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BABS1201 - Test 2 Flashcards

fuckin learn? idk

1
Q

Explain the semi-conservative model of DNA replication

A
  • Parental strands that are unzipped to create two template strands
  • The template strands create daughter strands which are semi-conservative because each strand is made up of old, conserved strands of DNA
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2
Q

Describe the basic steps involved in the process of DNA replication

A

Remember: Always synthesized from 5’ to 3’ direction!

In eukaryotes

Leading strand (made continuously):

  1. Replication begins at multiple origins where replication bubbles will merge - topoisomerase relieves strain by unwinding ahead of the replication fork
  2. Helicase unzips the DNA strands to create a replication fork
  3. Priming: Primase starts the process - makes a small piece of RNA called a primer that marks the starting point for the construction of a new strand of DNA
  4. Elongation: DNA polymerase binds to the primer and makes the new strand of the DNA - can only add bases from 5’ to 3’ ends

Lagging strand
1. Fragments called Okazaki fragments are started with RNA primers

  1. DNA polymerase adds a short row of DNA bases in 5’ to 3’
  2. A primer is added further down the lagging strand, another Okazaki fragment is made and the process repeats again

End of both strands
1. Exonuclease removes all RNA primers from both strands

  1. DNA polymerase fills the gaps with DNA bases
  2. DNA ligase seals up the fragments of DNA in both strands to form continuous double-strands
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3
Q

Describe the function of major enzymes involved in DNA replication

A

Helicase - unzips DNA

Single-strand binding protein - binds to and keeps strands separate

Topoisomerase - relieves overwinding strain ahead of replication

Primase - synthesises an RNA primer

DNA pol III - adds nucleotides to RNA primer or pre-existing DNA strand

DNA pol I - removes RNA primers and replaces with DNA nucleotides
- fills gaps between Okazaki fragments

DNA ligase
- the glue - seals remaining gaps

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4
Q

What are the requirements of DNA polymerase?

A
  • must have a 3’ OH group to add on to
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5
Q

What prevents the loss of DNA in linear eukaryotic chromosomes?

A
  • telomeres!
  • TTAGGG
  • they carry RNA which is used as a template to lengthen the ends of chromosome
  • extends out longer than necessary so if it is broken, important DNA is unaffected
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6
Q
  1. Explain the difference between a genes, chromosome and chromatin
A

Gene - segments of DNA that code for a specific molecule (typically a protein)

Chromosome - structures within cells that contain a person’s genes

Chromatin - a mixture of DNA and proteins that form the chromosomes

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7
Q

Describe the way DNA is packaged within a cell

A
  1. DNA wraps around proteins called histones. Done in groups of eight called an octamer of histones
  2. They form tight loops to create nucleosomes
  3. Many nucleosomes coil and stack to form chromatin fibres
  4. Chromatin fibres loops and folds again to form chromosomes (which prevents tangling and damage
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8
Q

Explain the process of binary fission, what is it?

A
  • type of asexual production in unicellular eukaryotes of prokaryotes
  • when parent cell splits into two identical daughter cells that are genetically identical
  1. DNA replication commences at origin of replication
  2. Two copies of the origin are separately attached to either end of the plasma membrane - this ensures the chromosome is moved into two daughter cells
  3. Cell elongates and plasma membrane pinches inwards in the middle
  4. A new cell wall is deposited and two daughter cells are made (one with each copy of the chromosome)
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9
Q

Provide an overview of the cell cycle

A

Two phases :

Interphase - growth and replication of cellular components

Mitotic phase - when the cell divides its copied DNA and cytoplasm to make two new cells

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10
Q

Explain the process of mitosis in animal cells, what is it?

A
  • the process of one cell dividing to form two identical cells (for growth and to replace worn out/damaged cells)

Mitosis in animal cells
1. G2 of interphase
- DNA has not yet been condensed into chromosomes (spaghetti-looking DNA)

  1. Prophase
    - DNA begins to be condensed and packed down
    - individual chromosomes start to become more visible
    - spinders begin to extend from centrosomes
    - asters surround centrosomes
    - centrosomes begin to move away from each other - at opposite ends of the cell
  2. Prometaphase
    - nuclear membrane is degraded
    - chromosomes are freed
    - centrosomes move to opposite poles of the cell
    - spindle fibers attach to centromeres, to their kinetochores
  3. Metaphase
    - spindle fibers extend from centrosomes at opposite poles
    - all chromosomes are lined up on the equator (metaphase plate)
    - spindle fibers exert the same amount of pressure which puts chromosomes in the middle of the cell
    - checkpoint! - the cell will not continue to the next phase until every single chromosome is lined up at the equator
  4. Anaphase
    - protein chews through the centre of chromosomes to release them
    - the pulling pressure applied from end of the cell splits the sister chromatids and they end up at opposite poles
  5. Telophase
    - the middle pinches in to form two new daughter cells
    - cell is separated into two and they begin to decondense
  6. Cytokinesis
    - division of cytoplasm
    - a cleaveage furrow appears first (comprised of a contracting ring of actin microfilaments and myosin)
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11
Q

Explain mitosis in a plant cell

A

Everything is the same, except for the cytokinesis phase
- has a cell plate form (instead of cleavage furrow)
- a cell plate is formed mid-cell at the end of telophase

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12
Q

What is apoptosis?

A
  • programed cell death
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13
Q

Explain the process of meiosis, what is it?

A
  • when the cell divides twice to form four daughter cells (2n to n)
  • produces sex cells (gametes)
  • they only have half the number of chromosomes in the parent cell and are haploid (single-set)

Numerical process: 2n, 4n, 2n, n

Meiosis inhumans
- somatic cells have 46 chromosomes
- 23 from mum, 23 from dad, hence are diploid (two sets)
- gametes have half this number (n), and are haploid

Meiosis I

  1. Interphase
    - growth and replication of chromosomes
  2. Prophase
    - chromosomes are duplicated
    - pair of homologous chromosomes in diploid parent cell
    - sister chromatids produced
    - crossing over (some parts of chromosomes swap parts for genetic diversity)
  3. Metaphase I
    - pairs of chromosomes line up at the metaphase plate
    - Mendel’s Second Law of Independent Assortment
  4. Anaphase I
    - pairs of homologous chromosomes are separated
    - sister chromatids remain attached at the centromere
    - Mendel’s First Law of Segregation
  5. Telophase I
    - splitting of cells to create two haploid cells

Meiosis II

  1. Prophase II
    - chromosomes and spindles start to form
  2. Metaphase II
    - single file line down metaphase plate
  3. Anaphase II
    - chromosomes split into sister chromatids by spindle fibres
  4. Telophase and Cytokinesis
    - 4 haploid daughter cells genetically different from the parent cell
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14
Q

Describe the genetic code

A

gene expression - the process by which the information encoded in a gene is used to dictate the assembly of a protein molecule

  • DNA is transcribed in messenger RNA (mRNA) using base pairing
  • mRNA is translated into a protein through a triplet code
  • 4 bases to code for 20 amino acids
  • a universal language
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15
Q

Explain how the instructions contained within DNA are transcribed into RNA

A
  • DNA contains the instructions for how a cell will function
  • proteins perform these functions
  • RNA is the intermediary
  • central dogma: DNA -> RNA -> Protein
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16
Q

Define the three stages of transcription (plus after mRNA transcription)

A
  • only one strand of the DNA is used as the template for mRNA synthesis

Stage 1: Initiation
RNA polymerase: binds to the promoter region (which marks where transcription starts)
- unwinds DNA strands
- initiates RNA synthesis
- makes a complementary RNA copy of the DNA sequence from the template strand
- transcribes DNA into RNA - mRNA

Stage 2: Elongation
- RNA polymerase moves downstream, unwinding the DNA and elongating the RNA transcript
- as soon as it is transcribed, the DNA forms a double helix

Stage 3: Termination
- RNA polymerase transcribes a terminator sequence which signals the end of the gene
- RNA polymerase detaches from the DNA and transcript is released

After transcription:

  1. mRNA processing
    - before export from the nucleus, mRNA are protected by the addition of a 5’ cap and a poly(A) tail
  2. Splicing
    - only occurs in eukaryotic cells
    - contain intervening sequences (intron) in the middle of expressed sequences (exons)
    - introns are spliced out before the mRNA leaves the nucleus (can be spliced in different ways to produce different proteins from the same gene)
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17
Q

State the main differences in gene expression between bacteria and eukaryotes

A

Bacteria
- transcription and translation occur simultaneously in the cytoplasm
- mRNA translated directly into protein

Eukaryotes
- transcription in the nucleus
- translation in cytoplasm

Initiation in eukaryotes
- TATA box -
- proteins called transcription factors mediate the initiation of transcription (an additional control for gene expression)

18
Q

Explain the process of translation and relate it to cell function and the role of ribosomes

A

Ribosome - assembles amino acids into a polypeptide chain based on the mRNA sequence
- made out of RNA and proteins and consists of two sub-units
- has sites for binding tRNAs
- A site for aminoacyl-tRNAs
- P site for peptidyl-tRNAs

Translation overview
- tRNAs carrying their amino acids move to the ribosome
- base-pair with mRNA
- place amino acids in correct sequence to form the protein coded in the mRNA (and hence in DNA sequence)

19
Q

Describe the basic structure and function of tRNA and ribosomes

A
  • one long molecule that has been folded to produce a particular shape to fit perfectly into the ribosome factory
  • amino acid is attached to one end of the tRNA
  • other side has an anticodon loop that pairs with the mRNA codon
  • separate tRNA for every amino acid
  • three sites - A, P and E
  • mRNA transcript runs between small and large units (like a conveyor belt with instructions)
  • A site = acceptor site, has a spot for incoming tRNAs
  • P site = holds the growing polypeptide chain
  • E = exit site - ejects the last tRNA to create an empty spot to move the process along

Aminoacyl-tRNA synthase
- synthesises a link between amino acids and tRNAs

20
Q

Describe the three main stages of translation

A

Stage 1: Initiation
- small sub-units binds the mRNA and the initiator tRNA
- large sub-unit then binds with the initiator tRNA in the P site
- 5’ to 3’ direction

Stage 2: Elongation
- 2 GTP is used up in codon recognition

  1. Codon recognition
  2. Peptide bond formation
    - New tRNA moves into A site
    - The tRNA in the P site attaches onto the peptide bond of the new tRNA
  3. Translocation
    - Old tRNA is moved into the E site and is ejected, new tRNA is moved into P site

Stage 3: Termination
- no tRNAs bind

  1. When a stop codon occurs in mRNA, it is recognised by a protein called a release factor
  2. Causes the last tRNA to leave the ribosome and the newly synthesised protein is released
  3. The ribosome sub-units separate (to be reused), the mRNA is released
21
Q

Explain the main differences between control of gene expression in bacteria and eukaryotes

A

Prokaryotes
- control of gene expression occurs at level of transcription, i.e. whether a gene is transcribed or not

Eukaryotes
- occurs at many more levels
- most important is at transcription, but can occur in processing, transport and degradation of the mRNA
- proteins can be modified, transported and degraded
- lifespan of mRNA molecules in the cytoplasm is important in determining the pattern of protein synthesis in a cell (eukaryotic mRNA is longer lived than prokaryotic mRNA)
- final opportunities for control occur after translation
- regulation might occur at any steps
- lifespan of each protein in the cell is regulated by selective degradation

22
Q

Describe the PCR including steps involved

A
  1. DNA with sequence of interest (target sequence)
  2. Denaturation at 95 celsius to separate strands
  3. Extension at 72 degrees
    - annealing occurs (primers are attached)
    - DNA synthesis
  4. More DNA polymerase (Taq polymerase) is added
    - each cycle doubles the previous amount sequenced

Electrophoresis
- DNA has a negative charge, therefore it moves towards the positive electrode
- separates DNA based on size
- electric current pulls DNA through the gel
- short molecules move faster and migrates farther (gets pulled down )

Visualising the DNA
- stain - fluorescent under UV when bound to DNA

23
Q

List applications of PCR

A
  • Disease testing (e.g. COVID)
  • paternal testing
  • disaster identification
  • crime (forensics)
  • historical cases
24
Q

Define mutation and mutagen in biological terms

A

mutation - a change in the nucleotide sequence of an organism’s DNA or in the DNA/RNA of a virus

mutagen - a chemical, biological or physical agent that interacts with DNA that can cause a mutation

25
Q

List and describe different types of mutations

A

Point mutations - change in a single nucleotide within a DNA sequence
1. Substitution of a base (different base)
2. Insertion of a base (extra base added)
3. Deletion of a base

Nucleotide mutations
1. Insertion
2. Deletion
3. Duplication of a sequence

Small-scale mutations
1. silent mutation - change in base creates the same protein
2. missense mutation - produces a different amino acid than usual on the polypeptide chain
3. nonsense mutation - creates a premature stop (stop codon), no protein is produced
- conservative - substituted amino acid has similar chemical proteins to original amino acid
- non-conservative - has different chemical properties
4. frameshift mutation - addition/deletion causes a shift in reading frame of mRNA (can cause other mutations to occur)

Large-scale mutation - occurs in larger regions of a chromosome (in chunks)
1. deletion - loss of a chunk
2. inversion - pieces of chromosome break apart, inverts and reattaches in opposite orientation but on same chromosome
3. duplication - identical chunk is added
4. translocation - a chunk breaks off and attaches or switches with another chunk of another chromosome

Sets of chromosomes
1. polyploidy - normally diploid cells acquire one or more additional sets of chromosomes (results in triploid or tetraploid sets)
2. aneuploidy - an abnormal number of only one chromosome

26
Q

Describe the way in which various mutations may arise

A

induced mutations - caused by external mutagens, e.g. physical (e.g. UV), chemical (e.g. tobacco) or biological (e.g. virus) mutagens

spontaneous mutations - arise in the absence of any specific external mutagens and are a result of natural cellular processes (e.g. from mistakes by DNA, spontaneous changes in structure of a nucleotide, unrepaired DNA damage from metabolites naturally produced)

27
Q

Describe a mechanism by which DNA can be repaired

A

Pyrimidine dimer function
- form when thymine or cytosine nucleotides covalently bond in adjacent bases, causing DNA damage (caused by UV radiation from the sun)

Nucleotide excision repair of DNA damage
1. damage recognition - specialised proteins bind to distorted DNA, marking it for repair
2. incision - endonucleases make cuts on both sides of damaged DNA and cuts it out
3. gap filling - DNA polymerase fills in gap
4. ligation - sealed by DNA ligase

28
Q

How do DNA changes lead to genomic diversity and the process of evolution?

A
  • some mutations occur in egg and sperm cells which creates hertiable variation
  • without heritable variation, natural selection cannot occur
29
Q

Provide examples of how DNA changes can be good or bad

A

Sickle cell anemia
Peppered moth

30
Q

Describe Mendel’s Laws

A

First Law: law of segregation (anaphase)
- alleles segregate into separate gametes, so that each gamete carries only one allele for each gene (one allele from each parent)

Second law: law of independent assortment (metaphase)
- genes located on different chromosomes assort independently of each other
- inheritance of one trait is independent of another trait
- only applies if different genes are on different chromosomes

31
Q

Explain the basis of inherited characteristics (the definition of phenotype and genotype)

A
  • centres on the transmission of genetic information from parents to offspring
  • we have 23 pairs of chromosomes
  • 22 of these pairs are autosomes
  • 1 of these pairs are our sex chromosomes

phenotype - refers to an individual’s observable traits
genotype - refers to the genetic makeup or set of genes that an individual organism possess

32
Q

Explain the factors contributing to genetic diversity

A
  1. segregation (Mendel’s first law)
  2. independent assortment (Mendel’s second law) of alleles during meiosis
  3. random fertilisation - genetic recombination in meiosis
  4. crossing over
    - leads to the recombination of genetic information
33
Q

Describe how Punnett squares and cross-analysis are used to predict genetic inheritance patterns (dihybrid, monohybrid and test crosses)

A

Dihybrid cross - appears in 9, 3, 3, 1 ratios
- dihybrid - cross involving individuals that are heterozygous for two traits

Monohybrid cross - appears in a 3 to 1 ratio
- monohybrid - cross involving individuals that are heterozygous for one trait

Testcross - involving a homozygous recessive individual of unknown genotype to determine the unknown’s genotype

34
Q

Explain the varied modes of inheritance in different organisms

A
  • using pedigrees
  • squares = males
  • circles = females

Autosomal recessive inheritance
- may skip one or more generations
- no gender bias

Autosomal dominant inheritance
- present in every generation
- no gender bias

X-linked recessive inheritance
- males more likely to be affected
- some generations skipped
- mothers pass to sons and daughters
- fathers only pass to daughters

X-linked dominant inheritance
- affected males pass the condition to all daughters but no sons
- affected mothers pass to sons and daughters
- present in every generation

Y-linked dominant inheritance
- only in males
- passed from father to son
- every affected male has an affected father

35
Q

Explain examples of extension of Mendelian principles

A

Incomplete dominance
- neither allele is dominant
- when an organism is heterozygous, both alleles contribute to the phenotype (e.g. creates mixes in colour in snapdragons)

Co-dominance
- both alleles are seen (e.g. roan cows)

Multiple alleles
- inheritance that involves more than 2 alleles for a trait (e.g. blood types)

Polygenic traits
- traits that are influenced by many genes (e.g. skin colour)

36
Q

Explain examples of challenges of Mendelian principles

A

Mitochondrial inheritance
- the maternal inheritance of mitochondrial genes

Epistasis
- when phenotypic expression of a gene at one locus alters that of a gene at a second, different locus (e.g. labradors)

Pleiotropy
- when a single gene influence multiple traits or characteristics (e.g. sickle cell alleles)

Polygenic inheritance
- when mulitple genes affect only single characteristic/trait

Genetic linkage
- alleles located close together on the same chromosome tend to be inherited together more frequently (they are less likely to be separated during meiosis)

Alternation in chromosome number or structure
- nondisjunction
- when chromosomes aren’t distributed to the poles as expected in meiosis I or II, resulting in an abnormal number chromosomes
e.g. aneuploidy - abnormal number of chromosomes in a cell (i.e. Down syndrome)

Multifactorial disorders
- some traits are dubbed complex because a complicated combinations lead to the phenotype
- environment has significant influence

Environment
- gene expression can be modified by interaction with the environment (e.g. Himalayan rabbit, hydrangeas)

37
Q

Explain evolutionary forces that influence population genetics using the Hardy-Weinberg model

A

The Hardy-Weinberg equilibrium describes a population that is not evolving

It assumes
1. no selection
- individuals that possess traits that offer advantages in their environment are more likely to survive and reproduce
- leads to adaptation
2. no mutation
3. a large population
- if small, chance events lead to changes in allele frequency, e.g. the bottleneck effect to the founder effect (subset of original population is isolated)
4. random mating
- individuals choose mates on the basis of phenotype (not randomly)
- because of sexual selection or human intervention in selective breeding
5. migration
- gene flow - the movement of alleles from one population to another through the migration of individuals and subsequent mating with members of the recipient population
- can occur without migration, e.g. pollen in seeds like in dandelions

Calculating allele frequency
- count all dominant alleles (as individuals, not in pairs)
- count all dominant alleles (as individuals, not in pairs)
- divide number of dominant/recessive alleles over total number alleles

38
Q

What are the component of a typical amino acid?

A

amino group, carboxyl group, variable R-group

39
Q

What is the role of tRNA in translation?

A
  • to carry amino acids and recognise the start codon
40
Q

What is the difference between homozygous and heterozygous?

A

Homozygous - when the same version of a gene is inherited from a parent

Heterozygous - when a different version of a gene is inherited from each parent.

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