Genome Flashcards
Is DNA semiconservative?
Yes
What is biderectional DNA?
Bidirectional replication.a type of dna replication where replication is moving along in both directions from the starting point. This creates two replication forks, moving in opposite directions
What are the enzymes called that make new DNA?
DNA polymerase
What is DNA polymerase and what does it do?
Consists of a template and a primer (starter), that synthesises DNA in the 5’ - 3’ direction
DNA replication requires other enzymes in addition to DNA polymerase, what are the others called?
DNA primase, helicase, ligase and topoisomerase
Summarise the process of DNA replication:
- Hydrogen bonds break the phosphate backbone of the double helix - essentially ‘unzipping’ the two strands
- Each strand of DNA acts as a template for synthesis of a new complementary strand
- Replication produces two identical DNA double helices, each with one new and one old strand
To which end of the DNA strand are nucleotides added?
3’ end
In DNA replication, what happens during both leading and lagging strand synthesis?
RNA primers help initiate DNA synthesis
At what point during normal DNA replication is genetic material lost from the telomeres?
Joining of adjacent Okazaki fragments
In what direction is DNA synthesised when catalysed by either DNA polymerase or reverse transcriptase?
Both DNA polymerase and reverse transcriptase catalyze the synthesis of DNA in the 5’ to 3’ direction
Which association between complementary bases would require the most energy to break (has the highest bond dissociation energy)?
Guanine and Cytosine (Adenine and thymine associate via two hydrogen bonds. Adenine and uracil associate via two hydrogen bonds)
Where within the eukaryotic cell might a drug which exclusively binds to tRNA binding sites exert its effects?
The cytosol, tRNA binds to ribosomes to be used in translation and translation occurs in ribosomes
What constitutes the phosphodiester bonds in DNA?
Covalently linked nucleotides, phosphodiester = phospho + di + ester = a phosphate and two esters
An Exon is a non-encoding section of DNA?
False
An intron-less gene is likely to have occurred by which mechanism?
Retrotransposition
Which represents the correct sequence of stages in mitosis?
Prophase, Prometaphase, Metaphase, Anaphase, Telophase
Which protein catalyses the formation of phosphodiester bonds between nucleotides?
Polymerase III
Which of the following carries an anticodon and a specific amino acid to a growing polypeptide chain?
tRNA
In what stage of meiosis do the chromosomes pair and cross over?
Prophase I
A mutation in a codon leads to the substitution of 1 amino acid for a STOP Codon. What type of mutation is this?
Nonsense mutation
In which stage of Mitosis do chromosomes align in the middle between spindle poles?
Metaphase I
Which type of bonding holds together the 2 anti-parallel strands of DNA?
Hydrogen bonds
DNA Replication occurs during which phase of the cell cycle?
S phase
Autosomal Recessive Disorders are rarer than Autosomal Dominant Disorders?
Yes
Intercalating agents insert into DNA and cause helix distortion?
True
Which are types of point mutation?
Neutral and missense
Crossing over in meiosis is an exchange of genetic material between…?
Non-sister chromatids of homologous chromosomes
Select the 3 correct sequences which encode for STOP Codons:
UAA, UAG and UGA
Recessive X-linked traits occur more frequently in males?
True
The Ribosome contains RNA binding sites known as…?
A Site, P Site, E Site
The process of translocation occurs during which phase of translation?
Elongation
Select the mechanisms by which new genes can originate in a genome:
gene chimerism, lateral gene transfer, motif multiplication and exon shuffling
What catalyses formation of peptide bond between amino acids?
Large ribosomal subunits
If mRNA has AAU what is the tRNA corresponding sequence?
UUA
What is regulatory DNA sequence part of the genetic switch called?
Operator
If wild type operon & LOW lactose levels, is lac operon ON or OFF?
OFF
If wild type operon & HIGH lactose levels, is lac operon ON or OFF?
ON
About how many adenine nucleotides are added to 3’ end on mRNA during polyadenylation?
Approx 150
What is lateral gene transfer?
Genetic material transferred across lineages horizontally
What is gene chimerism?
From 2 or more different ancestral genes by exon shuffling or retrotransposition
What is motif multiplication?
A specific motif is multiplied to make new gene
What is exon shuffling?
Exons moving to new regions of genome
Cell division is essential for any living organism. For which of these processes is it NOT absolutely necessary?
Preservation
There are three checkpoints in the cell cycle, what is their role?
Ensure that each phase is complete before the next phase
The cell contains two sets of chromosomes (2n). What is the correct name for such cells?
Diploid cells
What would happen if humans produced reproductive cells through mitosis instead of meiosis?
The number of chromosomes would double every generation
Unicellular organisms such as bacteria depend on asexual reproduction. Why is sexual reproduction so common in higher multicellular organisms such as humans?
Sexual reproduction and meiosis ensure genetic diversity in the population
Which bases are purines?
Adenine and guanine
Which bases are pyrimidines?
Thymine, cytosine and uracil
How many bonds do C and G have?
3 bonds
How many bond do A and T have?
2 bonds
Components of DNA nucleotides:
- Phosphate group
- Organic nitrogenous base (A, T, C, G)
- Pentose sugar (deoxyribose)
Semiconservative process of DNA replication:
- DNA unwound to separate template strands
2. Addition new nucleotides linked by covalent bonds
Stages of the cell cycle:
G1 (growth), S phase (DNA synthesis), G2 (preparation for mitosis) and M phase (mitosis cell division - prophase, metaphase, anaphase, telophase and cytokinesis)
What happens during G1 phase?
G1 = cellular content, excluding chromosomes, are duplicated
What happens during S1 phase?
each of the 46 chromosomes is duplicated by the cell (in S phase, the cell synthesizes a complete copy of the DNA in its nucleus. It also duplicates a microtubule-organizing structure called the centrosome. The centrosomes help separate DNA during M phase).
What happens during G2 phase?
he cell ‘double checks’ (regulates) duplicated chromosomes for error, making any needed repairs, the cell grows more, makes proteins and organelles, and begins to reorganize its contents in preparation for mitosis. G2phase ends when mitosis begins
What stages make up interphase?
G1, S1 and G2
What happend during M phase?
the cell separates its DNA into two sets and divides its cytoplasm, forming two new cells. M phase involves two distinct division-related processes: mitosis and cytokinesis.
Mitosis
Inmitosis, the nuclear DNA of the cell condenses into visible chromosomes and is pulled apart by the mitotic spindle, a specialized structure made out of microtubules. Mitosis takes place in four stages: prophase (sometimes divided into early prophase and prometaphase), metaphase, anaphase, and telophase.
What are nucleosomes?
A nucleosomes is the basic repeating unit of chromosomes in eukaryotes, in order for the DNA to fit within the nucleus. The nucleosomes are arranged like beads on a string. They are repeatedly folded in on themselves to form a chromosome. The DNA is complexed with histones in the centre to form nucleosomes, each nucleosome consists of 8 histone proteins around which the DNA wraps.
Proteins involved in DNA replication:
- Topoisomerase
- DNA helicase
- Single Stranded Binding Proteins (SSB)
- DNA polymerase III
- Primase
- DNA polymerase I
- DNA ligase
Topoisomerase
unwinds the double helix ahead of DNA replication forks (relieves supercoils), cuts the phosphate backbone of one of the strands
DNA helicase
binds to the origin (ori) of replication, uses energy from ATP molecules to break the hydrogen bonds, then DNA becomes single stranded - which gains access to the proteins involved
Single Stranded Binding Proteins (SSB)
bind to single strands of DNA
DNA polymerase III
catalyses the formation of phosphodiester bonds between nucleotides. It requires a DNA template (strand to copy), RNA primer (short piece of RNA) and four dNTPs (nucleotides). Chain elongation 5’ to 3’ direction, addition at 3’ end. Nucleotide added, 2 phosphates released. DNA polymerase catalyses the elongation of DNA chains
Primase
initiation of DNA synthesis requires an RNA primer
DNA polymerase I
Image result for dna polymerase 1 in dna replication
DNA polymerase I functions to fill DNA gaps that arise during DNA replication, repair, and recombination.
DNA ligase
DNA ligase, uses one ATP to join the Okazaki fragment into the growing lagging strand
DNA damage and repair
- DNA can occur spontaneously
- Can occur in response to mutation-inducing agents (mutagens)
- If DNA damage id not repaired it leads to mutations
When does most damage take place?
during DNA unwinding, as the single stranded DNA is prone to breakage (phosphodiester bond). During the DNA unwinding bases become exposed to damaging agents. DNA polymerase III also makes errors
Faults regarding DNA polymerase
- DNA polymerase makes mistakes - sometimes adds the wrong nucleotide, which leads to a mismatch (wrong pairing of bases) - distortion in helix formation (recognised by proteins)
- The incorporated nucleotide can contain modified bases
- Small deletions and insertions can occur
What are mismatch repair proteins (MMR)?
Mismatch repair proteins (MMR) are a group followed by DNA polymerase, proofread the new strand. The MMR proteins identify and remove mis-incorporated nucleotides.
Base oxidation damage
often induced by high levels of reactive oxygen species (ROS) increase mutation rate, usually affects guanine and cytosine, which causes misplacement of hydrogen
Base alkylation damage
adding chemical alkaline group to base, which change formation of nucleotide - problem during DNA replication
DNA adducts and crosslinks damage
induced by chemicals or radiation (not usually spontaneous), essentially induced by high dose of radiation or strong chemicals
Mutagens damage
eg alcohol, metabolites and ROS
Environmental mutagens damage
chemical - air/water pollutants, drugs, toxins (eg aflatoxin) and food preservatives
Radiation damage
UV and ionizing radiation
Anti-cancer Drugs Often Cause DNA Damage:
- Topoisomerase inhibitors - etoposide, camptothecin, irinotecan - prevent ligation resulting in ssDNA breaks
- Intercalating agents - doxorubin, daunorubicin, cisplatin - insert into DNA which leads to disortion
Repairing DNA damage
it’s often a multistep process and involves many proteins
- Direct reversal systems (correct damaged area by reversing damage)
- Excision repair systems (cut out damage and repair gap by new DNA synthesis and ligation)
What Can Happen if DNA damage Can’t be Repaired?
- Heritable change in the genetic material
- Mutation provide allelic variations
- Evolutionary change
- Can be harmful and often cause disease
- Essentially mutations are results of unrepaired DNA damage
Types of Mutations:
- Chromosome mutations (changes in chromosome structure)
- Genome mutations (changes in chromosome number)
- Gene mutations (small changes in DNA structures - affects a single gene)
Point Mutations
May be introduced by the addition of incorrect base in the first round of replication (at this stage it is not a mutation yet - mismatch repair). However, if the cell divides and replicates in the second round, it is a mutation. In the second round of replication - mutation is permanent part of DNA
Translation of a Normal Gene
- DNA sequence is transcribed into messenger RNA
- 3 bases of mRNA = codon
- Every codon encodes one amino acid
Point Mutations: Silent (same amino acid)
- Change in DNA (= change in RNA)
- Change in mRNA - same amino acid
- Essentially genetic code is degenerate, for example a few codons encode the same amino acid
Point Mutations: Neutral (different amino acid but functional)
- Change in DNA
- Change in mRNA - amino acid substitution
- No detectable change - amino acid with similar properties (small change as there is a different amino acid but with similar function)
- Proteins can be replaced by lysine, arginine and histidine
Point Mutations: Missense (completely different amino acid)
- Change in DNA
- Change in mRNA codon - different amino acid (has different chemical properties and can lead to improper folding of the protein and affect its function
- This can result in non functional protein
Point Mutations: Nonsense (change to STOP codon - shorter protein)
- Change in DNA
- Change in mRNA codon to STOP (UAG, UAA or UGA) - no amino acid
- This can result in too short/incomplete polypeptide
Larger Mutations: Insertion/Deletion
- Change in mRNA reading frame downstream
- May generate/lose STOP codons - shorter (deletion)/longer (insertion) polypeptides
- Can lead to frameshift mutations - leads to completely different amino acid sequence (proteins)
Summary of mitosis:
- Produces new cell via duplication of existing cell (somatic cells)
- Important in development, growth and healing
- Copy contents and divide into two - with 23 chromosomes each
Gap phases allow the cell to:
- Grow
- Monitor the internal and external conditions before committing to S phase or mitosis
G0 resting state
is a normal state for some cells (neurons and muscle cells)
Cell Cycle Control of System Triggers the Majors Events of the Cell Cycle
Receives info from the cycle events and external environment, can arrest the cycle at checkpoints. Near the end of G1 phase (checks the DNA for mutations and environment) and another checkpoint before M phase
- G1 and G2 checkpoints
The Cell Cycle M Phase
M phase - small fraction of the cell cycle
- Mitosis - nuclear division (prophase, metaphase, anaphase and telophase)
- Cytokinesis - cell division
- After S and G2 - enter M phase (IF CHECKPOINT PASSED)
- Sister chromatids separated into identical daughter cells
Prophase
- Replicated chromosome condense
- Outside the nucleus: centrosome replicate and move apart
- Microtubule-organising centre
- Mitotic spindle assembles between 2 centrosomes
Pro-metaphase
- Breakdown of nuclear envelope
- Chromosomes attach to spindle microtubules via kinetochore
- Kinetochore binds to the centromere of the chromosome
Metaphase
- Chromosome align in the middle of the spindle - between spindle poles
- Specific microtubules attach sister chromatids to opposite spindle pole
Anaphase
- Sister chromatids separate - 2 daughter chromosomes
- Kinetochore microtubules get shorter
- Spindle poles move apart
- Sister chromatids are pulled towards opposite poles
Telophase
- Daughter chromosomes arrive at poles of spindle
- Chromosomes decondense
- New nuclear envelope forms around each set of chromosomes (formation of nuclei)
- End of mitosis
Cytokinesis
- Cytoplasm divides into two
- formation of contractile ring - actin and myosin
- Pinches cell into two
- Two daughter cells each with one nucleus
- The same number of chromosomes as original cell
- Both daughter cells have identical genetic information
Meiosis
- Sexual reproduction occurs in diploid organisms - two sets of chromososmes
- Requires specialised haploid cells - one set of chromosomes
- A haploid cell cell of one individual fuses with haploid cell of another
- Restores diploid state
- Generates genetically distinct offspring
Mitosis single round of cell division
diploid cells
Meiosis two rounds of cell division
haploid cells
Meiosis I
Homologous chromosomes are separated (unique to meiosis)
Meiosis II
Sister chromatids are separated (same as mitosis)
Process of meiosis I:
Duplicated homologous chromosomes (paternal and maternal) pair up along side each other - same size, length, genes…Then there is an exchange of genetic information. They line up at the equator of the meiotic spindle. The duplicated homologous chromosomes (NOT sister chromatids) are pulled apart. Lastly they are segregated into two daughter cells.
Stages of meiosis I
- Prophase I = chromosomes were duplicated in S phase, chromosomes condense and become visible. Duplicated centrosomes separate and spindle forms
- Prometaphase I = Visible chiasmata, nuclear envelope breaks down, meiotic spindle is present and kinetochore microtubules are attached to chromosomes
- Metaphase I = Chromosomes shorten and thicken, homologous chromosomes (paternal and maternal) recognise each other. Associate along their length - pairing. Microtubules align each chromosome pair, paired homologous chromosomes at spindle equator (randomly oriented)
- Anaphase I = Homologous pairs separate, sister chromatids remain attached and move towards opposite poles
- Telophase I = Separated chromosomes (2 sister chromatids) at opposite poles of the cell, spindle disassembles, new nuclear envelope may form. Two nuclei - haploid with one mixed parental set of separated chromosomes
Process of meiosis II:
No DNA replication between meiosis I and meiosis II
Sister chromatids pulled apart and segregated to produce haploid daughter cells
End of meiosis diploid cells produces four haploid cells = which inherits either the maternal or paternal copy of each chromosomes
Stages of meiosis II
Meiosis results in genetic variation, the process generates different haploid cells (produces individuals with novel genetic combinations)
Genetic differences via two mechanisms:
-Independent assortment of maternal and paternal homologs during meiosis I
-Crossing over during prophase I (exchanges DNA segments between homologous chromosomes and reassorts genes on individual chromosomes)
Mendel
Mendel: basic principles of inheritance by breeding garden peas
- Tracked only characters that occurred in two distinct alternative forms
- Used varieties that were true-breeding
- Offspring same variety when they self-pollinate
Phenotype
physical appearance
Genotype
genetic make-up
How do Gene Sets Come Together in Offspring?
Mendel’s first law of segregation:
- Two alleles for each trait separate during gamete formation (meiosis)
- Alleles randomly reunite at fertilisation
Monohybrid crosses
one trait
Multihybrid crosses -
multiple unrelated traits
Transcription
The pathway from DNA to protein
Only one strand of DNA acts as a template (3’-5’)
(5’) C G G T A T A G C G T T T (3’) DNA non template (coding) strand
(3’) G C G A T A T C G C A A A (5’) DNA template (antiparallel) strand
(5’) C G C U A U A G C G U U U (3’) RNA transcript
Transcription
Nucleotide sequence of RNA determined by complementary base pairing to DNA template
DNA is transcribed by the enzyme RNA polymerase, it catalyses the formation of phosphodiester bonds between nucleotides. DNA is producing DNA strands and RNA is producing RNA strands
RNA polymerase uses the template strand to make mRNA
Transcription: RNA polymerase catalyses the same reaction as DNA polymerase but there are some important differences:
- RNA chains (like DNA) grow in the 5’ to 3’ direction
- RNA polymerase catalyses linkage of ribonucleotides
- RNA polymerase doesn’t require a primer (DNA pol require a RNA primer)
What is the name of the process which copies DNA to make messenger RNA?
Transcription
What type of bond does RNA polymerase catalyse the formation of?
Phosphodiester bonds
RNA polymerase performs multiple functions in transcription:
- Searches DNA for transcription start sites - promoters
- Unwinds ( to single strand) short stretch of dsDNA to ssDNA template
- Selects correct ribonucleoside triphosphate: ATP, CTP, UTP and GTP
- Catalyses phosphodiester bond formation between ribonucletides to join them together in a strand. Hydrogen bonds reform.
- Detects termination signals - transcript ends
Which transcription is more complicated?
Eukaryotic transcription is more complex than prokaryotic transcription
Transcription: Prokaryotic RNA polymerase
Prokaryotes don’t have a membrane bound nucleoid, they don’t contain junk information
RNA polymerase in two forms:
- Core enzyme (contains α α β β’ ) σ
- Holoenzyme enzyme (core enzyme (α α β β’) and sigma factor (σ) can leave and join whenever it wants). Once the sigma factor leaves it becomes the core enzyme again
Transcription: Signals Encoded in DNA Tell RNA Polymerase Where to Start and Stop
- Promoter - sequence upstream (before) - directs RNA pol to transcription start site. The promoter is always at the start
- Terminator - sequence downstream (after) - RNA pol stops and releases RNA chain, essentially a stop signal
Transcription: Prokaryotic Promoter Sequences
Prokaryotic promoter sequences:
- -35 sequence - TTGACA
- -10 sequence - TATAAT
Transcription: What is sigma factor required for?
In prokaryotes the sigma factor of RNA polymerase recognise promoter sites. Sigma subunit, part of holoenzyme (α α β β’ σ) binds to the promoter sequences at -10 and -35.
Transcription process
RNA polymerase unwinds dsDNA exposing the template strand. Closed promoter (has hydrogen bonds) to open promoter (broken hydrogen bonds). This doesn’t require energy as hydrogen bonds are covalent.
RNA polymerase moves into elongation phase of transcription. The RNA pol transcribes the DNA template strand, synthesising complementary RNA strand. After approx 10 nucleotides, the sigma factor (σ) leaves - core enzyme (α α β β’) continues to transcribe DNA.
The RNA polymerase continues to transcribe DNA until it encounters a termination signal. There are two type of termination in prokaryotes: rho dependent (p) which requires a protein called rho that helps the RNA polymerase to disassociate from the molecule and you get rho independent in which protein is not required. In both cases the RNA pol reaches the termination site and is forced to release the mRNA strand - therefore ending transcription of that specific gene.
Transcription: Statements of the promoter:
- It is located at the beginning of the gene
- It directs RNA polymerase to the transcription start site
- It contains consensus sequences
Transcription: Core enzyme of RNA Polymerase
α α β β’ subunits
Transcription: Holoenzyme of RNA Polymerase
α α β β’ and sigma (σ) subunit
Transcription: Sigma subunit
Helps RNA polymerase recognise promoter of gene. Released after initiation
Eukaryotic Transcription
RNA polymerase in eukaryotes recognises the promoter with the help of the other proteins. Eukaryotic promoter sequences are more complex and RNA pol in eukaryotes can’t find promoter on its own. Other proteins = general transcription factors (similar role to the sigma factor).
5’ RNA capping is the first modification of eukaryotic pre-mRNAs, addition of modified GTP (guanosine triphosphate) - with a 7-methyl group residue attached to it, which is the beginning of the messenger RNA.
Splicing: RNA splicing removes intron sequences from the newly transcribed pre-mRNAs. We have large amount of junk information (we don’t fully understand junk info), however they need to be removed - introns, from exon which are protein coding portion of the gene before it can be translated in the cytoplasm. The removal of the introns is called splicing - as the mRNA is being produced in eukaryotes it will be spliced and the introns will be removed and the exons will be stuck together.
Polydenylation is the final modification of eukaryotic pre mRNAs. At the very end of the RNA molecules polyadenylation takes place, which is when the cell will add a series of poly A Tail usually between 100 -150 or more adenine on to the end of the mRNA. The longer the poly A Tail the longer the mRNA in the cytoplasm - therefore the more it is translated.
Messenger RNA is processed in what type of cells?
Eukaryotic cells
Describe splicing:
Removal of introns from mRNA leaving exons
Eukaryotic transcription RNA Processing: 5’ Capping
Addition of modified GTP to 5’ (phosphate) end of mRNA
Eukaryotic transcription RNA Processing: 3’ Polydenylation
Addition of approx 150 nucleotides to 3’ (OH) end of the mRNA
Eukaryotic transcription RNA Processing: Splicing
Addition of approx 150 nucleotides to 3’ (OH) end of the mRNA
Translation
An mRNA sequence is decoded in sets of three nucleotides. The information mRNA nucleotide sequence used to synthesise protein. Each amino acid is encoded by three nucleotides - codon = dictates the amino acid.
Translation: mRNA sequence can be translated in three possible reading frames:
- Start signal (AUG) at beginning of mRNA set the reading frame at start of protein synthesis. All mRNA have a start codon. AUG also codes for the amino acid Methionine
- Stop signal (UAA, UAG, UGA = STOP), they don’t code for amino acids
Translation: Transfer RNA (tRNA) matches amino acids to codons in mRNA
- Codons do not directly bind to amino acids
- Use of adaptor molecule - tRNA
- Convert codon to amino acid
Translation: Where is mRNA decoded
The mRNA is decoded in the ribosomes, protein synthesis is performed at the ribosome. RER has ribosomes attached to its structure. Ribosomes which help translate proteins, sit in the endoplasmic reticulum.
Translation: Where are amino acids added?
Amino acids are added to the c-terminal end of a growing polypeptide chain. As tRNA comes together with amino acids attached to them we get a bond between the amino acid and tRNA - peptide linkage bond between the carboxyl group of the amino acid and amine group of the other amino acid - which will cause the tRNA to be released (which can be recycled and go back into the system and recharged).
Translation: The ribosome contains RNA binding sites:
- Binding site for mRNA
- Binding site for tRNA
Translation : A, P, E
- A site (aminoacyl-tRNA)
- P site (peptidyl-tRNA)
- E site (exit)
Translation: Where does the tRNA enter from?
tRNA will usually enter at the A site move into the P site and exit via the E site into the cytoplasm - and recharged. The messenger RNA (mRNA) sits in between the large and small ribosomal unit - in order to be read.
What is the name of the process which copies DNA into mRNA?
Transcription
What is attached to the transfer RNA (tRNA)?
Amino acid
Translation is most closely associated with which organelle?
Ribosomes
Translating an mRNA molecule involves 3 stages:
- Initiation = begins with the start codon AUG, initiator tRNA binds to AUG at P site of ribosome
- Elongation
- Termination
What catalyses the formation of peptide bond between amino acids?
Large ribosomal subunit by ribozyme
Translation in prokaryotes
In prokaryotes small ribosomal subunit aligns ribosome on mRNA. Shine -Dalgarno sequence in rRNA base pairs to sequence in mRNA. Binding of large ribosomal subunit. We have A site empty, the tRNA with amino acid binds to A site, forming a peptide bond between the two amino acids (Met in P site and amino acid in A site). Now the tRNA in the P site is uncharged it has its amino acid removed and everything is in the A site.
