IB Biology D1 Flashcards SL

D1.1.1—Name the process which produces exact copies of DNA with identical base sequences.

DNA replication.

D1.1.1—Name three life processes which require the process of DNA replication.

Reproduction, Growth, and Tissue replacement in multicellular organisms.

D1.1.2—In DNA replication each of the DNA molecules produced has one new strand and one strand conserved from the parent molecule, what words do we use to describe this?

Semi-conservative.

D1.1.2—What feature of DNA replication allows a high degree of accuracy in copying base sequences.

Complementary base pairing. A-T, C-G.

D1.1.3—Name the site where a parent DNA molecule is separated into two single strands, each of which is used as a template for the synthesis of a new strand. This site gradually moves along the parent molecule as it is replicated. The changes that occur here are carried out by multiple enzymes working together.

Replication fork

D1.1.3—Name the enzyme that unwinds the double helix and separate the two strands by breaking hydrogen bonds.

Helicase.

D1.1.3—Name the enzyme that links nucleotides together to form new

strands, using the pre-existing strands as templates. Each nucleotide in the new strand has the base that is complementary to the base of the nucleotide on the template strand.

DNA polymerase.

D1.1.4—Name the tool that is used for amplifying DNA. It is carried out in small tubes called eppendorf tubes which are loaded into a thermocycler.

Polymerase chain reaction (PCR).

D1.1.4—Name four things needed for PCR.

a) DNA sample

b) Taq DNA polymerase (heat-stable DNA polymerase)

c) Primers (short DNA strands which bind to DNA at the point where DNA polymerase should attach to the DNA and start copying, two primers are needed - one for each of the DNA strands)

d) DNA nucleotides.

D1.1.4—Describe the three stages of PCR, and the temperature at which they take place, which are repeated to amplify the DNA.

1. Separation of DNA strands - DNA is heated to 95ºC to separate the two strands.

2. Binding of primers - temperature reduced to 53ºC which allows primers to bind to DNA next to the sequence to be copied.

3. DNA replication - temperature increased to 73ºC the optimum temperature for Taq polymerase allowing both strands to be replicated.

This is repeated. The number of strands doubles for each round of replication: 1->2->4->8->16->32

D1.1.4—Name the tool that is used for separating DNA. It is carried out in an agarose gel, in an electrophoresis chamber, to which has an electric field applied.

Gel electrophoresis.

D1.1.4—On which basis are DNA fragments separated in gel electrophoresis?

Large, heavy, uncharged particles move the least. Small, light, charged particles move the most easily and therefore furthest. Intermediate particles are in the middle. A characteristic banding pattern is produced.

D1.1.4—Do DNA fragments move towards the positive or negative electrode? Give a reason.

Positive, DNA is negatively charged due to the phosphate group.

D1.1.5—Explain how a genetic fingerprint would be produced.

1. DNA sample is taken from person or scene.

2. PCR is used to amplify the sample, and primers are used to promote the amplification of around 15 short tandem repeats (STRs)

3. Gel electrophoresis is used to create a pattern of bands from the STRs which is likely to be highly unique to the individual.

D1.1.5—Name two applications of PCR and gel electrophoresis.

Forensic investigations, paternity testing.

D1.1.5—NOS: Reliability is enhanced by increasing the number of measurements in an experiment or test. In DNA profiling, how can we increase reliability and reduces the probability of a false match.

Increasing the number of markers used.

D1.2.1—What do we call the synthesis of RNA using a DNA template

Transcription.

D1.2.1—Name the enzyme needed for transcription.

RNA polymerase

D1.2.1—Describe the steps in transcription.

1. RNA polymerase binding - it binds to a promoter sequence on the DNA at the start of the gene.

2. Unwinding and unzipping - RNA polymerase unwinds the DNA and separates it into two single strands, exposing the bases.

3. RNA nucleotide base pairing - RNA polymerase pairs up free RNA nucleotides to DNA nucleotides on the template strand by complementary base pairing.

4. Formation of RNA backbone - RNA polymerase links adjacent RNA nucleotides with covalent bonds between the pentose sugar of one nucleotide, and the phosphate of the next.

5. mRNA separation - The assembled RNA strand separates from the template DNA strand.

6. Re-winding and re-zipping - DNA winds back into a double helix.

D1.2.2—DNA has one strand which is used to make mRNA, and a second. What do we call these two strands.

Template DNA strand - makes mRNA

Sense DNA strand - is not used to make mRNA

D1.2.2—What process is used to make a complementary copy of the DNA template?

Complementary base pairing. A-U, T-A, G-C, C-G.

D1.2.3—Explain how the structure of DNA templates is so stable, and explain why this is important.

Stable structure - bases of each strand are linked by strong covalent bonds, when the two strands are separated these covalent bonds (and so the base sequence they hold) do not change and are conserved.

Importance - the base sequence of a gene rarely changes during transcription, one gene can be transcribed many times (in the case of brain cells, which do not carry out cell division, but need to make proteins for a person's life).

D1.2.4—Transcription as a process required for the expression of genes. What does gene expression mean?

A gene is expressed when the information it holds is used and an observable characteristic is generated within a cell or organism.

D1.2.4—Are all genes expressed in all cells at the same time.

No, each cell should only express the genes it needs, when they need them.

D1.2.4—Name the steps in expression of an enzyme.

Transcription --> Translation --> Polypeptide (which acts on substrate) --> Product.

D1.2.4—In which of the steps of gene expression is a gene most likely to be switched off.

Transcription - this can be switched on / off.

D1.2.5—Name the process where the base sequence of mRNA is translated into the amino acid sequence of a polypeptide.

Translation

D1.2.6—Which type of RNA is a complementary copy of the template DNA (usually a gene), and contains a series of codons.

mRNA (messenger RNA).

D1.2.6—Which type of RNA are present in the cytoplasm in large numbers. They have a triplet of bases called an anticodon and carry the amino acide corresponding to the anticodon

tRNA

D1.2.6—Describe three features of the ribosome.

They have two subunits (small and large).

Small subunit - has a binding site for mRNA.

Large subunit - has three binding sites for tRNA (A,P,E) but only two tRNA can bind simultaneously; the large subunit also has a catalytic site for making peptide bonds.

D1.2.6—Describe the functional roles of the A, P and E sites (HL only, but useful for SL to know to visualise what is happening).

A site - where each tRNA initially attaches

P site - where the amino acid attached to the tRNA is added to the growing polypeptide chain.

E site - exit point for the tRNA moleucle after it has transferred its amino acid.

D1.2.7—What do we call three bases which code for a specific amino acid in mRNA?

Codon

D1.2.7—What do we call three bases which code for a specific amino acid in tRNA?

Anticodon

D1.2.7—Name three places where complementary base pairing is used.

DNA replication

Transcription od DNA to RNA

Matching of codons and anticodons in translation

D1.2.8—How many amino acids are there?

20

D1.2.8—The genetic code has more than one codon for each amino acid. What word describes this feature of the genetic code?

Degenerate.

D1.2.8—All organisms with a few exceptions share the same genetic code. What word describes this feature of the genetic code?

Universal - this means we can put a gene from a human into a bacteria and the bacterium will transcribe and translate it into the same protein as a human cell would.

D1.2.9—Using a table of mRNA codons, deduce the sequence of amino acids coded for by an mRNA strand with sequence CACAGAUGGGUC

histidine, arginine, tryptophan, valine

D1.2.9—Using a table of mRNA codons, deduce possible codons for the amino acid glutamine.

CAA CAG

D1.2.10—Name the three parts of translation.

Initiation ("beginning"): in this stage, the ribosome binds with the mRNA and the first tRNA so translation can begin.

Elongation ("middle"): in this stage, amino acids are brought to the ribosome by tRNAs and linked together to form a chain (SL focuses on this step).

Termination ("end"): in the last stage, the finished polypeptide is released to go and do its job in the cell.

D1.2.10—Describe the elongation stage of translation (we are less interested in initiation and termination at SL) by the stepwise movement of the ribosome along mRNA and linkage of amino acids by peptide bonding to the growing polypeptide chain

We start our description of elongation with a tRNA attached to a growing chain of amino acids bound to the P site.

1. new tRNA binding - a tRNA molecule, with specific anti-codon, binds to the open A site on the large subunit.

2. Peptide bond formation - the tRNA molecules in sites A and P bring amino acids adjacent and these are bonded by a peptide linkage by a catalytic site on the large subunit.

3. Stepwise movement of the ribosome - the tRNA in the A site moves to the P site, the tRNA in the P site moves to the E site where it detaches and exits the ribosome without an amino acid.

4. Steps 5-7 are repeated until the polypeptide is fully transcribed.

D1.2.10—What do we call the structure where multiple ribosomes are bound to the same mRNA molecule allowing many copies of the same polypeptide can be made at the same time.

Polysome (not sure if you need to know this).

D1.2.11—Describe how a point mutation in a gene can create a large change in protein structure.

If the codon changes from a hydrophilic amino acid to a hydrophobic one, or vice versa.

D1.2.11—Describe how a point mutation in a gene might create no change in protein structure.

If the codon changes but still codes for the same amino acid (same-sense mutation).

D1.3.1—What do we call structural changes to genes at the molecular level?

Mutations.

D1.3.1—What type of mutation is it when one or more extra nucleotides are inserted into the DNA of the gene?

Insertion

D1.3.1—What type of mutation is it when one or more nucleotides are removed from the DNA of the gene?

Deletion

D1.3.1—What type of mutation is it when one base is replaced by another base, changing one codon into a different one?

Substitution / point mutation

D1.3.2—Describe the three possible consequences of base substitutions.

1) neutral—no effects - because they affect non-coding DNA; or they are same-sense mutations, or they change a codon to another amino acid with a very similar properties.

2) deleterious (causing harm)—the most harmful mutations are lethal (cause death) e.g. they code for a nonsense mutation, or mis-sense mutation.

3) beneficial—these are far rarer than neutral and deleterious mutations.

D1.3.2—A base substitution will change one codon into another codon. Describe the three types of mutation that arise from this.

Same-sense (synonymous) mutations, Nonsense mutations or

Mis-sense mutations.

D1.3.2—If a base substitution mutation spreads by inheritance

until 1% or more of the population has it, then it is considered to be a single nucleotide polymorphism (SNP). This only happens if the consequences of the mutation have what consequence?

Neutral or beneficial.

D1.3.2—What type of base substitution mutation changes one codon for an amino acid into another codon for the same amino acid, and are possible because of the redundancy of the genetic code. They do not affect the phenotype.

Same-sense (synonymous) mutations

D1.3.2—What type of base substitution mutation changes a codon for an amino acid into a stop codon (ATT, ATC or ACT). Translation is therefore terminated before a polypeptide has been completed. The resulting protein is unlikely to function properly. The consequences depend on what the protein's function is.

Nonsense mutations

D1.3.2—What type of base substitution mutation changes a codon for one amino acid into a codon for a different amino acid. One amino acid in the polypeptide is therefore different.

This may not have much effect if the new amino acid has a similar structure and chemical properties to the original one (a synonymous substitution) or if it is positioned in part of a protein that is not critical in terms of function.

Mis-sense mutations can also have severe and even lethal effects. Many genetic diseases are due to missense mutations, for example sickle cell disease. A very small proportion of mis-sense mutations have a beneficial effect.

Mis-sense mutations

D1.3.3—Describe the consequences of insertions and deletions if 1,2,4,5 or another number of nucleotides which is not a multiple of 3 is inserted or deleted.

These create frameshift mutations where the reading frame is changed, so every codon is changed from the mutation point onwards.

The likelihood is that this will cause significant changes to the structure and function of the polypeptide.

D1.3.3—Describe the consequences of insertions and deletions if 3, 6 or another number of nucleotides which is a multiple of 3 is inserted or deleted.

These mutations where there are additional codons added or deleted, so amino acids are added or deleted.

This will likely cause significant changes to the structure and function of the polypeptide, even if only one amino acid is added or deleted.

D1.3.4—Name three causes of gene mutation

a) Errors in DNA replication or repair.

b) Chemical mutagens e.g. nitrosamines (cigarettes), benzene (solvent used in industry), mustard gas (gas used as chemical weapon).

c) Mutagenic forms of radiation e.g. gamma rays, x-rays, beta particles, medium and short-wave ultraviolet radiation (in sunlight).

D1.3.5—What doe we call random changes that can occur in any

gene of any cell.

Mutations.

D1.3.5—Is there any natural mechanism which is known for making a deliberate change to a particular base with the purpose of changing a trait.

No.

D1.3.5—Mutation is random, however some bases have a higher probability of mutating than others. Give four examples of this.

a) Changes between bases which are chemically similar: C and T (single-ringed pyrimidines), A and G (double-ringed purines).

b) Adjacent bases: An adenine between G and G (GAA) mutations much less frequently than a cytosine (ACG).

c) CpG sites and islands: Where C is followed by a G, and the C is methylated, the C can mutate into a T. CpG islands are where these hotspots repeat.

d) Function of DNA: i) protein-coding sequences have a higher average mutation rate than non-coding sequences, presumably because of differences in how these sequences are used within a cell. ii) Satellite DNA has a high mutation rate.

D1.3.6—Somatic cells are body cells which cannot develop into gametes, therefore their genes (and any mutations to those genes) are not inherited. Name two consequences of a mutation to somatic cells.

a) Nothing - that cell may be damaged or killed but only that one cell is affected and it can be replaced.

b) Cancer - if the mutation affects genes that control the cell cycle, it can cause uncontrolled cell division and tumor formation which can become cancerous.

D1.3.6—Germ cells are gametes or cells that can produce gametes. Name a consequences of a mutation to somatic cells.

All cells in the organism will be affected - the gamete will become part of a zygote and every cell in the organism will be formed from that zygote and so every cell in the body will inherit it.

D1.3.7—What is the original source of all genetic variation, and so they are essential long-term in a species for evolution by natural selection.

Gene mutation (although beneficial mutations are much rarer than neutral or harmful ones).

D1.3.7—NOS: Commercial genetic tests can yield information about potential future health and disease risk. Give two benefits and two disadvantages of this information.

Adv

1) Can make lifestyle choices to decrease their risk of that specific disease

2) Can have preventative surgery e.g. mastectomy.

Disadv

1) Anxiety - without expert interpretation, this information could be problematic to people receiving this information.

2) Expensive insurance.