2.3* Flashcards
(149 cards)
1
Q
What is a double helix?
A
Shape of a DNA molecule, due to coiling to two sugar-phosphate backbone strands into a right handed spiral configuration.
2
Q
What is a monomer?
A
A molecule that when repeated makes up a polymer. Amino acids are the monomers of proteins. Nucleotides are the monomers of nucleic acids.
3
Q
What is a nucleotide?
A
Molecule consisting of a five-carbon sugar, a phosphate group and a nitrogenous base.
4
Q
What is a large molecule containing many nucleotides?
A
A polynucleotide.
5
Q
What is a nucleotide?
A
Nucleotides are biological molecules that participate in nearly all biochemical processes. They are phosphate esters of pentose sugars, where a nitrogenous base linked to the carbon atom 1 of the sugar residue, and a phosphate group is linked to either carbon atom 5 or carbon atom 3 of the sugar residue, by covalent bonds formed by condensation reactions.
6
Q
What do nucleotides form?
A
Nucleotides form the monomers of nucleic acids, DNA and RNA. In RNA the nucleotide pentose sugar is ribose. In DNA the nucleotide pentose sugar is deoxyribose.
7
Q
When do nucleotides become phosphorylated nucleotides?
A
When they contain more than one phosphate group.
8
Q
Give some examples of phosphorylated nucleotides.
A
ADP adenosine diposphate
ATP adenosine triphosphate
ATP is an energy-rich end-point of most energy-releasing biochemical pathways, and it is used to drive most energy-requiring metabolic processes in cells.
9
Q
What do nucleotides help regulate?
A
Many metabolic pathways, for example by ADP and AMP (adenosine mono-phosphate)
10
Q
What may nucleotides be components of?
A
Coenzymes
11
Q
Give some examples of nucleotides that act as co-enzymes.
A
Adenine nucleotides are components of the co-enzymes NADP - nicotinamide adenine dinucleotide phosphate, which is used in photosynthesis, and of NAD (nicotinamide adenine dinucleotide), which is a co-enzyme used in respiration, and of FAD (flavine adenine dinucleotide) and co-enzyme A (both also involved in respiration).
12
Q
Where is DNA found?
A
DNA is found in the nuclei of all eukaryote cell, within the cytoplasm of prokaryotic cells and is also inside some types of viruses.
13
Q
What does DNA carry?
A
DNA is the hereditary material and carries coded instructions used in the development and functioning of all known living organisms.
14
Q
What is DNA one of the most important?
A
DNA is one of the most important macromolecules that make up the structure of living organisms, the others being proteins, carbohydrates and lipids.
15
Q
What is the structure of the polymer of DNA
A
DNA is a polymer as its made up of many repeating monomeric units called nucleotides.
16
Q
A molecule of DNA consists of two stands made up of?
A
Polynucleotide
17
Q
What does each DNA nucleotide consist of?
A
Each DNA nucleotide consists of a phosphate group, a five-carbon sugar called deoxyribose, and one of four nitrogenous bases; adenine, guanine, thymine or cytosine.
18
Q
What type of bond exists between the sugar residue and the phosphate group in DNA?
A
A covalent bond.
19
Q
What is the covalent bond between the sugar residue and the phosphate group in a nucleotide called? - DNA
A
A phosphodiester.
look at pg 87 for a diagram on condensation bonds.
20
Q
How do nucleotides in DNA differ?
A
DNA consists of just four types of nucleotide. In each nucleotide the phosphate and sugar groups are the same but the organic (nitrogen) base differs.
21
Q
What are the full names for the bases in DNA?
A
Adenine always pairs with thymine and Guanine always pairs with cytosine.
22
Q
How are the two anti-parallel DNA strands joined to each other?
A
Hydrogen bonds between the nitrogenous bases.
23
Q
Why do matching base pairs have to pair?
A
A purine always pairs with a pyrimidine to give equal sized rungs on the ladder.
24
Q
Why do the DNA ‘rungs’ twist around an imaginary axis into a double helix?
A
To give the molecule stability.
25
What bases are purines?
Adenine and guanine
26
What bases are pyrimidines?
Thymine and cytosine
27
What bonds allows the nucleotides to unzip for transcription and replication?
hydrogen bonds.
28
Nucleotides with adenine as the base can make how many bonds with nucleotides with thymine as the base?
Two
29
Nucleotides with guanine as the base can make how many bonds with nucleotides with cytosine as the base?
Three
30
What is the upright part of the large DNA molecule that resembles a ladder formed by?
A sugar-phosphate backbone of the anti-parallel polynucleotide strand.
31
What does 'opposite directions' of two strands refer to?
It refers to the direction that the the 3rd and 5th carbon molecule on the 5-carbon sugar, deoxyribose, are facing.
Diagram on pg 88.
32
What is the 5' end of the molecule?
Where the phosphate group is attached to the fifth carbon atom of the deoxyribose sugar.
Diagram on pg 88.
33
What is the 3' end of the molecule?
Where the phosphate group is attached to the third carbon atom of the deoxyribose sugar.
Diagram on pg 88.
34
What do the rungs of the ladder consist of?
Complimentary base pairs, joined by hydrogen bonds.
35
Is the information within the base sequence protected?
The molecule is very stable, and the integrity of the coded information within the base sequences is protected.
36
How should you refer to bases within nucleic acids?
You should always refer to the bases within nucleic acids as nucleotide bases or nitrogenous/nitrogen containing bases, or as organic bases, because bases on its own refers to another group of chemicals.
37
What did and didn't scientists know in the late 1800 about the nucleic acid DNA.
They knew that all nuclei of cells contained the nuclei acid DNA, but they did not know what it did. In fact it was referred to as 'the stupid molecule' as it was ubiquitous, but seemed to have no function.
38
At what time did which scientists help to work out the structure of DNA?
In 1953 the scientists James Watson, Frances Crick, Maurice Williams and Rosalind Franklin all helped to work out the structure of the DNA molecule.
39
When did which scientists receive the Nobel prize and why?
In 1963, Wilkins, Crick and Watson shared the Nobel prize for what was probably the most important biological discovery of the 20th century, and which spawned the beginning of modern molecular biology.
40
Who did not receive the Nobel prize?
Unfortunately, the x-ray crystallographer Franklin had already died of cancer, and the Nobel prize could not be awarded to her posthumously.
41
Explain the investigation that extracts and purifies DNA by precipitation.
All living organisms contain DNA, you can extract it from many sources for example strawberries and kiwifruit. The extracting process is very simple and involves simply macerating the tissue, adding a strong detergent (such as washing up liquid) and then adding ethanol so DNA precipitates out of solution. This DNA can be further purified by removal of unwanted salts and then can be concentrated.
42
How is DNA organised in a chromosome?
Each large molecule of DNA is round around special histone proteins into chromosomes. Each chromosome is therefore one molecule of DNA.
43
How is DNA organised in prokaryotic cells?
DNA is in a loop and is within the cytoplasm, not enclosed in a nucleus.
It is not wound around histone proteins, and is described as naked.
44
Where in the cell is there DNA that is not organised in chloroplasts?
There is also a loop of DNA, without the histone proteins, inside the mitochondria and chloroplasts.
45
What cells also have DNA in a loop?
Viruses that contain DNA also have it in the form of a loop of naked DNA.
46
What is DNA polymerase?
Enzyme that catalyses formation of DNA from activated deoxyribose nucleotides, using single stranded DNA as a template.
47
What is helicase?
Enzyme that catalyses the breaking of hydrogen bonds between nitrogenous pairs of bases in a DNA molecule
48
What is semi-conservative replication?
How DNA replicates, resulting in two new molecules, each of which contains one old strand and one new strand. One old strand is conserved in each new molecule.
49
Every time a cell divides why does the DNA need to be copied?
So each daughter cell receives a full set of instructions. Each molecule of DNA replicates.
50
When does cell replication take place?
This replication takes place during inter phase before the cell actually divides
51
What is a eukaryote?
A eukaryote is any organism whose cells contain a nucleus and other organelles enclosed within membranes.
52
What does cell division result in for eukaryotes.
This results in each chromosome having an identical copy of itself. At first they are joined together at the centro-mere, forming two sister chromatids.
53
To make a new copy of itself what is the first two steps each DNA molecule must follow?
DNA must;
unwind - the double helix is untwisted, a bit at a time, catalysed by a gyrase enzyme.
Unzips - hydrogen bonds between the nucleotide bases are broken. This is catalysed by DNA helicase, and results in two single strands of DNA with exposed nucleotide bases.
54
In semi-conservative replication what happens to free phosphorylated nucleotides?
Free phosphorylated nucleotides, present in the nucleoplasm within the nucleus, are bonded to the exposed bases, following complementary base pairing rules.
55
In semi-conservative replication what does the enzyme DNA polymerase do?
The enzyme DNA polymerase catalyses the addition of new nucleotide bases, in the 5' to 3' direction, to the single strands of DNA; it uses each single strand of unzipped DNA as a template.
56
In semi-conservative replication How is the leading strand synthesised?
The leading strand is synthesised continuously, whereas the lagging strand is in fragments (discontinuous) that are later joined, catalysed by ligase enzymes.
57
In semi-conservative replication what is the purpose of the hydrolysis of the activated nucleotides?
To release extra phosphate groups, supplies the energy to make phosphodiester bonds between the sugar residue of one nucleotide and the phosphate group of the next nucleotide.
58
What is the product of semi-conservative replication?
Two DNA molecules, identical to each other and to the parent molecule. Each of these molecules contains one old strand and one new strand, and so this is termed semi-conservative replication.
59
What is a prokaryote?
A prokaryote is a single-celled organism that lacks a membrane-bound nucleus (karyon), mitochondria, or any other membrane-bound organelle.
60
How does DNA in prokaryotes replicate?
The loops of DNA in prokaryotes, and inside mitochondria and chloroplasts, also replicate semi-conservatively. A bubble sprouts from the loop and this unwinds and unzips, and then complimentary nucleotides join to the exposed nucleotides. Eventually the whole loop is copied.
61
What did and didn't scientists know about semi-conservative replication?
Scientists knew that DNA was a self replicating molecule but did not know how the molecule made copies of itself. There were three theory's.
62
What were the three theory's for replication in the 1950's?
Conservative - the original molecules acts as a template and a new molecule is made.
Dispersive - The original molecule breaks up into nucleotides, each one joins to a complimentary nucleotide and new ones join up again..
Semi conservative - the new molecule consists of one original strand and one newly formed strand.
63
What scientist's carried out an investigation at which point in the 20th century into DNA replication.
Two scientists, Meselson and Stahl, carried out an experiment in 1958 which showed DNA is semi-conservative.
64
What was the first step of Meselson and Stahl's investigation?
They grew bacteria, E. coli, for 14 generations in a medium containing the heavy isotope nitrogen, 15N. This contains an extra neutron in every atomic nucleus. After 14 generations, most of the DNA in the bacteria would be heavy, as it contains 15N.
65
What was the second step of Meselson and Stahl's investigation?
They then transfer some of these bacteria into a medium containing the normal 14N isotope of nitrogen, and left them for long enough to undergo one replication.
66
After the 2nd step of Meselson and Stahl's investigation what could the scientists infer?
The DNA from these bacteria after one division was found to be a hybrid DNA. This showed that DNA does not replicate conservatively, as that would have produced two bands of DNA, one heavy and one light.
67
What was the final step of Meselson and Stahl's investigation?
The bacteria were allowed to divide once more and their DNA, one hybrid and one light, showing that replication is semi-conservative and not dispersive.
68
What is the sugar molecule in RNA?
The sugar molecule in each nucleotide is ribose.
69
In RNA what is the nitrogenous base?
The nitrogenous base uracil, which is a pyrimidine, replaces the pyrimidine base thymine.
70
Compare the polynucleotide chain in RNA and DNA.
The polynucleotide chain is usually single stranded.
| The polynucleotide chain is shorter.
71
What are the three forms of RNA?
Messenger RNA, (mRNA), Transfer RNA (tRNA) and ribosomal RNA (rRNA).
72
What is DNA polymerase?
Enzyme that catalyses formation of DNA from activated nucleotides, using single stranded DNA as a template.
73
When does the replication of DNA take place?
During inter-phase before a cell actually divides.
74
After DNA is replicated how is it joined at first ?
At the centromere, forming two sister chromatids.
75
What happens to DNA in the mitochondria and chloroplasts before a cell divides?
It replicates just before the organelles divide which is just before the cells divide.
76
How often does a mutation occur?
1 in 1000000000 or 10 to the 8 base pairs.
77
What is a mutation?
During DNA replication, errors may occur and the wrong nucleotide may be inserted. This could change the genetic code and is an example of point mutation.
78
What reduces the rate mutations are produced?
During the replication process there are enzymes that can proofread and edit out such incorrect nucleotides, reducing the rate that mutations are produced
79
If, due to a mutation a gene has a change to its nucleotide sequence what are the different versions of the same gene called?
Alleles or gene variants
80
Are all mutations harmful? give some examples.
Not all mutations are harmful, some appear to give neither an advantage or disadvantage - for example whether or not you can roll your tongue.
some can be advantageous - for example a white coat to an animal during winter when snow is in the ground.
81
What is a gene?
A length of DNA that codes for a polypeptide or a length of RNA that is involved in regulating gene expression.
82
What is a polypeptide?
A polymer made of many amino acid units joined together by peptide bonds. Insulin is a polypeptide of 51 amino acids.
83
What is a protein?
A large polypeptide of 100 or more amino acids. However, the terms are often used synonymously, and insulin may be described as a small protein.
84
What is transcription?
The process of making mRNA from a DNA template.
85
What is translation?
The formation of a protien, at ribosommes, by assembling aminno acids into a prticular sequence according to the coded instructions carried from DNA to the ribosomme by mRNA
86
What does each chromosomme in a eukaryotic cell nucleus contain?
A molecule of DNA
87
On each chromosomme what are each specific lenghts of DNA called?
genes
88
What does each gene contain?
A code that determines the sequence of amino acids in a particular polypeptide or protien.
89
How much of an organisims dry mass does protien account for?
75%
90
What are some functions of protiens?
Some proteins are structual, such as the cytoskeleton threads inside cells or the protien in the cell membrane; others make up the cells tool kit, such as enzymes, and these may catayse the formation of non-protien molecules such as lipids and carbohydrates,
91
What will enable a polypeptide to carry out its function.
Within each gene there is a series of DNA base triplets that determines the amino acid sequence, or primary structure, of a polypeptide. As long as this primary structure of a polypeptide is correct, it will then fold correctly and be held in its tertiary structure or shape, enabling it to carry out its funtion.
92
Give some eamples of where a protien molecule must be exactly right.
The shape of the active site of an enzyme molecule must be complimentary to the shape of the substrate molecule.
Part of an antibody molecule must have a shape complimentary to that of the antigens onthe surface of an invading pathogen.
Receptor on a cell membrane - cell signalling molecule such as a hormone or drug.
Ion channel protien must have hydrophillic amino acids lining the inside of the channel, and lipphillic amino acids on the outside portio that will be next to the lipid bilayer of the plasma membrane.
93
How do genes code for protiens outside of the nucleus?
As the instructions inside the genes, on chromsommes, cannot pass out of the nucleus, a copy of each gene has to be transcribed into a lenght of mRNA. In this form, the sequence of base triplets, now called codons, can pass out of the nucleus to the ribosomme, ensureing the coded instructions are translated and the protien is assemvled correctly from amino acids.
94
Is the genetic code universal?
The genetic code is near universal, because in almost all living organisms the same triple of DNA bases code for the same amino acid.
95
Why is the genetic code described as degenerate?
because, for all amino acids, except methioniene and tryptophan, there is more than one base triplet. This may reduce the effect of point mutations, as a change in one base of the triplet could produce another base triplet that still codes for the same amino acid.
96
Does the overlap? and in what diection is DNA read?
The code is also non-overlapping and is read starting from a fixed point in groups of three bases.
97
What happens if a base is added or deleted from DNA?
It causes a frame shift, as every base triplet after that, and hence every amino acid coded for, is changed.
98
There are few exceptions to the universal code theory. In nearly all living organisms what code starts of most proteins?
AUG codes for methionine
99
What does AUA code for?
Isoleucine
100
In our mitochondria give some examples of how codes change.
In our mitochondria, the mRNA codon AUA codes for methionine instead of coding for isoleucine, and codons AGA and AGG are stop codons instead of coding for arginine. UGA codes for tryptophan instead of being a stop codon.
101
What theory might the evidence that codons code for different in amino acids in mitochondria than they do in the nucleus support?
The endosymbiont theory of the origin of mitochondria, as in some other bacteria UGA also codes for tryptophan instead of being a stop codon.
102
What is the first step of transcription?
A gene unwinds and unzips
103
What is the second step of transcription?
Hydrogen bonds between complimentary nucleotide bases break.
104
In transcription which enzyme catalyses the formation of temporary hydrogen bonds?
RNA polymerase
105
In transcription what are the temporary hydrogen bonds formed between?
between RNA nucleotides and their complimentary unpaired DNA bases.
106
In transcription what does each base pair with?
A bonds with T; C with G; G with C and U with A, on a strand of unwound DNA.
107
In transcription what can the DNA strand be described as?
The template strand.
108
What is produced in transcription?
A length of RNA that is complimentary to the template strand of the gene produced. It is therefore a copy of the other DNA strand - the coding strand.
109
What is the last step of transcription?
The mRNA now passes out of the nucleus, through the nuclear envelope, and attaches to a ribosome.
110
Inside the nucleus how does a portion of a DNA molecule open up for transcription?
Inside the nucleus a portion of a DNA molecule opens up by breaking hydrogen bonds to reveal a sequence of nucleotide bases.
111
In transcription what happens to exposed DNA bases?
Free RNA nucleotides hydrogen-bond onto exposed bases, following complimentary base pairing rules so U bonds with A, A with T, C with G and G with C.
112
How are ribosomes formed? (Sorry Slug)
Ribosomes are made in the nucleolus, in two smaller subunits. These pass separately out of the nucleus, through pores in the nuclear envelope, and then come together to form the ribosome. Magnesium ions help to bind the two subunits together. Ribosomes are made of ribosomal RNA and proteins in roughly equal parts.
113
Translation;
| Where are transfer RNA molecules made?
In the nucleolus and pass out of the nucleus into the cytoplasm.
114
What is transfer RNA made of?
They are single stranded polynucleotides, but can twist into a hairpin shape.
115
What is at one end of a molecule of tRNA?
A trio of nucleotide bases that recognises abs attaches to a specific amino acid.
116
In tRNA what is at the loop if the hairpin?
Another triplet of bases, callee an anticodon, that is complimentary to a specific codon (triplet) if bases on the mRNA.
117
What does the anti codon bind to on mRNA?
The anticodon which binds to its complimentary codon on the mRNA.
118
What to tRNA molecules do in translation?
Transfer RNA molecules bring the amino acids and find their place when the anticodon binds by temporary hydrogen bonds to the complimentary codon on the mRNA molecule,
119
In translation what happens as the ribosome moves along the lenght of mRNA?
As the ribosome moves along a lenght of mRNA, it reads the code, and when two amino acids are adjacent to each other a peptide bond forms between them.
120
In translation why is energy in the form of ATP needed?
for polypeptide synthesis.
121
In translation; What is the amino acid sequence for the polypeptide ultimately determined by?
The sequence of triplets of nucleotide bases on the lenght of DNA - the gene.
122
In translation; What happens to the mRNA after the plypeptide is assembled?
The the mRNA breaks down. Its component molecules can be recycled into new lenghts of mRNA, with different codon sequences.
123
In transcription; what happens to the newly synthesised polypeptide?
It is helped by chaperone protiens in the cell, to fold correctly into its 3D shape or tertiary structure, in order to carry out its function.
124
What is a triplet of bases on a DNA molecule called?
A base triplet.
125
What is a triplet of bases on a lenght of mRNA called?
A codon.
126
What is a triplet of bases on a tRNA molecule, complimentary to the mRNA codon called?
an anticodon.
127
What might an investigation using methyl green-pyronin stain show?
The distribution of DNA and RNA within cells.
128
Why does an investigation using methyl - green show the distribution of DNA and RNA within cells?
Dna takes up methyl green and RNA takes up pyronin.
129
Give an exmple of where an investigation using methyl green-pyronin stain might show results?
You can make slides of root tips of bean or onion roots and stain them to show that DNA is in the nuclei and RNA is in the cytoplasm (and nucleus).
The cut tips have been of bean or onion roots have been fixed in acetic ethanol or absolute ethanol for at least thirty minutes.
130
In the investigation using methyl green-pyronin stain what is the first step?
Use a clean scapel or razor blade and cut thin longetudinal sections of the tip of the fixed root. Each section should be about 3 mm long.
131
In the investigation using methyl green-pyronin stain what is the second step?
Place the sections on a microscope slide and cover with methyl green-pyronin stain for 30 minutes.
132
In the investigation using methyl green-pyronin stain what do you do after using a pipette to remove the stain?
Then add distilled water to the root tips.
133
In the investigation using methyl green-pyronin stain what do you have to change sevaral times and what is the step after?
Change the water sevaral times to wash the root tip sections.
Then add a drop of distillled water and ac overslip.
134
In the investigation using methyl green-pyronin stain what must be done under high power?
Observe cells in the sections under low power and then under high power.
135
In the investigation using methyl green-pyronin stain what should you observe?
You should see DNA stained bule-green in the cells' nuclei and RNA stained red in the cytoplasm.
136
What is the scope of a human eye, giving measurements?
1 m, a hens egg 100 mm, Amoeba 1 mm, onion upper epidermis cell 100 um.
137
What is the scope of a light microscope, giving measurements?
Amoeba 1 mm, human cheek cells or a human ovum 1 um, influenza virus 100 nm.
138
What is the scope of a electron microscope, giving measurements?
Amoeba 1 mm, human cheek cells or a human ovum 1 um, influenza virus 100 nm, ribosome or protien 10 nm, lipids 1 nm, atom 0.1nm.
139
How far apart can your eye distinguish objects?
0.3-0.5 mm apart. This is the limit of its resolution, but it gives you quite good visual accuracy for everyday objects.
140
In the eye what produces visual acuity and sharpness?
In the retina, at the back on an eye, are photosensitive cells called cones that work in bright light and produce the visual accuracy (sharpness).
141
How many photosensitive cells do you have in the back of your eye.
You have about 200,000 cones per mm squared.
142
In the retina which animal has much higher amount of photosensitive cones per mm squared, and what does this mean?
Eagles and hawks have many more cones in their retinas, around 1 million per square mm, and therefore giving a greater resolution and visual accuracy.
143
Talk through the vision of Hawks and eagles.
When you see a rabbit 20 m high over a grass verge, it can clearly see an insect scurrying amongst the vegetation. An eagle can spot a rabbit 2 miles away and, although its much smaller than you, its eyes are about the same size.
144
Give three methods of viewing specimens in an optical microscope.
Living organisms such as Paramecium and Amoeba.
Smear preparations of human blood and cheek cells.
Thin sections of animal, plant and fungal tissue, such as bone, muscle, leaf, root or fungal hyphae.
145
Slides and photomicrograph's;
| Why do specimens need to be stained?
Many biological structures, including single-celled organisms such as Paramecium, are colourless and transparent.
146
Slides and photomicrograph's;
| How do microscopes work without a stained specimen?
Some microscopes use light interference, rather than light absorption, in order to produce a clear image without staining.
Some use a dark background against which the illuminated specimen shows up.
147
Slides and photomicrograph's;
| What are microscopes that do not need the organism to be stained particularly useful for?
These microscopes are particularly useful for studying living specimens. You can observe these specimens with a school light microscope by adjusting the iris diaphragm to reduce the illumination of the specimen.
148
Slides and photomicrograph's;
| What are stains?
Stains area coloured chemicals that bind to molecules in or on the specimen, making the specimen easy to see.
149
Slides and photomicrograph's;
| Give an example of an all purpose stain.
Methylene blue
