IB Biology Concepts
D1.1 - DNA replication
Copies DNA in order for an organism to grow
Semi-conservative
Each new strand contains one original strand, and one new strand
DNA replication steps
Eukaryotic DNA is supercoiled around Histones
Forms Nucleosomes
Coils unwind to make DNA accessible to enzymes
Helicase unwinds DNA
Breaks Hydrogen bond between strands, separating them
DNA polymerase III moves along strand, forming new DNA
PCR - Polymerase Chain Reaction
Step 8 - Isolate clean DNA libraries
Step 7 - Remove PCR reagents
Step 6 - Removing small DNA fragments
Step 5 - Removing large DNA fragments
Step 4 - Addition of primers and PCR
Step 3 - Wash tagmented DNA
Step 2 - Stop tagmentation
Step 1 - Cut and Tagment DNA
Rise in temperatures allow enzymes to cut DNA into smaller pieces
DNA is tagged with adapters
DNA binds with Bead-linked Transposomes (BLT), "tagged" with adapters
Stops enzymes from cutting DNA
Prevents DNA getting too small
Tagmentation stop buffer (TSB) is added
Removes enzymes used for tagmentation
Tagmentation wash buffer (TWB is used)
Magnet pulls BLT towards the bottom, enzymes remain in supernatant
Add index - Unique index added to each sample for identification by sequencer
Amplifies / Makes numerous copies of DNA
Temperature increased to denature DNA
Primers added to ends of DNA strands
Extension begins from primers, copies of DNA are produced
Sequencer works best with medium sized DNA fragments
Large fragments bind with BLT first in diluted solution
Magnet pulls BLT with large DNA downwards, transfer small and medium fragments to another tube
Desired DNA placed in chamber that contains
Primers for replication
Taq polymerase
Free Nucleoside Triphosphates
Found in Hot springs bacteria
Does not denature in high temp
Annealing
Denaturation
Extention
Occurs at 98C
DNA heated until denatures
Temperature lowered to 60C
Primers bind to complementary strands of DNA
Taq polymerase goes through DNA with primer as start point
Once replicated, begin Denaturation again
Concentrated solution has more beads
Medium-sized fragments bind to BLT
Same as large fragments
Add ethanol
Beads and DNA pulled downwards
Supernatant, PCR reagents, and ethanol removed
Resuspension buffer (RSB) added to DNA sample, separates from beads
DNA is left in supernatant, BLT pulled down by magnet
Gel Electrophoresis
DNA Digested with restriction endonucleases
Samples loaded into wells on gel
Gel submerged, electric current ran through gel
DNA begins near negative pole, spreads out to positive pole
Gel is porous, DNA has to move through holes - bigger DNA move slower, vice versa
Directionality of DNA replication (HL)
DNA made up of phosphodiester bonds attached to 5' Carbon
DNA polymerase III adds to the 3' end of the previous molecules - 3' - 5' directionality
Can ONLY do so in said direction due to shape
Lagging strand
Leading strand
Continuous replication
Discontinuous replication
Oriented 3' to 5'
Oriented 5' to 3'
Enzymes of DNA replication (HL)
DNA polymerase :
DNA ligase
DNA polymerase III
DNA polymerase I
Helicase
Gyrase
DNA primase
Unwinds / Unzips DNA molecule
Breaks H bonds holding bases together
Forms replication fork
Strands kept from rejoining via single-strand binding proteins
Goes in front of Helicase, relieves pressure from unwinding DNA; controls topological transition
Replicates DNA
Attaches RNA primers to template strand
Lets DNA polymerase begin replication
Single primer required for leading strand
Multiple needed on lagging due to discontinuous nature
Removes RNA primers, replaces with DNA
Leading strand
Lagging strand
Replicates continuously
Replicates in intervals - Okazaki fragments
5' to 3' directionality
Catalyses phosphodiester bonds between Okazaki fragments and primers - Turns lagging strand into a single strand
Proofreads DNA strands for errors, fixes them
D1.2 - Protein synthesis
Transcription
Translation
Produces mRNA from DNA
Transcription stages
Elongation
Termination
Initiation
RNA polymerase binds to DNA at the start of a gene
Separates two strands by breaking H bonds
RNA polymerase builds a molecule on one strand of DNA
Template / Anti-sense strand
Other strand is called sense strand
Terminator sequence is reached
mRNA released
DNA joins back together again
RNA polymerase moves along DNA, adds RNA nucleotides 1 at a time, complimentary base paired
Complimentary base pairs
G with C
C with G
A with U
T with A
2 H bonds
3 H bonds
mRNA moves outside the nucleus through nucleopores, is read and polypeptides synthesized
Occurs in cytoplasm w free ribosomes
Occurs in rough endoplasmic reticulum
Key components
mRNA
tRNA
Ribosomes
Brings code from nucleus
Enzyme thing with multiple active sites
80S and 70S
Eukaryotic 80S
Prokaryotic 70S
Small 40S subunit
Large 60S subunit
Small 30S subunit
Large 50S subunit
Proteins and rRNA
3 Binding sites for tRNA
2 subunits
Large subunit - 2 tRNAs bind at a time
Small subunit - mRMA binds
Single-stranded RNA molecule
Folds on itself to have a clover-lead structure with double stranded regions
Has three hairpin loops
Has specific corresponding amino acid attached
Has specific amino acid attached
Recognizes, binds to corresponding codon
Transfers acid to end of growing polypeptide chain, peptide bond is formed
3 - base combinations
Codons
3 - base combinations
Anti-codons
Complementary in nature
Features of genetic code
Degeneracy
different codons code for the same amino acid
20 Amino acids in total
Stop
Start
UGA
UAA
UAG
AUG
Universal - Every organism has the same system
Initiation
Elongation
Ribosome moves along mRNA 1 codon at a time
New codon - new tRNA attaches
New acids delivered. Condensation reaction catalysed, peptide bonds formed
Begins with tRNA binding to A site
Reaction catalysed by large subunit
Forms peptide bond with P site amino acid
Once bond forms, tRNA translocates by one codon
tRNA in P site moves to E site, exits ribosome
tRNA in A site moves to P site
A site available
Mutations
Point mutation
Mutations occurring onto one nucleotide
Frameshift
Substitution
Silent
Nucleotide changed for another
Changes in structure, but no change in expression
Insertion
Deletion
Nucleotide added
Nucleotide deleted
Sickle Cell Anemia
Directionality
RNA polymerase builds mRNA molecules in a 5′ to 3′ direction
Polymerase binds to Promoter
Promoter has transcription factors that bind
No transcription factors - no transcription
Non-coding DNA
DNA sequences that do not make proteins
98% of the human genome
Regulators for gene expression
Promoters
Enhancers
Silencers
Increase rate of transcription
Decrease rate of transcription
Introns
Telomeres
Genes for tRNA and rRNA
Sequences that get removed at the end of transcription
Repetitive sequences that protect the ends of the chromosome - ensure that DNA is replicated correctly. With every cell division, short stretches of DNA are lost from the telomeres.
Codes for RNA molecules that do not fold to form proteins
Post - transcriptional modification
Introns
Extrons
Codes for polypeptides
Steps
Transcription - synthesis of pre-mRNA
Addition of 5'cap and poly A-tail
Prevents mRNA degradation
Splicing
Excising introns, Ligating exons
mRNA
snRNP (Small nuclear ribonuclearproteins) forms base pairs with ends of intron
Spliceosome and looped intron form
Intron is excised
Exons are ligated, spliceosome disassembles
Alternative splicing
Exons combined differently, gives different protein
All proteins start with Met - start codon
5′ terminal of the mRNA binds to the small ribosomal subunit
Ribosome moves along until it binds AUG
anticodon of initiator tRNA binds to codon
Large subunit joins, completes assembly of translation complex
Aminoacyl-tRNA binding site
Peptidyl-tRNA binding site
Exit
Uses GTP
Uses GTP
D1.3 Mutations and Gene editing
Proteasomes
Recycle unwanted protein bits
Termination
Ribosome reaches stop codon, releases polypeptide chain
Polypeptides delivered via vesicles into golgi apparatus for modification and transport
Gene mutations
Single nucleotide polymorphisms (SNPs)
One nucleotide is replaced with another
Synonymous
Non-synonymous
Changes protein
No effect - no changes in protein
Types
Insertion
Deletion
Frameshift
Why mutate
Causes
Mutagens
Chemical mutagens
Radiation
DNA breaking
Single-strand break
Double-strand break
Impedes replication fork movement
Replication errors / Halt of replication
Completely halts DNA replication
Randomness
Some bases more likely to cave under mutagens
Cytosine can deanimate - amino group is removed
Environmental factors can contribute to mutation rate and frequency
Environment can favour specific mutations
Mutations as variation
Somatic cells
Germ cells
Heritable
Within a person's lifetime, inheritable
Types
Silent
Harmful
Beneficial
Neutral
Occurs in non-coding sections
Occurs in coding sections, does not alter amino acids
Have harmful consequences on organism
Increases fitness in a particular environment
Errors in DNA replication and repair
Genetic engineering
CRISP - Cas9
Gene knockout technique
Specific gene is intentionally removed
Determines function of gene
Cas9 - Enzyme that cuts DNA at specific target sites
CRISPR
Clustered Regularly Interspaced Short Palindromic Repeats
Specific regions found in bacteria that contain short repeated and unique spacer sequences
Bacterial uses
When foreign DNA matches a CRISPR spacer, a corresponding RNA sequence (CRISPR RNAs) bind to the DNA
Cas9 is guided to make precise cuts into the DNA
Induces double strand breaks that can be repaired by cell's repair system
Human uses
Single-guide RNAs
Targets a specific DNA sequence
Marks DNA for cutting
Lets scientists add or delete or modify sequences
Gene therapy
Agriculture
Disease modelling
Genetic engineering of microorganisms
Conserved sequences remain similar across species
Highly conserved sequences remain similar over long periods of evolution
D2.1 Cell and Nuclear Division
Cytokinesis
Animal cell
Plant cell
Actin and Myosin proteins form contractile ring
Assembly of cell plate
Pinches cell membrane together, forms cleavage furrow
Gradually deepens, splits membrane in half
Separates cytoplasm into two daughter cells
Important proteins involved in muscle contraction
Vesicles containing cell wall materials fusing
Cell plate grows outwards, dividing cytoplasm into two daughter cells
Equal, both daughter cells receive equivalent amounts of organelles
Unequal division
Oogenesis
Formation of egg cells
Produces first polar body, and secondary oocyte
If fertilisation occurs, second polar body produced, mature oocyte is made
Budding
Growth of a genetically identical daughter from parent
Daughter smaller than parent, receives half or less of cytoplasm
Parent left with scars when separated
Mitosis
Meiosis
Shared features of Mitosis and Meiosis
Before nuclear division, DNA duplicates
Forms two sister chromatids, held together by centromere
DNA supercoiled around Histone proteins when not replicating
Forms chromosomes
Both involve the movement of microtubule and microtubule motors
Long, thing cylindrical fibrous proteins that form spindle apparatus
Motors attach to microtubules, hydrolyze ATP for movement
Prophase
Chromatin condenses into chromosomes
Nuclear membrane breaks down
Spindle fibres form
Microtubule organising centres head towards opposing ends - centrosomes containing centrioles in animal cells
Metaphase
Anaphase
Telophase
Sister chromatids line up on metaphase plate
Spindle fibres bind to centromeres, moving them into position
Spindle fibres shorten, splits centromere, pulling sister chromatids apart
Chromosome decondenses, nuclear membrane reforms
Spindle fibres disintegrate, cell elongates
Produces identical diploid daughter nuclei
Meiosis I
Meiosis II
Prophase I
Anaphase I
Telophase I
Prophase II
Metaphase II
Anaphase II
Telophase II
Sister chromatids form tetrads / Bivalent pairs
Metaphase I
Homologous pairs form
Same genes at the same loci
Crossing over
Swaps alleles for the same gene
Random orientation
Orientation of one independent of the other
Sister chromatids remain connected
Homologous pairs separated
Chromosomes decondense, cytokinesis occurs, followed by interkinesis
Two non-identical haploid daughter cells
Nothing special
Fibres attach to centromeres
Sister chromatids separated, they're now called chromosomes
Chomosomes decondense, nuclear membrane reforms
Four haploid daughter cells
Non-disjunction
Failure of sister chromatids to separate
Gamete with three chromatids, and one
Trisomy
Monosomy
Trisomy 21 - Down's Syndrome
Genetic diversity
Crossing over
Independent assortment, Random orientation
Random fusion during sexual reproduction
Offspring inherit a random combination of alleles
Can occur multiple times in the same bivalent
Crossing over occurs between two non-sister chromatids over the chiasmata
Different places each time meiosis occurs
Chromatids not crossed over are called non-recombinant
Chromatids that cross over are recombinant
Cell cycle
Cell proliferation
Growth
Increase in cell number / organism size
In plants
Meristematic tissue
Regions of undifferentiated cells
Stimulated by auxin
Actively divide and differentiate
Cell at apex, the tip, remain undifferentiated
In animals
Embryonic division
Cleavage
Division of zygote into totipotent stem cells
Blastomeres
Continue to divide into blastula
Forms different cells through differentiation
Cell replacement
Skin turnover
Skin cells formed from epithelial cells
Asymetric division
1 Undifferentiated, 1 Differentiated
Mature skin cells move upwards through epidermis to replace dead skin cells
Tissue repair
When wounded, cells surrounding rapidly divide
Healing rate depends on cell turnover rate - some are non-dividing, and need to be stimulated
Stages
Control
Interphase
G1 (Gap 1)
S (Synthesis)
G2 (Gap 2)
Most active, longest phase of cell cycle
Happens in cytoplasm
Cell grows in size
Mitochondria and chloroplasts divide through binary fission
Supports endosymbiotic theory
Cell doubles in size
Checks internal environment for ability to synthesize DNA
DNA replication occurs
Doubles amount of DNA
Grows and prepares for Mitosis
Synthesizes microtubules and other proteins requires for mitosis
Acts as checkpoint to ensure DNA replication is properly carried out
Cyclins
Family of proteins that regulate the cell cycle
Binds to and activates CDKs - Cyclin dependent kinases
Enzymes that phosphorylate specific proteins to drive the cell forwards
Each cyclin only active in a specific stage
Certain concentration (Threshold) must be reached before new stage can continue
Mutations that happen in genes controlling cell cycle
Occurs in proto-oncogene
Uncontrolled cell division
Proto-oncogene becomes oncogene
Tumour suppressor genes
Codes for proteins that slow / prevent cell division
Develop cancer
Promote apoptosis (programmed cell death)
When mutated, no longer code for such proteins
Uncontrolled cell division
Uncontrolled division leads to formation of tumour
Derived from body's own cells - immune system might not activate
Secrete signalling molecules that stimulate blood vessel - gives tumour oxygen supply
Malignant
Benign
Non-cancerous abnormal growth
Have well-defined borders
Mostly harmless unless protruding into vital organs
Can be removed surgically with high success rates
If left untreated, can grow out of hand
Cancerous
Lack well-defined border
Can spread to other parts of the body through metastasis
Cells go into blood / lymphatic system
Original tumour called the primary tumour
Other tumours called secondary tumours
Treated with surgery, chemotherapy, radiotherapy
Harder to remove
Can spread throughout body, into vital organs
Presence indicates more advanced stage of cancer
Mitotic index
(Actively dividing cells / Total number of cells) x 100
D.3.2 Inheritance
Some organisms reproduce asexually - genetically identical offspring
Some reproduce sexually - genetically unique offspring
50% from each parent
Monozygotic twins the exception - identical genome
Individual reaches sexual maturity
Special organs - gonads undergo meiosis
Contains cells whose nuclei only has pairs of chromosomes
Two gametes fuse to become zygote - n to 2n
Hermaphrodite
Male and female gametes on the same organism
Mendel's experiments
True-bred pea plants
P generation
F1 generation
F2 generation
Mendelian laws
Law of Dominance and Uniformity
Law of Segregation
Law of Independent Assortment
Parent generation
Offspring 1
Offspring 2
Alleles of genes are separated independently - and are inherited independently of each other
Variants of genes found in loci are either dominant or recessive. if there is a dominant allele, its phenotype is expressed over recessive alleles
Two alleles from each gene separate during gametogenesis - parents only pass one down
Genotypes and phenotypes
Individuals have homologous chromosome pairs
One from each parent
Chromosomes have stretches of DNA called genes
Encode for specific proteins
Are in identical positions - individuals have two copies
Different forms of genes called alleles
Allele combination - Genotype
Heterozygous
Homozygous
Dominant
Recessive
BB
bb
Bb
Phenotype - External expression of genotype
Phenotypic plasticity
Ability to express variations in physical characteristics in response to changes in environment
Polyphenism
Environmental pressures result in two or more distinct phenotypes of one organism
Allele combinations
SNP mutations
Multiple alleles
Blood type - (Ia, Ib, i)
Co - dominance
Incomplete dominance
Neither is dominant over the other - both genes are expressed
Neither is dominant over the other completely - a blend of both is expressed
Gene bahaviour
Dihybrid cross
Monohybrid cross
Established in Metaphase 1
Exceptions - linked chromosomes
Rarely cross over separately
Chi-Squared analysis
Expected results vs Actual results
Determines linkage
X^2 is the whole value - solve for X^2
Steps
X^2 = 0, expected and observed are the same
Closer to 0 X^2 is, closer to expected it is
Can be statistically significant (Linked / Non-linked)
- Determine X^2
Formulate H0 and HA
Determine expected / observed values
H0 - There is no statistical significance between the expected and observed values
HA - There is a statistically significant difference between the expected and observed values
Identify no. alleles
- Calculate X^2
Degrees of freedom - # of categories - 1
Find critical value - use p=0.05
X^2 < critical value, there IS NO statistical significance
X^2 > critical value, there IS statistical significance
Genes unlinked
Genes linked
DEAB