Biological molecules pt 2 Flashcards
DNA stands for and structure
Deoxyribose Nucleic Acid
Two strands twisted in a double helix structure with hydrogen bonds between complementary base pairs
Phosphate group, deoxyribose,nitrogenous base of adenine thymine cytosine guanine
Phosphate group has a negative charge
Covalent bonds
C1 of deoxyribose to nitrogenous base
Monomer to polymer of nucleotides
Nucleotides form phosphodiester bonds in condensation reactions and are broken thriugh hydrolysis
DNA VS RNA formula and relate to stability
C5O4H10 is DNA loss of oxygen is more stable than C5O5H10
DNA vs RNA differences
Two strands (antiparallel) vs one strand Nucleus vs nucleus and cytoplasm Thymine vs uracil Replicates and stores in for vs converts to a format acceptable for protein synthesis One type vs three types
How/why is dna stable
Phosphodiester backbone protests the bases inside the double helix which fairies the genetic code so is protected from outside chemical and physical forces
Bases on each strand are linked by hydrogen bonds forming bridges between the sugar phosphate backbone
Many hydrogen bonds are string together
DNA function and properties
Very stable allowing it to pass from generation to generation without changing - rare mutations
Two strands that can be separated during replication and protein synthesis
Large so carry huge amounts of genetic info
Base sequence of a gene determines structure and function of protein
Semi conservative replication
DNA helicase enzyme breaks the hydrogen bonds between the complementary base pairs leaving them exposed and individual strands can act as a template for the new strand to be formed. Free activated nucleotides with two extra phosphate groups (which helps lower the activation energy and increase the likelihood of a reaction) binds to the complementary base pairs. DNA polymerase enzyme catalysts the synthesis of phosphodiester bonds starting on the strand ending on 3’ hence in the 5’ to 3’ direction. The new molecule formed retains half of the original DNA and half of the new.
2 features of DNA and explain how each one is important in semi conservative replication (2 marks)
Hydrogen bonds between complementary base pairs are important because DNA helicase needs to break them in order to separate the strands leaving the bases exposed, allowing each strand to act as a template. Complementary base pairing allows for accurate replication.
Dispersive model of DNA
Two molecules with old and new DNA dispersed between the strands
Watson and crick used other scientists results but pieced it all together
All DNA bases contain nitrogen 14…..when bacteria is grown in a medium they will absorb nitrogen from the medium and incorporate it into the new nucleotides and ultimately DNA. All bacteria grown in a heavy medium then spun in a centrifuge which allows the heavy and light DNA to separate. Results showed only one line in the middle hence ruling out the conservative model. The second generation showed 14N and 15N line hence ruling out dispersive because that would only be one line.
Why did many scientists not agree that nuclei acid contained the molecule of heritage
Proteins have 20 amino acids hence have numerous possibilities which seemed more suited to explain the genetic variation present in humans whereas there are only four nitrogenous bases.
Explain why new nucleotides can only be added in the 5’ to 3’ direction
The enzyme DNA polymerase is specific and has an active site of a complementary shape to the 3 OH group of 5’ strand and phosphate of growing strand hence can only work on substrate in that direction.
ATP stands for and is an…with an extra… which makes it …..
Adenosinetriphosphate
Activated nucleotide - extra phosphate bond makes it more reactive so easily broken down
Function of ATP
Stores chemical energy from glucose as chemical energy in ATP
ATP hydrolysis
Energy stored in ATP is released (exothermic) by breaking off third phosphate and small amounts of energy are steadily related to drive energy requiring process in the cell.
ATP hydrolyse catalyses the hydrolysis
ATP hydrolysis is exergonic meaning
Energy is released
Condensation of ATP
Adds phosphate group, ATP synthase catalyses the synthesis and is endergonic hence energy is required.
3 ways to make ATP
Phosphorylation in chloroplasts uses light energy in a condensation reaction
Oxidative phosphorylation uses glucose and other fuels in a condensation reaction
Substrate level phosphorylation is when the phosphate group is in a high energy bond with sugar substrate instead of dissolved in cytoplasm .
Base reaction is ADP plus Pi = ATP plus water with arrows for light or fuels upwards
Last reaction is sugar substrate plus ADP gives sugar substrate plus ATP
Functions ATP examples
Anabolism so protein synthesis
Muscle contraction - needed for filaments to slide past one and other
Active transport
Secretion of substances from cells - needed to form lysosomes
Activation if Molecules - glycolysis - add phosphate toe glucose molecules so can be broken into TP
Explain how the hydrolysis of ATP for energy requiring reactions (endergonic) is useful
ATP is an immediate source of energy for cells (better than glucose) and can be rapidly synthesised after hydrolysis and transfers small manageable amounts of energy for reactions that require it
What are enzymes
Enzymes are globular proteins that act as biological catalysts that speed up a reaction by lowering the activation energy without getting used up.
How is the function of enzyme reliant on its primary protein structure?
The primary protein structure is the sequence of amino acids that then fold in on each other forming a 3D molecule. An enzyme has a specific shape that will fit the substrate the enzyme is meant to work upon. A change to the primary structure would cause a difference in bonds formed during folding hence changing the shape rendering the active site useless and unable to form an enzyme - substrate complex.
What is the induced fit model of action?
Proposes that the decreased proximity of substrate is a change in the environment of the enzyme causes the shape of the enzyme to change , like a glove does to a hand, to accommodate the substrate. As the enzyme changes shape, strain is applied on the substrate molecule which distorts the bonds in the substrate, consequently lowering the activation energy.
Locke and Key model limitations
Older model than induced fit
Too rigid as enzymes are extremely specific hence does not explain scientists observing enzymes accommodating similarly shaped molecules to that of the intended substrate.
Describe and explain how temperature affects the rate of reaction (describe the graph).
Like a bell (rate on y optimum temp on x)
Rise in temperatures increases the kinetic energy of the molecules hence they move more rapidly which increases the frequency of successful collisions so more enzyme - substrate complexes are formed hence the rate of reaction increases. However too high temperatures cause denaturisation if enzyme, hence the rate of reaction slows down in human enzymes at around 45 degrees Celsius and becomes denatured at around 60 degrees C.
Birds have a ——- metabolic rate than humans because
Higher
For flight hence higher body temp
What is pH a measure of
Hydrogen concentration
Describe the graph of rate of reaction and pH and explain
Change in pH alters the charges of amino acids that make up an active site hence the substrate can’t form bonds to the enzyme.
Significant change in pH may cause bonds maintains the enzymes tertiary structure to break - more likely to reduce enzyme efficiency then denature.
Active site arrangement consists of hydrogen and ionic bonds between NH2 and COOH groups
Steep up and slow down a bit like a mountain.
Enzyme concentration and rate of reaction graph description and explanation
Enzyme concentration increasing will increase rate of reaction as long as there is an excess of substrate however if the substrate is limiting then no effect on rate of reaction.
Gentle rise then plateaus
Describe and explain the graph of substrate concentration and rate of reaction
Rate of reaction increases in proportion to the concentration of substrate until all enzymes are working at maximum speed then no effect p.
Gentle rise and plateau.
Competitive Inhibitors do what
Occupy the active site of an enzyme made for a different substrate
Non competitive inhibitors do what
Bind on an allosteric not active site) changin shape of molecule
Compare rate of reaction with competitive and non competitive inhibitors
Non competitive is a much more gentle slope and plateaus more quickly whilst competitive albeit slowly eventually reaches the plateau point for the intended substrate.
Inhibitors can be useful
Negative feedback loops inhibit starting product so that any increase in concentration is automatically regulated by the body.
Why is a dna molecule with more CG bases more stronger than AT?
CG has three hydrogen bonds AT has two so harder to break CG
Why is helix structure useful for function of DNA?
Helix is compact for storage of genetic info in nucleus
Relate the structure of mRNA to its functions
Breaks down quickly so no excess polypeptide forms
Ribosome can move along strand and tRNA can bind to exposed bases
Can be translated into a specific polypeptide by ribosomes.
Explain why ATP is a suitable energy source foer cellprocesses
High energy bonds between phosphate groups
Small amounts of energy released at a time means less energy wasted as heat
Single step hydrolysis means energy is available quickly
Readily re-synthesised.
Describe specificity of enzymes
Active site of a complementary tertiary structure to its substrate, allowing for enzyme substrate complexes to be formed. If not complementary then binding between will not occur properly and no catalysis will occur
RNA structure
Ribose sugar, phosphate group and Adenine,guanine,cytosine and uracil
Linear strand phosphodiester bonds
RELATIVELY SHORT
Structure of ATP and state two differences to dna nucleotide
Adenine bonded to ribose which is bonded to one phosphate which is bonded to two other phosphates in a line
One phosphate vs three phosphates
Deoxyribose vs ribose
Why is ATP useful in many biological processes? (5 marks)
Releases small amounts of manageable energy
Broken down in a one step process
Provides energy immediately
Hydrolysis provides phosphates which make a compound more reactive, lowering Ea which is useful for enzyme controlled reactions
Reformed after hydrolysis
Enzymes intracellular and extracellular reactions
ATP
Digestion
