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Flashcards in Unit 5 Deck (89):
1

What does ATP stand for

Adenosine triphosphate

2

What type of reaction is the synthesis of ATP

Condensation as it produces water

3

What type of reaction is the metabolism of ATP

Hydrolysis as it uses water to split the molecule, removing the terminal phosphate.

4

What is ATP used for in the cell?

Active transport (mineral uptake in root hair cells, absorption of AA's in PCT of kidney)
Anabolic reactions (protein synthesis from AA's, building polysaccharides from monosaccharides)
Mechanical work (muscle action, ciliary action, spindle action in nuclear division)

5

What are the stages of the biochemistry of respiration?

1- Glycolysis
2- Link reaction
3- Krebs cycle
4- ETC

6

Glycolysis

Glucose is converted into fructose bisphosphate, during this two molecules of ATP are converted into two molecules of ADP.
Then the fructose bisphosphate is converted into two molecules of triose phosphate. Each molecule of triose phosphate is converted into a molecule of pyruvate- during this two molecules of ATP are produced and a molecule of NADP is produced (with help from dehydrogenase enzymes catalysing dehydrogenation) per molecule of pyruvate produced.

7

Link reaction

Each molecule of pyruvate undergoes oxidative decarboxylation (releasing a molecule of CO2 and NADH) to produce a molecule of acetate, which reacts with coenzyme A (CoA) to produce acetyl CoA.

8

Krebs cycle

Acetyl CoA reacts with oxaloacetate to produce a molecule of citrate, which undergoes decarboxylation and dehydrogenation to produce a molecule of NADH and oxoglutarate, which under goes triple decarboxylation (making two NADHs and a FADH2) and substrate level phosphorylation to produce ATP and an oxaloacetate molecule. Cycle turns twice per glucose molecule.

9

Electron transport chain

Carriers:
!= ATP produced by oxidative phosphorylation
For NADH
NAD-NADH-!-flavoprotein-r.flavoprotein-CoQ-r.CoQ-!-cytochromes-!-r.cytochromes-cytochrome oxidase producing water

For FADH2
CoQ-r.CoQ-!-cytochromes-!-r.cytochromes-cytochrome oxidase producing water

10

How many molecules of ATP are produced per molecule of glucose

38
2 from glycolysis, 2 from Krebs and 34 from ETC

11

How are leaves adapted for ps

Palisade mesophyll cells directly under upper surface of the leaf- densely packed with chloroplasts maximising light absorption in chloroplasts
Spongy mesophyll cells lie underneath the palisade mesophyll which contain numerous air spaces forming a continuous pathway with the stomata facilitating gas exchange

12

What are the pigments in a chloroplast?

Chlorophyll-a, chlorophyll-b and carotene

13

Light harvesting

There are antenna complexes in the membrane of the thylakoids in the chloroplasts. Incident light reaches the antenna complex and the energy is funnelled toward the chlorophyll-a molecule in the reaction centre via accessory pigments by resonance transfer.
Energy causes the photo activation and emission of an electron from the primary pigment.

14

Light dependant reaction

The photolysis of water produces oxygen (waste) and protons. The electron released from the photosystem/antenna complex is accepted by an electron acceptor and then travels down an ETC by a series of redox reactions along cytochromes forming the carriers in the chain itself in progressively lower energy levels. As the electron loses energy while travelling down the ETC at a certain point enough energy is released to cause the photophosphorylation of adenosine diphosphate to form adenosine triphosphate. The electron the enters photosystem 1 and is emitted and subsequently accepted by an electron acceptor. The electrons combine with the protons to form hydrogen which combines with NADP to form NADPH

15

DNA

Deoxyribonucleic acid

16

RNA

Ribonucleic acid

17

Gene

A length of DNA that codes for a particular polypeptide

18

Description of DNA

Non overlapping each triplet read once
Degenerate each AA may be produced from more than one triplet
Three base

19

Why can't DNA be used for protecting synthesis directly?

It is too large to leave the nucleus
It is safer to keep it in the nucleus where it is better protective from damage as it the molecule of inheritance so it's important to protect
DNA can produce several copies of RNA allowing for more proteins to be produced simultaneously

20

Transcription

The two strands of DNA are separated by DNA helicase using energy from ATP
The RNA polymerase attaches near the beginning of the gene to be transcribed
The template strand is used for mRNA production. The RNA polymerase moves along the template strand attaching complementary ribonucleotides by the process of complementary base pairing
As the RNA polymerase moves along the DNA it reforms behind it- when the RNA polymerase reaches the end of the gene it releases the newly formed mRNA

21

Introns

Non coding regions of a gene

22

Exons

Coding regions of a gene

23

Translation

The mRNA contains a series of base triplets called codons. The ribosomes contain two sites, the aminoacyl site at and the peptidyl site, where the peptide bonds between adjacent amino acids are formed, this requires ATP. The first two codons enter the ribosome. The starting codon is AUG at the peptidyl site and the second at the A site. Then tRNA molecules carry complementary anticodons with corresponding amino acids and join with the complementary codon at the p site, then at the a site. tRNA is a single strand of DNA shaped like a clover with a specific anticodon and an amino acid. Then the ribosome moves along the mRNA by one codon, and the next codon enters at the A site. The tRNA is released and will travel to the cytoplasm to get another amino acid. This repeats until the ribosome reaches a stop codon.

24

Epigenetics

The study of the changes in gene expression that do not involve changes to the base sequence of the DNA. Caused by changes in the cell environment so that some genes are on and others are off.

25

Monohybrid inheritance

The inheritance at one gene locus, single charcteristic

26

Gene

Length of DNA that codes for a particular trait

27

Genetic Locus

The position of a gene on the chromosome

28

Allele

An alternative form of a gene

29

Dominant allele

An allele that has its instruction followed in the heterozygous condition

30

Recessive allele

An allele that has its instruction followed in the homozygous condition

31

Hereditiy

The transfer of genetic factors from one generation to the next.

32

Mendel's First Law

When any individual produced gametes, the alleles separate so that each gamete receives only one allele. Explained by anaphase 1 of meiosis.

33

Dominance

The heterozygote has the same phenotype as the homozygous dominant phenotype.

34

Codominance

The interaction of genes results in heterozygote with its own distinctive phenotype.

35

Lethal allelic combination

One allele in the heterozygous state causes death at an early age.

36

Multiple alleles

More than 2 alleles of a gene are possible.

37

Sex linkage

The gene and its alleles are located on a sex chromosomes most often the X chromosome.

38

Autosomal Recessive

Parents of an affected individual may not be affected.

39

X-linked recessive

More common in males, for a female to be affected the father must be affected. An affected female will pass the trait on to her sons.

40

Autosomal dominant

At least one parent must have been affected

41

X-linked dominant

At least one parent must be affected, an affected father passes it on to his daughters

42

Mendel's Second Law

The segregation of the alleles of a gene is independent of the segregation of the alleles of another gene. Explained by the random assortment of homologous pairs of chromosomes at the equator during metaphase 1 of meiosis, and the subsequent separation in anaphase 1.

43

Polygenic inheritance

More than 2 alleles are involved.

44

Epistasis

One gene influences the expression of another gene.

45

Dihybrid inheritance

The inheritance of alleles at 2 loci.

46

What are the characteristics that all animals share?

Eukaryotic, multicellular, heterotrophs lacking cell walls and chloroplasts.

47

What are the phyla that make up the kingdom Animalia?

Phylum Cnidaria, Phylum Platyhelminthes, Phylum Annelida, Phylum Arthropoda, Phylum Cordata

48

Cnidaria

Radially symmetrical, responds to environment through 360 degrees
Sac like enteron with only one entrance a mouth through which food may be ingested and undigested food egested.
Tentacles contain stinging cells (cnidicysts) to catch food which is then brought to the mouth.
Body supported by surrounded aqueous medium, and a hydrostatic skeleton formed by the fluid filled enteron.
Mvt limited, largely dictated by ocean currents (jellyfish) while Hydra can undertake cartwheels.

49

Platyhelminthes

Bilaterally symmetrical, dorsoventrally flattened, large surface area to volume ratio. Branched gut that permeates all parts of the body means that no cells are far from the gut or an exchange surface meaning that there is no need for a circulator system. Mouth used for egestion and ingestion. Supported by aqueous medium and well packed cells means there is no need for a hydostatic skeleton.

50

DNA Methylation

Addition of a CH3 group usually to cytosine, prevents RNApoly from binding and so inhibits gene expression, silencing the gene.

51

Histone modification

Addition of a methyl, acteyl or phosphate groups. Effects coiling of DNA around histones affecting the ease with which rnapoly can carry out transcription, Acetyl groups cause less winding.

52

Tumour suppressor gene

gene that protects a gene from uncontrolled cell division

53

Oncogene

Gene that can lead to uncontrolled cell division.

54

What does PCR need?

Thermostable (taq.) DNA polymerase
Free deoxyribnucleotides
Primers
DNA sample with region for replication

55

Primer

short strand of DNA (20 nucleotides) which is complementary to the sequence at the start of each strand to be amplified.

56

PCR method

Heat to 95 for 1 min, this denatures the DNA by breaking the H bonds between the stands separating them..
Cool to 50-60 for primers to anneal at the start of each strand of the complementary DNA region. They prevent the strands from rejoining and act as signals for the DNAp to start adding nucleotides. Heat to 72 for a min for the polymerase optimal temp. Repeat, doubles yield.

57

Anneal

To bind complementary sequences of single stranded DNA by H bonding.

58

Genetic markers

DNA sequences with know locations on chromosomes which are points of variation and so used to identify individuals. Examples incl. MRSs and SNPs.

59

What is used in genetic fingerprinting?

Introns between genes have variable nucleotide sequences which are similar in related individuals but are quite distinct in unrelated individuals, called satellite DNA.

60

Minisatellite

20-50 base pairs with 50 to several hundred repeats.

61

Microsatellite

2-5 base pairs with 5-15 repeats. Used in genetic finger printing pattern on any individual is unique except in identical twins.

62

DNA probe

A length of single stranded DNA with a particular base sequence, often located by addition of a tag.

63

DNA probe method

Extract the DNA from the sample.
Use restriction enzymes to cut out repeat sequences.
Gel electrophoresis to separate the fragments by size.
Transfer onto a nylon sheet
Add labelled probes
Detect using UV light or an X-ray
Barcode

64

Applications of genome sequencing

Phylogenetic trees, pharmacogenetics (personalised medicine) testing for genetic disease (CF), looking for genetic predisposition to disease (cancer), pathogen analysis, 3d protein structure

65

Gene expression

A gene is expressed when it is switched on so that mRNA is transcribed to encode the synthesis of a protein. Only some genes are switched on in each tissue type.

66

Genetic testing using microarrays

Hundreds to tens of thousands of dna probes anchored to a solid surface.
Each spot has many copies of the same probe, while different spots contain different probes.
Genes are made to be single stranded and are cut out and labelled, if the gene hybridises with a probe a colour change occurs or light is emitted if the tag is chemiluminescent. Computer analysis of the results will reveal a whole range of genes in a genome.
If testing for gene expression mRNA is extracted from the tissue and converted to cDNA using reverse transcriptase, with a fluorescent tag. If it shows up on the array it shows that the gene is expressed in that tissue.
For cancer genes, samples are taken from healthy and cancerous tissues and expression of oncogenes or tumour suppressor genes is measured and compared, different colour spots can be used.

67

To create a genetically modified organism

Obtaining the gene, inserting the gene into a vector, inserting the vector into the bacteria, identification of cells with correct vector.

68

What are the Hardy Weinburg assumptions?

No mutation - normally so slow it is ignored
No migration - effects equilibrium
No selection - no favourable genotype
Random mating - no advantageous genotype more likely to breed
Large population size - in small populations random mutations will skew results

69

Gene pool

Sum of all the genes and alleles in a population at a particular time

70

Allele frequency

proportion of a particular allele in a population at a particular time

71

Genome

All the DNA in an individual

72

How is meiosis a source of genetic variation

Crossing over during prophase 1 facilitates exchange of genetic material from one chromosome to another.

Independent assortment in metaphase 1, early alignment of homologous chromosomes at the equator of the cell is random and independent to that of any other homologous pairs causing a huge potential for variation. 2^23 possibilities.

73

How is cross fertilisation a source for genetic variation?

Many sperm cells (pollen) will attempt to fertilise an egg. Fusion of male and female gametes is entirely random. Produces new allelic combinations, not new alleles.

74

Neutral mutation

A point mutation that is a substitution that does not change the amino acid sequence due to degenerate nature of DNA.

75

How can frameshift lead to a shortened protein

Frameshift is a base deletion; as code read in threes a deletion effects every amino acid produced after it so a stop codon may be reached sooner than intended.

76

Chromosomal mutations

Chromosomes may break off an attach to other chromosomes, or get lost; too many/too few chromosomes may be present (Down's syndrome/Turner's syndrome)

77

Reasons for speciation/reproductive isolation

1) Behavioural isolation, courtship rituals in birds
2) Barriers to reproductive success, mechanical barriers, infertile offspring
3) Ecological isolation, different food sources, habitats

78

Species

A group of organisms with common ancestry that are capable of interbreeding to produce fertile offspring.

79

Speciation

Formation of species that are reproductively isolated from other species

80

How to insert genes into plants

Agrobacterium tumefaciens causes tumour like growths with desired gene by inserting a tumour inducing (Ti) plasmid, plant virus.

81

How to insert genes into animals

Microinjection into nucleus of fertilised egg.
Viruses adeno for gene therapy and retro can be used as RNA copied to DNA and is incorporated into the host's chromosome.

82

Phylum Annelida

Bilaterally symmetrical, round in transverse section.
Metamerically segmented allowing for independent but coordinated contraction of muscles for more efficient locomotion, repeating segments of identical nerve ganglia and muscle blocks.
Through gut; regional specialisation (pharynx, oesophagus, crop, gizzard and the intestine)
Hydrostatic skeleton supported by segmented fluid filled body

83

Phylum Arthropoda

Bilaterally symmetrical, metamerically segmented with different regions with fixed number of regions in each segment (6-head, 3-thorax, 11-abdomen)
Through gut, for regional specialisation.
Exoskeleton of chitin for protection, water retention and support. Muscles governing mvt are attached internally to the exoskeleton of the jointed limbs and to wings for flight.
Exoskeleton of insects limits the size of arthropods and creates a need for specialised exchange surfaces

84

Phylum Cordata

Endoskeleton of calcified bones
Vertebral spinal coloumn
Bilaterally segmented

85

Features of a moss

No vascular tissue; no true roots or leaves. Exchange with surrounding environment through cells, no cuticle or stomata. Rhizoids (filaments of cells) cannot penetrate deeply into soil so must be in moist area. Spores only germinate in moist conditions.

86

Features of a fern

Have a rhizome, horizontal stem. Due to horizontal stem leaves (Fronds) only extend to about a metre in height. Fronds have numerous spore producing structures.
Has vascular tissue with stomata and waxy cuticle and lignified xylem vessels. Roots can penetrate soil for anchorage and absorption of water and ions.
Support from xylem and turgor in cells.

87

Features of an angiosperm

Basically a fern with seeds.

88

Radially Symmetrical

Situation where body parts are arranged in a circle around an imaginary line through their mouth and gut cavity

89

Bilaterally Symmetrical

Situation where body parts are arranged on either side of an imaginary line through their mouth and gut cavity