Biological Molecules Flashcards
Hydrolysis
Breaking a bond using water
Covalent bond
A pair of electrons shared between two electrons
Hydrogen bond
Weak interaction can occur whenever molecules contain slightly negatively charged atom bonded to a slightly positively charged hydrogen atom
Carbohydrates elements, monomer, polymer
CHO Monosaccharides (glucose) Polysaccharides (starch)
Protein elements monomer polymer
CHONS
Amino acids
Polypeptides and proteins
Nucleic acid element monomer polymer
CHONP
Nucleotides
DNA and RNA
Properties of water
Liquid Density Solvent Cohesion and surface tension High specific heat capacity High latent heat of vaporisation Reactant
Use of water being liquid
Provides habitats for living things in rivers, lakes and seas
Use of water being dense
Provides aquatic organisms with a stable environment in which to live through the winter
Cohesion and surface tension use
Allows insects like pond-skaters can walk on water
High specific heat capacity
Provides aquatic organisms need a stable environment in which to live
Heat latent heat of vaporisation
Allows sweating to cool animals
Reactant
Extremely important for digestion and synthesis of large biological molecules
Carbohydrates
Functional group- three fold, store of energy
Main groups are: monosaccharides, disaccharides and polysaccharides. Common monosaccharides and disaccharides all have names ending in ose
Monosaccharides
Simplest carbohydrates
Disaccharides
Alpha glucose + alpha glucose-> maltose
Alpha glucose and fructose -> sucrose
Beta galactose + alpha glucose -> lactose
Beta glucose+ beta glucose-> cellobiose
Condensation
Reaction removal of water
How do you draw a glucose?
1) draw hexagon
2) put oxygen in corner
3) put carbons around in hexagon
4) flag pole
5) tail has
When OH
H
It is beta glucose
When H
OH
It is an alpha glucose
How do you draw haemglobin
Alpha beta
Beta Alpha
( all are glucose)
Collegan
Three twists
How do you draw cellulose?
Draw key for hexagon= circle
One Zigzag from each circle
Have a OH flagpole top then bottom all way through
Do two rows
How to draw glycogen?
Hexagons with O in centre of zig zag
Each needs flagpole
Put in v shape
How to draw starch?
Circle circle circle
Hexagon= circle
Name six functions of proteins?
Build cells Move muscles To fight bacteria and viruses Carry oxygen in blood Send chemical messages around the body Enzymes to speed up chemical reactions in body
What is special about myoglobin?
It allows the body to have own blood supply like haemoglobin
Name a protein messenger?
Adrenaline
What makes up proteins?
Amino acids
What must amino acids be bonded in to make a specific protein
A specific sequence
What do different amino acids have?
Different properties
What do the different properties of amino acids cause?
A different effect on the proteins effect
How many different amino acids with different R groups?
20 different amino acids
Give an example of how different properties of a amino can affect the protein?
If proteins contains a number of amino acids with hydrophobic R-groups then the final protein will have a specific shape
Name the protein structure levels
Primary
Secondary
Tertiary
Quaternary
What’s the bond and description of primary level of protein structure?
Bond is peptide
Sequence of o-o-o-o
Helix shape
Secondary bond and description
hydrogen bond
Alpha helix beta pleated sheets
Tertiary bond and description
Hydrophobic/hydrophilia , hydrogen bonds, disulphuric, van der waals
3D shape properties of aa
Quaternary bonds and description
Hydrophilia/ hydrophilia, hydrogen bonds, disulphuric, van der waals
Haemoglobin, four proteins two alpha two beta multiple protein polypeptides, collagen
What structure do gobular have?
Tend to roll up in compact ball shaped structure
Haemoglobin
Any hydrophobic R groups turned inwards towards centre of structure
Hydrophilic R-group tend to be on outside
Makes protein water soluble
Water molecules can easily cluster around them
Fibrous proteins
Form fibres
Most have regular repetitive sequences of amino acids usually insoluble in water
pH denatures ionic-tertiary, Avateraory temporary
Hydrogen bonds destroyed by heating
Give some examples of gobular proteins
Haemoglobin, insulin, pepsin (named enzyme)
Fibrous protein examples
Collegan
Keratin
Elastin
Primary structure of gobular proteins
Tend to roll up into compact globe or ball shaped structure
Hydrophobic R groups turned inwards towards centre of structure
Hydrophilia
Fibrous proteins primary structure
Form fibres
Most have repetitive sequences of amino acids
skin, tendons, Collegan injections
Every third amino acid in Collegan is
Solubility of gobular proteins
Soluble in water
Solubility of fibrous proteins
Insoluble in water
Gobular protein typical functions
Carrying oxygen hormone
Fibrous proteins
Structural proteins
What is carbohydrates
Glucose
Monosaccharide
Made of oxygen hydrogen and carbon
Glucose
Single sugar
Found in blood and in cells
Function source of energy made available from respiration source of raw material to make each other substances
Features of monosaccahides
Soluble in water
Sweet tasting
Form crystals
Role of monosaccahides in living organisms
To release energy through process of respiration
Used to make storage molecules starch (plates)
Compare between monosaccahides and polysaccharides
Similarities- hydrogen at top right, both have OH at bottom right, have six carbons, both carbohydrates
Differences- polysaccharides has two really big groups
Monosaccahides- pentagon ring
Are glucose and glycogen monosaccahides or polysaccharides
Glucose -monosaccahides
Glycogen polysaccharides
Getting glucose
Gluconeogenesis
Reducing glucose
Glycogenolysis
Polysaccharides what’s its role in living organisms?
Respiring substance
Alpha glucose broken down during respiration to make energy available
Used by cells to make new substances
Beta glucose to make cellulose
Alpha glucose to make glycogen and starch (amylose and amylopectin)
How does polysaccharides carry out their role?
Contains large number of bonds that can be broken to form simple molecules
Released energy used to make ATP through a series of enzyme controlled steps in the process of respiration
ATP is
The universal energy molecule
What must an organism have to be able to use glucose in respiration?
Enzymes that can specifically break down the glucose molecule
What type of glucose do animal and plants break down?
Alpha glucose only
Why can’t animals and plants break down beta glucose?
Because of its different arrangement of OH and H group at carbon 1
Why does the different arrangement of OH and H matter in breaking down glucose?
The different shape of the beta glucose molecule means that it doesn’t fit in the active sites of respirate tissues
Features of amylose
Many alpha glucose molecules
Via 1,4 glycodisic bond
Long chains can coil into spring-quite compact molecule
Not water soluble
What can iodine become in amylose and what is it the basis for?
Iodine molecules can become trapped in the coils of the spring causing the iodine to change colour
Basis of the starch test
Glycogen features
Many alpha molecules
Via a 1,4 glycosidic bonds for straight chains
Via a 1,6 glycosidic bonds for branches
Shorter chains than amylose
Highly branched so not as coiled as amylose
Not water soluble
Cellulose
NOT me Many beta glucose molecules Straight chained molecules Many H-bonds between the cellulose molecules go form bundles called microfibrils Not water soluble
Amylose and glucose both are:
Alpha glucose storage molecules 1-4 and 1-6 glucosidic If branched allows high density got storage Cross- linked High strength Structure will complement the enzymes
Calcium symbol and charge
Ca2+
Functions of calcium in the body
Increases rigidity of bone, teeth and cartilage and is a component of the exoskeleton of crustaceans (crabs)
Activator for several enzymes such as lipase, ATPase and cholinesterase
Regulates permeability of cell membrane
Sodium symbol and charge
Na+
Functions of sodium
Contributes to nervous transmission and muscle contractions
Constituent of vacuole in plants which helps maintain turgidity
Affects absorption of carbohydrates in the intestine and water in the kidney
Potassium symbol and charge
K+
Potassium functions
Contributes to nervous transmission and muscle contractions
Involved in control of water levels in body fluid and maintenance of pH
Assists active transport of materials across the cell membrane
Hydrogen symbol and charge
H+
Hydrogen functions
Involved in photosynthesis and respiration
Involved in transport of oxygen and carbon dioxide in the blood
Involved in regulation of blood pH
Ammonium symbol and charge
NH4 +
Ammonium functions
Some hormones are made of proteins e.g. Insulin
A component of the nitrogen cycle
Essential part of nucleic acid
Nitrate symbol and charge
NO3 -1
Nitrate functions
A component of the nitrogen cycle
An essential component of nucleic acids
Component of amino acids, proteins, vitamins and chlorophyll
Hydrogencarbonate symbol and charge
HCO3 -1
Hydrogencarbonate functions
Involved in regulation of blood pH
Involved in transport of carbon dioxide into and out of the blood
Chloride symbol and charge
Cl-
Chloride functions
Used to produce hydrochloric acid in the stomach
Helps in production of urine in the kidney, and maintaining water balance
Involved in regulation of blood pH
Phosphate functions
Component of phospholipids, ATP, nucleic acid and several important enzymes
Involved in regulation of blood pH
Helps root growth in plants
Phosphate symbol and charge
PO4 3-
Hydroxide charge and symbol
OH-
Hydroxide functions
Involved in regulation of blood pH.
How to test for starch
Add iodine solution (in potassium iodide) to sample
If starch is present what will happen
Colour change of yellow-brown to blue-black
What causes this colour change?
When dissolved in potassium iodide (I2) forms triiodide ion (I3. -) which slips into middke of amylose helix causes colour change
Reducing sugars what are they?
All monosaccahides, some polysaccharides
Why are they known as reducing sugars?
They can reduce or give electrons to other molecules
How do you do Benedict’s test?
Add Benedict’s reagent (blue) to sample and heat it make sure solution doesn’t boil. If test’s positive will form coloured precipitate (solid particles supended in solution)
Colour of precipitate changes from: blue-> green-> yellow-> orange-> brick red
Higher the concentration of reducing sugar further the colour change goes use this to compare amount of reducing sugar in different solution
How would you do reducing sugars last step more efficient?
More accurate way of doing this to filter solution and weigh precitate
How would you test non-reducing sugars?
First break them down into monosaccahides
Do this by boiling test solution with dilute HCL and then neutralising it with sodium hydrogencarbonate then carry out Benedict’s test as reducing sugars
What’s annoying about testing for non-reducing sugars?
If result positive sugar could have been reducing or non-reducing
To check you have to do reducing sugar test to
How do you test for proteins?
Biuret test
1) test solution needs to be alkaline do add few drops of sodium hydroxide solution
2) then add some copper (II) sulfate solution
What happens if protein present?
Purple layer forms
What happens if no protein is present?
Solution will stay blue
Why do you need to look carefully?
Because colours are pale
How do you test for lipids?
Shake test substance with ethanol for about a minute then pour the solution in water.
What shows a positive result for the emulsion test?
Solutions turn milky
The More lipid there is the more noticeable the milky colour will be
What shows a negative result for the emulsion test?
Solution will stay clear
How much of ions are required in humans and plants?
Some in large amounts (macronutrients/main elements)
Some in small amounts (micronutrients/ trace nutrients)
Who can display deficiency symptoms?
Plants and humans
How can humans and plants show deficiency sighs?
If they don’t consume enough of a particular ion
Give some examples of deficiency symptoms
Humans and plants Deficiency of trace element cobalt causes anaemia
Deficiency of copper in plants causes young shoots to die back.
What does Benedict’s reagent detect the presence of?
Reducing sugars
What does Benedict’s test show if there are more reducing sugars?
Amount of precipitate increases
Amount of copper (II) ions remain in solution decrease
How can we quantify concentration of sugar in original sample?
Assessing how
Amount of precipitate
Amount of copper (II) in solution vary
Colorimetry
How does a colorimeter work?
Shining a light through a sample
What would we use to separate the precipitate from the Benedict’s solution?
A centrifuge
What is Benedict’s solution in this example?
Supernatant
How can we use a colorimeter?
Using pipette take the supernatant
Place it in curvette
Which is placed into colorimeter
What’s a curvette and what’s it made from?
Small vial
Made of glass/ plastic
What should you ensure you don’t do with the curvette?
Leave a greasy fingerprint on the surface of the curvette as could affect transmission of light
What are often used for greater accuracy?
Colour filters
What would using a red filter in this example do?
Can shine red light through solution
Detect percentage transmission
Solution can reflect blue light but absorbs red light.
What is percentage transmission?
How much passes through
What happens to the percentage transmission and absorption of light if there’s a lot of unreacted copper sulfate?
Supernatant still quite blue
Absorption of red light is high
Percentage transmission is low
What happens to the percentage transmission and absorption of light if there’s little unreacted copper sulfate?
Supernatant less blue
Absorption of red light is low
Percentage transmission is high.
What usually happens between readings?
Device usually zeroed between each reading by placing appropriate blank sample to reset 100% transmission/ absorption
Blank would be water
What does using a colorimeter give us?
A semi-quantitative test for sugar
Can compare how much sugar contained in different samples
What do you need to do to find exact amounts?
Create a calibration curve
How do we create a calibration curve?
Take series of known concentrations of reducing sugar
Using each sample carry out Benedict’s test
Use colorimeter to record light percentage transmission through each supernatant
Plot graph to show transmission of light against concentration of reducing sugars
What does plotting a graph provide?
Calibration curve
Can use with other unknown samples to determine concentration of sugar in original sample
How do biosensors work?
Take biological/chemical variable which can’t be easily measured and convert it to electrical signal
What applications do biosensors have?
To detect
contaminants in water
Pathogens and toxins in food
Airborne bacteria (e.g. Counter-bioterrorism programmes)
Fibrous proteins are like:
Repetitive sequences of amino acids
Usually insoluble in water
Able to form fibres
(structural function, Collagen, elastin, keratin)
Gobular proteins are like:
Tend to roll up into almost spherical shape
Hydrophobics R groups turn inwards, hydrophilia groups on outside
Water soluble
Often specific shapes helps them take up specific roles -enzymes, hormones, haemoglobin
Functions of collagen?
Artery walls
Tendons
Bones
Cartilage and connective tissue
Why is collagen helpful in artery walls?
Prevents artery bursting under high pressure from blood pumped by heart
Why do tendons have collagen?
Connect muscles to bone allowing them to pull on bone
How are bones made from collagen?
Reinforced with calcium phosphate
What is keratin rich in?
Cysteine so lots of disulfate bridges form between polypeptide chains alongside hydrogen bonding makes molecule strong
Where is keratin found?
Finger nails Hair Claws Hoofs Horns Scales Fur Feathers
What does keratin provide?
Mechanical structure
Impermeable barrier to infection
Waterproof prevents entry of water-borne pollutants
What makes the structure of elastin strong and extensible?
Cross-linking and coiling
What does the structure of elastin cause it to be?
Strong and extensible
Where is elastin found?
Where there is a need for stretch/ adapt shape as part of life processes
What is skin like with elastin?
Can stretch around bones and muscles
Without it skin wouldn’t go back to normal after being pinched
Where else does elastin work in the body?
Lungs- allows to inflate and deflate
Bladder- helps expand to hold urine
How is elastin like collagen?
Helps blood vessels stretch and recoil as blood pumped through them
Helping maintain pressure wave of blood as passes through
What’s haemoglobin made up of?
4 polypeptides Two alpha glucoses Two beta glucoses Has own tertiary structure When fitted together form 1 molecule Interactions between polypeptides gives molecules specific shape
Chain of haemoglobin?
One position outside chain space for haem group
Groups like prosthetic groups essential part without couldn’t function
Aren’t made of amino acids
Haem contains iron ion
Protein associated with conjugated protein
Function of haemoglobin?
Carry oxygen from lungs go tissues
What happens in lungs that allows this to happen
Oxygen molecule associates haemoglobin turns from purple red to red colour
Oxygen released by haemoglobin when reached tissues
Insulin made of
2 polypeptide chains
A chain begins with section of alpha helix
B chain ends with section of beta pleat
Both chains fold into tertiary structure joined together by disulfide links
What makes insulin soluble in water?
Amino acids with hydrophilia R groups on outside of molecule makes it soluble in water
Insulin binds to glycoprotein receptors on outside of muscle and fat cells increases uptake of glucose from blood increases consumption of glucose
Pepsin is?
Enzyme digests protein in stomach
What’s pepsin made of
Single polypeptide gushy of 327 amino acids folds into symmetrical tertiary structure
How many amino acids with basic R group and acidic R group?
Four -basic
43- acidic
What does this help explain?
Why it’s stable in acidic environment of stomach as there are few basic groups that accept H+ ions therefore can be little effect on enzymes structure
What’s the tertiary structure held together by?
Hydrogen bonds and two disulfide bridge
Give an example of how predicting the shape of a protein molecules from its primary structure is useful for biochemistry?
Predicting occurrence of biologically active binding sites in protein molecule can help identifying new medicines
How can scientists predict protein shapes?
Using computer modelling techniques
Why can scientists do this?
Techniques for prediction of secondary structure developed based upon probability of amino acids or sequence of amino acids in particular secondary structure
How are these probabilities derived?
Already known protein molecular structures
What makes this so exciting?
Usually tertiary structure of protein molecules contributes directly to bioactive function
What are the two broad approaches?
Ab initio protein modelling
Comparative protein modelling
Ab initio protein modelling
Model built based on physical and electrical properties of atoms in each amino acid in sequence
With this technique can have multiple solutions to same amino acid sequences and sometimes other methods need applying to reduce number of solutions
Comparative protein modelling
Protein threading
Scans amino acids sequence against database of solved structures and produces set of possible models which would match sequence
What is the aim of chromatography?
To separate a mixture into constituents
What are the two components?
Stationary phase
Mobile phase
What is the stationary phase?
Either chromatography paper or thin-lined chromatography plate
What is the TLC plate usually coated in?
Either sheet of plastic with thin layer of silica gel
Aluminium hydroxide
(Either way have free OH group)
Mobile phase is what?
Solvent
Can use alcohol or water
Flows through and across stationary phase
Things to remember?
Wear eye protections draw line in pencil
Spot solution mixture onto pencil dot several times using capillary tubing
Wait for spot to dry to make smaller dot
Cover beaker with watch glass/watch plate
Let run until solvent reached just underneath top of paper. Then remove solvent and lay on tile to dry
What happens as solvent travels up the paper/plate?
Components of solution mixture travels with it.
What happens by the time the solvent reaches the top?
Some travelling slowly and some quickly so different positions on the plate
What can you use to identify pigments?
Relative distance
Rf value
How to calculate the Rf value
Rf= distance from pencil line to centre of spot of pigment/ distance from pencil line to solvent front.
What will have the same value if you repeat the investigation?
Each pigment’s Rf value
How can you identify a certain pigment?
Rf value of this pigment
What are the three solutions to seeing colourless molecules finish using thin-layer chromatography?
Ultra violet light
Ninhydrin
Iodine
How is uv light a solution?
Thin layer chromatography have chemical which fluoresce a under UV light. If you look at the plate under UV light most will glow except places where spots travelled to. Plates mask from UV light.
How is ninhydrin a solution?
See amino acids allow plate to dry then spray with ninhydrin. Binds to amino acids which are then visible as brown/ purple spots
How is iodine a solution?
Allow plate to dry
Place in enclosed container with few iodine crystals
Iodine firms gas the same binds to molecules in each of spots
What does the speed of molecules along paper/ TLC plate depend on?
Solubility in solvent and polarity
In paper chromatography may also depend on size
How does this happen?
Exposed -OH groups make surface of paper/plate very polar
Allow it to form hydrogen bonds with molecules along other dipole interactions
Highly polar solute will tend to stick to surface move more slowly
Non-polar solute travel very quickly
How can it be difficult to tell between two molecules?
Same speed
If this happens different solvent or change pH
What is thin-layer chromatography used for?
To monitor progress of reactions because works relatively quickly.
What is it also used for?
Urine testing of athletes for illegal drugs
Analysing drugs for purity of components
Analysis of food to determine presence of contaminants
Function of amylase?
Storage
Function of cellulose?
Plant structure
Why does pH falls during reaction and why did it stop?
Fatty acids formed which is acidic meaning the acid levels rise. Enzyme denatured due to low pH.
Bond holds sucrose together is?
Glycosidic
