Module 2 Flashcards
Sample preparation
FIXING: chemicals like formaldehyde used to preserve specimens
DRY MOUNT: embedded in wax and cut with microtome knife to preserve shape. cryostat cuts specimens frozen in liquid nitrogen
WET MOUNT: suspended in water or oil and cover slip placed on at an angle. drop of stain at one edge and paper towel at other to draw stain across.
SQUASH SLIDES: wet mount is prepared and lens tissue used to press down cover slip
SMEAR SLIDES: edge of slide smears sample onto another slide
Why is staining needed
Examples of stains
images have low contrast as the cells absorb little light
resolution is limited by wavelength of light an diffraction
cell structures often transparent but different ones take up different stains due to chemical nature
Eosin stains cytoplasm
methylene blue stains DNA
electron microscopes use heavy metal compounds that absorb electrons like phosphotungstic acid
Cell theory
- all living things consist of one or more cells
- new cells are formed by the division of preexisting cells
- the cells contain information that acts as instructions for growth and can be passed onto new cells
Magnification
how many times larger an image is compared to the actual object itself
size of image/size of object WILL I AM
resolution
the ability to distinguish between 2 things very close together (limited by diffraction of light ass cases through lenses and samples)
Units
1 meter
- 001 millimetres
- 000001 micrometers
- 000000001 nanometers
measuring cells method
An eyepiece graticule is fitted into microscope eyepiece (100 EPU)
its scale must be calibrated for each magnification using a stage micrometer
it has 100 divisions and it 1mm long, so each division is 10 micrometers
1 graticule division= number of micrometers/ number of graticule divisions
Compound microscope
2D high magnification (1500) low resolution (0.2 um) living or dead eyepiece lens then objective lens to change magnification using visible light
Laser scanning confocal microscope
3D
colour
laser beams focused by dichromatic mirrors
specimens tagged with fluorescent dye and laser light causes it to give off light which is shone onto detector
small and portable
Scanning electron microscope
3D high magnification (500,000) high resolution (less than TEM 0.002um) dead specimen black and white electromagnetic lenses beam of electrons knocks electrons off specimen which are collected in a cathode ray tube forming a image of exterior artefacts hard to use and large vacuum mounted on aluminium stubs and coated in gold
Transmission electron microscope
2D high magnification (1,000,000) high resolution (0.0002um) electromagnets focus a beam of electrons transmitted through specimen denser parts absorb more so darker ultramicrotome used to create thin slices vacuum films of collodion on copper grids
microfilaments: monomer structure function size
MONOMER- actin STRUCTURE- contractile fibres made from 2 intertwined strands. grown and shrink as monomers added and removed. networks form a matrix FUNCTION- maintain cell shape contraction cell movement cytokinesis of cell division SIZE- 7nm
intermediate filaments: monomer structure function size
MONOMER- fibrous proteins like keratin STRUCTURE- fibres would into thicker cables and form a dense network within and around nucleus FUNCTION- maintain cell shape give strength to cell as resists tension anchor nucleus and organelles SIZE- 10nm diameter
Microtubules
MONOMER- globular tubular proteins (alpha and beta dimers)
STRUCTURE- hollow tubes which grow or shrink in length as subunits are added or subtracted from ends
FUNCTION-
maintain cell shape
act as tracks for movement of organelles
cilia and flagella motility
spindle fibres in cell division
SIZE- 25nm diameter
Types of protein threads
Types of microtubules (made of microtubules)
Microfilaments, intermediate filaments, microtubules
Centrioles, flagella, cilia
Centrioles
- structure
- function
- location
- numbers
FUNCTION- organising spindle in cell division
STRUCTURE- ring of 9 triplets of microtubules
LOCATION- near nucleus in cytoplasm
NUMBERS- in pairs at right angles to each other
Flagella
What is different about bacteria?
FUNCTION- move cells like sperm
STRUCTURE- ring of 9 pairs of microtubules surrounding a pair in the centre
LOCATION- on surface of cells
NUMBERS- 1 long one sometimes 2
no microtubules in bacteria though as prokaryotes don’t have organelles or cytoskeleton
Cilia
FUNCTION- wafting liquids across cell
STRUCTURE- ring of 9 pairs of microtubules surrounding a central pair
LOCATION- surface of cells
NUMBERS- usually shorter and in large numbers
cell wall structure and function
STRUCTURE- made of cellulose microfibrils embedded in a layer of pectins (adhesive) and hemicelluloses (fluid)
calcium pectate cements one cell to the next
may also contain plasmodesmata- a cytoplasmic link between cells
FUNCTION- provides share and support
protection against pathogens
lets substances in and out
Division of labour
- mRNA copy of the gene is made in nucleus
- mRNA leaves nucleus (MRNA nucleotide goes in) through nuclear pore
- mRNA attaches to a ribosome which reads gene to assemble protein into correct 3D shape
- protein molecules are pinched off in vesicles and travel towards the Golgi apparatus on the cytoskeleton
- vesicles fuse with Golgi and become part of it
- Golgi processes and packages insulin molecules , adding stuff like carbohydrates through an enzyme which makes a glycoprotein
- packaged insulin molecules pinched off in vesicles and move to surface membrane
- fuse with cell surface membrane
- cell surface membrane opens to release molecule to outside
Features of prokaryote (bacteria)
- 1-5um
- 1 membrane- cell wall made of peptidoglycan formed from aa and sugars
- polysaccharide capsule helps it cause disease
- no membrane bound organelles or nucleus
- ribosomes 70S (80S in eukaryote as bigger and dense to make more complex proteins)
- DNA in cytoplasm in a loop- nucleoid
smaller loops of DNA called plasmids - mesosomes are enfolded regions of the cell membrane where ATP is produced- site of respiration. increase SA for enzymes
- flagella are attached to the plasma membrane by a basal body and rotated by a molecular motor. the main body is a filament and hook, which gets energy to rotate from chemiosmosis unlike ATP in eukaryotic
- pilus used for attachment and shorter and straighter than flagella
- genes in chromosomes groupes into operons so a number of them can be switched off at once
Endosymbosis
the theory that mitochondria and chloroplasts and maybe other eukaryotic organelles were formerly free-living bacteria. They were taken inside another cell as an endosymbiont. Eventually evolved to form eukaryotic cells.
Advantages and disadvantages of prokaryotes
DISADVANTAGES:
some are resistant to antibiotics - MRSA. this is coded for on plasmid DNA and can be transferred between cells
ADVANTAGES:
food industry for cheese and yogurt
used in mammalian intestines to digest food and break down vitamin K
skin on flora to help prevent microorganisms getting on
used in sewage treatment and natural recycling
Difference between prokaryotic and eukaryotic cells
Feature Prokaryotic cell Eukaryotic cell Cell size: P-Small (1-5micro) E-Larger (20-40 (or 100) micro) Genetic material: P-Nucleoid. 1 circular chromosome free in cytoplasm but super coiled to make compact. E-True nucleus. Multiple linear chromosomes wrapped around proteins called histones creating chromatin, which coils and condenses to form chromosomes. Organelles: P-No E-Membrane bound/many Ribosomes: P- 70S (smaller)- 10-20nm E-80S (larger)- 25nm Respiration: P-Mesosomes E-Mitochondria Flagella: P-Simple, no microtubules (20nm) E-Complex, microtubules (200nm) Photosynthesis: P-May take place on unstacked membranes E-Chloroplasts Examples: P-Bacteria E-Plant, animal, fungi Cytoskeleton: P-Present E-Present, more complex Reproduction: P-Binary fusion E-Asexual or sexual Cell type: P-Unicellular E-Uni or multi cellular
What are the 2 nucleic acids
deoxyribonucleic acid
ribonucleic acid
polynucleotides
What is in the nucleotide
- phosphate group- PO4 2-, an inorganic negative acid. bonds to carbon 5 and 3
- organic nitrogenous base containing 1 or 2 carbon rings and nitrogen
- pentose sugar
each component is joined by a strong covalent bond in 2 condensation reactions
(image of phosphate, sugar and base joined)
Types of bases
Purine: Adenine and Guanine
Pyrimadine: Cytosine, Uracil and Thymine (only one carbon ring- longer word but smaller molecule as its been CUT)
(draw out images of the bases)
purine bonds to pyrimidine so its symmetrical
Types of bonding
-nucleotides are joined by phosphodiester bonds to form a sugar phosphate backbone
chains of nucleotides join together to form nucleic acids
only nucleotides of the same sugar can join
-hydrogen bonds hold the double helix 3D structure between the bases. easily broken and reformed to allow DNA to replicate. complementary base pairing A-T 2 hydrogen bonds, C-G have 3.
What is the name for how the strands are held together
anti-parallel strands
Similarities and differences between DNA an RNA
S-Pentose sugars
D-deoxyribose sugar and ribose sugar on carbon 2
S-nitrogenous bases
D-RNA has U instead of T
S-sugar phosphate backbone
D-Double/single strand
S- Phosphodiester bonds/condensation reactions
D-3 types of RNA-messenger, ribosomal and transfer
S-nucleotides
D-DNA/RNA nucleotides
S-Order of nitrogenous bases forms a code on the nucleic acid (DNA+mRNA)
D-DNA stores genetic information long term and bases code for aa which make proteins/RNA doesn’t store code but copies it-protein synthesis
D-DNA is big and stable RNA is small and unstable especially mRNA
D-DNA in nucleus/ RNA in nucleolus and cytoplasm
What is ATP and it uses
- phosphorylated nucleotides that are made up of a ribose, adenine (nitrogenous base) and 3 inorganic phosphates
energy storage molecules where energy can be released by breaking bonds between phosphates.
-immediate store as used up as soon as made. instability of phosphate bonds in ATP means not good long term store.
-A small amount of energy is needed to break (hydrolyse) the bond, but lots is released when the phosphate undergoes other reactions involving bond formation 30.6KJmol-1 - occurs simultaneously with energy requiring reactions
-energy used in the breakdown of these molecules (respiration) is used to create ATP by attaching a phosphate to an ADP molecule-phosphorylation
Properties of ATP
- Small- moves easily in and out of cells
- Water soluble- energy requiring processes occur in aqueous environments
- Contains bonds between phosphates with intermediate energy- large enough for useful cellular reactions but not large enough that energy is wasted as heat
- Releases energy in small quantities- for same reason as above
- Easily regenerated- can be recharged with energy
Semi-conservative DNA replication
- The DNA helix unwinds
- The 2 polynucleotide strands of DNA separate as the hydrogen bonds between the bases are broken by the enzyme helicase, which catalyses reactions to break them.
- This unzips the DNA exposing the nitrogenous bases
- Each new strand now acts as a template for the formation of a new molecule of DNA
- Free DNA nucleotides base pair with the unpaired complementary bases. Complementary base pairing ensures exact copies are made
- Then phosphodiester bonds form between the phosphate of one DNA nucleotide and the sugar of the next
- The enzyme DNA polymerase catalyses the condensation reaction to covalently bond each nucleotide to the next. The sugar phosphate backbones of each new DNA strand are joined to form a DNA polymer
- 2 genetically identical DNA molecules are formed, each containing one strand from the parent DNA and a new complementary strand- half parental DNA Is conserved.
The strand that codes for a protein to be synthesised is a sense strand and rund from 5’ to 3’. The other strand is from 3’ to 5’ and is complementary to the sense strand and is also known as the antisense strand or the template strand. RNA is same bases as sense.
DNA replication
- The copying of DNA so that following cell division each new cell will have a full copy of all the original DNA. It is semi conservative replication, and produces geneticall identical sister chromatids
- occurs during S phase
- Must be copied accurately to conserve genetic information
- Mutations are random an spontaneous changes in the sequence of bases in the DNA
Experiment showing semi-conservative replication
Started growing bacteria in a medium containing heavy nitrogen isotope 15N, which the bacteria used to make nucleotides. The bacteria where then transferred to a normal 14N growth medium, and DNA samples were extracted over time and centrifuged. This separated the DNA according to density.
The lowest strip contains purely 15N, the medium is hybrid DNA with 1 parental strand and 1 new DNA strand and the top is light DNA with just new strands.
- Bacteria are used for this experiment as the replicate very fast so multiple generations and changes can be seen in a short period of time
- Few ethical concerns
- Reproduce asexually so less variation
Genetic code to polypeptides
Types of polypeptides
A gene is a sequence of bases in DNA that codes for the codon which determine the sequence of aa in the primary structure of the polypeptide. this codes for enzymes which catalyse reactions to build a whole person.
DNA contains the genetic code which codes for the synthesis of all polypeptides
its contained in the nucleus to be conserved and protected
Types of polypeptides are:
- Structural proteins (keratin, collagen, actin, myosin)
- Channel proteins
- Enzymes
- Cell surface receptors
- Electron carriers
- Haemoglobin
- Antigens, immunoglobulins
Genetic code to polypeptides
A gene is a sequence of bases in DNA that codes for the codon which determine the sequence of aa in the primary structure of the polypeptide. this codes for enzymes which catalyse reactions to build a whole person.
in-between genes is non coding DNA
DNA contains the genetic code which codes for the synthesis of all polypeptides. genome is entire sequence of DNA with 25,000 genes
its contained in the nucleus to be conserved and protected
Types of polypeptides are:
- Structural proteins (keratin, collagen, actin, myosin)
- Channel proteins
- Enzymes
- Cell surface receptors
- Electron carriers
- Haemoglobin
- Antigens, immunoglobulins
Features of the genetic code
o A triplet code
o Is degenerative (more than 1 codon codes for the same aa, which means mutations can be silent if the new triplet code codes for the same amino acid as the previous one)
o It has punctuation
o It is widespread but not universal ( most organisms have same code but different sequence of bases)
o A non overlapping code (always in threes ensured by start codon)
There are 4 bases arranged into triplets.
43 =64 options
There are 20 amino acids
64-3 stop codons =61
61-1 met (start codon) = 60 options
Transcription
- The part of the DNA molecule to be transcribed unwinds and unzips as DNA helicase breaks the H bonds between bases, exposing unpaired nucleotides. Happens 3’ to 5’ of template strand.
- Free RNA nucleotides form complementary base pairs with the unpaired bases on the template strand – hydrogen bonds. This starts at 5’ end of nucleotide and 3’ of mRNA
- A binds with U and C binds with G, with 2 and 3 hydrogen bonds, purine to pyrimidine
- Phosphodiester bonds (covalent) form between nucleotides to make the sugar phosphate backbone using the enzyme RNA polymerase. This occurs 5’ to 3’.
- The template and coding strand reform hydrogen bonds, A-T ect.
- The mRNA is complementary to the template strand and a copy of the coding strand
- mRNA leaves to go to the ribosomes through the nuclear pore
tRNA
- made in the nucleus and passes into the cytoplasm
- it is a length of RNA that folds into hairpin shapes to form a clover leaf
- it can bind to a specific amino acid in the cytoplasm where 3 exposed bases are
- it can recognise the specific mRNA codon for the amino acid it carries by having 3 unpaired nucleotide bases at the other end which are anticodons for the amino acid
- the other clover leaf recognises a specific activation enzyme
- is the smallest RNA and there are over 20
After protein synthesis the RNA molecules are degraded in the cytoplasm- the phosphodiester bonds are hydrolysed an the RNA nucleotides are released and reused
Translation
- mRNA attaches to the small subunit of a ribosome in the groove exposing 6 bases of the mRNA to the large subunit. Several ribosomes may attach to the mRNA at once forming a polysome. This means many identical polypeptides can be synthesised at once. and each makes a bit of the polypeptide all one polypeptide or several different
- the first exposed mRNA codon is always AUG (start codon methionine)
- the tRNA molecule with the amino acid metaphase has an anticodon complimentary to the 1st codon, and lines up in position P.
- complimentary base pairs form H bonds between the codon and the anticodon (UAC with AUG)
- another tRNA (pro) forms complimentary base pairs with the next codon in the ribosome at position A
- the enzyme peptidyl transferase forms a peptide bond between the two amino acids (met and pro)
- the first tRNA is released and leaves the ribosome without its amino acid
- the next ribosome moves along the mRNA 3 bases exposing the next codon
- the second tRNA molecule (pro) is now in position P
- a new tRNA molecule pairs with the mRNA in position A bringing its amino acid (Tyr)
- a growing polypeptide is formed in this way until a stop codon is reached
- a stop codon (UAA, UAC or UAG) on the mRNA signals the ribosome to leave the mRNA. These work by having no tRNA with a complementary anticodon or the tRNA is codes for is not carrying an amino acid
- a newly synthesised protein is now complete and can take up its tertiary structure ect. Needed for structure and fucntion
- some proteins need to be activated by cAMP to take a 3D shape that is the best fit to their complementary molecule eg. By binding to an allosteric site on an enzyme
Comparing replication and transcription
R-Both processes have DNA as template but both strands are used as template strands
T-Has a template strand and a coding strand
R-Whole molecule is unzips and unwinds and is replicated
T-Only part of a DNA molecule (gene) unzips and unwinds at a time
R-Activated free nucleotides to bond to, but DNA nucleotides
T-Activated free nucleotides to bond to but RNA nucleotides
R-Both use polymerase to form phosphodiester bonds to produce a backbone but DNA polymerase
T-Both use polymerase but RNA polymerase
R-Both use complimentary bases with hydrogen bonds but AT GC
T- AU GC
R-Product is 2 daughter strands identical to templates
T-Product is 1 mRNA strand
R-DNA stays in nucleus
T-mRNA leaves through nuclear pore to go to cytoplasm
R- both unwinds and unzips
T- unwind and unzip
Protein synthesis
o DNA stays in nucleus
o Proteins are made on ribosomes in the cytoplasm (ribosomes made in nucleolus from rRNA and protein)
o Genetic code is copied to messenger RNA which can leave the nucleus by nuclear pores as its smaller taking the code to the ribosomes transported by the cytoskeleton
Cell cycle
INTERPHASE
Growth 1: normal cell growth and specialisation. proteins from which organelles are synthesised are produced
Synthesis: DNA replication
Growth 2: synthesis of organelles so there’s enough in new cells. DNA starts to coil into visible chromosomes at end.
MITOSIS (cytokinesis)
Difference between mitosis and cytokinesis
mitosis is when the nucleus splits (growth, repair and asexual reproduction)
cytokinesis is when rest of cell splits and is the end of mitosis
how are cells formed
by asexual reproduction or form a zygote from a female and male gamete
differentiation
the process by which a cell develops to become more distinct in form and function
Cell cycle checkpoints
enzymes check replicated DNA for errors
if errors are detected they are repaired or the cell destroys itself to stop mutations being passed on
G1:chromosomes checked for damage and DNA repaired before S phase. If the cell doesn’t satisfy the requirements of the checkpoint, then it enters the resting state G0.
s: check that all chromosomes have been replicated- the cycle will stop if not
G2:another check for DNA damage that may have occurred during replication, and cycle may be delayed to repair
Metaphase:check whether chromosomes have attached correctly to spindle fibres before anaphase
interphase
the part of the cell cycle where the cell is not undergoing cell division
what is G0 and why does it happen?
The phase when the cell leaves the cycle either temporarily or permanently. It does this because:
• Differentiation: a cell that becomes specialised to carry out a particular function is no longer able to divide so will not renter the cycle. red blood cells can’t divide as they loose their nucleus in development
• The DNA may become damaged so is no longer viable and cant divide so enters permanent cell arrest
• The majority of normal cells only divide a limited number of times and eventually become senescent. As you age, the number of these cell in your body increases leading to age related diseases like cancer and arthritis
• Lymphocytes can be stimulated to go back into the cell cycle and start dividing again in an immune response
Homologous chromosomes
homologous chromosomes are 2 chromosomes with the same sequence of genes on them- one from father and one from mother. they may have different alleles
chromatin
DNA wrapped around histone proteins
when it becomes supercoiled it forms visible chromosomes. after G2 as they can’t function when coiled
sister chromatids
before cell divides the DNA replicates (synthesis) producing a chromosome made of a pair of sister chromatids
held together by a centromere. they need to be kept together during mitosis so they can be segregated equally, one to each daughter cell
examples of mitosis
- Replacement of cells EG. outer layer of skin replacement of epidermal cells, red blood cells, intestinal lining cells
- Growth of tissues by producing new extra cells – EG. epithelial tissue, plant meristem cells (stem and root growth).
- Division of zygote into a multicellular organism where, all cells are genetically identical.
- Formation of clones of T and B lymphocytes and plasma cells in the immune response
- Asexual reproduction where mitosis produces individual organisms which are genetically identical to each other (clones) and the parent cell – EG. binary fission in bacteria(not asexual as no nucleus), budding in yeast.
- The production of genetically identical cells in multicellular organisms allows certain cells to retain the ability to develop into any other type if needed as a result of damage.
- Sometimes, abnormal cells divide by mitosis in an uncontrolled way giving rise to tumours, and if the cells are malignant, cancers.
cytokinesis method
the equator of the cell is constricted by a ring of contractile proteins (actin) in the process of cleavage to create 2 cells
in plant cells, cleavage can’t form as there is a cell wall and no centrioles. so vesicles from the Golgi assemble at the equator and fuse with each other and the cell surface membrane to divide the cell
new sections of wall form along the new sections of membrane. if they were formed before daughter cells separated lysis would occur
some vesicles remain intact to make connecting channels- plasmodesmata, through the new cell wall
Mitosis
INTERPHASE: chromosomes replicated and its checked for errors
PROPHASE (plump):
start- chromosomes supercoil, nucleolus starts to disappear, centrioles move to opposite poles and organise formation of microtubules that will form the spindle- spindle starts to form
end- chromosomes consist of a pair of chromatids joined by a centromere, nucleolus disappears and nuclear envelope breaks down
METAPHASE: (middle)
start-Microtubules of the spindle attach to the centromeres from either side which are aligned in the middle. The attachment involves a protein structure on each chromatid called a kinetochore.
end-The microtubules pull in opposite directions on the centromere so that they pull apart
Homologous chromosomes don’t associate.
ANAPHASE: (apart)
start- The chromatids are pulled to opposite poles of the cell by spindle fibres which shorten, centromeres leading (V-shape).
end-chromosomes reach their destination
TELOPHASE: (two)
start-Chromatids now called chromosomes.
The spindle fibres break down. The cells start to constrict around the middle
end-New nuclear envelopes and nucleolus’ form around each group of chromosomes.
The chromosomes slowly uncoil
I Peed on a MAT, C?
Meiosis
• The first stage is when homologous chromosomes are separated into two cells, each containing 1 full set of genes so are haploid due to reduction division
• The second stage is where pairs of chromatids are separated forming 4 haploid daughter cells that are unidentical providing genetic variation
PROPHASE 1: centrioles replicate and move to poles to form spindle, chromosomes condense as sister chromatids after replicating in interphase, nucleolus disappears, and nuclear envelope disintegrates. Crossing over as chiasmata form between homologous pairs of chromosomes (X X) (bivalents when they are close together, 4 chromatids- tetrad). When exchange occurs it forms recombinant chromatids. They may be different alleles of the same gene so sister chromatids are no longer identical.
METAPHASE 1: bivalents line up randomly along the metaphase plate and independent assortment occurs. Microtubules attach to centromeres.
ANAPHASE 1: Separation of homologous chromosomes in each bivalent by contracting microtubules. Each chromosome still has 2 sister chromatids joined together.
TELOPHASE 1: usually telophase 1 and interphase 2 doesn’t occur in plants but in animals chromosomes assemble at each pole, cytokinesis occurs (leaves small cytoplasmic bridges between cells) and new nuclear membranes forms during telophase, chromosomes uncoil and a very rapid interphase may occur.
PROPHASE 2: centrioles replicate and move to poles whilst new spindle fibres form at right angles to previous spindle axis. The chromosomes condense and become visible again and nuclear envelope breaks down if it reformed. No chiasmata
METAPHASE 2: individual chromosomes consisting of 2 sister chromatids line up alone on the metaphase plate. Microtubules attach to centromeres. Independent assortment occurs.
ANAPHASE 2: individual chromosomes are now separated into chromatids by being pulled to opposite poles after division of centromeres
TELOPHASE 2: 4 haploid genetically different cells are produced as chromatids assemble at poles. Chromosomes uncoil and form chromatin again. Nuclear envelope reforms and nucleolus becomes visible.
diagram
Sources of variation
asexual: environmental influences
Sexual: CROSSING OVER
A pair of joined homologous chromosomes – a bivalent with a chiasmata may exchange DNA between non sister chromatids of homologous chromosomes during prophase 1. This creates a new combination of alleles in chromatids, but doesn’t change genetic information as chromosomes have identical sequences. They come together in a process called synapsis
INDEPENDENT ASSORTMENT
The random orientation of homologous chromosomes on the equator in metaphase 1 determines the direction in which the pairs of chromatids move in anaphase 1. different combo of alleles. 2n genetically different gametes could be made where n is the haploid number of chromosomes
In metaphase 2 the random orientation of pairs of chromatids determines which chromosomes migrate to opposite poles of the cell.
FUSION of male (spermatozoa)and female gametes(secondary oocyte) which are genetically different to produce a zygote is completely random creates a large number of allele combinations
RANDOM MUTATIONS
cause different bases so different polypeptides as DNA checks don’t recognise damage
Similarities and differences between mitosis and meiosis
mitosis: no chiasmata form
Meiosis: bivalents are formed when homologous chromosomes are paired up in prophase 1 and chiasmata may form
Mitosis:Individual chromosomes line up along equator in metaphase
Meiosis: Homologous pairs of chromosomes assemble along the equator in metaphase 1
Mitosis:Chromatids are pulled to opposite ends of cell
Meiosis: Homologous chromosomes are pulled to the opposite poles and chromatids stay joined together in anaphase 1
first division ends up with haploid
mitotic index
measures ratio of cells in mitosis to the number of cells counted
used to diagnose cancer as a measure of cell proliferation
high in growing areas like tips and roots
number of cells in mitosis/ total number of cells
blastocyst
a structure formed in the early development of mammals containing embryonic stem cells that will create body cells as well as placenta and umbilical cord. (totipotent) It is not yet implanted in the womb. It is made of an outer layer of cells, a fluid filled space and a group of cells called the inner cell mass, which is where the embryo cells are found
stem cell division
starts with the fertilised egg- 1 cell
divides in 2 to produce 2 daughter cells then divides again and so on
they can self renew by making copies of themselves and also differentiate to make specialised cells. when they divide they produce 2 stem or 2 specialised, not one of each
the DNA in stem cells and the daughter specialised cell is the same, as there are lots of other molecules inside and around cells that can change the way cells behave in the case of differentiated cells
specialised cells can’t divide and make copies of themselves, so stem cells are needed to replace specialised cells that die, get damaged or used up(liver and T cells can)
2 Types of stem cells
embryonic found in the blastocyst
tissue/adult found in tissues of the body(foetus, baby child or adult)
4 types of stem cells
pluripotent:
Can make all types of specialized cells in the body. Embryonic stem cells are pluripotent
Multipotent:
Can make multiple types of specialized cells, but not all types. Tissue stem cells are multipotent as they can only make the kind of cells found in the tissue they belong to- blood cells can make cells found in blood
Totopotent:
can differentiate into all types of specialized cells in the body PLUS cells that are needed during development of the embryo only: placenta, yolk sac, umbilical cord. Eg. Zygote
Unipotent:
can only differentiate into one type of specialized cell. For example, spermatogonial stem cells (found in the testicles) are unipotent because they can only form sperm cells.
Uses of embryonic stem cells
What factors should be considered to assess effectiveness of stem cell therapy?
- To treat diseases
- Understand how diseases develop
- Test drugs in lab
- Umbilical cord stem cells are very good because they are plentiful supply and non-invasive surgery, and can be stored in case the individual ever needs them without rejection
gender, age
Diseases which may betreated by stem cells
diseases which are treated by stem cells
• HEART DISEASE- muscle tissue in the heart damaged from heart attack
• TYPE 1 DIABETES- grow insulin producing cells to transplant into a patient with diabetes
• PARKINSON’S DISEASE- Replacing dopamine producing brain cells that die causing shaking and rigidity.
• ALZHEIMER’S DISEASE- brain cells destroyed from build up of abnormal proteins. Stem cells are beig grown into nerve cells. Hard because damage to brain is widespread.
• MACULAR DEGENERATION- condition responsible for causing blindness in elderly and diabetics. Can grow retinal cells.
• BIRTH DEFECTS- have successfully reversed birth defects in mice
• SPINAL INJURIES- some movement has been restored in rats by introducing stem cells into site of spinal injuries to repair damage
• BLOOD DISEASES- eg. Sickle cell disease using bone marrow and stem cells
CURRENT:
• BURNS- stem cells grow on biodegradable meshes to produce new skin quicker than normal graft process
• DRUG TRIALS- potential new drugs can be tested on cultures of stem cells before being tested on animals and humans
• DEVELOPMENTAL BIOLOGY- the study of the changes that occur as multicellular organisms grow and develop from a single cell like a fertilised egg and why things sometimes go wrong
what are Induced pluripotent stem cells
how may they be used for Alzheimers
• Cells from the body go through genetic reprogramming- certain genes are added to their cell so that the iPS behaves like an embryonic stem cell. These are then cultured in a lab so that they differentiate into specialised cells. From multipotent to pluripotent.
Parkinson’s or Alzheimer:
• Take cells like skin cells from body
• Make iPS cells
• Use those iPS cells to grow specialised cells needed eg. Brain cells. They wouldn’t be rejected as they would be from their own body
What did shimmy yamanaka do
won Nobel prize for adding 4 genes and in a few weeks the cells behaved like stem cells
Ethics of stem cells
- Embryos used to be donated from left over fertility clinics, but the law has changed recently so that embryos can be specifically created in the laboratory as a source of stem cells
- Usually the removal of stem cells from embryos destroys the embryos but techniques are being introduced to prevent damage- moral and religious objections as murder. There are debates over weather the embryo has rights and who owns the genetic material being used for research
- The use of umbilical cord stem cells overcomes the ethical debate, but these cells are only multipotent, not pluripotent like embryonic
- Adult stem cells could also be used but don’t divide as well as umbilical and are more likely to have mutations, therefore iPS is occurring
- Plant stem cells don’t have the same ethical issues and are used to create drugs cheaply and unlimited supply
differentiation
specialisation
The process of physical changes by which a cell develops to become more distinct in form to carry out a particular function
how the physical changes of differentiation allow an organism to perform its function
red blood cell features (erythrocytes)
o Flattened biconcave shape to increase SA to vol ratio for transport of oxygen
o No nuclei or many other organelles increasing space for haemoglobin
o Flexible, elastic membrane to change shape to squeeze through narrow capillaries
o Cytoplsam contains lots of haemoglobin (280mill molecules) pigment binds with oxygen and relases it when concentrations are low
develop large numbers of ribosomes early in differentiation to make haemoglobin
white blood cell features (neutrophil)
o indentation of nucleus to make it multi-lobed so it’s easier to squeeze through small gaps to get to sight of infection. May be due to flexible membrane.
o development of granular cytoplasm contains many lysosomes containing hydrolytic enzymes used to attack pathogens
o Flexible nuclear membrane shape allowing them to penetrate between junctions of the cells of the capillary wall and to form pseudopodia to engulf microorganisms
o Called neutrophils as granules don’t stain darkly with acidic or basic dyes
o Destroy foreign bodies by engulfing them by phagocytosis and secreting enzymes
xylem features
o Responsible for transport of water and minerals throughout plants
o Tissue is composed of vessel elements which are elongated dead cells
o Walls strengthened with lignin providing structural support and waterproof
o Wide lumen and absent end walls allows water flow without blockages
o No cytoplasm as its unnecessary for strengthening and would obstruct water transport
what elements are found in the xylem
o Parenchyma cells are not specialised and form a packaging tissue between other cells
o Vessel elements are the main water transporting cells and have a wide lumen and end walls are perforated or completely absent. Pits allow water to move laterally, which can be helpful for avoiding blockages. Vessels are aligned so are continuous and stretch the length of the plant.
o Tracheid’s transport water in angiosperms they also help strengthen tissue. Don’t have a wide lumen but have perforated end walls and pits where cell wall is very thin, and water can move easily between cells.
o Fibres don’t transport water they just provide support. They have hardly any lumen and are just strips of lignin.
phloem features
o Responsible for transport and of organic nutrients, particularly sucrose, from leaves and stems where it is made by photosynthesis to all parts of plants where it is needed
o Composed of columns of sieve tube cells separated by perforated walls called sieve plates connecting cytoplasm of cells
o Few organelles
o Reduction of cytoplasm means they cannot support themselves so have companion cells
o Plasmodesmata allows molecules to pass between plant cells through cytoplasm
what elements are found in the phloem?
o Sieve tube elements are the cells that transport nutrients
o Companion cells help support the sieve tube elements, and have a large number of mitochondria and ribosomes so we think they play a role in transport
o Phloem parenchyma also are packed between cells
fibres and sclereids with thick. cell walls for support
How are xylem and phloem produced
o Cambium tissue in stems and roots divides to form phloem cells on the outside and xylem on the inside
o Cambium is an example of meristem- undifferentiated plant tissue and is pluripotent
o The production of xylem and phloem is stimulated by hormones.
o The balance of different hormones can shift production between xylem and phloem
o The outer cambium cells produce phloem and the inner produce xylem
o The cells that become xylem lose their cytoplasm and deposit lignin in their cell walls. The end cell walls may be lost.
o The cells that become phloem loos some cytoplasm and organelles and develop sieve plates at the end of cells.
squamous epithelium features
o Made of specialised squamous epithelial cells
o Very thin due to flat/squat cells and is only 1 cell thick, helping rapid diffusion across a surface
o Forms lining of lungs and allows rapid diffusion of oxygen into blood
ciliated epithelium
o Made of ciliated epithelial cells
o Cells have hair like structures called cilia on one surface that move in a rhythmic manner to move substances
o Lines trachea to sweep mucus away from lungs
o Goblet cells are also present releasing mucus to trap any unwanted particles in air like bacteria, so they don’t reach the alveoli
sperm cells
o Male gametes that deliver genetic information to female gamete (ovum)
o Have a flagellum to help with movement
o Contain many mitochondria to supply the energy needed to swim
o Acrosome head contains digestive enzymes released to digest the protective layers around the ovum allowing the sperm to penetrate
Palisade cells
o Many chloroplasts to absorb as much light as possible for photosynthesis. They can also move within the cytoplasm in order to absorb more light
o Cell is tall and thin to allow light to penetrate further before having to go through a second cell wall, as cell walls absorb or reflect some light
o Rectangular box shapes can be closely packed to form a continuous layer
o Thin cell wall, increasing rate of diffusion of carbon dioxide
o Large vacuole to maintain turgor pressure
Guard cells
o Form small openings called stomata
o Close when loose water by osmosis
o Cell wall is thicker on one side so doesn’t change shape symmetrically as its volume changes
root hair cells
o Root hairs are long projections from cell penetrating between soil particles to reach more water and increases surface area for absorption of minerals and water
vacuole contains cell sap with ions and sugars to lower water pot.
o Present at the surfaces of roots near the growing tips
muscle
o Made of muscle and nerve tissue blood and connective tissue.
o Have skeletal (voluntary), smooth (involuntary), cardiac (in heart).
o Skeletal muscle cells are highly specialised and are multinucleate, and often referred to as muscle fibres, which group together to form a fascicle, and groups of these form muscle.
o The muscle fibres contain the contractile protein myofilaments called actin and myosin which are formed into structures called myofibrils.
cartilage
o A connective tissue composed of specialised cells called chondrocytes that produce extracellular matrix consisting of collagen fibres stiffening and strengthening the tissue, and elastin fibres giving it flexibility.
o Function is to protect and strengthen, found in joints, nose, ear, rib cage, trachea. Many fish have no bone, only cartilage
what is a tissue
examples in plants and animals
a group of differentiated cells that work together to perform a specialised function
o Plant:
- Epidermis- adapted to cover plant surfaces (single layer of closely packed cells covered by waterproof waxy cuticle. Contains stomata)
- Vascular- adapted for transport of water and nutrients eg. Xylem and phloem
o Animal:
- epithelial- adapted to cover body surfaces, internal and external
- nervous- transmission of electrical impulses
- muscle-adapted to contract
- connective- adapted to hold other issues or as a transport medium
what is an organ
examples in plants and animals
Organ: a group of different tissues that work together
o Plant: the leaf carry’s out photosynthesis and gas exchange. It has xylem to bring water, phloem to take organic nutrients away, palisade and spongy parenchyma carrying out photosynthesis, epidermis waterproofing leaf and has stomata.
o Animal: the heart pumps blood around the body. Cardiac muscle requires nutrients and oxygen for respiration, supplied throughout the blood. Coordination is provided by nervous tissue.
what is a system
examples in plants and animals
a number of different organs working together to carry out a major function in the body
o Plant: gaseous exchange system
o Animal:
- Digestive system takes in food, breaks down large insoluble molecules into small soluble ones, absorbs nutrients into blood, retains water and removes undigested material. Involves oesophagus, stomach, small and large intestine, liver, pancreas, and gall bladder.
- Cardiovascular system moves blood around body to provide an effective transport system for the substances it carries
formation of red blood cells
Erythropoiesis- the process by which an erythrocyte is formed
always formed from stem cells as have no nucleus so can’t divide themselves
Multipotent bone marrow stem cells differentiate
Proerythroblast- changes to have a large nucleus containing several nucleoli surrounded but a small amount of cytoplasm so now only able to become an erythrocyte
Haemoglobin then accumulates in the cytoplasm
Nucleus is ejected from the cell
Undergoes further changes like changing shape to biconcave disk to become a mature erythrocyte
advantages of mitosis
- only 1 parent required so saves time and energy finding a mate or waste of gametes- pollen that doesn’t result in fertilisation
- genetically identical offspring if an organism is well adapted its passed on
- dispersal and spread is quick
- rapid multiplication so large numbers of individuals can be produces very quickly to help survival
disadvantages of mitosis
- no genetic variation unless mutation so evolution my natural selection doesn’t occur so unlikely to survive changes in environment
- rapid colonisation may lead to overcrowding and exhaustion of resources
advantage of meiosis
genetic variation through natural selection
disadvantage of mitosis
requires a lot of time and energy in comparison to asexual reproduction
elements in carbs:
lipids:
proteins:
nucleic acids:
carbon, hydrogen, oxygen
carbon, hydrogen, oxygen
carbon, hydrogen, oxygen, nitrogen, sulfur
carbon, hydrogen, oxygen, nitrogen, phosphorus
what happens in a polymerisation condensation reaction?
what type of reaction is it?
what happens to water molecule?
what happens to covalent bond?
o Monomers are joined together to form a polymer
o Anabolic
o Water molecule is released
o Covalent bond formed- oxygen bridge
what happens in a hydrolysis reaction?
what type of reaction is it?
what happens to water molecule?
what happens to covalent bond?
o A chemical reaction that splits polymers into monomers
o Catabolic
o Water molecule is used
o Covalent bond is broken- enzyme needed
carb monomer and polymer?
protein monomer and polymer?
nucleic acid monomer and polymer?
monosaccharide and polysaccharide
amino acid and polypeptide
nucleotides and DNA+RNA
bonding in water:
o Hydrogen bonds form between polar molecules
o They break and reform constantly between the moving water molecules
o Polar molecule occur when in a covalent bond, the electrons are not shared equally amongst atoms of different elements. When atoms spend more time closer to one atom than other, you get polar molecules, with slightly negative and slightly positive ends.
o Weak individually but strong in large numbers
o Shown by a dotted/dashed line
o Liquid at room temp, but densest at 4 degrees Celsius
what are the uses of water?
habitat solvent transport temperature regulation reactant
Why is water used as a habitat?
o High specific heat capacity due to hydrogen bonds restricting the movement of water molecules so aquatic habitats are stable. Mammals don’t have to endure rapid and extreme temperature changes, and can keep internal body temperature constant- enzymes and metabolic rate
o Ice has lower density than water because of its lattice arrangement-4 hydrogen bonds to other water molecules, which provides a habitat (swim and move) and an insulating layer so organisms in water can survive. Prevents bottom of water freezing too which would kill organisms and allows currents/nutrients to circulate.
o Surface tension due to cohesion between water molecules below rather than air creates a skin which insects such as pond skater can be supported on
o Colourless nature means photosynthesis can occur at depth
Why is water a good solvent?
EG
o When chemical dissolves in water its free to move and react with other chemicals- cytoplasm
o Water is polar so can attract other charged or polar covalent molecules
EG. In blood and sap used for transport, glucose and sucrose are polar molecules
o Stability to cell membrane is obtained as its hydrophobic
why is water a good transport medium?
EG
o Blood and tissue fluid transport many substances in and out of cells as is a solvent
o Water helps xylem and phloem function as the hydrogen bonds that hold water molecules together give it cohesive properties, making long columns of water molecules that don’t break. Adhesion occurs between walls of xylem and water helping water get drawn up vessels- capillary action.
o viscosity allows water to flow byt slows doewn water loss from pores in plants
Why is water used for temperature regulation?
o High latent heat of vaporisation so when you sweat it transfers a lot of energy when it evaporates due to hydrogen bonds being broken
o Transpiration stream in plants is similar
general formula for carbs
Cn(H2O)n
when drawing sugars must…
number carbons
C must bond to O but H can be either side
pentose sugars:
Pentose sugars have 5 carbons
o RNA- 5 membered ring with 4 carbons
On carbon 2 there is a hydroxyl group
o DNA- 5 membered ring with 4 carbons
On carbon 2 there is just hydrogen
Hexose sugars:
Hexose sugars have 6 carbons
o Glucose- 6 membered ring with 5 carbons
Soluble as OH group is free to interact with water
o Fructose- 5 membered ring with 4 carbons- naturally found in fruit
o galactose
properties of monosaccharides
water soluble
reducing sugars
what is the difference between alpha and beta glucose?
What are the properties of alpha and beta glucose?
Alpha glucose:
o Down, down, up, down-OH
o Hydroxyl group is below carbon 1 in alpha
Beta glucose:
o Up, down, up, down
o Hydroxyl group is above carbon 1 in beta
Animals and plants have enzymes that can only break down a glucose to release energy needed to make ATP in respiration
B glucose cannot be used for energy but is used for structure and cellulose
Benedicts test
o Place the sample in a boiling tube with an equal amount of benedict’s reagent. Either dissolve or grind it if not liquid.
o Must heat at 80 degrees for reaction to occur for about 5 minutes
o The reducing sugars will react with the blue copper sulphate solution in the benedict’s reagent reducing cu2+ ions to brick red cu+ ions.
o Green- yellow-orange-brick red precipitate shows increasing quantities
o For non-reducing sugars, you need to boil them with HCL it will then test positive as it is hydrolysed by the acid to form reducing sugars. You must neutralise the acid first.
o Can be made quantitative by using a colorimeter- a piece of equipment used to quantitatively measure the absorbance or transmission of red light- more concentrated will be less blue as the blue benedict’s solution is used up in the reaction with the sugar. Therefore more red light is transmitted.
o You put a filter in the colorimeter then calibrate it using distilled water. The solutions being tested must be filtered first to remove precipitate.
o Reagent strips can be used to test the presence of reducing sugars. With the use of a colour coded chart, the concentration of the sugar can be determined. An alternative to this is to filter the precipitate, dry it and weight it, where more precipitate means more concentrated
monosaccharide condensation reactions:
form disaccharides then polysaccharides
1-4 glycosidic bond is formed
What are the reducing and non reducing sugars?(disaccharides)
maltose- 2 alpha glucose
sucrose- alpha and fructose
lactose- alpha/beta glucose and beta galactose
reducing sugars like maltose and lactose as can donate electrons to another molecule
sucrose is non reducing sugar as the glycosidic bond formation is different so must first be hydrolysed by acid in hot water bath/enzyme into its constituent where once neutralised will test positive for Benedict’s
similarities between lactose and maltose
differences
- Maltose and lactose both contain the same number of each element
- Both bonded by 1-4 glycosidic bonds
- Have 2 6 membered rings each
- Have 2 CH2OH groups
- Rings contain 1 oxygen atom
- Lactose has 1 glucose monomer and one galactose monomer whearas maltose has 2 glucose monomers
- Lactose has beta glucose maltose has alpha glucose
- Beta glycosidic bonds alpha glycosidic bonds
- Monomers flipped in lactose and same direction in maltose
test for water
cobalt chloride paper goes from blue to pink
iodine test
iodine dissolved in potassium iodide solution
o The long chains of amylose coil into a spring shape making the amylose molecule quite compact
o Iodine molecules can become trapped in the coils of the spring to form an amylose-iodine complex
o The formation of this complex changes the colour of iodine from brown to blue/black
starch is a heteropolysaccharide: amylose structure function bond shape properties
Structure:
Chain of alpha glucose monomers. Compact and stable because of coils so good storage molecule
Function:
Energy store in plant. Glucose made by photosynthesis is stored as starch.
bond:
1-4 glycosidic bond with hydrogen bonds holding the OH groups inside coil together making it more compact
shape:
Linear molecule that coils due to angle of bond.
properties:
Slightly soluble as OH group sticks out so can make hydrogen bonds with water, but some are bonded. Less soluble than amylopectin or glycogen.
starch: amylopectin
structure:
Chains of alpha glucose monomers with other chains branched off. Compact.
function:
Energy store in plants eg. In potato tuber its stored in amyloplasts within cells and in chloroplasts
Bond:
1-4 glycosidic bond between alpha glucose and 1-6 gylcosidic bonds to add a new strand (to join the 2 chains of amylose)
shape:
Branched molecule every 25 glucose subunits
Properties:
Slightly Soluble as OH group sticks out so can make hydrogen bonds with water
Glycogen polysaccharide
Structure:
Similar to amylopectin but has many more branches (1-6 bonds) which make the ends more accessible to enzymes giving a quicker release of energy and makes it more compact.
Function:
Energy storage in animals- stored as granules in animal cells like liver and muscle cells. Large molecule so doesn’t leave liver cell where made but bonds are hydrolysed to release alpha glucose into blood
Bond:
1-4 glycosidic bond between alpha glucose. These chains tend to be shorter so less likely to coil, and more compact. 1-6 gylcosidic bonds to add a new strand
Shape:
Branched molecule
Properties:
Doesn’t change osmotic potential of cell when stored as glycogen as it is insoluble.
Most soluble as has the most branches so can make the most OH bonds
Cellulose polysaccharide
Structure:
Alternating molecules of beta glucose rotate 180 degrees, preventing spiral. Bundles of microfibrils (40-70 cellulose chains) are also crosslinked by hydrogen bonds to form macrofibrils then fibres. This is a very stable and strong structure.
Function:
Structural support and rigidity in plants eg. Cell walls
Bond:
Beta glucose held together by gylcosidic bonds and chains held together by hydrogen bonds forming microfibrils.
Shape:
Straight chains to form microfibrils
Properties:
Insoluble as the OH groups are involved in hydrogen bonds so can’t make hydrogen bonds with water
High tensile strength
How Many amino acids are there?
what are amino acids?
How are they joined?
o There are 20 amino acids, 8 essentials and 12 non essentials. 20x20x20 for all combo’s
o Amino acids are basic monomer units of proteins made of an amino and carboxyl/organic group
by condensation reactions which create dipeptides then polypeptides main peptide bonds and releasing water
plants and aa
animals and aa
plants can manufacture their own amino acids using nitrates from the soil and organic molecules made by photosynthesis
Animals can only make non-essential amino acids from essential amino acids obtained from the diet.
Can’t store excess amino acids because the amino group makes them toxic- in solution is ammonia
They are transported to the liver where the amino group is removed (deamination) and then converted into urea and excreted in urine via the kidney.
keto acid is respired
if the R group contains C, O or H it can also be respired
if if was amine it would be converted into urea
Biuret test
DO NOT HEAT
o Detects presence of peptide bonds
o Contains copper sulphate and alkaline potassium hydroxide
o A blue ring first appears and when shaken will turn the solution purple
o Relies on reduction of cu(II) ions to cu(I), which forms a violet complex with the nitrogen component of the peptide bond in an alkaline solution
roles of enzymes in protein breakdown
o Protease enzymes control formation and breakage of peptide bonds in organisms
o Pepsin is a type of protease and digests protein in the stomach
o Protease regulates the breakdown of protein hormones, so their affects are not permanent
o Older skin is less able to build the protein collagen as it lacks enough of the correct enzyme resulting in aging.
Primary protein structure
the sequence of aa in a polypeptide
o It determines the structure and function of the protein
o The sequence is coded for in the DNA in the nucleus
o Held together by peptide bonds- this reaction is catalysed by the enzyme peptidyl transferase present in ribosomes, the sites of protein synthesis
Secondary protein structure
the chain of amino acids takes one of these 2 shapes:
o An alpha helix or a beta pleated sheet (chains lie parallel an appear pleated due to pattern formed by individual amino acids)
o This is determined by the R groups and the order of amino acids determines where the bonds form so what shape occurs
o There are hydrogen bonds between chains in both structures creating these shapes
Tertiary protein structure
the secondary structure then further coils into its final 3D shape
o Determines the 3D shape of the and therefore its function- give active site
This causes the following interactions between R groups:
o Disulphide bonds- the amino acid cysteine contains sulfur (R group) where 2 cysteines are found close together and a covalent bond forms
o Ionic bonds- R groups sometimes carry a charge and where opposite charged amino acids are close together, they form an ionic bond (affected by pH as affects charge ratio) (strongest)
o Hydrogen bonds- where slightly positive groups are found near slightly negative groups (weakest). O- H+
o Hydrophobic and hydrophilic reactions- proteins are assembled in a water-based cytoplasm, so the way in which the protein folds depends on whether the R groups are hydrophilic or phobic. Hydrophilic amino acids tend to be found on the outside in globular proteins and hydrophobic in the centre
o Van der waals forces- several aa have large hydrocarbon groups in their side chains which can attract or repulse each other creating weak bonds
Quaternary protein structure
o Quaternary structure: When a protein is made from more than 1 polypeptide chain or subunit- they can be the same or different. Enzymes have identical subunits whereas insulin has 2 different.
o A sub unit is a single polypeptide
o The polypeptides are bonded together by ionic, hydrogen and hydrophilic/phobic bonds like tertiary, but these interactions occur between different protein molecules rather than within 1 molecule
fibrous protein
is formed from long parallel insoluble molecules, due to presence of a high proportion of amino acids with hydrophobic R groups in their primary structures. Linked by disulphide bonds. They contain a limited range of amino acids with small r groups and is very repetitive leading to organised structures. They make strong long molecules not folded into complex 3D shapes.
EG keratin
Elastin
Collagen
globular protein
similarities between globular and fibrous proteins:
is a polypeptide chain coiled and folded into a spherical shape
are compact, water soluble. Form when proteins fold into their tertiary structures so that hydrophobic R groups are on the inside away from aqueous environment. Used for metabolic reactions, immunity, muscle contractions
EG. Haemoglobin has 4 subunits, with 2 sets of identical subunits.
Insulin
Catalyse/ enzymes
Similarities: a number of different types of bond stabilise the molecules and hold it in place and are both polypeptides made from combinations of 20 amino acids
what is a biosensor used for and what are the features of it?
example of one
o An analytical device for the quantitative measurement of a biological response.
o Molecular recognition- It usually uses an immobilised antibody which can specifically interact with an analyte and produce physical, chemical or electrical signals that cause a change in a transducer, causing it to release an immobilised dye on a test strip or an electric current in a glucose testing machine (transduction) signal is amplified.
o An analyte is a compound (e.g. glucose, urea, drug, pesticide) whose concentration is being measured.
o Display- this then produces a visible qualitative or quantitative signal such as a particular colour on a test strip or reading on a machine.
o A blood glucose biosensor uses FAD combined with the enzyme glucose oxidase which oxidises the glucose and the released electrons reduce the FAD (enzyme) and leads to an electrical current being generated as the transducer takes the electrons by oxidising the FAD. The current is a measure of glucose concentration. Blood is put on a test strip which is inserted into the biosensor meter which displays it as a digital figure.
Roles or inorganic cations:
Ca2+: Bone structure, Muscle contraction Synaptic transmission Amylase cofactor Na+: Nerve transmission Counter current multiplier in LOH/CD Kidney function K+: Nerve transmission Guard cell opening H+: H bonds Blood pH ETC in resp and phs Catalysis NH+ 4: Formed from deamination of amino acids Needed for production of nitrate ions by bacteria
Roles of inorganic anions:
NO-3:N source for plants to build AA HCO-3:CO2 transport Plasma buffer Blood pH Cl-: Cl- shift in CO2 transport Amylase cofactor Balances positive charge of K and Na ions in cells PO-3 4: In phospholipids, cell membrane ATP and nucleic acids formation Bone formation OH-:Involved in bonds pH determination catalysis of reactions
Serial dilutions:
Dilution factor: volume added/total volume
serial dilution: volume added/total volume x previous answer for concentration
rf value:
distance moved by solute/distance moved by solvent
functions of membranes
o They are partially permeable barriers, controlling what passes through them.
o They are involved in cell signalling (communication between cells)-target cells
o Site of chemical reactions
o They provide attachment sites for enzymes and other molecules involved in metabolism. E.g. Cristae in mitochondria
o They can allow electrical signals to pass along them.
o They produce different compartments inside cells. (compartmentalisation) e.g. In lysosomes it can provide right conditions like PH of 4.8
development of membrane model
gorter and grendel in 1925 a the phospholipid bilayer
1935 Davson-danielli proposed model with proteins
1970s singer and Nicholson showed fluid mosaic model
Describe the fluid mosaic model
o They have a polar phosphate group which is hydrophilic and faces the aqueous solution so outside
o Fatty acid tails are non-polar and move away from an aqueous environment so are inside
o Both tissue fluid and cytoplasm is aqueous so phospholipids firm 2 layers with hydrophobic tails facing inward attracting each other and phosphate group facing outwards interacting with aqueous environment
proteins which can move freely and are randomly distributed
Features of the fluid mosaic model
o Glycoproteins are involved in cell adhesion for aggregating cells into tight junctions in tissues.
They also act as receptors for chemical signals (cell signalling). When the chemical binds to the receptor it causes a response from the cell provoking a direct response or a cascade of events
o Glycolipids act as cell identity markers or antigens allowing immune system to recognise them as self or non self
Also help with stability by forming hydrogen bonds with surrounding water molecules but can be receptors sometimes
o Cholesterol regulates fluidity of membrane- high temps make the membrane less fluid and at low ones maintains fluidity. Is a lipid with a hydrophilic and phobic end interacting with philic and phobic ends respectively. It stops the phospholipid molecules grouping together and crystallising, by partially immobilising nearby phospholipids
o Intrinsic proteins have amino acids with hydrophobic R groups keeping them in place by interacting with the hydrophobic core - channel and carrier. They span the entire phospholipid bilayer and are free to move about so have a random arrangement
o Extrinsic proteins have hydrophilic R groups on outer surfaces to interact with polar heads of phospholipids or with intrinsic proteins. Can move between layers.
o Channel proteins allow the movement of large or hydrophilic molecules to diffuse by providing a hydrophilic channel e.g. Glucose. They can be gated and are passive
o A variety of carrier proteins allow for the controlled movement of substance through the membrane using both passive diffusion or active transport- ATP. They have specific shapes for certain molecules, and then the protein changes shape to allow molecules through. Usually for polar molecules. Can be denatured.
o Receptor proteins can act as binding sites for hormones and other substances and can transmit the information to the interior of the cell.
how do polar and non polar molecules pass through the phospholipid bilayer?
o Polar molecules need channel proteins to enable them to pass through the membrane as they can’t get through the hydrophobic surface of the bilayer as they are not fat soluble
o Non polar molecules diffuse/dissolve through the phospholipid bilayer eg. Steroid hormones
How does temperature affect cell membranes
o Cell membranes are given kinetic energy when they get hot, so they vibrate
o Lipids become more fluid so membranes become more fragile
o Proteins are formed of coiled and folded strings of amino acids, held together by hydrogen bonds and disulphide bridges. When they get hot they untangle and break apart due to the vibrations, forming holes that destroy the structure, and the inner pigment/ cytosol can spill out as vacuole is damaged.
o Carrier and channel proteins will be denatured at higher temperatures which also affects membrane permeability
How does organic solvents affect membranes?
o Slightly polar organic solvents like alcohol can denature the membrane, but weaker ones such as drinks wont dissolve the membrane but cause damage. Combination of alcohol and higher temperature can dissolve lipids.
o Nonpolar alcohol molecules can enter the cell membrane and the presence of these molecules between the phospholipids disrupts the membrane
How do polar and non polar signals get received?
o Non polar signals can diffuse through the phospholipid bilayer and bind to intracellular receptors. Steroid hormones are fat soluble EG. testosterone
o Polar signals must bind to membrane bound receptors (intrinsic proteins)
Hormone cell signalling process
EG
o Chemical messengers transported in the blood
o Target cells are any cells with a receptor for that hormone
o Hormone and receptor on target cell bind due to their complementary shape
o Binding causes the target cell to respond in a certain way
1) The change in the receptor may cause the release of a second messenger inside the cell
2) The change in the target cell may result in an opening of a protein channel that was previously closed, or close one that was open
3) The change may activate an enzyme within the cell, or the membrane protein itself may be an enzyme itself which is activated
EG. Insulin
o Under normal circumstances there are some glucose channel proteins present, and some being held in vesicles inside the cell
o When blood glucose levels rise the hormone insulin is secreted into the blood by the Pancreas
o The insulin binds to its complementary receptor in the glycocalyx of target cells (liver, muscles)
o This sets off a series of events that causes the vesicles to fuse with the cell surface membrane
o This means many more glucose channel proteins are on the surface so there’s a greater uptake of glucose from the blood into the cell
o The insulin hormone is then broken down and vesicles reform by pinching off from the plasma membrane reducing number of glucose pores to normal level
Glucose is big and hydrophilic, so channel proteins are specific
Examples of drugs that use receptors
o Eg. Beta blockers block receptors and prevent the heart from increasing the heart rate when it could be dangerous for patient
o EG. For schizophrenia drugs mimic natural neurotransmitters that patients cannot produce
o Viruses on the other hand enter cells by binding with receptors on cells plasma membrane EG HIV can enter cells of the immune system (T lymphocytes) which can prevent cells doing there job and may destroy the cell
o Botox uses a toxin from a bacteria which binds with receptors on muscle fibres and prevents them from working causing paralysis
diffusion
EG
the overall movement of atoms or molecules from an area of higher concentration to an area of lower concentration, though phospholipid bilayer not through channel/carrier proteins.
molecules move randomly as have kinetic energy to bump into other particles - Brownian motion
move both ways but majority 1 way
passive
oxygen into red blood cells
Which particles go by facilitated diffusion and normal diffusion?
o Other very small charged particles like water (polar) and small ions (calcium, sodium, potassium) can also diffuse directly through the lipid bilayer. (for nerve cells) but at slower rates
o Larger or charged particles like glucose or amino acids are unable to pass through the lipid bilayer, and so must pass through membrane proteins to cross the membrane. This is known as FACILITATED DIFFUSION. It is still passive as the molecules are moving from an area of high concentration to an area of low concentration down a concentration gradient. This is because the hydrophobic interior or the membrane repels substances with charges.
Facilitated diffusion methods
o Rate is also affected by how many channel proteins are present
Channel proteins:
o Pores in the membrane with a specific shape that only allow a certain shaped ion or small polar molecule through. They can also be gated, so they can open or close.
o Passive
o They can limit a reaction
o EG. Glucose into blood to cells
Carrier proteins:
o Specific shape so that only a certain (usually larger) molecule fits into it at the membrane surface. The molecule binding causes a change in shape of the protein that delivers the molecule to the other side of the membrane.
o Active or passive Control:
o Different membranes have different carrier and channel proteins in them, allowing a measure of control over what enters and leaves the cell.
o NET diffusion will stop when there are an equal number of one type of particle on one side of the membrane as on the other. NB. This does NOT mean diffusion STOPS, but that molecules are entering at the same rate as they are leaving.
Factors affecting rate of diffusion:
Temperature- the higher the temperature the higher the rate of diffusion as particles have more kinetic energy and move at higher speeds
Conc. Gradient- the greater the difference in concentration the faster the rate as the overall movement will be larger.
Stirring/ moving- provides kinetic energy
SA- the larger the exchange surfaces the higher rate as more particles can interact at once and more likely to collide.
Distance/ thickness- thinner means higher rate as takes less time to cross
Size of molecule – small diffuses fastest
Active transport:
EG
o Against a concentration gradient
o Carried out by carrier proteins
o Adenosine triphosphate (ATP) provides energy, which is generated by mitochondria in aerobic transpiration
o If cells are deprived of oxygen then there is less ATP so active transport slows
o Each carrier is specific to a certain substance/ substance
o They can be involved in 2-way active transport – pump 1 in and 1 out at same time
o Faster, allows accumulation
o Inhibitors are usually to do with active transport
o EG. Ions from soil to root hair cells – ions can diffuse through bilayer as they are small even though they are polar
Active transport method
- The molecule or ion to be transported binds to receptors in the channel of the carrier protein on the outside if the cell- complementary shape
- On the inside of the cell, ATP binds to the carrier protein and is hydrolysed into ADP and phosphate
- Binding of the phosphate molecule to the carrier protein causes the protein to change shape opening up to the inside of the cell
- The molecule or ion is released into the cell
- The phosphate molecule is released from the carrier protein and recombines with ADP to form ATP
- The carrier protein returns to original shape
Primary and secondary active transport
o Primary is when ATP is directly used for the energy to transport molecules
o Secondary is when energy is stored in a concentration gradient and the transport of one molecule is coupled to the transport of another down its concentration gradient and ATP is not directly involved in the transport process
What type of materials are transported by bulk transport?
What is the process?
How come it can happen?
Examples
o A form of active transport so requires ATP
o Large molecules like enzymes, hormones and whole cells like bacteria are too large to move through channel or carrier proteins so are moved into and out of cell by bulk transport
o Endocytosis- the bulk transport of material into cells
o The 2 types are phagocytosis for solids and pinocytosis for liquids
o The cell surface membrane invaginates when it comes into contact with the material to be transported. The membrane enfolds the material until eventually the membrane fuses, forming a vesicle. The vesicle pinches off and moves into the cytoplasm to transfer material for further processing within the cell- e.g. vesicles containing bacteria are taken to lysosomes where its digested by enzymes.
o Some endocytosis is receptor mediated and is triggered when receptor proteins on the extracellular surface bind to specific substances
o Exocytosis is where vesicles usually formed by the Golgi apparatus move towards and fuse with the cell surface membrane releasing the contents of the vesicle outside of the cell
o Energy from ATP is needed for the movement of vesicles along the cytoskeleton, changing the shape of cells to engulf materials and fusion of cell membranes as vesicles form or as they meet the cell surface membrane.
o Endocytosis and exocytosis can occur because the membrane is fluid so it can break and form allowing vesicles to form and break off
o Examples: hormones like insulin released into blood by pancreatic cells
pinocytosis: Microvilli in the gut use this process to absorb nutrients from food
Phagocytosis: Uptake of lipoproteins by mammalian cells
Foreign material and cell debris by neutrophils and macrophages
o Plant cell vesicles carry materials to make cell wall
o WBC phagocytes engulfing foreign invaders and fusion with lysosomes
Osmosis
EG
Osmosis is the net movement of WATER particles from an area of high Ψ to an area of low Ψ by diffusion, across a partially permeable membrane.
EG: water into root hair cells
water potential
o The amount of ‘free’ water molecules in a solution.
o Pure water has the highest water potential, as all its water molecules are free to move. The Ψ of pure water = 0 kPa
o Water potential is the pressure exerted by water molecules as they collide with the membrane or container measure in Pa or kPa
o When substances dissolve in water, the water molecules cluster around the solute particles and are no longer free to move, so don’t count in water potential. The water potential has decreased i.e. it gets more negative.
o The smaller the number (bigger no. before the -) the more concentrated, so the higher water pot. Will be the lower number before the -
o Continues till reaches equilibrium- no net movement
Animal cells and water potential
o Animal cells burst in hypotonic- high water pot as they have thin (7nm) cell surface membrane and no cell walls so cant stretch or withstand the pressure increase. It will break and burst- lysis.
o Crenation in hypertonic – low water pot.
o Animal cells must therefore be bathed in a solution having the same osmotic strength as their cytoplasm.
o We therefore need kidneys to regulate the amount of salt and water in our blood, under the control of our hypothalamus- this regulation process is called osmoregulation
o Animals that live on dry land and salty sea water must conserve water but animals living in fresh water must get rid of excess water as fast as it gets in by osmosis
plant cells and water potential
o Plants can’t control the water pot of the fluid around them e.g. roots are usually surrounded by pure water
o When water enters the increased hydrostatic pressure pushes the membrane against the rigid cells walls – turgor pressure which resists the entry of more water and it becomes turgid. This provides support for plants that aren’t woody – prevents wilting
o During plasmolysis, cells can die as the cytoplasm pulls away from the cell wall. The incipient point is where the cell membrane just begins to move away from the cell wall. It is assumed this is when 50% of the cells have been plasmolysed.
o Flaccid is when the cell is not turgid but not yet plasmolysed. Plasmolysis is irreversible.
If you define hypertonic, isotonic or hypotonic, you must define them in terms of water pot.
The increase in pressure caused by the movement of water into a fixed volume is called hydrostatic pressure measured in kPa
ion pumps
o Transmembrane proteins that use energy to move ions and some molecules across a membrane across their concentration gradient
proton pump: ATP is used to remove hydrogen ions from inside the cell to the outside, creating a large difference in proton conc. either side of the membrane, with the inside being very negative. This potential difference can be coupled to the transport of other molecules.
Sodium potassium pump:
A specific protein in the membrane that uses ATP to exchange sodium ions for potassium ions across the membrane. The large conc. difference can be used to drive the transport of other substances like glucose.
Cotransport-sodium-glucose symport:
A gradient in sodium ions drives the active transport of glucose in intestinal epithelial cells. The specific transport protein couples the return of sodium ions down its conc. gradient with the transport of glucose into the intestinal epithelial cell. The low intracellular conc. of sodium is maintained by the sodium potassium pump.
what are enzymes and what do they do
o Enzymes are very specific catalysts made by cells that catalyse (speed up) metabolic reactions without undergoing permanent change so it can be used again
o In small quantities they reduce the need for high pressures, temperatures and extreme pH as well as high concentrations of reactants which would kill organisms. need water as need aqueous solution for movement of enzymes and substrates
o Reactions that enzymes catalyse are reversible. Enzymes don’t determine the direction if the reaction, only the speed
o Enzymes are globular proteins with complex tertiary structures. Some are single polypeptides, and some have 2 or more polypeptides so have quaternary structure
o Enzymes form the biological molecules that make up living tissues and break down the biological molecules that provide organisms with energy and building materials
EG. Polymers like cellulose forms the cell walls of plant cells and long protein molecules form the contractile filaments of muscles in animals. Different cell components are synthesised and assembled into cells, tissues, organs and organisms. Anabolic reactions needed form growth are catalysed by enzymes - structure
o EG. Cells in the organs in the abdomens of fireflies make the enzyme luciferase. They also make luciferin, the only substrate to it can catalyse. When cells are stimulated by nerve impulses to release luciferin, which is broken down un the presence of ATP bound to magnesium ions. The reaction releases light.
Energy is realised from large organic molecules like glucose in metabolic pathways consisting if many catabolic reactions catalysed by enzymes - function
intracellular enzymes
EG
o Performs its function within the cell that produces it
o Many reactions that occur simultaneously inside cells at low temperatures, low concentrations and pH 7 are catalysed by intracellular enzymes
o Some are free in the cytosol, nucleoplasm, mitochondrial matrix and stroma, others are fixed in place, like either side of cell surface membrane and inner membrane in mitochondria and chloroplasts.
EG. Sucrase is an enzyme of the digestive system and is fixed to the cell membrane of cells lining the gut
EG. Catalase acts on hydrogen peroxide, a waste product of metabolic processes in cells that is a powerful oxidising agent so very toxic.
It breaks it down to oxygen and water in seconds, compared to the months it would take to degrade by itself, found in plants and animals.
Some cells use hydrogen peroxide to kill pathogens, cells infected with viruses and cancer cells
Extracellular enzymes
EG
o An enzyme that functions outside the cell which it originates
o Substrates are raw materials and found in diet or environment
o Catalyse reactions that occur out of cells like those involved in breakdown of food In the gut, as large molecules cannot be absorbed unless broken down into small ones
o Many digestive enzymes are secreted from the cells that make them into the gut lumen
EG. Amylase hydrolyses starch to maltose in mouth and pancreas in saliva and pancreatic juice. Maltase then breaks down maltose into glucose in the small intestine. Glucose can be absorbed by cells lining digestive system into bloodstream. 2 enzymes are needed as each is specific to a reaction.
EG. Trypsin is a protease which breaks down protein molecules into peptides and then can be further broken into amino acids by other proteases. Released by pancreas into small intestine. Again can be absorbed into blood.
EG. Some organisms rely entirely on extracellular digestion where the enzymes are secreted outside their body to digest food, like single celled organisms. Fungal hyphae secrete the enzymes onto the food then absorb the simple molecules through hyphal walls.
Lock and key hypothesis
o Proposed in 1890
o The idea of the substrate fitting exactly into the active site
o The active site is an area within the tertiary structure of the enzyme
o The substrate acts as the key fitting into the lock of the active site of the enzyme
o Interactions between the R groups within the active site and the substrate stabilise the enzyme substrate complex
o The substrate is held so that the right atom groups are close enough to react
o The R groups within the active site of the enzyme will also interact with the substrate forming temporary bonds which put strain on the bonds with the substrate helping the reaction along
o The substrate is altered and forms a product forming an enzyme product complex
o The enzyme is unchanged so releases the substrate and is a free enzyme molecule ready to accept another substrate molecule
why is the lock and key theory not accurate Induced fit hypothesis
o Proposed in 1959
o The lock and key theory doesn’t explain how the substrate and enzyme are able to collide successfully to form he enzyme substrate complex
o As collisions are so random, it would be hard for them to collide to form the complex if the active site were a fixed shape
o Proteins are not fixed structures like the other theory suggests
o The active site doesn’t have a complementary shape to the substrate until it has moulded around the substrate so the 2 fit closely together and the amino acids with specific r groups within the active site are close to the substrate holding it together. The initial interaction between the enzyme and substrate is by weak chemical bonds, but they rapidly induce changes in the enzymes tertiary structure (active site) that strengthen bonding putting strain on the substrate molecule bonds so it breaks/makes bonds and creates the product(s) (break or make depends if catabolic-respiration or anabolic-photosynthesis)
o This can weaken a particular bond or bonds in the substrate therefore lowering the activation energy for the reaction as les energy is required to overcome the bonds
what are active sites
o Active sites determine the specificity of an enzyme
o The active site is a specific shape complementary to a substrate or part of a substrate, allowing a complementary fit
o Active sites are groves or clefts, composed of as small number of amino acids within a polypeptide
o The features of the active site and the type of substrate it accepts are dependent on the r groups of the amino acids
o R groups can no polar which provides a hydrophobic interior to the active site accepting non-polar substrates
o R groups can also be polar which means they form temporary ionic bonds with substrate molecules
o Specificity comes in different degrees- either for 1 reaction or for a few of the same type or act on a particular linkage EG. Protease acts on peptide bonds
activation energy
o Reactions that occur in organisms involve compounds that are very stable
o There is an energy barrier that prevents a chemical reaction happening or only allows it to happen very slowly
o EG. Hydrogen peroxide takes 6 months to decompose due to the amount of kinetic energy it has to build up.
o Activation energy is the amount of energy required to overcome the barrier
o This can be done by increasing temperature and or pressure or by adding a catalyst
o Enzymes don’t lower the overall energy change of the reaction, they provide an alternative pathway with a lower activation energy
o This allows reactions to occur without the extreme conditions that could kill cells
o Once the enzyme substrate complex is formed, the activation energy is lowered as a different reaction pathway is followed. The energy of the substrate and product stay the same
o This is possibly due to the tensions formed within the complex by the charges within the amino acids at the active site and the links between the amino acids and the substrate
cofactors
EG
o Some enzymes are inactive until they combine with a non protein substance that changes their tertiary structure to that their active site is able to bind with substrate molecules and ESC is catalysed/more likely to form. Ionic interactions and hydrogen bonds can be affected by charges too. This is a cofactor.
o Some enzymes require inorganic ions to function which stabilise the enzyme structure or take part in the reaction at the active site EG. Amylases digests starch into maltose, require the presence of calcium ions and chloride ions to function correctly and form correct active site shape obtained via diet
co enzymes
examples
o Larger organic cofactors are called coenzymes.
o Some of these are bound permanently to the enzyme often in or near the active site. Others only bind temporarily to the active site during the reaction. o Many of the B groups of vitamins are used to make important coenzymes in metabolic reactions:
Pantothenic acid or B5 is a component of coenzyme A
Nicotinic acid or B3 is used in the synthesis of the coenzymes NAD and NADP
The coenzyme FAD is based on vitamin B1- riboflavin
o NAD and FAD are alternatively reduced and oxidised in the reactions of which they take part, which transfers energy in the form of hydrogen ions in respiration
o NADP does a similar thing in chloroplasts during photosynthesis
o Other coenzymes like ATP and coenzyme A transfer chemical groups, ATP transferring phosphate groups between respiration and energy consuming processes in cells
o coenzyme A transfers the acetyl group (-CH3CO) from glucose and fatty acids during respiration. (breaks down fatty acids and carbs)
prosthetic groups
o Prosthetic groups are when any cofactor becomes a permanent part of an enzyme- tightly bound
o These contribute to the 3D shape of the enzyme so are vital for its ability to function
o Carbonic anhydrase, an enzyme found in red blood cells is important in the conversion of CO2 and water into carbonic acid (metabolism of CO2)
o Its prosthetic groups is a zinc 2+ ion that forms an important part of its active site
what are precursor enzymes
types of precursor enzymes
example
o Many enzymes are produced in an inactive form, known as inactive precursor enzymes, particularly enzymes that cause damage within cells producing them or to tissues where they are released, or whose action needs to be controlled and only activated under certain conditions
o Precursor enzymes often need to undergo change in shape (tertiary structure) to be activated
o This can be done by adding a cofactor
o Before the cofactor is added, the precursor is called an apoenzyme
o When the cofactor is added its activated its called a holoenzyme
o This can be brought about by the action of another enzyme like protease which cleaves certain bonds in the molecule
o A change in conditions can also cause a change in tertiary structure and activates a precursor enzyme- these types are called zymogens or proenzymes
o EG. When inactive pepsinogen is released into the stomach to digest proteins, the acid pH brings about the transformation into the active enzyme pepsin, protecting body tissues against the digestive action of pepsin
Effect of temperature on enzyme activity
o Molecules in solution move randomly and continuously, colliding with each other (Brownian Motion)
- Low temperatures so less kinetic energy so molecules move slower and collide with less force, so lower frequency of successful collisions (enough activation energy) so less ESC formed so less product and slower rate of reaction.
- Increasing temperature so more kinetic energy and increasing frequency of successful collisions so more ESC formed so more product (EPC) and increasing rate of reaction
- This is the optimum where all the active sites are occupied (unless lack of substrates). This is the highest temperature before they denature and they have the most kinetic energy, and the highest frequency of successful collisions (with enough AE), with the most ESC formed and the most/ more product with the fastest rate of reaction. Usually between 35-40 for humans and mammals, 20 for plants and 80 for bacteria, which have thermostable/philic enzymes. Psychrophilic organisms live in very cold areas and can have optimums of 5.
- Hydrogen bonds and ionic bonds in the tertiary structure break first as the heat vibrates the molecules as they have more KE straining the bonds, so the 3D shape of the active site changes so is no longer specific/ complementary to substrate so can’t form ESC and is permanently denatured, ROR decreases rapidly and reaction stops. Usually higher than 60 but can depend how long they are left in the heat for.
enzymes adapted to hot and cold.
o Enzymes adapted for the cold tend to have more flexible structures like the active site, making them less stable than enzymes that work at high temperatures. Smaller temperature changes will denature them.
o Thermophiles are adapted to live in hot environments and are more stable than other enzymes due to more bonds, like hydrogen bonds and sulphur bridges, in their tertiary structures. The active sites and shapes are more resistant to change as temp rises.
what is the name when almost all the active sites are occupied?
burst phase
when is the rate of enzyme catalysed reaction fastest and why?
the start because the concentration of substrate molecules is higher at the start so there is more chance they will enter the active site
what is Q10 and how is it measured?
o Between 0oC and 40oC any change in tissue temp causes problems for animals
o Most biochemical reactions are temp sensitive
o The sensitivity is described by the temperature quotient or coeffient Q10
o The Q10 is a measure of the rate of change of a biological or chemical system as a consequence of increasing the temperature by 10°C.
o A temperature increase of 10⁰C is equal to the Q₁₀ coefficient for that enzyme and can be used to compare the rate of reaction for different enzymes.
o It is calculated by dividing the rate of reaction at a certain temp by the rate of reaction of the same enzyme at a temp 10oC lower
o Q10 = RT/RT-10
o If a reaction is not temp sensitive, it has a Q10 of 1
o Most biological Q10 values are between 2 and 3
o A Q10 of 2 means that for every 10oC rise in temperature the rate of reaction doubles and for a value of 3 it triples
o So the larger the Q10 the faster the rate of a reaction rises in response to a temperature increase
o The graph produced is a curve
o If there is no scale for ROR you can calculate Q10 by measuring distances using a ruler and using these as equivalent to rates
what is pH and how does it affect enzyme activity?
examples
what is a control for investigating effect of pH?
o pH is a measure of H+ ion concentration. (H must be small at top)
o it’s a logarithmic scale so a change in 1 pH unit is x10 in conc. Of hydrogen ions
o The higher the H+ concentration the lower the pH (acidic)
o The H+ ions can disrupt the bonding, so active site is less effective
o Ionic interactions and H bonds are primarily affected between R groups of amino acids in the active site
o The active site will only be the right shape at a certain hydrogen ion concentration – optimum
o In the induced fit model, the charges allow the substrate to enter and become linked with the active site allowing the enzyme substrate complex to form. Changes in the charge therefore effect the ability of the active site to successfully link with the substrate.
o pH range can be wide or narrow, and optimums vary EG. Pepsin stomach acid or Trypsin alkaline small intestine or urease catalyses the hydrolysis if urease at neutral
o a control for a reaction investigating the effect of pH on enzyme ROR would be no enzyme
where are these enzymes found, pH and function: Amylase pepsin trypsin lipase maltose what is the pH of most intracellular enzymes how can pH be maintained?
neutral, saliva, starch to maltose
acidic (1-2), gastric juice in stomach, protein to polypeptide
alkaline (8), pancreatic juice in small intestine, proteins to polypeptides
triglycerides to glycerol and fatty acids
amylase, starch to maltose
maltase, maltose to glucose
o most intracellular enzymes have an optimum of 6.5 which is the pH of cytosol
o lysosomal enzymes have a lower optimum so rarely function if released into cytosol
o Buffer solutions can maintain different values of pH
how does pH affect enzyme activity?
1- The optimum
o The solution contains the ideal no. of H+ ions.
o The ionic bonding of the enzyme is not disrupted.
o The shape of the active site is not changed it is specific and complementary
o Substrate fits forming ESC then EPC
o Product is released
o Rate of reaction is at its maximum
2- Either side of the optimum
o Change in pH either side of the optimum provides less/more H+ ions
o Ionic bonding is disrupted changing the tertiary protein structure
o Active site changes its 3D shape so it is no longer specific and complementary
o the substrate no longer fits
o Less or no ESC are formed
o So less or no product formed
o Mild pH change effects are reversible
o Extreme pH can cause irreversible denaturation
effect of substrate concentration on ROR
o For a fixed enzyme concentration, the rate of reaction increases with increasing substrate concentration.
o An increase in the number of substrate molecules results in an increase in the frequency of successful collisions between enzyme and substrate molecules.
o More ESC will be formed.
o Rate of reaction increases.
o The rate of reaction is limited by substrate concentration.
o The rate of reaction continues to increase (directly proportional) with increases in substrate concentration.
o a point is reached when further increase in substrate concentration no longer produces a significant change in the rate of reaction.
o The active sites of all the enzyme molecules are saturated with substrate molecules.
o Any extra substrate molecule has to wait until the ESC has released the products before it can enter the active site of the enzyme.
o The rate of reaction is now limited by enzyme concentration, and can only proceed at the enzyme turnover rate.
Effect of enzyme concentration on ROR
o If the substrate concentration is maintained at a high level and other conditions such as temperature and pH are kept constant, the rate of reaction is proportional to the enzyme concentration
o As enzyme concentration increases, the frequency of successful collisions between the enzyme and substrate molecules increases.
o More ESC are formed
o The rate of reaction increases.
o At very high enzyme concentrations, if the concentration of substrate molecules is limiting, an increase in enzyme concentration would not result in any further increase in the rate of reaction.
What are competitive inhibitors?
examples
o Molecule or part of a molecule that is structurally similar to the substrate and compete with substrate for active site- enters into, binds or blocks it preventing ESC forming
o Can still reach v max but may take longer, if the substrate is increased so much more than the inhibitor
o Temporary
o The inhibitor competes with the substrate to occupy the active site, so the substrate can’t bind. The higher the inhibitor concentration the less likely the ESC will form so the slower the rate of reaction, but doesn’t change the v max
o The inhibitor doesn’t have to be exactly the same shape as the substrate
o Statins inhibit an enzyme used in the synthesis of cholesterol. They are prescribed to help people reduce cholesterol levels in blood, to prevent heart disease
o Aspirin irreversibly inhibits the active site of COX enzymes, preventing the synthesis of prostaglandins and thromboxane, the chemicals for producing pain and fever.
what are non competitive inhibitors?
examples
o The enzyme binds to an allosteric site which changes the 3D tertiary shape (conformation) of the active site preventing it from catalysing a reaction as it is no longer complementary to the substrate
o This means a proportion of the enzyme molecules are out of action so the effective enzyme concentration is decreased
o Can be permanent and not leave but some are reversible
o The inhibitors have no structural resemblance to the substrates
o Cofactors also bind to an allosteric site
o You can also have allosteric activators which bind to activator sites to change the shape of an enzyme so that the substrate fits (cofactor)
o Reaction hasn’t stopped so some will be reversible but doesn’t reach v max as others are irreversible
o EG. Organophosphates used in insecticides and herbicides irreversibly inhibit the enzyme acetyl cholinesterase, an enzyme necessary for nerve impulse transmission, leading to muscle cramps, paralysis and death
o EG. Proton pump inhibitors are used to treat long term indigestion as they irreversibly block an enzyme system responsible for secreting hydrogen ions into the stomach, preventing excess acid which can lead to stomach ulcers
When can enzymes be good?
When can they be bad?
o Enzymes must be controlled otherwise can be fatal
EG. In multiple sclerosis the immune system starts destroying nerves by allowing destructive enzymes to attack nerve cells, often resulting in paralysis
o Many poisons work by inhibiting the action of enzymes involved in metabolic processes
E.g. Potassium Cyanide is an irreversible inhibitor of the enzyme Cytochrome C Oxidase, used in respiration reactions in cells. It forms strong covalent bonds with the enzyme. The only way to reverse the inhibition is to make new enzymes, which takes time. Is a metabolic poison as it prevents metabolic reactions occurring.
o Some Enzyme Inhibitors can be used as Medicines
o Infection by viruses can be treated by inhibitors to the viral enzyme Protease. This means that the viruses cant build new protein coats and so cant replicate.
EG. Penicillin irreversibly inhibits a bacterial enzyme (transpeptidase) responsible for forming cross-links in bacteria cell walls halting reproduction.
what is end product inhibition?
example
When the end product of a metabolic pathway builds up and inhibits the first reaction as a non competitive inhibitor- negative feedback
prevents excess product and waste as reaction controls itself
EG.o Respiration is a metabolic pathway resulting in the production of AT. The 1st step involves the addition of 2 phosphate groups to a glucose molecule. The addition of the second phosphate group which results in the breakdown of the glucose molecule is catalysed by the enzyme phosphofructokinase (PEK). The enzyme is competitively inhibited by ATP, so it regulates its own production, so when ATP levels are high more ATP binds to the allosteric site on PEK
Nucleus structure function size found in significance
bound by a double nuclear membrane
nuclear pores
Chromosomes or chromatin- DNA wrapping around proteins called histones
nucleolus which is a dense solid structure composed of
nucleic acid and RNA
RNA produces rRNA which is combined with proteins to form ribosomes
contains coded genetic information in the form of DNA which provides the template for making RNA needed to make proteins so indirectly controls metabolic activities
10-20 um Diameter
animals and plants
mitochondria structure function size found in significance
membrane bound organelles with a double membrane
inner membrane folded into cristae creating larger SA fir enzymes used in aerobic respiration
fluid interior is matrix
contain own DNA with 70S ribosomes
produce own enzymes and reproduce themselves
resemble bacteria
carry out final stages of aerobic respiration where ATP is produces- cytosol is anaerobic
1um diameter and 1um length.
plants and animals
metabolically active cells like muscle and nerve and liver
chloroplasts structure function size found in
membrane bound organelles with a double outer membrane
internal membranes form thylakoids, grouped into stacks called grant, joined by internal lamellae- thin flat pieces of thylakoid membrane
chlorophyll pigments found in thylakoids
thick fluid stroma is found in space between grand
have own DNA and 70S ribosomes so can make own proteins
starch granules found just outside where carbs are stored in amyloplasts
grana contain green pigment chlorophyll which absorb light energy for photosynthesis
2 um diameter
10 um long
plant cells
rough endoplasmic reticulum
part of the endomembrane system containing ER and golgi
network of membranes through cytoplasm enclosing a series of connected flattened sacs called cisternae
these membranes join with outer nuclear membrane to form a continuous membrane
ribosomes embedded in outer membrane
the cells transport system
ribosomes here make proteins destined for transport and secretion out of the cell
30-50nm diameter
plants and animals
pancreas and liver produce a lot of hormones and enzymes
smooth endoplasmic reticulum
long network of folded tube-like structures with no ribosomes
makes and stores lipids like phospholipids for cell membranes and steroid hormones
also makes and stores carbs
contains enzymes that detoxify lipid-soluble drugs and some harmful products of metabolism
30-50nm diameter
plants and animals
liver produces lipids and steroid hormones
ribosomes
free in cytoplasm and and attached to RER membrane s
made of ribsosomal ribonucleic acid and protein
large subunit and small subunit which are separate and come together in protein synthesis
80S in eukaryotic not 70S
to manufacture proteins my assembling aa
if found in cytosol is use to make proteins withn the cell itself
if found in RER makes proteins for usage outside cell (protein synthesis)
25nm
plants and animals
liver cells as protein synthesis occurs here
Golgi apparatus
A series of membranous flattened sacs known as cisternae, separated from cytoplasm by a membrane. Similar to SER but the cisternae are not interconnected. There are 2 sections: the cis Golgi network and the trans Golgi network.
vesicles delivered from RER join at cis face
proteins and lipids are processed, packaged and transported.
processed and modified in cis network then passed to trans network where they are packaged into vesicles ready for transport and secretion
2.5um
animals and plants but fewer and larger in animals
centrioles
a component of the cytoskeleton constructed of microtubules arranged in 9 triplets forming a cylinder
occur in pairs near nucleus and form the centrosome
Centrosomes help with formation and organisation of spindle fibres during cell division. 2 centrioles are found in each centrosome.
Celiogenesis is the formation of cilia and flagella on the surface of cells, which help the cell move. Centrioles play a role in the positioning of these structures.
250nm length
animal only
lysosomes
contain 40-50 hydrolytic enzymes
acidic environment unlike neutral cytoplasm
digest cellular material- food and foreign matter. may come from outside cell like bacteria or inside like damaged or old organelles
part of immune system as break down pathogens ingested by phagocytic cells
have a part in apoptosis
100nm
animal cells
liver, kidney, pancreas as have stuff to be broken down
white blood cell lysosomes break down microorganisms
acromosome in spr=erm to penetrate egg
vacuole
membrane bound sac (tonoplast) within cytoplasm
semi permeable membrane
filled with solution of salts and sugars called cell sap
in plants are large and provide structural support (turgor)
store water, nutrients and waste and gets rid of them
1-10 um
smaller and more and transient in animals
cell wall
made of cellulose, a complex carb for plants and algae
freely permeable
fungal cells have wall of chitin which is pitted and composed of cellulose fibres to let water and dissolved substance through
gives shape, supports and protects cell from pathogens and prevents is bursting when water flow in
5-20 nm thick
plants
what does a plant cell not have
what does an animal cell not have
what is cytosol
no centrioles of lysosomes
no cell wall or chloroplasts
the liquid part whereas cytoplasm includes organelles
functions of lipids
1) High energy yield so acts as an important energy source to be respired
2) Act as an energy store- lipid droplets in plants and fat in adipose tissue in animals. Insoluble (don’t affect water potential of cell vital for storage of molecules)
3) Thermal insulation under skin of mammals
4) Electrical insulation around some nerve cells in vertebrates and some invertebrates as it’s a poor conductor of heat
5) Waxy cuticle around leaves and stems and waterproofing of birds feasthers
6) Forms biological membranes as are hydrophobic
7) Group of hormones called steroids are lipids
8) When oxidised during respiration, triglycerides release hydrogen molecules which combine with the oxygen to form metabolic water, relied on my desert animals to survive
9) Aids buoyancy so useful for aquatic animals like whales
10) Protection of vital organs
what are lipids
Lipids are macromolecules (not polymers) as they are not formed of many similar monomer units.
why don’t lipids dissolve in water
They dissolve in organic solvents like alcohol, but no in water- hydrophobic. This is because the electrons in their outer orbitals that form the bonds are more evenly distributed than in polar molecules no there are no positive or negative areas.
what are saturated fats?
examples
o When all the carbon atoms in a fatty acid are joined by single bonds
o When combined with glycerol forms a saturated fat
o Usually animal fatty acids such as stearic acid and butyric acid.
what are unsaturated fats?
example
why are they liquid at room temperature?
o Where the hydrocarbon chain has at least one double bond, forming a mono-unsaturated fatty acid.
o When there are many double bonds it’s called a poly-unsaturated fatty acid (often in plants- oleic acid)
o The double bond changes the shape of the hydrocarbon so that it kinks at the bond.
o They hydrocarbon chains do not lie straight together and push apart, making unsaturated fatty acids liquid at room temperature so are oils.
What type of reaction forms triglycerides? What type of bond is formed? What molecules are involved? What reacts with what? Why is the chain hydrophobic? How many of everything are there?
o Formed by a condensation reaction between fatty acids and glycerol.
o An ester bond is formed
o The glycerol molecule is an alcohol
o The fatty acid molecule is different depending on molecule of fat or oil formed- is a long molecule consisting of a hydrocarbon chain and a carboxyl group on the end- carboxylic acid
o The carboxyl group reacts with the OH group of glycerol to form the ester bond in an esterification reaction
o The methyl group(-CH3) at the other end makes the whole chain hydrophobic.
o Because there are 3 -OH groups on the glycerol, 3 fatty acids bond to bond to three glycerol by 3 condensation reactions, so 3 molecules of water are lost and 3 ester bonds form in each for each triglyceride.
o The chain is usually between 14 and 22 carbon atoms long
What is a phospholipid? how does the phosphate fit on and where does it come from? how is it hydrophilic? What structures can they form? what is their function?
o Modified triglycerides containing carbon, hydrogen, oxygen and phosphorus.
o Inorganic phosphate ions (PO4 3-) are found in the cytoplasm of every cell.
o They have extra electrons so are negatively charged and soluble in water
o One of the fatty acid chains in a triglyceride is replaced with a phosphate group
o The phosphate group is usually attached to an nitrogen containing water soluble group like choline- creates a hydrophilic head
o Form a layer on the surface of the water with phosphate heads in water and tails sticking out. They are called surface active agents or surfactants
o Can also produce a bilayer (2 layered sheet formation) with tails pointing toward the centre of the sheet, protected from water by hydrophilic heads.
o Form cell membranes due to bilayer arrangement. They can separate the aqueous environment which the cells usually exist from the aqueous cytosol within cells
what are glycolipids?
o Lipids with a carbohydrate attatched by a glycosidic bond
Haemoglobin structure and function
Structure:A quaternary protein structure made from 4 polypeptides, 2 alpha, and 2 beta subunits, which create 2 alpha helixes and 2 beta pleated sheets. It is a conjugated protein, so contains a non-protein component called a prosthetic group (permanently attached to the molecule and is vital for the normal functioning of the molecule). Each subunit contains a prosthetic haem group, which contains iron II ions, which can combine with oxygen.
Function: Transports oxygen around the body; picks up oxygen at the lungs and transports it to cells where it is needed for respiration and released.
Insulin structure and function:
Structure: It is a globular protein, with a quaternary structure. It is composed of 2 polypeptide chains with 21 amino acid residues in chain A and 30 amino acid residues in chain B. The chains are held together by 3 disulphide bridges in alpha helixes.
Function: Hormone involved in the regulation of blood glucose concentration. Insulin’s solubility allows it to be dissolved and transported in the blood. The specific shape means that it fits into specific receptors on cell surface membranes.
Catalase structure and function:
Structure: Catalase is an enzyme and is a quaternary protein containing 4 haem prosthetic groups.
Function: Catalase is an enzyme, so its main function is to speed up reactions, and its 3D structure means that it is specific to this particular reaction (active site): the iron II ions allow catalase to interact with hydrogen peroxide and speed up its break down, which is a common by-product of metabolism but can be damaging if it accumulates.
Collagen structure and function:
Structure: Have 3 polypeptide chains wound round each other in a triple helix structure to form a tough rope like protein.
Every third amino acid in the polypeptide chain is glycine, which is a small amino acid, allowing 3 protein molecules to be closely packed in the triple helix.
Hydrogen bonds form between the polypeptide chains forming long quaternary proteins with staggered ends, allowing proteins to join end to end forming long fibrils called tropocollagen. These fibrils cross link to produce strong fibres.
Collagen also contains high amount of the amino acids proline and hydroxyproline, and the R groups in these repel each other adding to stability of collagen.
Function: When multiple fibres of collagen create larger bundles, they are found in ligaments, tendons, heart, arteries, bone and cartilage providing strength and support, as well as in skin forming a mesh resistant to tearing. Also found in nervous system.
Elastin structure and function:
Structure: A quaternary protein made by linking many soluble tropoelastin protein molecules to make a very large insoluble and stable cross-linked structure.
The multiple tropoelastin molecules aggregate through interactions between hydrophobic areas.
The cross links are covalent bonds which involve the amino acid lysine.
Tropoelastin molecules contain alternate hydrophobic and lysine rich areas.
Function: A connective tissue able to stretch and recoil without breaking like small springs. Each elastin provides strength and elasticity to the skin and other tissues and organs in the body, such as walls of blood vessels and in the alveoli in lungs. They can therefore expand when needed but also return to their normal size.
Keratin structure and function:
Structure: Has lots of the sulphur containing amino acid- cysteine. It has lots of strong disulphide bridges forming strong, inflexible and insoluble materials. The amount of disulphide bond determines flexibility, so hair contains less and nails contain more
Function: Found in hair, skin and nails
what determines how freely the proteins can move through the phospholipid bilayer?
the number of phospholipids with unsaturated fatty acids in their tails
unsaturated are bent so don’t fit together as closely so is more fluid and allows proteins to move more easy
erythropoiesis
o As a mature red blood cell has no nucleus it can’t divide so new cells have to be constantly formed from multipotent stem cells in bone marrow to maintain erythrocyte count in blood
