Unit 1 Flashcards
What are the two strands of DNA held together by?
Weak hydrogen bonds between the bases
How do bases pair?
complementary base pairing
adenine-thymine
cytosine-guanine
What are the subunits of DNA called?
nucleotides
Draw the structure of DNA
-phosphate
-deoxyribose sugar
-base
-nucleotide
-3’ end
-5’ end
-weak H2 bond
-sugar forms strong bond with phosphate below: sugar-phosphate backbone
-carbons are numbered 1-5
-double stranded
-anti-parallel: the 2 strands run in opposite directions to each other (5’—>3’ / 3’—>5’)
Prokaryotes
organisms which lack a true membrane-bound nucleus e.g. bacteria
Eukaryotes
organisms which have a membrane-bound nucleus that stores their genetic material e.g. animal cells
ribosome
nucleus
cell membrane
chloroplast
mitochondria
ribosome-site of protein synthesis
nucleus-controls cell division and cell chemistry
cell membrane-controls the movement of materials in and out of cells
chloroplast-site of photosynthesis
mitochondria-site of aerobic respiration
Prokaryote DNA
circular chromosome and structures called plasmids
Eukaryote DNA
linear chromosomes held inside the nucleus
Where can circular chromosomal be found in eukaryotic cells?
mitochondria and chloroplasts
What is special about yeast cells?
-Eukaryotic
-Can have plasmids
structure of a linear chromosome (eukaryotes)
-DNA
-Histone Protein
-Nucleosome
(beads ion a string-Dna wound on nucleosomes)
-double helix
Why is DNA unique?
It can copy itself exactly. This is essential for replication of chromosomes before any cell division
Semi conservative?
DNA replication is semi conservative-each new molecule contains one new and one original strand
What are the two enzymes involved in DNA replication?
DNA pyolymerase
DNA ligase
DNA replication steps
1-DNA unwinds
2-H2 bonds break
3-DNA strands separate to form 2 template strands (lagging and leading)
5-Primer binds to 3’end
4-DNA polymerase adds DNA nucleotides, using complementary base pairing, to the 3’end of the template DNA strand
5-H2 bonds form between bases
6-sugar-phosphate bond forms between nucleotides
7-DNA molecule recoils in double helix
What does DNA polymerase require to start replication and what isn’t it?
A primer-a short strand of nucleotides which binds to the 3’end of the template DNA strand allowing polymerase to add DNA nucleotides
-Primers are complementary to specific target sequences at the two ends of the region of DNA to be amplified
Describe the formation of the leading strand
Replication of the parental DNA strand which has the 3’end at the bottom is continuous and forms the leading strand
Describe the formation of the lagging strand
The lagging strand has to be replicated in fragments and its formation is described as discontinuous.
5’end at bottom
What does ligase do? (and what is it?)
Enzyme that joins the fragments in the lagging strand
bonds fragments of replicated DNA into lagging strand
Direction of replication
5’ to 3’
‘nucleotides added to the 3’ end of template strand)
What does DNA polymerase do? (and what is it?)
Bonds nucleotides into backbone
Enzyme which adds nucleotides to the 3’end of the template strand to form a new strand
What is required for DNA replication?
DNA-Acts as a template
Primer-start point for replication
Free nucleotides l-used to make the new complementary strand
DNA polymerase
Ligase
ATP(energy)
What is PCR?
The Polymerase Chain Reaction
(It is a useful tool in DNA technology.)
It is a way of amplifying (making copies of) target regions of DNA.
Steps of PCR
1-DNA is heated between 92-98 to separate the 2 strands (DNA is denatured)
2-It is then cooled to between 50-65 to allow the primers to bind (anneal) to target sequences
3-It is then heated to between 70-80 for the heat-tolerant polymerase to replicate the region of DNA (heat-tolerant so that it does not denature)
Uses of PCR
PCR can amplify DNA to:
-help solve crimes
-settle paternity suites
-diagnose genetic disorders
What can DNA samples be analysed with?
Gel electrophoresis
How is a cell’s genotype determined?
By the sequence of DNA bases in its genes
How is a cell’s phenotype determined?
By the proteins that are synthesised when two genes are expressed
How much of an organism’s genome is expressed?
A fraction of the gene
What is the structure of a protein (coded for by a gene) determined by?
By the sequence of amino acids
What are amino acids linked by?
peptide bonds to form polypeptides
What do polypeptide chains do?
Fold to form the three-dimensional shape of a protein, held together by hydrogen bonds and other interactions between individual amino acids
Two types of polypeptide chains
fibious-long parallel strands
globular-folded together in a spherical shape (or incorporates another chemical)
What does gene expression involve?
The creation of a protein from a gene through 2 stages:
-transcription
-translation
Chromatography
A technique that can be used to separate amino acids
3 types of RNA involved in transcription and translation
mRNA (messenger), tRNA (transfer), rRNA (ribosomal)
What is RNA?
-single-stranded
-composed of nucleotides containing ribose sugar, phosphate and one of the four bases: cytosine, guanine, adenine, uracil
What is Transcription?
The process in which a copy of DNA is made, mRNA, in the nucleus
Steps of transcription
1-RNA polymerase moves along the DNA, unwinding the helix
2-The weak H2 bonds, between the bases, break
3-RNA polymerase adds free RNA nucleotides pair up with their complementary bases on the DNA
4-RNA polymerase enzyme controls the formation of the backbone between adjacent RNA nucleotides forming an RNA chain
5-Weak H2 bonds between DNA and RNA break. This leaves a single strand of mRNA. This is called the primary transcript
6-The 2 strands of DNA come together again and wind up.
What is the mRNA primary transcript made up of?
coding (exons) and non-coding regions (introns)
What is RNA splicing?
The introns of the primary transcript are removed. The exons are joined together to form the mature transcript. The order of exons is unchanged during the splicing.
Alternative RNA splicing
Different proteins can be expressed from one gene (as a result of alternative splicing)
Different mature transcripts are produced from the same primary transcript depending on which exons are retained.
What happens during translation?
mRNA is translated into proteins by ribosomes in the cytoplasm
What is used to determine the sequence of amino acids in the protein?
codons on the mRNA
What are codons?
A triplet of bases on mRNA that code for one amino acid
tRNA
-transfer RNA
-found in the cytoplasm
-folds due to complementary base pairing
-a tRNA molecule had an anticodon (triplet of bases) at one end and an attachment site for a specific amino acid on the other end
-transfers amino acid from cytoplasm to ribosome
Where is the site of translation?
ribosome
What are ribosomes made up of?
-rRNA (ribosomal RNA)
-protein
Steps of translation
-Begins at a start codon in mRNA and ends at a stop codon on mRNA
-The ribosome reads three bases (codon) at a time
-tRNA carries a specific amino acid to the ribosome and anticodons on tRNA bond to codons by complementary base pairing
-Peptide bonds join the amino acids together (polypeptide chain) (to form proteins)
-Each tRNA then leaves the ribosome (discharged) as the polypeptide is formed
What is cellular differentiation?
The process by which a cell expresses certain genes to produce proteins characteristic for that type of cells
This allows a cell to carry out specialised functions
What directs a cell’s development?
The selective switching on and off of genes
What are stem cells?
Unspecialised cells in animals that can divide (self-renew) and/or differentiate
What are meristems?
regions of unspecialised cells in plants that can divide (self-renew) and/or differentiate
Embryonic stem cells
-cells in the very early embryo can differentiate into all the cell types that make up an organism
—>PLURIPOTENT
-All the genes in embryonic stem cells can be switched on so these cells can differentiate into any cell type
Where do we find tissue stem cells?
-bone marrow
-brain
-testes
-ovary
-skin
-intestines
-muscles
What are tissue stem cells involved in?
growth, repair, and renewal of the cells found in that tissue
What is a property of tissue stem cells?
They are multi potent as they can differentiate into all of the types of cell found in a particular tissue type.
For example, blood stem cells located in bone marrow can give rise to all types of blood cell.
Therapeutic uses of stem cells
-bone marrow transplant to tread leukaemia
-cornea repair
-regeneration of damaged skin
-repair of damaged or diseased organs or tissue
research value of stem cells
-embryonic stem cells can self renew, under the right conditions, in the lab
-stem cells research provides information on how cell processes such as cell growth, differentiation and gene regulation work
-research uses stem cells being used as model cells to study how diseases develop or being used for drug testing
controversy surrounding stem cell use
-Use of embryonic stem cells invokes destruction of embryos
-Some people believe that life begins at fertilisation and using embryonic stem cells is destroying a potential life
What is an organism’s genome?
Its entire hereditary information encoded in DNA
What is a gene?
A sequence of DNA that codes for a protein
What parts make up the genome?
coding (code for proteins)
non-coding (do not code for proteins)
Most of the eukaryotic genome consists of non-coding sequences
What do non-coding regions of DNA do?
-regulate transcription
-transcribed but never translated
Non-translated forms of RNA are not translated into protein (e.g. tRNA and rRNA)
-no known function
What are mutations?
Changes in the structure or mass of an organism’s DNA.
/changes in the genome
They are rare.
What do mutations result in?
no protein or an altered protein.
What do you call an organism possessing a mutation?
Mutant
What is a mutagenic agent? + examples
Something that increases the frequency of mutations
-chemicals e.g. mustard gas
-radiation e.g. gamma rays
What does a single gene mutation involve?
A change in one of the base pairs in DNA sequence of a single gene
What can single gene mutations be the result of?
-substitution (one base/nucleotide replaced with another in DNA)
-insertion (nucleotide/base added to DNA)
-deletion (nucleotide/base removed from DNA)
of nucleotides within a gene
Frameshift mutations
insertions or deletion
cause all of the codons and all of the amino acids after the point of mutation to be changed
major effect in the structure of the protein produced
substitution
point mutatjon
major or minor effect
base replaced with anorher
examples-missense or nonsense, splice site
Missense mutations
result in one amino acid being changed for another
may result in a non-functional protein or have little effect on the protein
Nonsense mutations
result in a premature stop codon being produced which results in a short protein
Splice site mutations
inclusion of introns in the mature mRNA transcript
exclusion of exons in the mature mRNA transcript
may in turn be translated into an altered protein (longer or shorter) which does not function properly
Chromosome structure mutations
Deletion
duplication
inversion
translocation
deletion (chromosome structure mutations)
where a section of a chromosome is removed
protein not produced
duplication
where a section of a chromosome is added from its homologous partner
set of genes being repeated
can be detrimental
one copy of gene functions normally
one copy can mutate
inversion
where a section of a chromosome is reversed (flipped 180)
often results in formation of non-viable gametes
Translocation
where a section of a chromosome is added to another chromosome (not its homologous partner)
evolutionary importance of gene duplication
allows potential beneficial mutations to occur in the second/ duplicated copy of gene which is free from selection pressures (it can become altered without affecting the original genes function)
The original gene will still be expressed (function will not be lost)
What is evolution?
The changes in organisms over generations as a result of genomic variations
These variations take the form of changes in the frequencies of certain genetic sequences (or alleles of genes)
What does evolution result in?
the formation of new species over time
vertical transfer of genetic material
genetic sequences are inherited vertically from parent to offspring (down the generations) as a result of sexual or asexual reproduction
horizontal transfer
Prokaryotes (bacteria and viruses) can exchange genetic material horizontally (between members of the same generation). This can then result in rapid evolutionary change
e.g. the spread of antibiotic resistance in bacteria
spread of antibiotic resistance
A significant amount of horizontal gene transfer still occurs in modern day promaryotes
Resistance to antibiotics has occurred through the transfer of plasmids carrying antibiotic resistance genes from bacteria to bacteria
What is natural selection?
The non-random increase in frequency of DNA sequences that increase survival and the non-random reduction in the frequency of deterioration sequences
Traits that are advantageous are selected for and traits which are disadvantageous are selected against
Types of selection
stabilising
directional
disruptive
stabilising selection
an average phenotype is selected for and extremes of the phenotype range are selected against
mean remains unchanged
directional selection
one extreme of the phenotype range is selected for
a new mean is created in the population
disruptive selection
two or more phenotypes are selected for
two or more new means are created in the population
2 types of speciation
allopatric speciation
sympatric speciation
Allopatric speciation
occurs when gene flow between two (or more) populations is prevented by a geographical barrier
examples of geographical barriers
rivers
mountain ranges
sea
sympatric speciation
two (or more) population live in close proximity in the same environment but still become genetically isolated
This happens due to a behavioural or ecological barrier
examples of ecological barriers
temperature
pH
salinity
humidity
altitude
examples of behavioural (reproductive) barriers
if individulas in a population become fertile at different times of the year
their organs change
or their courtship is different or unattractive
Then individuals cannot mate
What is the genomics?
The study of genomes
What does genomic sequencing involve?
Determining the sequence of bases individual genes or entire genomes
What happened in 2003?
The DNA sequence of the human genome was completed
Since the Human Genome Project, the genome of several organisms has been sequenced e.g. pathogenic bacteria/virus which helps to create vaccines
What can computer programs be used to do in genomic sequencing?
To identify base sequences by looking for sequences similar to known genes
Bioinformatics
The fusion of molecular biology, statistical analysis and computer technology to compare genomes of organisms
After sequenced, the genome of organisms can be compared for a variety of purposes. Name one of these purposes.
Members of disease causing micro-organisms - do they have important genetic sequences in common?
What has comparison of many genomes revealed?
That DNA sequences of important genes are highly similar (conserved) from one organism to the next
e.g genes coding for proteins involved in aerobic respiration, or for key enzymes
What is phyologenetics
The study of evolutionary history and relationships
Phylogenetically-what can genetic sequence data be used for?
To study the evolutionary relatedness among groups of organisms
Over time, what happens to a group of closely related living organisms?
They accumulate mutations e.g. nucleotide substitutions which gradually alter the genome
What is evolutionary distance?
A measure of how related two genomes are.
The number of differences per unit length of DNA between two genomes.
This can be used to produce phylogenetic trees
What can be used as a molecular clock?
The number of substitutions which differ between 2 groups. This indicated the length of time since the group diverged and can be used as a molecular clock
If genetic sequences differ by only a few bases, it suggests the groups share a common ancestor and diverged recently
What is the main sequence of events in evolution?
Evolution of life on earth
Evolution of cells similar to prokaryotes
Evolution of last universal ancestor
Evolution of prokaryotes able to photosynthesise
Evolution of eukaryotes
Evolution of multicellular organisms
Evolution of animals
Evolution of vertebrates
Evolution of land plants
What is pharmacogenetics?
The use of genome information in the choice of drugs
What can an individual’s personal genome sequence be used to do?
Select the most effective drugs and dosage to treat their disease (personalised medicine)
Why is mRNA so much shorter than DNA?
because they are copied from only a limited region of the DNA
(only transcribes one gene)
