Topic 1 - Biological Molecules And Nucleic Acid Flashcards
Monomer
The smaller units from which larger molecules are made
Polymer
Molecules made from a large number of monomers joined together
Monosaccharide
The monomers from which larger carbohydrates are made
e.g. glucose, fructose, galactose
Disaccharide
Formed by the condensation of two monosaccharides
held together by a glycosidic bond
e.g. maltose, sucrose, lactose
Polysaccharide
Formed by the condensation of many glucose units
held by glycosidic bonds
e.g. starch, glycogen, cellulose
Cellulose
Polysaccharide in plant cell walls formed by the condensation of
β-glucose
Glycogen
Polysaccharide in animals
formed by the condensation of
α-glucose
Starch
Polysaccharide in plants
formed by the condensation of α-glucose
contains two polymers - amylose and amylopectin
Glycosidic bond
C–O–C link
between two sugar molecules formed by a condensation reaction
it is a covalent bond
Amylose
Polysaccharide in starch made of α-glucose
joined by 1,4-glycosidic bonds
coils to form a helix
Amylopectin
Polysaccharide in starch
made of α-glucose
joined by 1,4 and 1,6-glycosidic bonds
branched structure
Condensation reaction
A reaction that joins two molecules together
with the formation of a chemical bond
involves the elimination of a molecule of water
Hydrolysis reaction
A reaction that breaks a chemical bond
between two molecules
involves the use of a water molecule
Microfibrils
Long, straight chains of β-glucose running parallel to one another
Cross linked by hydrogen bonds
These molecules joined to form microfibrils which in turn are grouped to form fibres
Triglyceride
Formed by the condensation of one molecule of glycerol and three molecules of fatty acids
forming 3 ester bonds
Phospholipid
Formed by the condensation of one molecule of glycerol and two molecules of fatty acid
held by two ester bonds
a phosphate group is attached to the glycerol
Induced-fit model
The enzyme active site is not initially complementary to the substrate
the active site moulds around the substrate
this puts tension on bonds lowers the activation energy
Competitive inhibitor
A molecule that is the same/similar shape as the substrate
binds to the active site
prevents enzyme-substrate complexes from forming
Non-competitive inhibitor
A molecule that binds to an enzyme at the allosteric site
causing the active site to change shape
preventing enzyme-substrate complexes from forming
Primary structure
The sequence of amino acids on a polypeptide chain
Secondary structure
The folding or coiling
to create a β pleated sheet or an
α helix
held in place by hydrogen bonds
Tertiary structure
The further folding to create a unique 3D shape
held in place by hydrogen, ionic and sometimes disulfide bonds
Quaternary structure
More than one polypeptide chain in a protein
Can also have prosthetic group
Peptide bond
Covalent bond joining amino acids together in proteins
C–N link between two amino acid molecules
formed by a condensation reaction
What is the effect of temperature on enzyme-controlled reaction
At low temperatures, there is not enough kinetic energy for successful collisions between the enzyme and substrate.
At too high a temperature, enzymes denature, the active site changes shape and enzyme- substrate complexes cannot form.
What is the effect of pH on enzyme-controlled reaction
Too high or too low a pH will interfere with the charges in the amino acids in the active site.
This breaks the ionic and hydrogen bonds holding the tertiary structure in place
therefore the active site changes shape and the enzyme denatures
Different enzymes have a different optimal pH
What is the effect of substrate concentration on enzyme-controlled
reaction
At low substrate concentrations, there will be fewer collisions between the enzyme and substrate.
At high substrate concentrations, the rate plateaus because all the enzyme active sites are saturated.
What is the effect of enzyme concentration on enzyme-controlled
reaction
At low enzyme concentrations, there will be fewer collisions between the enzyme and substrate.
At high enzyme concentrations, the rate plateaus because there are more enzymes than the substrate, so many empty active sites.
Ester bond
–COO– chemical bond
formed between glycerol and fatty acids
Hydrophilic
The ability to mix, interact or attract water
Hydrophobic
The tendency to repel and not mix with water
Glucose
Monosaccharide that exists as two isomers β glucose and α glucose.
Alpha is -oh group below and beta is -oh group above
Galactose
An example of a monosaccharide that forms lactose
Fructose
An example of a monosaccharide that forms sucrose
Isomer
Molecules with the same molecular formula
but the atoms are arranged differently
Maltose
Disaccharide
formed by the condensation of two glucose molecules
Lactose
Disaccharide
formed by the condensation of a glucose molecule and a galactose molecule
Sucrose
Disaccharide
formed by the condensation of a glucose molecule and a fructose molecule
Polypeptide
Polymer chain of a protein
made up of amino acids
bonded together by peptide bonds following condensation reactions
Amino acid
The monomer of a protein formed from C,H,O,N
contains a carboxyl group, amine group and an R group
Carboxyl group
COOH group
made up of a C with hydroxyl (OH) and carbonyl (double-bonded O) group bonded to it
found in amino acids and fatty acids
Amine group
NH2 group found on amino acids
R group on amino acids
The variable group
the part of each of the 20 amino acids that is different
α helix
A secondary structure in proteins a coiled shape held in place by hydrogen bonds
β pleated sheet
A secondary structure in proteins
a folded, pleated shape
held in place by hydrogen bonds
Hydrogen bonds
Weak bond
forms between H and O
in many biological molecules e.g. proteins, water, DNA, tRNA
Ionic bonds
A bond that forms between the R groups of different amino acids in the tertiary structure of proteins
Disulfide bonds
A strong covalent bond
between two sulfur atoms in the R groups of different amino acids
in the tertiary structure of proteins
Active site
Unique-shaped part of an enzyme that the substrate binds to
Activation energy
The minimum amount of energy required for a reaction to occur
Enzyme-substrate complex
Forms when an enzyme and substrate collide and bind resulting in a lowered activation energy
Denature
When the active site changes shape so the substrate can no longer bind
Enzyme-inhibitor complex
The structure that forms when an enzyme and inhibitor collide and bind
prevents enzyme-substrate complexes from forming
Saturated fatty acid
A long hydrocarbon chain with a carboxyl group at one end only single bonds between carbon atoms
Unsaturated fatty acid
A long hydrocarbon chain with a carboxyl group at one end
at least one double bond between carbon atoms
Polar molecule
A molecule that has an uneven distribution of charge
Phospholipid bilayer
Phospholipids have two charged regions
in water, they are positioned so that the heads are exposed to water and the tails are not
Plasma membrane
Phospholipid bilayer
cell surface membranes and organelle membranes
Reducing sugar
Sugars that can reduce Cu2+ ions in Benedict’s reagent to Cu+ ions in the form of copper (I) oxide
which forms a brick-red precipitate
Test for reducing sugar
Add Benedict’s reagent
heat
observe green/yellow/orange/brick red precipitate
How does the structure of a triglyceride relate to it’s function? (4)
Large ratio of energy-storing carbon-hydrogen bonds compared to the number of carbon atoms; a lot of energy is stored in the molecule
High ratio of hydrogen to oxygen atoms they act as a metabolic water source
Do not affect water potentials and osmosis - non polar
Have a relatively low mass
How does the structure of a phospholipid relate to it’s function?
Phospholipids have two charged regions, so they are polar
In water, they are positioned so that the heads are exposed to water and the tails are not.
This forms a phospholipid bilayer which makes up the plasma membrane around cells.
How does the structure of a triglyceride and phospholipid differ?
A phospholipid has one fewer fatty acid chain
which is replaced by a phosphate group
What is the difference between saturated and unsaturated fatty acid?
A saturated fatty acid has no double bonds between carbon atoms
where as unsaturated fatty acids had at least one double bond between carbon atoms
Non-reducing sugar
a sugar unable to reduce Cu2+
the glycosidic bond must be hydrolysed to expose the reducing group
e.g. sucrose
Test for non- reducing sugar
Following a negative Benedict’s test boil sample in acid (hydrolyse glycosidic bonds)
and then neutralise with alkaline ( Benedict’s cannot work in acidic conditions)
add Benedict’s reagent and heat observe orange/brick red colour
Test for starch
Add iodine
turns blue/black
Test for lipids
Add ethanol and shake to dissolve
then add water
white emulsion forms
Test for protein
Add biuret (blue)turns purple
Nucleotide
The monomer of DNA and RNA contains a pentose sugar, a phosphate group and a nitrogenous base
Nitrogenous base
Part of a nucleotide
adenine, guanine, cytosine, thymine and uracil
Attached to first carbon
Adenine and guanine - purine bases (double ring structure)
Cytosine, uracil and thymine - pyrimidine (single ring structure)
DNA nucleotide
The monomer of DNA
contains a deoxyribose sugar, a phosphate group(5th carbon) and a nitrogenous base(1st carbon)
Polynucleotide
DNA polymer many nucleotides joined together via a condensation reaction
joined by phosphodiester bonds
Phosphodiester bond
Bond joining two nucleotides together
forms between a phosphate group and the pentose sugar
Complementary base pairs
The base pairs that align opposite each other and form hydrogen bonds
adenine and thymine/uracil (2 H-bonds)
guanine and cytosine (3H-bonds)
Purine (double ring)- pyrimidine (single ring)→complementary base pairs
Ribose
Pentose sugar
found in RNA nucleotide and ATP
Uracil
Nitrogenous base
found in RNA instead of thymine
mRNA
a copy of a gene
single-strand polymer of RNA
tRNA
Found only in the cytoplasm single-stranded but folded to create a shape that looks like a cloverleaf
held in place by hydrogen bonds
rRNA
rRNA combines with protein to make ribosomes
DNA template strand
A DNA strand that is used to make a new DNA copy from
both DNA strands in the double helix are used as templates in DNA replication
DNA polymerase
An enzyme in DNA replication
joins together adjacent nucleotides by forming phosphodiester bonds
Semi-conservative replication
DNA replication is semi- conservative replication
one strand is from the parental DNA and one strand is newly synthesised
DNA helicase
Enzyme that breaks hydrogen bonds between the two chains of DNA in a double helix
causes the two strands to separate involved in DNA replication and transcription
Large latent heat of vaporisation
A lot of energy is required to convert water from its liquid state to a gaseous state
This is due to the hydrogen bonds, as energy is needed to break these to turn it into a gas
means water can provide a cooling effect
High specific heat capacity
a lot of energy is required to raise the temperature of the water
because some of the heat energy is used to break the hydrogen bonds
between water molecules
important so water can act as a temperature buffer
Metabolite
Water is involved in many reactions such as photosynthesis, hydrolysis, and condensation reactions
Solvent
Water is a good solvent
meaning many substances dissolve in it
polar (charged) molecules dissolve readily in water due to the fact water is polar
Strong cohesion
Water molecules ‘stick’ together due to hydrogen bonds
results in water moving up the xylem as a continuous column of water
provides surface tension, creating a habitat on the surface of the water for small invertebrates
ATP synthase
Enzyme that catalyses the synthesis of ATP from ADP + Pi
ATP hydrolase
Enzyme that catalyses the hydrolysis of ATP into ADP +Pi
Phosphorylation
The addition of a phosphate group to a molecule
making the molecule more reactive/it gains energy
Structure of water
Water is a polar molecule
the oxygen atom is slightly negative
the hydrogen atoms are slightly positive
Dipeptide
Two amino acids bonded together by a peptide bond
formed by a condensation reaction
RNA nucleotide
monomer of RNA
composed of a phosphate group, ribose and a nitrogenous base
has the base uracil instead of thymine
Role of hydrogen ions
determine the pH
the more hydrogen ions, the more acidic the conditions are
an important role in chemiosmosis in respiration and photosynthesis
Role of iron ions
a compound of haemoglobin
involved in oxygen transport
Role of sodium ions in co-transport
involved in co-transport for absorption of glucose and amino acids in the ileum
Role of phosphate ions
as a component of DNA, RNA and ATP
phosphodiester bond in DNA and RNA forms between the phosphate group and the pentose sugar
Structural function in DNA - PO4 3-
ATP- for storing energy
Fatty acid structure
carboxyl group and a long hydrocarbon chain
can be saturated or unsaturated
Properties of ATP which makes it good source of energy (6)
- Immediate source of energy as ATP to ADP is a single reaction
-Bonds in ATP is weak so broken down easily to produce energy
-Releases energy is small and manageable units so less energy list as heat
-It’s small and soluble so easily transported in body
-Can make other molecules more reactive - phosphorylation
-It cannot pass out of cell so cells always have immediate source of energy
3 ways synthesis of ATP occurs
Photophosphorylation - photosynthesis
Oxidative phosphorylation - respiration
Substrate level phosphorylation - in plant and animal cells when phosphate groups are transferred from donor groups to ADP
Why are DNA strands anti-parallel?
The 5’ or 5prime - where phosphate group is attached
3’or 3 prime - where hydroxyl group present.
When DNA forms double helix - they are arranged so one strand runs 5’ to 3’ and the other strand is 3’ to 5’ - antiparallel.
This is because in vivo DNA polymerase which forms DNA molecules can only attach nucleotides to hydroxyl group on 3’ carbon.
DNA polymerase active site is complementary only to the 3’ end of the molecule with hydroxyl group
Stability of DNA
-The phosphodiester bonds protect the chemically reactive bases from corrruption
- C to G has 3 H-bonds. Larger the no.of C to G more stable the DNA
There are other interactive forces between the bases which holds them together
What’s a quantitative and qualitative way of measuring concentration of sugars?
Benedict’s colour change with reducing sugars - semi quantitative as colour change depends on concentration of sugars. Blue-> Green->Yellow->Orange->Brick red
Quantitative-
Colorimeter- gives absorbance value
Filter ppt and dry it and weigh it - concentration of sugars
What are the two basic types of proteins? Structure
- Fibrous protein - eg collagen carry out structural functions
-Globular protein -eg enzymes and Hb carry out metabolic functions
Basic structure of fibrous protein.
-Long, straight chains running parallel to one another
-Cross bridges formed - makes them a very stable molecule
-eg collagen
Molecular structure of fibrous protein
Primary- sequence of amino acids - unbranched polypeptide
Secondary - polypeptide chain very tightly wound
Lots of amino acids, glycine helps packing them closely
Tertiary-chain is twisted into second helix
Quaternary - 3 polypeptide chains wound together the same way individual fibres are in a rope
Where is collagen found
-Tendons
-Tendons connect muscles to bones
-As muscles contract bone is pulled in the direction of the contraction
-Individual polypeptides in collagen held together by bonds between amino acids in adjacent chains
What is end product inhibition
Type of non competitive inhibition
In metabolic pathways
Helps keep steady concentration of particular chemical in a cell
The same chemical often acts as an inhibitor of an enzyme at the start of the reaction
Eg- If concentration of end product is higher than normal, more of enzyme at start inhibited and therefore concentration of chemical back to normal
-If concentration of end product is lower than normal, less of enzyme at start inhibited and therefore concentration of chemical back to normal
Why did scientists doubt DNA carried the genetic code
It was a relatively simple molecule
Later experiment with mice and bacteria carrying pneumonia was used to prove DNA carried the genetic code
As DNS transformed dead harmful strain bacteria to living harmful ones
4 requirements for semi conservative replication of DNA
4 types of nucleotides
Enzyme dna polymerase
Both strand acts as a template
Source of chemical energy to drive this process
Process of semi conservative replication
-DNA helicase breaks the H-bonds between the bases
-Exposes the bases and now both the strands acts as a template strand
-Free nucleotides align with complementary bases
-DNA polymerase runs along the free nucleotides and catalyses the reaction of forming phosphodiester bonds by condensation reaction
-This leaves us with new DNA molecule with one parental and one new strand - semi conservative replication
What’s the hypothesis given by Watson-Crick model of DNA replication? What does it mean?
What was his experiment depended on?(3)
-They hypothesised that DNA must replicate either conservatively or semi conservatively
This experiment depended on:
-DNA has a nitrogenous base
-Nitrogen has 2 isotopes N14 and N15 (heavier)
-Bacteria will incorporate nitrogen from their growing medium into the DNA
If bacteria grown in N14 medium will only have DNA which only contains this isotope and be lighter
If bacteria grown in N15 medium will only have DNA which only contains this isotope and will be heavier
-When DNA is centrifuged - N14 DNA will settle higher up while N15 will settle further down as its more dense
What’s the method of experiment to prove semi conservative replication
-Grow normal bacteria-N14 in a growth medium N15 -G0. Centrifuge to measure density
-Transfer this bacteria into growth medium with N14 and let it replicate for one generation -G1. Centrifuge to measure density
- Do the same and let the bacteria replicate for 3 generations - G2 and G3. Centrifuge to measure density
This proves its semi conservative as DNA always has one parental and one newly synthesised DNA.
Where are inorganic ions found in the body
In solution in the cytoplasm and body fluids
5 processes in cells which requires ATP
-Metabolic process - used in cells for forming macromolecules from monomers eg starch from glucose or polypeptides from amino acids
-Movement- ATP used in muscle contraction. Gives energy to filaments to slide past one another and shorten the muscle fibre.
-Active transport- Used in changing the shape of carrier molecule which helps in movement against concentration gradient
-Activation of molecules- phosphorylation makes molecules more reactive- lowering activation energy eg Glycolysis
-Secretion- necessary to form lysosomes for cell secretion
