AS-Biological molecules Flashcards
Which bases are pyramidines?
Cytosine and Thymine
Which bases are purines?
-Pure Silver-Ag
-Adenine and Guanine.
What is the 5’ end of a DNA strand?”
-5 carbon of deoxyribose unattached to another nucleotide
“What is the 3’ end of a DNA molecule?”
-The end where the 3 carbon of deoxyribose is unattached to another nucleotide.
What is the difference between purines and pyramidines?
-Pyramidines - one nitrogenous ring (one point of pyramid)
-Purines - two nitrogenous rings
What is the advantage of purines binding with pyamidines?
-even molecule width
-more stable
What does DNA strands being anti-parallel mean, and what is the advantage of this?
-upside down relative to one another
-5’ end of one strand and 3’ end of other strand on the same side of the double helix
-bases in close proximity
-more stable
What does DNA strands being anti-parallel mean, and what is the advantage of this?
-upside down relative to one another
-5’ end of one strand and 3’ end of other strand on the same side of the double helix
-bases in close proximity - more stable
What are Monomers?
Small basic molecular units that join together to form a polymer
What are polymers?
Large complex molecules composed of long chains of monomers joined together
Examples of monomers
monosaccharides, amino acids and nucleotides
Examples of polymers
Carbohydrates, proteins and nucleic acids
How many types of glucose are there?
2
What are the names of the types of glucose?
Alpha-glucose and beta-glucose
Structure of Alpha Glucose
Hydrogen to the right of ring is in the ‘attic’
Structure of Beta glucose
Hydrogen to the right of ring is in the ‘basement’
What are alpha and beta glucose relative to glucose?
Isomers of gluose
What are Isomers?
Compounds with a single chemical formula but different forms
What is a condensation reaction?
When 2 molecules join together with the formation of a new chemical bond, releasing a water molecule
Condensation reactions join which molecules?
Monosaccharides
What type of chemical bond forms between 2 monosaccharides?
Glycosidic
What is formed when 2 monosaccharides join together?
Disaccharide
Which 2 molecules make maltose?
Alpha glucose and alpha glucose
What is sucrose made from?
Alpha glucose and fructose
Which 2 molecules make lactose?
Alpha glucose and galactose
What is a hydrolysis reaction?
When 2 molecules are broken apart using a water molecule
What is broken down by hydrolysis to form monosaccharides?
Carbohydrates
Benedict’s Test for Reducing Sugars [step1]
Add Benedict’s reagent to a sample and add it to a water bath which is boiling
Benedict’s Test for Reducing Sugars [step2]
-If the test is positive, it will form a coloured precipitate
-if it’s negative, it’ll stay blue
Benedict’s Test for Non-Reducing Sugars [step1]
-Get a new sample of the test solution,
-add DILUTE HCl
-heat it in a hot water bath
Benedict’s Test for Non-Reducing Sugars [step2]
Neutralise the solution with sodium hydrogencarbonate
Benedict’s Test for Non-Reducing Sugars [step3]
Carry out the Benedict’s test as normal
positive result= blue to brick red precipitate colour change
what is a Polysaccharide?
Formed when more than 2 monosaccharides are joined together by condensation reactions
Function of Starch
Energy Store
What makes up starch?
Amylose and amylopectin
Structure of amylose
-Long, unbranched chain of alpha-glucose
-has a coiled structure
-making it compact and good for storage
Structure of amylopectin
-Long, branched chain of alpha-glucose
-side branches allow the enzymes that break the molecule down to access the bonds easily
-meaning glucose can be released quickly
Features of starch
-Insoluble in water
-doesn’t affect water potential so water doesn’t enter the cell, which would make them swell
The iodine test
-Add iodine dissolved in potassium iodide solution to the test sample.
-If starch is present, sample turns from yellow to blue black
What do animals store glucose as?
Glycogen
What structure is glycogen similar to?
Amylopectin, except it has more side branches, meaning stored glucose can released quickly, very compact
What is a major component of cell walls in plants?
Cellulose
Structure of cellulose
Long unbranched chains of beta glucose
What is formed when beta glucose molecules bond?
Straight cellulose chains
Advantage of cellulose chains
They’re linked together by hydrogen bonds to form microfibrils, providing structural support for cells
Structure of a triglyceride
1 glycerol and 3 fatty acid chains
What are triglyceride tails made of?
Hydrocarbons
Are the triglyceride tails hydrophobic or hydrophilic?
Hydrophobic
Are lipids soluble or insoluble in water?
Insoluble
What’s the basic structure of a fatty acid?
O
||
C
/ \
OH R
Triglycerides are formed by what type of reaction?
Condensation
What is a saturated fatty acid?
A fatty acid with no double bonds between the carbon atoms
What is an unsaturated fatty acid?
A fatty acid with at least one double bond between the carbon atoms
What’s the difference between a triglyceride and a phospholipid?
A triglyceride has 3 fatty acid tails. A phospholipid has 2 fatty acid tails and a phosphate group attached to the glycerol
Is the phosphate group hydrophilic or hydrophobic?
Hydrophilic
Triglycerides are used as what?
Energy storage molecules
What do the hydrocarbon tails of triglycerides contain which is useful for us?
Chemical energy
Lipids contain how much more energy than carbohydrates?
Double
Are triglycerides insoluble or soluble?
Insoluble, don’t affect water potential
How do triglycerides act in cells?
They clump together as insoluble droplets, the tails face inwards and the heads face out
What do phospholipids do?
Make up the bilayer of cell membranes, meaning they control what enters and leaves the cell
What do phospholipids form?
A double layer, heads outside and tails inside, forming a barrier against water soluble substances
How do you do the emulsion test?
Shake the test substance with ethanol for a minute so it dissolves and pour the solution in water. Any lipid will show as a milky emulsion
What are the monomers of protein?
Amino acids
How is a polypeptide formed?
Formed by more than 2 amino acids join together
How are proteins made up?
Made up of one or more polypeptides
Structure of amino acids
Carbon bonded to a hydrogen, amino group, R-group and Carboxyl
How many amino acids do all living things have?
20
What is the name of the bonds formed between 2 amino acids?
Peptide bond
Protein Structure: Primary Structure
Sequence of amino acids in the polypeptide chain
Protein Structure: Secondary Structure
Hydrogen bonds form between the amino acids in the chain, making it coil into an alpha helix or a beta pleated sheet
Protein Structure: Tertiary Structure
The coiled or folded chain is coiled further, more hydrogen and ionic bonds form.
When do disulfide bridges form?
Whenever 2 molecules of cysteine come close together
Protein Structure: Quaternary Structure
Made of several different polypeptide chains, held together by different bonds
How do you do the biuret test?
-Make the solution alkaline by adding sodium hydroxide solution
-Add copper(II) sulfate solution
-If protein is present, the solution colour changes from blue to purple
What are enzymes?
Biological catalysts
What do enzymes do?
They catalyse metabolic reactions at both a cellular level and across the whole organism
What can enzymes affect?
Structures in an organism (such as collagen production) and functions (such as respiration)
What makes each enzyme different?
Their active site, which has a specific shape
How are enzymes specific?
Their tertiary structure
How do enzymes speed up a reaction?`
If the substrate is being joined, the substrates being attached to the enzyme brings them closer together, reducing any repulsion significantly
If the enzyme is catalyzing a breakdown reaction, fitting into the active site puts strain on the bonds in the substrate, allowing the molecule to break up more easily
What is the induced fit model?
Where the substrate fits into the enzyme, then the enzyme changes it’s shape slightly to lock the substrate even tighter to itself
What is it called when an enzyme and a substrate are joined together?
Enzyme-substrate complex
What determines the primary structure of a protein?
A gene
How does pH affect enzyme activity?
=All enzymes have an optimum pH (usually 7)
-Above and below the optimum temperature messes up the ionic and hydrogen bonds that hold the tertiary structure in place
-denaturing the enzymes
How does enzyme concentration affect enzyme activity?
-The more enzyme molecules there are, the more likely there are to be collisions between enzyme and substrate molecules
-forming more enzyme-substrate complexes
How can enzyme activity be inhibited by competitive inhibitors?
Competitive inhibitor molecules have a similar shape to substrate molecules
-so will compete with the substrate to bind with the enzyme and block the active site.
-The higher the competitive inhibitor concentration, the more active sites are filled and less enzyme-substrate complexes are formed
How can enzyme activity be inhibited by non competitive inhibitors?
-Non-competitive inhibitors bind to the enzyme away from its active site
-causing the active site to change shape so substrate molecules can’t bind to the enzyme
Nucleotide structure (DNA)
Phosphate group, deoxyibose (pentose sugar) and a organic nitrogenous base
polynucleotide
repeating units of a nuclotide
What is the general structure of monosaccrides?
(CH20)n
What does DNA strands being anti-parallel mean, and what is the advantage of this?
-upside down relative to one another
-5’ end of one strand and 3’ end of other strand on the same side of the double helix
-bases in close proximity - more stable
Describe DNA replication.
- DNA helicase breaks H bonds, unwinding helix
-Each DNA strand used as a template for a new strand
-Free DNA nucleotides align with complementary base, form H bonds
-adenine forms 2 H bonds with thymine, cytosine forms 3 H bonds with guanine
-DNA polymerase forms phosphodiester bonds between nucleotides
-by condensation reactions
-forms sugar-phosphate backbone
-continues along DNA molecule
What direction does DNA polymerase act in and why?
- 5’ to 3’ direction of the developing strand specific tertiary structure
-binding site with specific shape that is
-only complementary to nucleotide to 3’ end of developing strand
-5’ end of developing strand has differently shaped nucleotide
What is the advantage of DNA replication being semi-conservative?
ensures genetic continuity between generations of cells
What does semi conservative replication mean?
Each stand from the parent DNA molecule acts as a template for the formation of a new complementary stand
Recall the semi conservative hypothesis experiment
-Use 2 isotopes of nitrogen
-Heavy nitrogen [15N] -light nitrogen [14N]
-bacteria will take up nitrogen from their surroundings into the DNA they make (bases are made from nitrogen)
-The composition of the DNA was analysed using density gradient centifugation
-The bacteria was taken out of the broth and put in a broth containing only light nitrogen and left to replicate
-When spun in centrifuge again where DNA hybrids (of light and heavy nitrogen) settles in the center of the centrifuge
Structure of ATP
adenine, ribose sugar (pentose sugar) and 3 phosphate groups
what is ATP used for?
-short term energy storage
-active transport
-phosphorylation of molecules
ATP properties
-small and water soluble (can be easilt transported)
-provides energy for metabolic reactions
importance of water in Biology
-liquid medium (habitat for aquatic organisms)
-metabolite (used in hydrolysis and condensation reactions)
-High specific heat capacity (keeps aquatic/ cellular environments stable)
-Good solvent and transport medium
-good reaction medium
-impressionable (provides structural support in plants)
-penetrateable (light can pass through it)
-transparent (aquatic plants can photosynthesis)
How do water molecules attract to eachother?
-oxygen slightly negatively charged
-hydrogen slightly positively charged
-attracts to other water molecules
Where do ions occur?
in solution in the cytoplasm and body fluids of organisms
what is the role of Fe 2+ in hemoglobin?
-They bind with oxygen
-allow hemoglobin to load oxygen forming ‘oxyhaemoglobin’
what is the role of Fe 2+ in photosynthesis and respiration?
-involved in electron transfer chains
what are the roles of H+ in PH
-Concentration of H+ determines the PH
-More H+ = lower PH
-Fewer H+ = higher PH
What are the roles of H+ in enzyme controlled reactions?
-maintenance of PH is crucial for metabolic reactions
-change in PH can effect enzyme structure
-abnormal levels of H+ can effect side chains of amino acids and change the secondary/tertiary structure.
What are the roles of Na+ in co-transport?
-required for the transport of glucose and amino acids across cell-surface membranes (e.g. in the small intestine)
-glucose and amino acids can only enter cells via carrier proteins with Na+
What is the role of PO43- in forming phosphate groups?
-PO43- attaches to other molecules to form phosphate groups, which are an essential component of DNA, RNA and ATP
Are cellulose chains straight or branched?
Straight
Describe the structure of maltose
Two alpha glucose’s’ bonded by a glycosidic bond (oxygen bridge)
Adaptations of glycogen
-compact ( lots can be stored in a small volume)
-insoluble (doesn’t effect osmosis)
-insoluble (so doesn’t diffuse out of cells)
- branched chains (increase surface area)
- and provide more ends for enzymes to hydrolyse glycogen faster
- to release glucose faster
How is starch adapted for its function?
- compact helical shape, lots of starch stored in small volume
- insoluble so osmotically inactive
- large and insoluble so doesn’t diffuse out of cells
- branched chains increase surface area
- provide multiple ends for enzymes to hydrolyse starch
- to rapidly release glucose
What do starch and cellulose have in common?
- C H O
- hydrogen bonding
- 1,4 - glycosidic bonds
Why is glycogen more highly branched than starch?
- glycogen is stored in animals
- branching increases surface area and number of ends for enzymes to hydrolyse
- faster release of glucose
- to maintain higher metabolic and respiratory rates in animals
What are the similarities between phospholipids and triglycerides? (4)
- both contain ester bonds
- both formed from glycerol
- both insoluble in water
- both contain C H and O
What are the similarities between phospholipids and triglycerides? (4)
- both contain ester bonds
- both formed from glycerol
- both insoluble in water
- both contain C H and O
What is the test for lipids?
- grind with ethanol
- add water
- milky white emulsion
What determines binding site shape?
- tertiary structure not quarternary structure
What is the difference between different amino acids?
- R group varies
Why would an enzyme become more effective?
- change in tertiary structure of enzyme
- change in active site shape
- successful E-S complexes form more quickly
Why would one amino acid substitution have a greater affect than another amino acid substitution?
- change in amino acid charge
- amino acid involved in hydrogen/ionic/disulfide bond
- larger effect on tertiary structure
What are the key words for enzymes? (5)
- specific
- complementary
- only
- fit
- substrate
What are zymogens?
- inactive form of enzymes
What control is used for enzyme experiments?
- boiled enzyme
Where does a non-competitive inhibitor bind?
- allosteric site
Nucleotide structure (RNA)
Phosphate group, ribose (pentose sugar) and organic nitrogenous base
Evidence for semi-conservative replication of DNA
- All organic bases in DNA contain nitrogen
- Nitrogen has forms: [14N] &[15N]
- Bacteria takes up any nitogen in their surroundings into any new DNA they make
Evidence for semi-conservative replication of DNA
- All organic bases in DNA contain nitrogen
- Nitrogen has forms: [14N] &[15N]
- Bacteria takes up any nitogen in their surroundings into any new DNA they make
