1B - More Biological Molecules Flashcards
What are DNA and RNA? What do they carry?
DNA (deoxyribonucleic acid)
- stores genetic information
—> all the instructions an organism needs to grow and develop from a fertilised egg to a fully grown adult
RNA (ribonucleic acid)
- similar in structure to DNA
- one main function is to transfer genetic info from DNA to ribosomes
Ribosomes synthesise the body’s proteins
Reading RNA to make polypeptides in translation
Ribosomes are made of RNA and proteins
What are nucleotides
A type of biological molecule. Are made from
- a pentose sugar (5 C atoms)
- a nitrogenous organic (containing carbon) base
- a phosphate group
They’re monomers that make up DNA and RNA
(diagram no.1)
What’s unique about DNA and RNA nucleotides
DNA
Each DNA nucleotide has same sugar and phosphate group
Base varies though.
- Pentose sugar in DNA nucleotide is called deoxyribose
- four possible bases are adenine, thymine, cytosine, guanine
.
RNA
these nucleotides also have a phosphate group
And one of four bases (uracil replaces thymine)
- nucleotides have ribose sugars
What do both types of nucleotides form when joining
Form polynucleotides, a polymer of nucleotides.
- nucleotides join by condensation reactions
- between phosphate group of one nucleotide
- and sugar of the other
- Forms a phosphodiester bond
(consisting of the phosphate group and two ester bonds - one already there) - chain of sugars and phosphates is the sugar-phosphate backbone
How to describe DNA’s structure
Made up of two polynucleotide chains
In a double helix
— two dna polynucleotide strands join
By hydrogen bonding between bases
— each base can only join with one particular base
This is complimentary base pairing (AT, CG)
Two anti parallel (running opposite directions)
polynucleotide strands twist to form double helix
.
DNA was first observed in the 1800s
Many scientists doubted it could carry genetic code
As it has relatively simple chemical composition
—> some argued genetic info was carried by proteins (more chemically varied)
By 1953, experiments showed DNA carried genetic code
This was the year double helix structure (helps DNA with function)
Was determined by Watson and Crick
How is RNA structure described
It’s a relatively short nucleotide chain
It’s made from a single polynucleotide chain (not double)
And much shorter than most DNA polynucleotides
How does DNA replicate by semi conservative replication
DNA copies itself before cell division (so each new cell has full amount of dna)
—> semi conservative as half strands in new dna molecule
Are from original dna molecule
— means genetic continuity between generations of cells
..
- Enzyme DNA Helicase breaks hydrogen bonds
Between the bases (on the 2 polynucleotide dna strands)
Making helix unwind forming two single strands - Each original single strand acts as template for new strand
- Complimentary base pairing means free floating dna nucleotides
- are attracted to complimentary exposed bases
On each original template strand (A-T and G-C) - Condensation reactions join nucleotides of new strands together
With DNA Polymerase
- hydrogen bonds form between bases, connecting original and new strands - Each new dna molecule contains one strand from original DNA
and another new strand
(DIAGRAM NO.2)
How does DNA Polymerase travel along DNA (which’s antiparallel)
Each end of one dna strand is slightly different in structure
—> one end is called the three prime end (3’) and the other is the five prime end (5’)
In a dna helix, the strands run in opposite directions (are antiparallel)
As aren’t identical directly opposite, they still are, but running the other way
- active site of DNA polymerase = complimentary to 3’ end of a strand
- so the enzyme can only join the nucleotides at 3’ end of original strand
New strand made = 5’ to 3’ direction
DNA moves down template original strand opposite way
In a 3’ to 5’ direction, as doesn’t need to join that side
Because strands in double helix are antiparallel
DNA polymerase working in one of the template strands
Moves in opposite direction to DNA polymerase working on other template strand
DIAGRAM NO3
What is chromatography?
-> a method used to separate a mixture of (multiple) soluble substances and identify them.
- chromatography involves two phases..
- mobile phase (where molecules can move , attracted to a gas/liquid - SOLVENT IN PAPER CHROMATOGRAPHY)
- stationary phase (where molecules can’t move , attracted to solid/really thick liquid - PAPER IN PAPER CHROMATOGRAPHY)
- The components of the mixture separate out , as they all go through both phases. Some substances stay in different phases longer/shorter than others, causing them to move at different differences.
How is paper chromatography done
- [ ] PAPER CHROMATOGRAPHY ..
In paper chromatography the stationary phase is where the substance is attracted to filter paper ; the mobile phase is where the substance is attracted to a solvent (water or ethanol). - Draw line near bottom of paper in pencil (baseline) because pencil marks are insoluble so won’t move with solvent. Put a spot of mixture (eg. Ink) to separate on the line.
- Put some of solvent into beaker and dip bottom of paper below line into solvent and leave it
- Put a watch glass on top of beaker to prevent solvent evaporation. The solvent will start to move up paper - when chemicals in mixture / ink dissolve in solvent , they’ll move up paper too.
- You will see different chemicals in the sample separate out , forming spots at different places on paper.
- if any are insoluble in one solvent, like stay on baseline, use another type of solvent with the same mixture , so they all separate and Rf values can be found
- If chemicals in your mixture are colourless (eg. Amino acids) you may have to spray the chromatogram / end result paper with locating agent to see them
How do you find the identity of chemicals in chromatograms / interpret chromatograms ?
Rf values are the ratio between distance travelled by solute and solvent.
They’re always between 0-1!! 1 is really soluble/0 is insoluble.
Rf Value 🟡 = distance travelled by substance / travelled by solvent
-> from the baseline!
- Different substances have different Rf values!
- controlled by two things : how soluble they are in the solvent (how attracted to mobile)
AND how attracted to stationary phase/paper - for example, substances with higher solubility in the solvent (and which are less attracted to the paper) will spend more time in mobile phase , so will be carried further up paper
- Different substances will spread out and will have different Rf values
- Comparing Rf Values
- if you run a pure sample of a substance alongside actual mixture,
that pure substance is confirmed to be in the mixture if one substance has the same Rf. - some chemists do this with multiple pure substances alongside mixture to identify substances.
These pure substances are called standard reference materials (SRMs)
they have controlled concentrations and purities. - [ ] ALSO, you can check if a substance is pure or not
- if pure, it won’t separate/will move as one blob during chromatography; a mixture will move as multiple blobs
How did meselson and stahl (validated Watson and crick’s theory) provide evidence for semi conservative replication in dna
Some throughout dna replication was conservative (original strands stay together, new molecules have two new strands)
Here’s how they proved dna replication is semi conservative (one strand orignal and the other, new)
..
- Two bacteria samples grown; one in nutrient broth of light N-14, the other heavy N-15
- as bacteria reproduced, it took up nitrogen from broth to make nucleotides for dna
- so nitrogen gradually became part of its dna - Sample of dna taken from each batch and spun on centrifuge
DNA from heavy nitrogen bacteria settled lower in tube than light
As denser/heavier - Then bacteria grown in heavy were taken out and put in light nitrogen broth
Bacteria were left there for one round of dna replication
And then another sample was taken from this bacteria then into centrifuge - If conservative, original heavy dna (still be together)would all settle at bottom
And new light dna would settle at top - As semi conservative, new bacterial dna have one strand heavy and other light
So dna would settle halfway between where light and heavy sit separately (but would all settle together) - DNA settles in middle, showing dna molecules contained mixture of heavy and light nitrogen
Bacterial dna replicated semi conservatively in light.
Other scientists proved it was same for all living organisms
What’s practical for trypsin is added to a dilute solution of milk power ?
Casein is a protein found in milk , which is digested by trypsin
And the solution goes clear
1.make 2 concentrations of 5cm3 trypsin from 1mmoldm-3 trypsin and distilled water
Either 0.5-1.0 mmoldm-3
— put each one into a separate test tube
- Take 2 more test tubes; add 2cm3 of each trypsin solution
And 2cm3 of a buffer solution to each test tube (label tubes) - Place cross on back of each trypsin/buffer test tube
Then add 3cm3 of milk to two other test tubes - Take the 0.5mmoldm-3 trypsin and buffer solution from one test tube
And add to the solution of milk powder in an other tube
Place on bung and mix by inversion (set amt time) - time how long it takes for milk to clear
Y seeing how long it takes to see cross through test tube - Repeat previous 2 steps to the other trypsin conc
How is water vital to living organisms
Makes up about 80% of a cells contents.
—> lots of important functions in and out of cells.
- Water is a metabolite in lots of metabolic reactions
(a chemical reaction that happens in a living organism
To keep alive. A metabolite is a substance involved in it.)
- eg. Condensation and hydrolysis - Water is a solvent (substances dissolve in it)
Most metabolic reactions take place in solution, like in cytoplasm - Water helps with temperature control, having
high latent heat of vaporisation and specific heat capacity - Water molecules are cohesive (stick together)
Helping water transport in plants and other organisms
What is the structure of water molecules
A water molecule (H2O) is one atom of O
And joined by two H atoms by shared electrons
- because the shared negative H electrons are pulled
to O atom, the other side of H atoms = left with delta+ charge
- the unshared negative electrons on O atom
Give it a delta- charge
Making water a polar molecule (partial negative charge on one
side and partial positive on other) - the delta- O attract delta+ H of other water molecules
- this attraction is called hydrogen bonding
What are some useful properties of water
• water is a metabolite
Many metabolic reactions involve a condensation (releases water molecule as new bond is formed)
or hydrolysis reaction (requires water molecule to break bond)
- like amino acids join to make polypeptides by condensation rs.
ATP is released by hydrolysis
• water has high latent heat of vaporisation
Takes lots of energy to break H bonds between water molecules
So water has high LH of vaporisation (lots of energy needed to evap)
- useful as organisms can use water loss through evaporation
To cool without losing too much water, like sweat
• water can buffer/resist temp changes
H bonds between water molecules absorb lots of energy
So water has a high SHC (takes lots of energy to heat up)
- useful as water doesn’t experience rapid temp change
- making good habitat as temp is less likely to change/constant
- and water inside organisms remains fairly stable temp
—> helping maintain constant internal body temp
• water is a good solvent
A lot of important substances in metabolic reactions are ionic (salt)
Meaning made from one positive and negative atom/molecule
- as water is polar, the + end will be attracted to the negative ion
- and negative end will attract positive
—> ions will get surrounded by water and dissolve
(Waters polarity makes it a useful solvent)
• strong cohesion between water molecules
Cohesion is that attraction between molecules of same type
Water is cohesive as are polar
- strong cohesion helps water flow - great for transporting substances
- like how water travels in columns up xylem
- it also means water has high surface tension when contact with air
- its reason why sweat forms droplets, wch evaporate to cool
- and why pond skaters and other insects can walk on pond
What is atp?
Plant and animal cells release energy from glucose (respiration)
- a cell can’t get its energy directly from glucose
- so in respiration, energy released from glucose is used to make atp
(Adenosine triphosphate)
- ATP is made from nucleotide (same structure as nuc.) base adenine,
with a ribose sugar and three phosphate groups
—> it’s a nucleotide derative as modified form of a nucleotide
Once made, atp diffuses to the part of the cell that needs energy
The energy in ATP is stored in high energy bonds
Between the phosphate groups; it’s released by hydrolysis..
How is atp used
When energy is needed by a cell, ATP breaks down
=ADP (adenosine diphosphate) and P (inorganic phosphate)
This is a hydrolysis reaction.
> A phosphate bond is broken and energy is released.
The reaction is catalysed by ATP hydrolase
- ATP hydrolysis can be coupled to other energy requiring reactions
In the cell, meaning energy released can be used directly to make
The coupled reaction happen (instead of lost by heat)
The released inorganic phosphate can also be used,
Added to another coumpound (phosphorylation)
—> makes compound more reactive
ATP can be resynthesised in a condensation reaction between ADP and P
(happens in respiration and photosynthesis;catalysed by ATP synthase)
DIAGRAM NO.4 ATP CYCLE
What are inorganic ions
An ion is an atom/group of atoms with electric charge
- +ion is a cation; -ion is an anion
An inorganic ion is an ion not containing carbon
- each ion has a specific role depending on properties.
An ions role determines whether its found in high or low concs
• iron ions are part of haemonglobin
Haemoglobin = large protein carrying O2 round body (in red blood cells)
- it’s made up of four different polypeptides
Each with Fe2+ in centre
- it’s the Fe2+ that binds to O2 in haemoglobin
- when oxygen’s bound, Fe2+ becomes Fe3+ until released
• hydrogen ions (H+) determine pH
pH is calculated based on H+ conc in environment
- the more H+ present, the lower the pH and more acidic environment
- Enzyme controlled reactions are all affected pH
• sodium ions (Na+) help transport glucose/amino acids over membranes
Glucose molecules and amino acids can be transported into cells
Alongside Na+ ions (this is co-transport)
• phosphate ions are an essential component of ATP and DNA
When PO4 3- / phosphate ions are attached to another molecule
It’s known as a phosphate group
—> it’s the bonds between phosphate group that store energy in ATP
> The phosphate groups in DNA and RNA allow
nucleotides to join up to form the polynucleotides
What is the practical where the water potential of potato tissue is identified?
Preparing the dilution series
1. You’re provided with a 1 mol dm-3 solution of sucrose. Plan 6
Concentrations, including pure water, in a dilution series
- that you can make from initial stock solution, that
- that will help you determine potato cells’ water potentials
- Label six test tubes with your concs (0-1 mol dm-3 in 0.2s)
- Use the 1.0 mol dm-3 of sucrose solution and distilled water
To make up 10cm3 of each of your solutions - Cut six pieces from potato with scalpel; use ruler to ensure
All same lengths on a tile. - Blot potato pieces dry with paper towel and put each potato back
On cleaned white tile - Weigh each piece and record initial masses in table. Then transfer
Each piece to its own labelled boiling tube filled with diff concs
Taking measurements
7. After incubation period , remove all pieces and blot dry.
Store them on a numbered white tile
- Re weigh and record final masses in table
- Calculate change in mass and then calculate the
Percentage change in mass
What kind of molecules diffuse through membranes easily and not easily?
Easily
- lipid soluble substances
- small substances
- oxygen and CO2
NOT easily
- water soluble/not lipid soluble
- large molecules
- molecules that have same charge as protein channel (repel)
- charged molecules electrically
- glucose and amino acids
What is facilitated diffusion
Large polar molecules (glucose, amino acids, ions)
Can’t diffuse across membrane
- must pass through protein channels or carriers
- diffusion through these channels =
FACILITATED DIFFUSION
It’s still passive but involves proteins that
Are specific to the substance crossing
What are channel and carrier proteins
• channel proteins
Form a channel in the membrane
Allowing specific water soluble ions to diffuse over
- most channels can be gated (opened/closed)
- allowing cells to control entry/exit of ions
• carrier proteins
They have a binding site for a specific solute
And constantly flip between 2 states so
site is alternately open to opposite sides of membrane
- the substance will bind on the side where
- it’s high conc; moves to low
Both these tend to be specific for 1 molecule type
Why may facilitated diffusion be limited
Carrier proteins may become the limiting factor
In facilitated diffusion
- because they can become fully saturated
- with molecules (can’t carry any more across)
This is why graphs show…
With molecules passing by simple diffusion,
Fick’s law is used, making graph direct prop / linear
With molecules passing by facilitated diffusion,
Carrier proteins become limited factor
So it increases direct proportionally then plateaus
