Topic 2- molecular biology Flashcards
Draw water molecule
Labels and clear arrow showing hydrogen bond
Polar
Uneven distribution of molecule charge
Hydrogen bond
Bond formed between the - charge from the oxygen of one water molecule and the + from the hydrogen atom of another water molecule
3 properties of water
- Water is liquid
- Water is a solvent
- Specific heat capacity of water is very high & remains relatively stable
Water also has high heat of vaporisation and fusion
Cohesion
Water molecules ‘sticking’ together
Result of the polarity of a water molecule and its ability to form hydrogen bonds
Adhesión
‘Sticking’ to other molecules that are charged or polar, ex) water molecules sticking to beaker surface
(Result of the polarity of a water molecule and its ability to form hydrogen bonds)
Monosaccharide
= one sugar unit
- fructose, glucose, galactose (found in milk)
B glucose diagram
OH on top
A glucose
OH on the bottom
Disaccharide
= two sugar units
-maltose, lactose, sucrose
Ex) glucose+glucose—(condensation)>maltose + water
Polysaccharide
- starch, glycogen, cellulose
Cellulose
- high tensile strength
- unbranched
- condensation reaction links carbon 1 and carbon 4, (1,4) glycosidic bond
- made by linking B glucose molecules
- subunits oriented alternatively upwards and downwards
Starch
- made by linking a glucose molecules
- all the glucose molecules can be oriented in the same way, curved rather than straight
- (1,4) glycosidic bond
Amylose & amylopectin
Amylose: unbranched, forms helix
Amylopectin: chain is branched, globular shape
- starch is only made by plants
- too large to be soluble in water (useful in cells where large amount of glucose needs to be stored as starch in seeds and storage organs, ex) potato cells)
- doesn’t affect osmotic balance
Glycogen
- branches many times, making the molecule more compact
- made by animals and also some fungi’s
-stored in the liver and some muscles in humans - same function as starch in plants
(Acts as a store of energy in the form of glucose), because it is insoluble, large amounts can be stored - like starch, it is easy to add or remove extra glucose molecules
Lipids
= fats (solid at room temp) and oils (liquid at room temp)
- used for long term energy storage
General formula:
H3C—(CH2)n—C=0, -OH
Label general formula as chain of carbon and hydrogen atoms, carboxyl group
Triglycerides
Formed by condensation from 3 fatty acids and one glycerol
Cis-isomers
- more loosely packed, hence lower melting point
- found in nature
- double bond causes a kink, curve in the chain
- hydrogen atoms are on the same side of the two carbon atoms
Trans-isomers
- rare to be found in nature, artificially made
- hydrogen atoms on different sides of the two carbon atoms
- double bond does not cause kink, thus more compact with higher melting point
Saturated
Draw as ^^^^^, all single bonds
Monounsaturated
Draw as ^—-^^^^^, one double bond
Polyunsaturated
Draw as ^——^—^, contains more than 1 double bond
BMI formula
Mass (kg)/ height (m)^2
Units= kgm ^-2
Draw protein diagram
Label with amino group, variable (20 different types), carboxylate group
Anabolic reaction
Getting more complex molecules from simple molecules
Draw formation of peptide bond
Clearly label peptide bond
Amino acid
Monomers of protein
Primary structure
- the order/unique sequence of the amino acids in a polypeptide
- controls all subsequent levels of structure
Secondary structure
- chain of amino acids fold in different structures; a helix and B pleated sheets
- structures are held by hydrogen bonds for structural stability
B pleated sheets: two or more segments of a polypeptide chain line up next to each other
A helix: backbone follow helical structure, R groups stick outwards (free to interact)
Tertiary structure
-polypeptides folds and coils to form a 3D shape, held by ionic bonds
- caused by interaction between R groups
Ex) disulphide bridges, caused by interactions between sulfur atoms
Quaternary structure
- single peptide chain has only 3 levels of structure unlike proteins made from multiple polypeptide chains
Fibrous proteins
- have a structural (strength and support) role
- long and narrow in shape
- insoluble in water
- less sensitive to changes in PH, heat
Ex) collagen, keratin, myosin - repetitive amino acid sequence
Globular protein
- functional role
- rounded/spherical in shape
-soluble in water
-irregular amino acid sequence - more sensitive to changes in PH and heat
Ex) insulin, haemoglobin
Rubisco (enzyme)
Catalysts the photosynthesis reaction that fixes carbon dioxide from the atmosphere
Insulin (hormone)
Produced by the pancreas, triggers a reduction in blood glucose
Immunoglobulins (antibodies)
Produced by plasma cells that are capable of targeting specific antigens
Collagen (structural)
Used in skin to prevent tearing, in bones to prevent fracturing, tendons and ligaments to give high tensile strength
Spider silk (structural)
High tensile strength, becomes stronger when stretched
Enzyme
- biological catalyst
- globular protein
Diagram with labels:
- active site + substrate, enzyme substrate complex, product, enzyme remains unchanged
- enzymes are specific to their substrates
Lock and key hypothesis
- structurally, substrates that don’t fit wont react
- functionally, substraes that are not chemically attracted wont react
Desaturation
Permanent change of active site so that the substrate cannot bind/bond
- affected by temp, PH level, substrate concentration
Temp enzyme affecting diagram
Optimum temp labelled as 37*
- increase in temp increases kinetic energy, meaning there’s more successful collisions
- due to heat, active site changes shape meaning substrate cannot bind as easily
PH level enzyme affecting diagram
Label optimum PH level as 7
- change in PH can alter shape resulting in a diminished rate of reaction
Induced fit model hypothesis
- as substrate approaches the enzyme, it induces a conformational change in the active site/changes shape to fit the substrate. This stresses the substrate, reducing the activation energy of the reaction
Draw labelled diagram; attraction, reaction/conformation change, enzyme reverts to original shape/release
Advantages of enzyme immobilisation
- enzymes can be resumed, saving money
- products are not contaminated with enzymes
- enzymes are resistant to desaturation over greater ranges of PH and temp
- concentration of substrate can be increased as the enzyme isn’t dissolved
Collision
- the coming together of a substrate molecule and active site
- successful collisions only happen when substrae and active sites are correctly aligned
Methods of enzyme immobilisation
- attachment to surface such as glass (adsorption)
- entrapment in a membrane or a gel
- aggregations of enzymes bonded together
Substrate concentration enzyme effect diagram
Correctly drawn diagram
- as substrate concentration increases, there is more chance of collision, hence rate of reaction increases
- at high substrate concentration, many active sites are ‘occupied’ so raising the substrate concentration has little to no effect on enzyme activity
Making lactose free milk
Lactos—> glucose+galactose
- lactase is bound to the surface of alginate beads
- milk is passed repeatedly over beads
- the lactose is broken down into glucose and galactose
- the immobilised enzyme remains to be used again and doesn’t affect milk quality
DNA 4 bases
Adenine with thymine
Guanine complementary with cytosine
DNA nucleotide
Single unit of a nucleic acid
Draw a DNA nucleotide
Clearly labelled with; phosphate (negatively charged), deoxyribose sugar base (5 carbon atoms, pensase sugar), base (contains nitrogen)
DNA key points/structure wise
- Is a double helix
- has a sugar phosphate backbone
- bases join the two strands by hydrogen bonds
- two strands run in opposite directions/anti parallel
- nucleotides are linked into a single strand via a condensation reaction
Purines and pyrimidines
Adenine and guanine are purines
Thymine and cytosine are pyrimidines
Draw a DNA sequence diagram
Clearly labelled; covalent bond ( phosphodiester bond), sugar phosphate backbone, 5’ (5-prime) on the left top corner, 3’ (3-prime) on top right corner, hydrogen bonds, phosphate, base, deoxyribose sugar base
Watson and Crick
- stick and ball models
- first model (triple helix) was rejected:
Ratio of adenine to thymine was not 1:1 and it required too much magnesium
From their setbacks they realised - DNA must be a double helix
- strands must be anti parallel to allow base pairing to happen
- relationship between the based and base pairing
Rosalind Franklin and Maurice Wilkins
Used x ray diffraction to understand the physical structure of the DNA molecule
DNA helicase
- unwinds the DNA helix (ATP is needed)
- separates the two polynucleotide strands by breaking the hydrogen bonds between complementary base pairs, two separated strands become the parent/template strands
DNA polymerase
- always moves in a 5’ to 3’ direction
- creates complementary strands
Polymerase chain reaction (PCR)
- used to amplify small samples of DNA (segment)
Occurs in thermal cycles:
1. Denaturation: DNA sample is heated to separate it into 2 strands
2. Annealing: DNA primers attach to opposite ends of the target sequence
3. Elongation: a heat tolerant DNA polymerase (TAS) copies the strands
Meselson and Stahl
- two theories of DNA replication was suggested, conservative and semi conservative
- DNA from bacteria E.coli that had been grown in medium containing N15 was cultured and appeared as a single band
- It was then transferred to a medium with the less dense N14, where it then replicated
- After a second round of replication, DNA appeared as two bands (one as half N15 and half N14)
Draw clear diagram as example
Protein synthesis
Creation of proteins by cells that uses DNA, RNA etc..
Transcription
-occurs in the nucleus
(Process by which an RNA sequence is produced from a DNA template)
RNA polymerase binds to a site on the DNA at the start of the gene and separated it into two strands, RNA polymerase assembles the free nucleotides and links them to form a single strand of mRNA.
The completed strand of mRNA detaches from the DNA and RNA polymerase ‘zips’ up the two strands of DNA again.
(In mRNA, the base Uracil, U, replaces Thymine, T)
Translation
-takes place in the cytoplasm on ribosome
(Process that uses the coded information in mRNA to construct polypeptide chains/mRNA translated into a sequence of amino acids in a polypeptide chain)
- each triplet of bases on the mRNA= codon
- each triplet of bases on the tRNA= anticodon
Ribosome is composed of two halves, large subunit (binding site for tRNA) and small subunit (binds to mRNA)
- MRNA binds to a site on the small subunit of the ribosome
- The larger subunit binds to the smaller subunit/come together
- There are 3 binding sites for tRNA molecules on the large subunit but only two bind at once, the bases on the codon and anticodon link together by forming hydrogen bonds.
- The amino acids carried by the tRNA molecules are bonded together by a peptide linkage and released/detached. As the ribosome moves along it form a growing peptide chain.
Draw clearly labelled diagram
Start codon
The coding region starts with a start codon, AUG
Stop codon
The coding region terminates with a stop codon, it does not add an amino acid, instead it causes the release of the polypeptide
Cell respiration
The controlled release of energy from organic compounds in cells (to form ATP)
Aerobic respiration equation
C6H12O6+6O2—> 6H2O+6CO2 + energy
ATP
(Adenosine triphosphate) is the immediately available energy source for a cell, made in the mitochondria
- broken down to ADP (adenosine di phosphate) and inorganic phosphate, this conversion releases energy
Glucose—> 2 pyruvates diagram
Clearly label with;
- glycolysis (occurs in the cytoplasm)
- small ATP yield
- occurs in mitochondria
- high ATP yield
Respirometer
Device used to measure the rate of respiration by measuring the rate of oxygen consumption
Aerobic VS Anaerobic
Aerobic:
- occurs in cytoplasm and mitochondria
- requires oxygen
- produces CO2 and H2O
- produces around 38 ATP molecules
Anaerobic:
- occurs in cytoplasm
- produces a small yield of ATP
- no oxygen is used
- produces lactate, ethanol and CO2
