Biological Molecules Flashcards
Define monomer and give some examples
Monomers are smaller units that join together to form larger ones.
Monosaccharides (glucose, fructose, galactose)
Amino acids
Nucleotides
Define polymer and give some examples
Molecules formed when many monomers join together.
Polysaccharides
Proteins
DNA/RNA
What happens during a condensation reaction?
2 molecules join together and form a chemical bond and a water molecule is removed
What happens during a hydrolysis reaction?
A water molecule is used to break a chemical bond between 2 molecules.
Name the 3 hexose monosaccharides and their chemical formula.
glucose
fructose
galactose
C₆H₁₂O₆
Name the type of bond formed when monosaccharides react
glycosidic bonds (1,4) or (1,6)
2 monomers = disaccharide
multiple monomers = polysaccharide
Name 3 disaccharides and describe how they form
Maltose: glucose+glucose
Sucrose: glucose+fructose
Lactose: glucose+galactose
condensation reaction forms glycosidic bond between 2 monosaccharides
Describe the structure of starch
amylose:
1,4 glycosidic bonds
helix with intermolecular hydrogen bonds meaning it is compact (can fit into small spaces)
amylopectin:
1,6 glycosidic bonds
branched structure so there is a larger surface area for quick hydrolysis to glucose
Describe the functions of starch
Storage polymer of alpha-glucose in plant cells
it is insoluble so no osmosis can happen
large so does not diffuse in and out of cells
Describe the structure of glycogen
1,4 and 1,6 glycosidic bonds
Describe the structure of glycogen
insoluble so no osmosis occurs
compact
Describe the functions of glycogen
main storage polymer of alpha-glucose in animal cells (also found in plant cells)
found in muscle and liver cells
Describe the structure of cellulose
1,4 glycosidic bonds
straight chain/unbranched molecule
hydrogen bonds between layers to form microfibrils for increased strength
Describe the function of cellulose
polymer of beta-glucose
provides strength to plant cell wall (holds stem up, prevents bursting) Describe the function of cellulose
Describe the benedicts test for reducing sugars
- Add an equal volume of benedicts reagent to a sample
- Heat the mixture in a water bath at 100 for 5 minutes
- A positive result will show a colour change from blue to brick-red, orange, yellow or green.
(brick-red shows there are a lot of reducing sugars, green shows there aren’t as many)
Describe the benedicts test for non reducing sugars
- Prove it is a non reducing sugar by carrying out the benedicts test and getting anegative result (colour blue)
- Hydrolyse non reducing sugars by adding acid and heat in a water bath.
- Neutralise the mixture by adding an alkali
- Redo the benedicts test for a positive result
Describe the test for starch
- Add iodine solution
- A positive result will show a colour change to black/blue
Describe how to test for lipids in a sample
- Dissolve solid sample in ethanol
- Add water and shake gently
- Positive result is milky white emulsion
How do triglycerides form?
condensation reaction between 1 molecule of glycerol and 3 fatty acids to form ester bonds
Contrast saturated and unsaturated fatty acids
saturated:
contain single bonds only between carbon atoms
higher melting point
solid at room temp
unsaturated:
has atleast one double bond between carbon atoms
lower melting point
liquid at room temperature
Relate the structure of triglycerides to their functions
Insoluble hydrocarbon chain = no effect on water potential hence used for waterproofing.
slow conductor of heat + used as a thermal insulation.
Describe the structure and function of phospholipids
a glycerol backbone attached to 2 hydrophobic fatty acid tails and 1 hydrophilic polar phosphate head.
Tails splay outwards for waterproofing.
Compare phospholipids and triglycerides.
Both have a glycerol backbone.
Both may be attached to saturated/unsaturated/polyunsaturated fatty acids
Contrast phospholipids and tryglycerides.
phospholipids:
2 fatty acids and 1 phosphate group.
Hydrophylic head and hydrophobic tail.
Used primarily in membrane formation.
Triglycerides:
3 fatty acids
Entire molecule is hydrophobic.
Used primarily as a storage molecule.
What does hydrophobic mean?
Doesn’t like water
What does hydrophilic mean?
Likes water
Are phospholipids and triglycerides polymers? Why?
No because they are macromolecules
Why is water a polar molecule?
Oxygen is more electronegative than hydrogen so it attracts the electron density more strongly to form oxygen with a slightly negative charge and hydrogen with a slightly positive charge.
State 4 biologically important properties of water.
Metabolite/solvent for chemical reactions in the body.
High specific heat capacity.
High latent heat of vaporisation.
Cohesion between molecules.
How does the fact that water is a metabolite/solvent for chemicals in the body make it useful?
Needed for hydrolysis or condensation.
Essential substances such as vitamins, amino acids, glucose, etc are transported in the body as a substance dissolved in a solvent.
How does specific heat capacity make water useful?
Means that water can buffer temperatures.
Allows temperatures to be stable for living organisms and protects them from rapid changes in the external environment.
How does latent heat make water useful?
Serves as a sink for living organisms and cools when evapourated from living organisms as perspiration. (important for hot conditions)
How does a strong cohesion between molecules make water useful?
Important for transport of water in xylem cells because plants rely on water being pulled up.
What are inorganic ions and where are they found in the body?
Ions that do not contain carbon atoms.
Found in cytoplasm and extracellular fluid.
May be high or very low concentrations
Explain the role of hydrogen ions in the body
lower the pH of solutions and impact enzyme function and haemoglobin function
Explain the role of iron ions in the body
Forms haem group in the haemoglobin.
Haem group has binding site to transport oxygen molecules around the body.
4 haem groups per haemoglobin molecule
Explain the role of sodium ions in the body
Involved in co-transport for absorption of glucose and amino acids in lumen of gut.
Explain the role of phosphate ions in the body.
Component of:
DNA
RNA
NADP
cAMP
What is the general structure of an amino acid?
COOH carboxylic acid group.
R variable side group consists of carbon chain and may include other functional groups (-OH (alcohol))
NH₂ amino group
Describe how to test for proteins in a sample.
Biuret test confirms presence of peptide bond
Add biuret reagent to sample.
A positive result: colour change from blue to purple.
A negative result: solution remains blue.
How many amino acids are there and how do they differ from eachother?
20.
Differ only by side R group
How do dipeptides and polypeptides form?
Condensation reaction forms peptide bond (-CONH-) and eliminates molecule of water.
A dipeptide is 2 amino acids and a polypeptide is 3 or more amino acids.
How many levels of protein structure are there?
4
Define secondary structure of a polypeptide.
Hydrogen bonds form between O (slightly negative) attached to -C=O & H (slightly positive) attached to -NH
Describe the 2 types of secondary protein structure
a-helix:
All N-H bonds on the same side of protein chain
Spiral shaped
H-bonds parallel to helical axis
B-pleated sheet:
N-H & C=O groups alternate from one side to the other
Define tertiary structure of a protein and name the bonds present
3D structure formed by further folding of polypeptide
•disulfide bonds
•ionic bonds
•hydrogen bonds
Describe each type of bond in the tertiary structure of a protein
•Disulfide bridges: strong covalent S-S bonds between the molecule of the amino acid cysteine
•ionic bonds: relatively strong bonds between charged R groups (pH changes which causes these bonds to break)
•Hydrogen bonds: numerous and easily broken
Define quaternary structure of a protein
Functional proteins may consist of more than one polypeptide.
Precise 3D structure held together by the same types of bond as tertiary structure
May involve addition of prosthetic groups (metal ions, phosphate groups)
Describe the structure and function of globular proteins
spherical & compact
Hydrophillic R groups face outwards & hydrophobic R groups face inwards (water soluble)
Involved in metabolic processes (enzymes and haemoglobin)
Describe the structure and function of fibrous proteins
Can form long chains or fibres
Insoluble in water
Useful for structure and support (collagen in skin)
How can chromatography be used identify amino acids in a mixture
•Use capillary tube to spot mixture onto pencil origin line and place chromatography paper in solvent.
•Allow solvent to run until it almost touches other end of paper. Amino acids move different distances based on relative attraction to paper & solubility in solvent.
•Use UV light or revealing agent to see spots.
•Calculate Rf values & match to database
What are enzymes?
enzymes are tertiary structure proteins which lower the activation energy of the reactions they catalyse
Explain the induced fit model of enzyme action
Shape of active site is not directly complementary to substrate and is flexible.
Comformational change enables ES complexes to form which puts a strain on substrate bonds, lowering the activation energy
How have models of enzyme action changed?
Was lock and key model which showed a rigid shape of active site which was complementary to only 1 substrate.
Now it is the induced fit model which also explains why binding at allosteric sites can change the shape of the active site
How can you identify the activation energy of a metabolic reaction from an energy level diagram
the difference between free energy of substrate & peak of curve
Name 5 factors that affect the rate of enzyme-controlled reactions.
enzyme concentration
substrate concentration
concentration of inhibitors
pH
temperature
How does temperature affect rate of reaction
Rate increases as kinetic energy increases & increases number of successful collisions. Above optimum, bonds break so active site isn’t complementary anymore and result in denature.
Compare competitive and non competitive inhibitors
Competitive inhibitors:
Similar shape to substrate = bind to active site
Do not stop reaction - prevents enzyme-substrate complexes from forming
Increasing substrate concentration decreases their effect.
Non-competitive inhibitors:
Bind at allosteric binding site.
May permanently stop reaction because it triggers the active site to change shape.
Increasing substrate concentration has no impact on their effect.
How do you calculate rate of reaction from raw data?
Change in concentration of product or reactant / time
Name the pentose sugars in RNA and DNA
RNA: ribose
DNA: deoxyribose
State the role of DNA in living cells
holds genetic information
State the role of RNA in living cells
mRNA: complementary sequence to 1 gene from DNA with introns (non coding regions) spliced out. Codons can be translated into a polypeptide by ribosomes.
rRNA: combines with proteins to make ribosomes.
tRNA: supplies complementary amino acid to mRNA codons during translation.
How do polynucleotides form?
Condensation reactions between nucleotides form strong phosphodiester bonds (sugar-phosphate backbone)
Describe the structure of DNA
Double helix of 2 polypeptide strands (deoxyribose)
H-bonds between complementary purine and pyramidine base pairs on opposite strands:
(A)denine + (T)hymine
(G)uanine + (C)ytosine
Which bases are purine and which are pyramidine?
A & G = 2 ring purine bases
U & C & T = 1 ring pyramidine bases
Name the complementary bases in DNA
2 H-bonds between:
Adenine + Thymine
3 H-bonds between:
Guanine + Cytosine
Name the complementary bases in RNA
2 H-bonds between
Adenine + Uracil
3 H-bonds between
Guanine + Cytosine
Relate the structure of DNA to its functions
sugar-phosphate backbone & many H-bonds provide stability.
helix is compact for storage in nucleus.
double stranded for semi conservative replication.
weak H-bonds break so strands can seperate for replication
Describe the structure for mRNA
Long ribose polynucleotide (shorter than DNA)
Contains Uracil instead of Thymine
Single stranded and linear (no complementary base pairs)
Relate mRNA structure to its functions.
Long ribose polynucleotide breaks down quickly so no excess polypeptide forms.
Single stranded so ribosomes can move along the strand and tRNA can bind to exposed bases.
Describe the structure of tRNA
Single strand of 80 nucleotides.
Folded into clover shape with some paired bases.
Anticodon on one end, amino acid binding site on the other.
Why is DNA replication ‘semi’- conservative?
strands form original DNA molecule act as a template
new DNA molecule contains 1 old strand and 1 new strand
Outline the process of semi conservative DNA replication
•DNA helicase breaks H-bonds between base pairs.
•Each strand acts like a template.
•Free nucleotides from nuclear sap attach to exposed bases by complementary base pairing.
•DNA polymerase catalyses condensation reaction that join adjacent nucleotides on a new strand
•Hydrogen bonds reform
Describe the Meselson-Stahl experiment
Bacteria was grown in a medium containing heavy isotope ¹⁵N for many generations.
Some bacteria was moved to a medium containing light isotope ¹⁴N. Samples were extracted after 1 & 2 cycles of the DNA replication.
Centrifugation formed a pellet - heavier DNA (¹⁵N) settled closer to the bottom of the tube.
Describe the structure of ATP
nucleotide derivative of adenine with 3 phosphate groups
Explain the role of ATP
ATP hydrolase catalyses ATP -> ADP + Pi
Energy released is coupled to metabolic reactions.
Phosphate groups phosphorylates compounds to make them more reactive.
How is ATP synthesised in cells?
ATP synthase catalyses condensation reaction between ADP & Pi
During photosynthesis & respiration
Explain why ATP is suitable as the ‘energy currency’ of cells
High energy bonds between phosphate groups.
Small amounts of energy released at a time = less energy wasted as heat.
Single step hydrolysis = energy available quickly.
Readily resynthesised
Outline how colorimetry could be used to give qualitative results for the presence of sugars and starch
- Make standard solutions with known concentrations. Record absorbance or % transmission values.
- Plot calibration curve: absorbance or % transmission (y-axis), concentration (x-axis)
- Record absorbance or % transmission values of unknown samples. Use calibration curve to read off concentration
what type of bond is between complementary base pairs?
hydrogen bonds
what type of bond is between adjacent nucleotides in a DNA strand
phosphodiester bonds
what are 3 differences between tRNA and mRNA
mRNA is a linear structure, tRNA is a clover shape
mRNA has codon, tRNA had anticodon
tRNA has hydrogen bonds, mRNA does not
explain difference between DNA in chloroplast and DNA in nucleus
DNA in chloroplast is shorter, has fewer genes, is circular (not linear) and has no introns
