IB Biology HL D1

DNA replication

reasons for DNA replication (2)

reproduction

growth/tissue replacement

semi conservative

DNA is composed of one new strand and one old strand

how does replication begin along DNA

starts at replication origin

opens to form replication bubble

replication fork forms where ends of parent DNA separated

enzymes in DNA replication

helicase

polymerase I

polymerase III

ligase

primase

helicase

unwinds DNA by breaking hydrogen bonds

primase

adds primers of ~10 bases of RNA to allow DNA replication to begin

polymerase I

replaces RNA primers with DNA

polymerase III

adds deoxyribonucleoside triphosphates to DNA strand in a 5’ to 3’ order by covalent bonds

removes 2 phosphates from triphosphates to provide energy for replication

proofreads incorrect base pairs

ligase

connects Okazaki fragments together

PCR

polymerase chain reaction

artificial method to amplify/copy DNA

used for genome rather than entire DNA sequence

PCR mechanism

DNA placed in solution of primers and Taq polymerase

1. denaturation to break hydrogen bonds and create two template strands by increasing temperature

2. DNA is cooled so primers can bond to complementary bases

3. Heat increased to ideal temperature of Taq polymerase that adds complementary dNTPs

gel electrophoresis

lab technique to separate DNA or other charged molecules by size using an electrical field

shorter base pairs travel further ‘down’ gel

gel electrophoresis mechanism

1. DNA samples placed in wells at the negative end of electric field

2. place DNA fragments of known sizes (ladder) into extra well

3. add electrolyte buffer to support electrical current

4. plug into power and wait until DNA samples spread

paternity testing

to determine biological father of child

amplifies short tandem repeats

coronavirus testing

1. throat or nose swap to collect virus particles

2. swab rinsed with saline solution to create liquid sample

3. reverse transcriptase converts viral RNA into DNA

4. PCR used to amplify base sequences specific to covid. fluorescent tags attached to show if amplification is taking place

5. if florescent level exceeds certain level, test is considered positive

protein synthesis

transcription → translation → folding

types of RNA

messenger RNA - translated into protein sequence

transfer RNA - delivery system of amino acids to translate mRNA

ribosomal RNA - structural component of RNA

promotors (2)

section of DNA where transcription is initiated

has site for binding of RNA polymerase and transcription factors

transcription factors

proteins that regulate gene expression by helping or hindering transcription

non protein coding genes

genes for tRNA and mRNA

promotors, silencers, enhancers, and introns

centromeres and telomeres

phases of transcription

initiation → elongation → termination

transciprtion initiation

RNA polymerase binds to promotor

RNA polymerase breaks hydrogen bonds to unwind DNA to form transcription bubble

transcription elongation

RNA polymerase pairs complemtary NTPs on template strand to create coding strand

uracil used instead of thymine

transcription termination

RNA polymerase detects terminator sequence that causes it to release the mRNA molecule

modifications to mRNA

5’ cap

poly-A-chain

RNA splicing

5’ cap (2)

guanosine added to mRNA’s 5’ end

protects it from digestion by exonucleases

poly A tail (4)

chain of 100-200 adenine ribonucleotides on 3’ end of mRNA

added by poly-A polymerase

acts as structural timer (how many times mRNA can be replicated)

protects mRNA from being digested too quickly

RNA splicing

introns being cut out and connects exons

alternative splicing

single gene with multiple exons can code multiple proteins

translation phases

initiation → elongation/translocation → termination

translation initiation

small subunit of ribosome binds methionine carrying tRNA

small subunit binds to mRNA

large subunit binds to small subunit so tRNA is in P site (middle), this forms initiation complex

translation elongation and translocation

next complementary tRNA hydrogen bonds to next codon in A site

large subunit advances which detaches amino acid from P site and attach to polypeptide chain in A site

small subunit slides across large subunit to move 3 base pairs

tRNA holding polypeptide shifts into P site and empty tRNA released in E site

translation termination

ribosome reaches stop codon

release factor aid disassembly of ribosome to release mRNA

polypeptide modification (6)

removal of methionine

changes to side chains of amino acids

folding

removal of part of polypeptide chain

combining polypeptide chain

combining non-polypeptide components

insulin modifications

begins as 110 base preproinsulin

24 amino acids cleaved at N terminus → proinsulin

3 disulfide bridges to maintain folding

35 amino acids removed that leaves two chains held together by disulfide bonds

gene mutation (2)

change in base sequence that codes for polypeptide

unpredictable and can occur anywhere in genome

sickle cell anemia

gene mutation (single base substitution) in hemoglobin

GAG → GTG, glutamic acid (hydrophilic) → valine (hydrophobic)

sickle cells clump together and cause reduced flow of blood

shorter lifespan and fewer RBCs

when oxygen is high, will function normally

types of gene mutations

base substitution

frameshift

base substitution(2)

one base in gene’s code is changed to a different base

most common is G to T

frameshift mutation

insertion - extra base added to sequence

deletion - base lost from sequence

occur less than substitution because it requires breaking phosphodiester linkage

consequences of base substitution (5)

nonsense mutation - codon changes to stop codon

missense mutation - results amino acids with different properties

silent mutations - codon changes to codon for same amino acid

synonymous missense mutations - codon changes to amino acid with similar properties

some missense mutations can be beneficial and favoured by evolution

consequences of frameshift

change of one or two bases will cause entire reading frame

change of three causes amino acid change which generally isn’t as harmful

mutagen

external agent that increases the risk of gene mutation

UV rays - strong energy can cause mutation

chemical substances - can react with sugar-phosphate backbone or bases

germ cells (mutation)

can differentiate into egg or sperm/pollen cells

mutation will be all cells in offspring

somatic cell

all body cells except for germ cells

mutation will only be in its daughter cells, cannot be transferred to germ cells

cancer

mutation in proto-oncogenes (cell that controls cell cycle)

cell division may be uncontrollable resulting in tumours

gene knockout

technology that makes gene inoperative to investigate its possible function

gene knockout mechanism

1. segment of DNA (neoR) is amplified by PCR relative to the gene of interest

2. neoR DNA is used to replace gene of interest in embryonic stem cell

3. cells where replacement was successful are injected into blastocyst of desired organism (generally mice)

4. organism is bred with individual that underwent same process (heterozygotic to gene of interest)

5. gene is knocked and experiments done to observe differences in characteristics

CRISPR

gene-editing technology

sequence of DNA in bacteria that contain remnants of viral DNA separated by palindromic repeats

two key parts: guide RNA and CAS-9 enzyme

CRISPR mechanism

1. gRNA for desired gene is created

2. CAS-9 and gRNA is delivered into the cell

3. gRNA binds to matching DNA sequence

4. CAS-9 cuts off both strands of DNA

5. other enzymes will repair DNA, but this is where gene editing occurs