C3 Biological molecules Flashcards
light microscope
-Poor resolution due to the long wavelength of light
-living samples can be examined and a colour image is obtained
Transmission electron microscope
-High magnification and resolution
-Electrons pass through the specimen to create an image
Scanning electron microscopes
-High magnification and resolution
-Electrons bounce of the surface of the specimen to create an image
Laser scanning confocal microscopes
-High resolution and 3D imaging
-Laser light is used to create an image
Types of microscopes (4)
-Light microscopes
-Transmission electron microscopes
-Scanning electron microscopes
-Laser scanning confocal microscopes
What is the definition of resolution?
- minimum distance between two objects in which they can be viewed as separate.
- Optical microscope = determined by the wavelength of light
- Electron microscope = determined by the wavelength of the beam of electrons
What is the definition of magnification ?
Refers to how many times larger the image is compared to the object
What is an eyepiece graticule ?
inside light microscopes , there is a scale on a glass disc called the EPG
what do we use the eyepiece graticule for?
Used to measure the size of objects you are viewing under the microscope
Why do we need to calibrate our eye piece graticule?
We need to calibrate the eyepiece each time we change the objective lens as the magnification changes
How do we calibrate? (3)
1) Line up the stage micrometer and eye piece graticule looking through the eyepiece whilst looking through the eyepiece
Why is water represented in a v shape?
- Each bond represents a pair of shared electrons
- 2 lone pair of electrons on the oxygen
What is more electronegative in water?
O is more electronegative than H
- electrons will orbit around the o a lot more than the H
what is a polar molecule
Unequal share of electrons
Example of polar molecules
glucose
HCL
What bond is formed between different polar molecules ?
hydrogen bond
why do we represent hydrogen bonds as dotted lines?
they are weak bonds, straight lines are covalent bonds
Important functions of water
Using examples of E and P
- they can be a solvent , mainly dissolve polar molecules EG: enzymes
- Medium for chemical reactions
-transport medium
-coolant for your body
-habitat
Prokaryotes use water to obtain some elements and compounds for their survival.
Water’s solvent properties allow it to dissolve and transport many biological molecules, such as carbohydrates, proteins, and nucleic acids
what is cohesion ?
hydrogen bonds between water molecules
What is adhesion
Force between water molecules and the surface it is attached to
What is glucose known as?
a hexose (6carbon) monosaccharide
What are the two different types of glucose molecules?
-alpha
-beta
What bonds do glucose molecules form
glycosidic bonds
How do we form glycosidic bonds between glucose molecules?
condensation - when two glucose molecules join together and produce a water molecule
how do you bring down a glycosidic bond ?
Hydrolysis- breaking down using water
What two types of glycosidic bonds can we form?
1,4 glycosidic bonds - form straight chains of glucose molecules
1,6 glycosidic bonds- forms branches
example of alpha glucose in plants
starch (made up of two different parts)
-amylose (straight chain 1,4)
-amylopectin (branched chain 1,4 and 1,6)
difference between glycogen and amylopectin
glycogen is more branched
Example of an alpha glucose in animal
glycogen - branched 1,6 and 1,4
Why is a branched molecule ideal for energy storage?
compact (stable) and hence doesn’t react with water or any other molecule, wont lose glucose as quick , we can retain more stuff to do respiration or anything else
What are the different types of lipids?
-triglyceride (1 glycerol molecules and 3 fatty acid chains)
-phospholipid
ESQ: They mixed oil and pH indicator Jan practical, when they added lipass, why did the PH drop?
A triglyceride is broken down by lipase to release glycerol and fatty acids , the fatty acids are what make the mixture acidic
How is an ester bond formed in a triglyceride ?
Triglycerides are formed by the condensation of one molecule of glycerol and three molecules of fatty acid. A condensation reaction between glycerol and a fatty acid (RCOOH) forms an ester bond.
What are the three different types of fatty acids that you can find in a tryglyceride?
-saturated (no double bonds)
-unsaturated (double bonds)
-ployunsaturated ( more than one double bond)
Why are phospholipids so important ?
it makes up the plasma membrane
In a phospholipid bilayer what properties do the phosphate and fatty acids have?
-the phosphate head is hydrophilic
(can deal with charged molecules Eg: Water )
-fatty acid tails - hydrophobic
What molecules can not go through the hydrophobic layer?
polar molecules- EG: An oily layer
what do we have in a plasma membrane?
-phosphate heads and fatty avid tails
(phospholipid bilayer)
-cholesterol
-protein channels (passage of polar molecules)
Facts we need to know about cholesterol
- 4-ring structure
-dual hydrophobic and hydrophilic properties
-provides stability to a plasma membrane
protein channel for water
aquaporins
What is an amino acid made of ?
- left = amine group
-bottom= R group
-Right = carboxyl group
How many different types of amino acids are there ?
20
What is the R group in an amino acid and what does it change depending on?
-the R group is the variable group
-changes depending on the 20 different types of amino acids
What reaction will make amino acids into a protein?
condensation reaction
What bond is formed between two amino acids when making a protein?
A peptide bond
What is a dipeptide ?
A dipeptide is a molecule that consists of two amino acids joined together by a peptide bond
What is a polypeptide?
A polypeptide is a chain of amino acids
What are the different levels of protein structure?
- primary
-secondary (alpha helix)
-secondary (beta pleated sheet)
-tertiary
-quaternary
What is a primary protein and what bonds does it make ?
- the sequence of amino acids linked together to form a polypeptide chain.
- Covalent, peptide bonds which connect the amino acids together maintain the primary structure of a protein
What is a secondary protein and what bond does it make?
- hydrogen bonds , between amine group, carboxylic group and the hydrogen but not the variable group
- A protein’s secondary structure prepares it for the further three-dimensional folding required to establish its tertiary structure
What is a tertiary protein structure and what bonds does it form?
- 3D structure
-The tertiary structure of a protein refers to the overall three-dimensional arrangement of its polypeptide chain in space
-hydrogen bonds, London forces, ionic binds, covalent bonds , disulphide bridges (example of a covalent bond), hydrophobic interactions (amino acids)
What is a quaternary structure and what bonds does it make?
-The quaternary structure of a protein is the association of several protein chains or subunits into a closely packed arrangement. Each of the subunits has its own primary, secondary, and tertiary structure
(different subunits joining up)
- same bonds tertiary
-hydrogen bonds, London forces, ionic binds, covalent bonds , disulphide bridges (example of a covalent bond), hydrophobic interactions (amino acids)
Examples of a quaternary protein
-haemoglobin
-DNA polymerase
-ribosomes
-antibodies
-ion channels
One haemoglobin subunit :
- Contains a haem group in the centre
- the haem group is hexagonal shape
- the haem group contains an iron ion (sometimes require non-protein components to function)
- Without the haem group, the haemoglobin wont function
How to test for starch?
-iodine solution (iodine in potassium iodide solution)
-brown to blue/black
-pasta, rice , potatoes
How to test for reducing sugars?
-Benedict solution
-Heat with the benedict solution in a water bath
-blue to brick red precipitate
-copper 2+ to copper + (reduction)
-green = low concentration of reducing sugars
-yellow = medium concentration
-brick red = high concentration
-EG: fructose and glucose
How to test for non reducing sugars?
-Benedict solution has no results
-boil with HCl
-HCL with hydrolyse the sucrose to fructose and glucose (reducing sugar)
-Idea is that we convert the non-reducing sugar to a reducing sugar so we can use the benedict solution to test for reducing sugars (Blue to brick red)
How to test for lipids?
-emulsion test
-mix ethanol and water and sample
-white emulsion layer is formed
-EG: butter or oil
What is the test for protein?
- biuret solution (alkaline solution ,contains copper sulphate hence is blue)
- Blue to lilac
What is the first enzyme in semi conservative replication ?
DNA helicase
What does DNA Helicase do?
DNA Helicase unzips DNA (separates the two strands) by breaking hydrogen bonds between the complementary bases
What are the four bases in DNA and who do they pair up with?
adenine (A), thymine (T)
cytosine (C), guanine (G)
What happens in step 2 of the DNA semi-conservative replication?
Free moving nucleotides floating around will be attracted to the exposed bases by complementary base pairing (AT and CG)
What happens in step 3 of semi Conservative replication?
Free nucleotides joined together by phosphodiester bonds by DNA polymerase
-this forms our sugar-phosphate backbone of new DNA strand
What happens in stage 4 of semi Conservative?
each DNA molecule gains a new strand
Why is it called semi Conservative replication?
Because in stage 4 we get a DNA molecule with one old strand and one new strand
ESQ what is proof for semi Conservative replication ?
the first DNA strand is made of nitrogen 14 as part of the nitrogenous bases)
Free nucleotides would have N15 (modified and heavier nitrogen)
What is the first step in protein synthesis?
Transcription
What is the structure of a nucleotide?
1- Nitrogenous bases – Purine and Pyrimidine
2- Pentose Sugar – Ribose and Deoxyribose
3- Phosphate – monophosphate, diphosphate, triphosphate
In a nucleotide, what is the bond between a pentose sugar and phosphate?
Ester
What are the four bases in RNA?
adenine, guanine, cytosine and uracil (U)
In a nucleotide, what is the bond between a pentose sugar and a base?
glycosidic
Which bases are purine bases?
adenine and guanine
Which bases are pyrimidine bases?
cytosine, thymine and uracil
What is the difference between a purine base and a pyrimidine base?
- They are different shapes
- Purines are 6+5 membered rings
-pyrimidine are 6 membered rings
Why must a purine always pair with a pyrimidine ?
A purine must always bond with a pyrimidine if the ‘rungs’ of the DNA ‘ladder’ are to be the same length –
adenine always pairs with thymine, and guanine always pairs with cytosine
How many hydrogen bonds are there between complementary bases in a nucleotide?
A-T = 2 bonds
C-G = 3 bonds
What is a phosphate ladder?
The phosphate and sugar section of the nucleotides form the ‘backbone’ of the DNA strand (like the sides of a ladder) and the base pairs of each strand connect to form the rungs of the ladder
Similarities and difference between a RNA and a DNA pentose sugar?
- RNA and DNA pentose sugar are both 5 sugar molecules
- Pentagon structure
- BUT both the 2nd carbon on the DNA is deooxy hence is a H wheras in RNA it is oxy hence the second carbon is OH
What is the difference between a nucleoside and a nucleotide?
-Nucleoside = nitrogenous base + pentose sugar
-Nucleotide = nitrogenous base + pentose sugar + phosphate
What does a gene code for ?
A protein
What is ATP and how is it used in RNA and DNA?
ATP is the energy currency of the cell. The energy required for metabolic processes is derived from ATP. It also acts as a coenzyme and is a precursor of DNA and RNA synthesis.
What are the steps in protein synthesis in order?
-Transcription
-Translation
What is the goal of transcription ?
To produce mRNA
What are the key steps in transcription?
1- Transcription factor binds to promoter region. The binding of a transcription factor to a promoter leads to the recruitment of several key enzymes to the area
2- DNA helicase unwinds the gene region - by breaking the hydrogen bonds between the two strands. This exposes the bases on each strand.
3- Enzyme RNA polymerase binds. The enzyme RNA polymerase binds in a region just before the start codon of the gene.
4- RNA polymerase transcribes the mRNA. RNA polymerase reads the nucleotides on the unwound template (antisense) strand of DNA. It then recruits nucleotides and continually makes a strand of RNA. The growing mRNA strand lengthens in the 5’ to 3’ direction.
5- RNA polymerase reaches the stop codon. RNA polymerase stops transcribing mRNA once it reaches the stop codon
6- The resulting strand of RNA is known as pre-mRNA. The pre-mRNA will have the complimentary sequence to the coding strand, except all thymine bases will be will be replaced with uracil bases
What happens in translation (fancy)?
1- After leaving the nucleus via a nuclear pore, the mRNA molecule attaches to a ribosome
a) Ribosomes consist of
ribosomal RNA (rRNA)
b) rRNA is a stable molecule that
allows mRNA to attach to the
ribosome and is aligned correctly
ready for the synthesis of the
polypeptide chain
2- In the cytoplasm, there are free molecules of tRNA (transfer RNA)
3- These tRNA molecules have a triplet of unpaired bases at one end (known as the anticodon) and a region where a specific amino acid can attach at the other
4- There are about 20 different tRNA molecules, each with a specific anticodon and specific amino acid binding site
What is translation (easy)?
1- Ribosomes bring over the tRNA
2- Ribosomes moves up in threes and reads the bases
3-
What does a ribosome consist of ?
- A large subunit and a small subunit
What are the two types of proteins?
Globular and fibroses
What do fibrosis proteins compared to globular proteins do?
Fibrous proteins are often have a structural purpose in the body, which means they help maintain shape and provide scaffolding.
In comparison to globular protein which plays a greater role in biological function and chemical processes.
What is a polysaccharide ?
Polysaccharides are macromolecules AKA polymers that are formed by many monosaccharides joined by glycosidic bonds in a condensation reaction to form chains
Examples of polysaccharides
Starch, glycogen and cellulose
How does the structure and function of cellulose relate to their functions in living organisms?
Cellulose molecules are arranged parallel to each other and are joined together with hydrogen bonds
Cellulose is used to provide strength and rigidity to the plant cell wall.
How does the structure and function of glucose relate to their functions in living organisms?
How does the structure and function of glycogen relate to their functions in living organisms?
How does the structure and function of starch relate to their functions in living organisms?
Examples of fibrosis proteins
Examples of globular proteins
How to calculate the Rf value in chromtography?
Distance moved by the solute/distance moved by the solvent
