1: Biological Molecules Flashcards
What’s a monomer and a polymer?
monomer- one of many small molecules combining to form a larger one (polymer)
polymer- large molecules made up of small repeating units (monomers)
What are prefixes of different polymers?
1: mono-
2: di-
3: tri-
4: tetra-
5: penta-
6: hexa-
many: poly-
What is a biological molecule?
an organic molecule including carbohydrates, proteins, lipids and nucleic acids (e.g. DNA and RNA)
What are examples of biological molecules?
- carbohydrates- store and supply energy, can be structural
- proteins- transport and structure, basic component of enzymes, hormones and more
- lipids- part of cell membranes, insulators and protection
- water- formation of molecules and metabolic reaction
- nucleic acid- made of nucleotides to form RNA and DNA
- enzymes- made of proteins, act as biological catalysts by lowering activation energy
What bonds form between all biological molecules?
carbohydrates- glycosidic
proteins- peptide
lipids- ester
water- hydrogen
nucleic acids- phospohodiester
What bonds are present in polymers?
- covalent- share electrons (e.g. carbon froms 2 covalent bonds- C2)
- ionic- 2 oppositely charged ions, lose and gain electrons
- hydrogen- slightly positive and negative charges, more hydrogen bonds, stronger attraction
What monomers and polymers make up biological molecules?
carbohydrates, proteins, nucleic acid, lipids
carbohydrates- monosaccharides –> polysaccharides
proteins- amino acids –> proteins/ polypeptides
nucleic acid- nucleotides –> DNA/RNA
lipids- fatty acids/ glycerol –> triglycerides
What monosaccharides make up carbohydrates?
monosaccharide- single sugar/ carbonhydrate
carbohydrates–> sugars/ polysaccharides
sugars:
- single- glucose, fructose, galactose
- double- sucrose, maltose, lactose
polysaccharides:
- glucose/ starch are carbohydrates for storage
- cellulose and chitin are important for structural carbohydrates
What’s the difference between alpha and beta glucose?
C6H12O6
alpha- H,OH
beta- OH, H
CH2OH top left, O top right
What are different disaccharides made up of?
maltose, sucrose, lactose
maltose- 2 alpha glucose
sucrose- 1 glucose, 1 fructose
lactose- 1 glucose, 1 galactose
How do polysaccharides form?
- a condensation reaction between 2 monosaccharides forms a disaccharise through a glycosidic bond and a water molecule being produced
- if these condensation reactions continue to occur, then a long chain called a polysaccharide will form, held together by multiple glycosidic bonds
What are different adaptations of carbohydrates?
- energy source allow for cellular respiration
- building blocks (structural carbohydrates)
- small monosaccharides can easily transport in and out of the cell
- polar molecule, soluble in water, easy to transport
- only breaks down to release energy when catalysed by the enzyme, can be controlled (as it’s unreactive)
starch: structure, function and properties
STRUCTURE:
- (C6H12O6)n
- most basic form is linear polymer amylose
- alpha 1-4 glycosidic bonds
FUNCTION:
- help plants to store energy
- source of sugar, mainly in plants
- broken down by enzyme amylaase
PROPERTIES:
- turns inky black with iodine
- insoluble, good for storage
- branched,can easily be broken for energy
glycogen: structure, function and properties
STRUCTURE:
- highly branched glucose polymer
- made of long chains of monosaccharides (simple sugars)
- connected by alpha 1-4 glycosidic bond and an alpha 1-6 glycosidic bond
FUNCTION:
- backup supply of energy reserve for body
- made when insulin converts excess glucose to glycogen
- important in blood glucose homeostatis
PROPERTIES:
- has many side branches to release energy quickly, enzymes can act on many branches at once
- highly soluble, easily broken down, compact
cellulose: structure, function and properties
STRUCTURE:
- connected by beta 1-4 glycosidic bonds
- unbranched long, straight chain (linear)
FUNCTION:
- strengthen the cell wall, making it turgid and rigid
- help plants remain stff and upright
- can’t be digested, kept for fibre
PROPERTIES:
- linear, arranged parallel
- joined by hydrogen bonds
- long chaing can combine with other cellulose molecules to provide support
What is a protein and what’s it made up of?
- made of monomer of amino acids
- 20 different amino acids
- soluble all with the same basic structure
basic amino group- NH2
acidic carbpxyl group- COOH
r group- side/ variable group (e.g. H)
NH2-HCR-COOH
How do proteins form?
PROTEINSYNTHESIS
- amino acids join in a condensation reaction between amino group and carboxyl group of 2 different amino acids
- dipeptides are formed by condensation of 2 amino acids (breaking of bonds uses water)
- polypeptides form during the condensation of many amino acids
What is the primary structure of proteins?
- sequence of amino acid bases
- makes up polypeptide chains
- structure coded for by cell DNA
What is the secondary structure of proteins?
- form when polypeptide chain takes up a particular shape (in folding)
- most common shapes are alpha helix (like half DNA) of a beta pleated sheet (zig zag)
- these are stable structures maintaines by hydrogen bonds between different amino acid groups
What is the tertiary structure of proteins?
- forms when secondary structure folds more to form a complex shape
- irregular folding results from formation of different bonds between amino acids
- all globular proteins and amino acids are tertiary from secondary and are essential for functon
e.g. myoglobin, WHERE ACTIVE SITE/ ENZME FORMS
How do R groups affect the structure of amino acids?
- vary (20 different)
- make amino acids different
- affect the way amino acids bond with other amino acids
- play vital roles in determining and maintaining specific protien shapes due to different charges and attractions
BONDS: disulphde, ionc, hydrophillic/ hydrophobic, hydrogen
e.g. glycine- simplest amino acid (just H)
What bonds form between proteins?
- disulphide bridges- R groups of 2 amino acids with sulfurs
- hydrogen- electronegative oxygen (of COOH) and electronpositive hydrogen (ofNH2) of another amino acid
- ionic- oppositely charged groups form
What is the quaternary structure of proteins?
- proteins of more than one polypepide chain folded of the same or a different polypeptide
- attatch to form haem groups
-e.g. iron found (Fe2+) to attract oxygen to attatch polypeptide to polypeptide
e.g. haemglobin/ collagen (stretchy/ fold protein)
What is the biochemical test for reducing sugars?
benedicts
- place sample in clean test tube, if sample is solid, prepare a test solution by crushing the food and adding a moderate amount of distilled water
- add an equal volume of Benedict’s reagent (copper (II) sulfate) is added
- the solution is heated in a water bath for 3-5 minutes
- if reducting sugars are present, they will reduce the Cu2+ ions to Cu+ ions, forming the orange-red precipitate copper (I) oxide.
blue–> orange/red based on initial concentration
What is the biochemical test for non-reducing sugars?
benedicts
- add hydrochloric acid to sample
- test tube is heated in water bath for 3-5 mins resulting in the hydrolysis of non-reducing disaccharide into 2 monosaccharides (there are reducing sugars)
- sample is neutralised with sodium hydrogen carbonate solution
- sample is tested with benedicts
- if colour change now occurs, non-reducing sugars were present in the original sample
blue –> orange/red
What is the biochemical test for starch?
iodine
- place sample in a clean test tube
- potassium iodide solution is added to the test tube
- gently shake tube
- if starch is present, solution chnages yellow –> inky black
yellow/brown –> inky black
What is the biochemical test for proteins?
biuret
- sample placed in clean test tube
- biuret a (sodium hydroxide) is added to the test tube
- add a few drops of biuret b (copper (II) sulfate) are added and the solution is mixed
- if protein’s are present, colour change blue –> violet
blue–>purple/ violet
What is the biochemical test for lipids?
ethanol
- sample placed in clean test tube
- add ethanol and then add water and mix/ shake gently
- should priduce white/ milky substance or emulsification that indicated lipids are present
emulsion (lipids are soluble in water, insoluble in alcohol)
What are lipids?
- organic compound made of fatty acid and glycerol monomers
- used for cell support, energy storage, insulation, source of metabolic water
What’s a triglyceride?
- made of glycerol and 3 fatty aicds
- condensation reaction produces 3 water molecules
- forms an ester bond between glycerol and fatty acids
- occurs between akcohol and carboxylic acid
What’s a phospholipid?
- long hydrocarbon tail with lots of chemical energy
- forms lipid bilayer for membrane, acts as barrier
- hydrophillic head, hydrophobic tail
- made of phosphate group, glycerol and 2 fatty acids
- polar and water soluble
BILAYER: - acts as barrier with water
What is an enzyme?
- a biological catalyst that speeds up a reaction without being used up by lowering activation energy with an alternative reaction pathway
- has an active site with a complementary shape to the substrate to bind and be broken down into products
What’s the difference between the lock and key theory and the induced fit model?
LOCK AND KEY:
- every enzyme has complementary active site to complementary substrate
- fit together like a lock and key to make an enzyme-substrate complex
- so enzyme can break substrate into products
INDUCED FIT:
- active site can change shape over time to be more complementary to the substrate
- changes as substrate binds to the active site
- improves fit of the enxyme and substrate to be broken down
What factors affect the rate of enzyme controlled reactions?
- temperature
- pH
- substrate concentration
- enzyme concentration
- competitve inhibitor conc.
- non-comp. inhibitor conc.
What is the effect of temperature?
- proportional to enzyme activity
- as temp. increases, so does enzyme activity (kinetic energy)
- increases till reaches optimum temp., then the enzyme denatures and stop working
What is the effect of pH?
- increase or decrease in optimum pH, reduces rate of enzyme activity
What is the effect of substrate concentration?
- when there’s few substrates, rate is low as there’s less for enzyme to breakdown
- when there’s too many substrates, the rate is constant and levels off
What is the effect of enzyme concentration?
- when there’s few enzymes, the rate is half the maximum
- when there’s enough, enzyme rate is doubled
- when there’s too many, there’s no effect.
What is the effect of competitive inhibitor conc.?
- increase in substrate concentration decreases inhibitor (substrate) effect, increasing the rate of reaction.
- increasing the inhibitor decreases the rate of reaction as more substrates compete to bond to an enzyme
What is the effect of non- competitive inhibitor conc.?
- increasing substrate conc. has no impact on the rate of reaction as they don’t compete to bond to an enzyme
- increasing inhibitors decreases the rate of reaction as less substrates to break down
What are genes, alleles and mutations?
gene- a section of DNA nucleotides that codes for a propolypeptide chain
allele- a different version of the same gene
mutation- a change in DNA base sequence
What are nucleic acids?
e.g. DNA or RNA
- DNA stores genetic information, RNA transfers genetic info. from the nucleus to the ribosomes
- nucleotides are made up of phosphate,
pentose sugarand a nitrous base
- these join together to form polynucleotides by a condensation reaction
- this forms a phosphodiester bond between the sugar and the phosphate
- the chain of sugars + phosphates is a sugar-phosphate backbone
What is the structure of DNA?
- double helix (2 strands / helical structure)
- polymer forming long chains several billions base pairs long
- DNA molecules are coiled tightly in the cell nucleus
- held together by weak hydrogen bonds holding bases, chains run with antiparallel strands (5’ and 3’)
what are the base pairs of DNA codes?
- adenine, guanine, cytosine, 1 and thymine (Uracil in RNA)
- AT (AU) & GC
- apples in the tree & cars in the garage
What is the difference between a purine and a pyrimidine?
- purine- has a 2 ring structure
- pyrimidine- has a 1 ring structure
- All Gold is Pure (Adenine and Guanine are Purines)
- C, T and U are pyrimidines
What is the structure of RNA?
- similar to DNA: phosphate group,sugar and base
- has ribose insteadof deoxyribose
- base uracil(U) replaces thymine (paired with adenine in RNA)
- RNA polynucleotides are mostly single stranded
What is the genetic code?
- DNA carries genetic code (set of molecular instructions to make proteins)
- structure of DNA discovered by James Watson/ Francis Crick in 1953
- helped by Maurice and Franklin’s X-ray diffraction
- simplicity of DNA led scientists to doubt if it carried genetic code
What is the process of DNA replication?
- An enzyme called DNA helicase attaches to the DNA molecule and moves along its length. Hydrogen bonds holding the DNA strands together are broken and the two strands of the helix begin to separate to form two single strands
- Each original single strand acts as template for a new
strand, free nucleotides from the Nucleoplasm (part of nuclear envelope) are attracted to their complementary bases on each separated strand of DNA - Condensation reactions join the nucleotides of the new strands together- catalysed by the enzyme DNA polymerase. Hydrogen bonds form between the bases of the new and original strands.
- Each new DNA molecule consists of one strand from the original DNA double helix and one newly synthesised strand. This mechanism is called SEMI-CONSERVATIVE REPLICATION
Who proposed the hypothesis for DNA replication?
- An important property for any molecule that passes genetic information from one generation to the next is that of self-replication
- When Watson and Crick first proposed the structure of DNA, this was accompanied by an explanation as to how DNA might replicate.
- Watson and Crick proposed that, during replication, the strands of DNA separate and each strand acts as a template for the formation of a new strand of DNA
How does DNA polymerase replicate?
- The strands of DNA run in the opposite direction 5’-3’
- The active site of DNA polymerase is only complementary to the 3’ end of the newly synthesised strand.
- This means that the new strand is made in a 5’ to 3’ direction and that DNA polymerase moves down the template strand in the 3’ to 5’ direction.
- DNA polymerase moves in the opposite directions on the template and the new strand because the strands are antiparallel.
What evidence is there that DNA is semi-conservative?
- If DNA was conservative and not semi-conservative, the new DNA would contain two newly synthesised strands.
- Messelson and Stahl carried out an experiment to show that DNA contains one original strand and one new strand.
- They grew two samples of bacteria- one in nutrient containing light nitrogen and one containing heavy.
- As the bacteria, produced they took up the nitrogen from the broth.
- They then took out the bacteria in the heavy broth and put it in the light broth.
- They spun a DNA sample in a centrifuge and saw it separated in the middle- containing both light and heavy nitrogen.
What is ATP made up of?
- ribose, sugar, adenine base and 3 phosphate groups (adenine+ribose= adenosine)
- a phosphorylated nucleotide (similar to DNA and RNA structure)
- ATP can’t leave the cell
What are phosphate groups?
- negatively charged
- high energy unstable bonds between phosphate groups
- when phosphate bonds are hydrolysed (broken), energy is released
How is ATP produced?
- light energy is converted by plants into chemical energy in photosynthesis
- chemical energy from photosynthesis in the form of organic molecules is converted into ATP during respiration
- this is then used to perform useful work
How does ATP release energy?
- ATP can be hydrolysed to break a bond between phosphate groups releasing large amounts of energy
- hydrolysis of ATP to ADP is catylased by enzyme ATPase
ATP –> ADP+ Pi +30KJmol-1
break with water, make with ATPase
What reactions occur using ATP?
- metabollic processes
- movement
- active transport
- activation of molecules
- bioluminesence
What is a phosphorylation group?
the addition of a phosphate group
- ATP can be reformed from ADP+Pi in a condensation reaction. this occurs in 3 ways
- 3 methods: photophosphorylation, oxidative photophosphorylation, substrate level photophosphorylation
- this makes them more reactive
Describe the 3 phosphorylation groups?
photophosphorylation- occurs in chlorophyll in photosynthesis
oxidative photophosphorylation- occurs in the mitochondria during electron transport chain (a part of respiration).
substrate level photophosphorylation-- when phosphate groups are transferred from donor molecules to ADP
this makes them more reactive
Where does energy come from that changes ATP->ADP?
- respiration provides energy required for condensation reaction converting ADP to ATP
- for each 30.5KJmol-1 of energy released by hydrolysis of ATP the same energy must also be input from respiration to reform the ATP
- energy for condensation reactions come from chemical energy in glucose
What occurs in ATP synthase?
Hydrolysis: ATP -> ADP+Pi
energy released for use by cells to do work
Condensation: ADP+Pi -> ATP
energy released from organic substrate, during respiration
What is water?
H2O
- 2 atoms of hydrogen covalently bonded to an oxygen atom
- polar molecule- electrons not evenly distributed across the molecule, seperation of charge
- attraction between charges form hydrogen bonds between water molecules
- oxygen’s slightly negative, hydrogen’s slightly positive
What are properties of water?
- high specific heat capacity- can abosrb lots of energy before changing temperature, good for global warming and creates a stable environment
- large latent heat of vapourisation- due to hydrigen bonding, needs lots of energy to connvert to gas, good cooling mechanism
- strong cohesion- water molecules form hydrogen bonds and continuous mass flow to flow in xylem and also create surface tension
- important metabolic solvent- positive and negative charges attract molecules to react causing them to seperate and dissolve (moveable)
- metabolite in chemical reactions- water molecules, digestion and synthesis of molecules.
condesation- make bond, makes water
hydrolysis- breaks bonds with water
What’s an inorganic ion?
- ions necessary for living organisms and cellular organisms
- doesn’t contain carbon (few exceptions)
- in solution: in cytoplasm of cells and bodily fluids
What is the concentration of inorganic ions?
- some are high in conc. others are low
- each ion has different role based on its properties
- role of ion determines conc. its found in
What is the role of phosphate lons (PO4)3- ?
Essential component and backbone of nucleic acids DNA and RNA attached to the molecules as a phosphate group
- in DNA nucleotides enabling nucleotides to join together forming phosphodiester bonds
- In ATP where bonds between them store and release energy
What is the role of hydrogen ions (H+)?
Determines pH levels and acidity
- the more H+ ions the lower the pH and the more acidic
- pH level is determined by concentration of hydrogen ions in the environment
- This controls enzyme reactions therefore changes in pH effect enzyme activity and structure
What is the role of iron ions (Fe2+)?
A very important part of hemoglobin and our key to how oxygen is transported around the body by red blood cells
- Haemoglobin is a large globular protein carrying oxygen around the body in red blood cells
- Made of four different polypeptide chains (each with the Fe in the middle, binding oxygen to hemoglobin)
- Oxygen turns ion into three plus
What is the role of sodium (Na+)?
Involved in coach transport of glucose and amino acids across membranes
- Glucose and amino acids need help Crossing membranes as they’re too large
- A molecule of glucose or an amino acid can be transported into a cell by sodium ions in co transport proteins
