch used for/composed of?
- main storage polysaccharide in plants
- amylose
- amylopectin
67
Structure/properties of cellulose:
- 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
Testing for non-reducing sugars:
- 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
Testing for reducing sugars (Benedict's + Reagent strips):
- 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
Iodine test for starch
- add few drops of iodine (mixed with potassium iodide) to sample
- colour change from yellow/brown to purple/black shows starch is present
71
What are lipids?
- 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
What are triglycerides?
- 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
What is a saturated fatty acid chain?
- no double bonds present
- all carbons form max. bonds with hydrogen
74
What is an unsaturated fatty acid chain?
- 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
What are phospholipids?
- (modified triglycerides) they contain phosphorus, carbon, hydrogen and oxygen
- charged phosphate head (hydrophilic)
- non-polar tails (hydrophobic)
76
How do phospholipids interact with water?
- 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
What are sterols?
- complex alcohol molecules with hydrophobic/philic characteristics
- hydroxyl is polar (hydrophilic) and the rest is hydrophobic
78
What is the function of cholesterol?
- 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
What are the roles of lipids?
- 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
What is the test for lipids?
- emulsion test
- sample is mixed with ethanol and then with water
- white emulsion = lipid is present
81
What is the basic structure of an amino acid?
- amine group (NH2)
- carboxyl group (COOH)
- R-group (different in each amino acid)
82
What do amino acids form?
- peptides (polymers)
- polypeptides/proteins consist of long chains of amino acids
83
What elements do proteins contain?
- C, H, O, N
84
How many amino acids are there?
- 20 different amino acids
- 5 = non-essential
- 9 = essential
- 6 = conditionally essential
85
How is a peptide formed?
- 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
How is a polypeptide formed?
- when many amino acids are joined together by peptide bonds
- **catalysed by *peptidyl transferase*, which is present in ribosomes**
87
How are peptides broken down?
- hydrolysis reaction (water molecule is used to break the peptide bond)
- proteases are enzymes that catalyse the reverse reaction
88
What are the levels of protein structure?
- primary
- secondary
- tertiary
- quaternary
89
What does the primary structure consist of?
- the sequence of amino acids (influences the final shape of the protein)
- peptide bonds
90
What does the secondary structure consist of?
- O, H, and N atoms interact
- hydrogen bonds may form (alpha helix or beta pleated sheet)
91
What does the tertiary structure consist of?
- 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
What does the quaternary structure consist of?
- association of two/more individual proteins (subunits)
- same as tertiary structure but is between *different protein molecules*
93
What are the two main types of proteins?
- globular (+ conjugated)
- fibrous
94
What are globular proteins?
- compact
- water soluble
- spherical in shape
- tertiary structure (hydrophobic R-groups are kept away from aqueous environment)
95
Example of a globular protein
- 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
What is a conjugated protein?
- 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
Example of a conjugated protein
- 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
What are fibrous proteins?
- 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
Examples of fibrous proteins
- 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
What are nucleic acids?
- large molecules discovered in cell nuclei
- made up of 30% C, 20% O, 20% N, 20% P, 10% H
101
What are the 2 types of nucleic acids?
- DNA (deoxyribonucleic acid)
- RNA (ribonucleic acid)
102
What is a nucleotide made up of?
- 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
What is DNA (deoxyribonucleic acid)?
- contains one fewer O atom than ribose
- nucleotides have four different bases:
- adenine (+ T)
- thymine (+ A)
- cytosine (+ G)
- guanine (+ C)
104
What are pyrimidines?
- smaller bases (single carbon ring structure)
- thymine and cytosine
105
What are purines?
- larger bases (contain double ring structures)
- adenine and guanine
106
What is the structure of DNA?
- 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
What are the base pairing rules?
- cytosine + guanine = three hydrogen bonds
- adenine + thymine = two hydrogen bonds
- (complementary base pairing)
108
What is RNA (ribonucleic acid)?
- 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
How does DNA leave the nucleus?
- 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
What is DNA replication?
- 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
What is semi-conservative replication?
- 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
What are the enzymes in replication?
- 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
What is a replication error?
- where sequences of bases are not matched correctly
- mutation = a random/spontaneous change in the sequence of a base
114
What is the genetic code?
- 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
What is transcription?
- 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
What happens in transcription?
- 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
What do eukaryotic ribosomes consist of?
- 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
What is translation?
- where the mRNA binds to a specific site on the ribosome subunit and is decoded into a sequence of amino acids
119
What is tRNA?
- 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
What happens in translation?
- 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
Why do cells need energy?
- synthesis (of large molecules)
- transport (pumping molecules/ions by active transport)
- movement (protein fibres that cause muscle contraction
122
What is ATP?
- 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
How does ATP release energy?
- 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
What are the properties of ATP?
- 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
