Molecules Flashcards
What is a macromolecule?
Large biologically important molecules inside cells.
They are composed of sub units and have structural, enzymatic or other functions.
Organelles are a collection of macromolecules that carry out functions in the cell.
Examples of macromolecules?
Polysaccharides, Nucleic acids, Protein
Specifically - Hb, DNA, Glycogen, Collagen
Water works well as a solvent for?
Ionic and polar compounds.
This is due to the hydrogen bonding in water.
(The electronegative O and the electron with its lone pair of electrons and the deficient H)
What type of intermolecular forces does water have?
- Hydrogen bonding
- Induced dipole - dipole interactions
- Permanent dipole - dipole interactions
Due to all three unique 0–100 as a liquid
Carbohydrates general formula?
Cn(H20)n
Made up of carbon, hydrogen and water only
What is a glycosidic bond?
A condensation reactions between the a carbohydrate (sugar) with another group which is often another sugar.
In this case the 2 OH groups form a covalent bond with the loss of a water molecule.
What is a disaccharide?
Oligosaccharide?
Polysaccharide?
Di - 2 monosaccharides
Oligo - 3 - 12 monosaccharides
Poly - 1000s of MS e.g glycogen and proteoglycans
What is a proteoglycan?
A structure made up of long unbranched polysaccharides (glycosaminoglycans) radiating from a core of protein.
Tend to have structural functions e.g in cheeks
Can also contain sulphur in which case they soak up lots of water and are used in protection e.g bones and joints
General overview of lipids…
Contains a carbon chain usually 16-20 C
They contain a methyl and a carboxyl group at the ends
Unsaturated lipids have lower melting points
Steroids general overview…
Multicyclic and complex structures
Involved in cell signally and as they are lipids they can pass into cells and their nuclei.
They stem from 3, 6C rings and 1 5C ring.
Eicosanoids…
20 C atom acids
Lipid derivative
Inhibit inflammation and have many more functions
Which bases are purines and which are pyrimidines?
Purines = Adenine and Guanine - have 2 rings
Pyrimidines = Uracil, Cytosine, Thymine - all have 1 ring
A 2 T
C 3 G
A.A overview
2 different types of side chain and hence 20 different a.a
They can be charged in certain PH’s
COOH — COO-
NH2 — NH3+
They can be polar and can be aromatic
Peptide bond?
A peptide bond is a covalent bond between the NH2 and COOH group of 2 amino acids to form a dipeptide and — polypeptide.
A condensation reaction
Polar definition?
Dipole definition?
Polar = uneven distribution of electrons
If a bond in a molecule is polar (large difference in electronegativity) then the molecule will be polar. Unless the bonds are symmetrical and hence cancel out.
Dipole = separation of opposite charges
In a protein which way do you name the a.as?
From the amine to the carboxyl terminal
Protein
Primary, secondary, tertiary, quaternary structures…
- Sequence of a.a
- H bonds from causing the formation of an alpha helix of a beta pleated sheet
- Disulphide bridges and ionic bonds can form, leading to a 3D specific structure
- Tertiary + more a.a chains +/or a prosthetic group
Name the different types of intermolecular forces and bonds found in a protein.
Induced dipole - dipole interactions - electrons moving about in atom cause instantaneous dipole which induces further dipoles in neighbouring molecules that attract.
Permanent dipole - dipole interactions - permanent delta + and delta - attraction
Hydrogen bonding - between electronegative atom, (N, O, F) with a lone pair of electrons that attracts a delta + Hydrogen.
Ionic bonds - atoms lose electrons to form ions that attract one another
Disulphide bridges - only found in cytosine, when the protein folds and it brings two of these molecules together a bridge will form. Provides extra support.
Note - hydrophobic side chains form tight cores in the interior proteins when in water.
How to determine the structure of proteins?
X-ray diffraction of protein crystals. This produces spots of light that can be analysed and used to rebuild the protein.
Enzymes
Biological catalysts, increases the rate of reaction, but can also control the rate.
Work by the lock and key or induced fit theory…
Sickle cell anaemia, what is it and symptoms?
Genetic disorder that is characterised by the formation of hard, sticky sickle shaped red blood cells.
Pain in chest, legs etc as they can block them and also shortness of breath and energy as they transport less oxygen.
Antibodies/ immunoglobulins
What is the CDR and what is its job?
= Complementarity determining region
It is responsible for the range of boding effects - ionic, MF’s etc
Also has loops that compliment the surface of the antigen.
This ensures a very tight bond/ antigen-antibody complex.
The portion of antigen bound is known as the epitope.
DNA function?
The genetic material of an organism that acts as a template for transcription and hence protein synthesis. It is all the structural basis for heredity and genetic diseases.
Prokaryotes vs Eukaryotes DNA?
In prokaryotes the DNS has no nuclear membrane, one circular strand, non linear and is not associated with histones.
DNA structure?
It is made up of 4 nucleotide bases, a phosphate group and deoxyribose.
It is made of two anti parallel strands and grows from the 5 to the 3 prime end, via the phosphate group binding with the OH and hence forming a phosphodiester bond.
Epigenetics
How environmental factors such as jet and stress can cause heridedible changes to DNA without changing the DNA base sequence.
This is due to methylation and acylation.
Oncogenes
Proto-oncogenes
A mutated gene that can cause cancer
A gene involved in normal cell growth (regulate division and death)
DNA Replication:
DNA opens at the replication fork and DNA helicase splits the strands.
Topoisomerase unwinds the strands and then DNA nucleotides activated using ATP join via complimentary base pairing.
Each strand has one new and one old strand and this is why it is called Semi-conservative replication.
The strands are shut via DNA Polymerase - forming the phosphodiester bonds
DNA has multiple origins of replication.
Polymerase Chain Reaction
- Select DNA to be amplified
- Heat to separate the strands
- Cool and add primers
- Add heat stable DNA polymerase
- Heat and cool with primers and DNA nucleotides and repeat to produce more copies
What damages DNA?
Chemicals
Radiation - ionising and UV
DNA adduct = reacts with bases to form a bulky group that disrupts replication
DNA repair:
The base or nucleotide is taken out (excision)
Then the strand is corrected
What are the differences between DNA and RNA?
Double stranded
1 x type
More stable
No Uracil
3 types of RNA and their function?
MRNA - (messenger) - template for protein synthesis
RRNA - (ribosomal) - 4 types and protein are used to form ribosomes
TRNA - (transfer) - complimentary anticodon to codon on mRNA brings specific a.a to ribosome
Transcription process:
DNA helicase separates the two strands
Topoisomerase unwinds it
RNA nucleotides join to their complimentary base pairs
RNA polymerase forms the sugar phosphate backbone.
Pre mRNA detaches and is spliced in the nucleus
It then passes out the nuclear pore and will travel to a ribosome most likely on the RER
Introns
Exons
Introns = non coding sections of DNA Exons = coding sections of DNA
The code is…
Almost universal
Degenerate
Non overlapping
What turns expression off?
What turns expression on
Represors that inhibit RNA polymerase binding
Enzymes no longer activated
RNA stability
Methylation acylation
On = TFs
Retro virus =
a virus that can produce DNA from RNA using an enzyme known as reverse transcriptase
Hb
Haemoglobin is a quaternary protein involved in transporting oxygen around the body via red blood cells.
At the core of Hb is a porphyrin ring which golds an iron atom this iron atoms forms ligand with oxygen.
increase temperature decreased affinity of Hb for oxygen - enhance unloading.
What is the job of glycosylases?
Glycosylases are involved in the repair of damaged bases in DNA
