Exam study Flashcards
(158 cards)
1
Q
What is photosynthesis?
A
The process of using light energy to produce a carbon compound (glucose)
2
Q
What are the two processes of photosynthesis?
A
Energy transduction and carbon assimilation
3
Q
Which process of photosynthesis is light-dependent?
A
Energy transduction
4
Q
What is the original equation of photosynthesis?
A
6CO2 + 12H2O > C6H12O6 + 6H2O + 6O
Carbon dioxide and water form glucose, water and oxygen.
5
Q
What is being oxidised during photosynthesis?
A
Water (H₂O) into oxygen (O₂)
6
Q
What is being reduced from the electrons that are lost during photosynthesis?
A
Carbon dioxide into glucose
7
Q
What colour light is absorbed by chloroplasts?
A
Red and blue
8
Q
What is energy transduction?
A
Chloroplasts capture light energy which is absorbed by chlorophyl molecules
Energy from photons of light is trapped and transferred to form a high-energy state. Oxidation of H₂O to O₂: electrons are captured and transferred to compounds along an electron transport chain to form NADPH, which is the final electron acceptor. ATP produced by ATP synthase enzyme complex from ADP and Pi
9
Q
Where does carbon assimilation take place?
A
In the stroma of the chloroplast
10
Q
What happens to hydrogen ions during energy transduction, and what are they used for?
A
As the electrons are passed from one molecule in the ETC, hydrogen ions are transported from the stroma to the thylakoid lumen. The high concentration of hydrogen ions is used to drive ATP synthase
11
Q
What is the light independent reaction of photosynthesis?
A
Carbon assimilation
12
Q
What happens during carbon assimilation?
A
NADPH and ATP are used to fix CO₂ into CH₂O (sugars/carbohydrates); carbon is incorporated into organic molecules to produce sugars.
13
Q
What enzyme is used during carbon assimilation?
A
Rubisco
14
Q
Where does carbon assimilation take place?
A
It occurs in the Calvin cycle in the stroma matrix of chloroplasts.
15
Q
What are the similarities between aerobic respiration and photosynthesis?
A
Use similar specialised organelles
- the chloroplast and mitochondria both are ovoid in shape, have a double membrane and acts as sites of electron transport chains and ATP synthesis
Use similar electron transport chains
Use chemiosmosis and ATP synthase
Generate energy in the form of ATP
16
Q
What are the differences between aerobic respiration and photosynthesis?
A
Reactants
▪ Aerobic respiration: Glucose + O₂
▪ Photosynthesis: CO₂ + H₂O
Products
▪ Aerobic respiration: CO₂ + H₂O
▪ Photosynthesis: Glucose + O₂
17
Q
What are the similarities between the ETC in photosynthesis and aerobic respiration?
A
In both pathways, energy released by electrons is used to actively transport H+ across membrane (chemiosmosis), for an electrochemical gradient to generate ATP
Both uses ATP synthase as the transport protein
They have similar electron carrier for both ETCs
- Aerobic respiration: NAD+ and FAD
- Photosynthesis: NADP+ (a phosphorylated NAD+)
18
Q
What are the differences between the ETC in photosynthesis and aerobic respiration?
A
In aerobic respiration, hydrogen ions are pumped from the intermembrane space, across the matrix and into the intermembrane space.
In photosynthesis, hydrogen ions are pumped across the thylakoid membrane from the thylakoid space to the stroma
Different final electron acceptor
- Aerobic respiration: O₂ reduced to H₂O
- Photosynthesis: NADP+ reduced to NADPH
19
Q
How can the metabolic diversity of prokaryotes be classified?
A
By energy source, electron source, and carbon source.
20
Q
What are the two energy source classifications?
A
- Phototrophs – Use light as energy source
- Chemotrophs – Obtain energy from oxidation of compounds
21
Q
What are the two electron source classifications?
A
Lithotrophs – Use reduced inorganic substances as their electron source
Organotrophs – Extract electrons from reduced organic compounds
22
Q
What are the two carbon source classifications?
A
Autotrophs – Use carbon dioxide as their sole carbon source
Heterotrophs – Use reduced, preformed organic molecules as their carbon source
23
Q
What are the classifications of a photolithoautotroph?
A
Light, inorganic electron donor and carbon dioxide as the carbon source.
24
Q
What are the classifications of a photoorganoheterotroph?
A
Light, organic electron source, and organic carbon source
25
What are the classifications of a chemolithoautotroph?
Inorganic chemical energy source, inorganic electron donor source, and carbon dioxide carbon source.
26
What are the classifications of a chemolithoheterotroph?
Inorganic chemical energy source, inorganic electron donor source, and organic carbon source.
27
What are the classifications of a chemoorganoheterotroph?
Organic chemical energy source, organic electron donor source, and organic carbon source.
28
How do bacteria reproduce?
Binary fission: a single bacterial cell divides into two identical daughter cells.
29
What happens during binary fission?
DNA replication
Cell elongation, when the cell wall and cell membrane are enlarging
Cell division: a septum is formed and divides the cell into two daughter cells
30
How would you describe bacterial growth?
Exponential increase: 2 > 4 > 8 > 16 > 32
31
What are the four phases of growth in bacteria?
Lag, log, stationary, and death
32
What happens in the lag phase?
Calls are alive but the population is not increasing. The cells are synthesising new components such as ribosomes. This is a period of adjusting due to new conditions.
33
What happens in the log phase?
Cells are growing and dividing at the maximum rate possible. Growth is measured and cells are increasing at a constant exponential rate.
34
What is Mean Generation Time?
Time required for one generation of bacteria to double.
35
How is mean generation time calculated?
When looking at a log graph of the exponential growth, find two points on the y-axis where cell number doubles, trace a line to the linear growth line and trace down to the x-axis to find the difference in time between the two.
36
What does mean generation time depend on?
Bacteria species, type of growth medium, and environmental conditions such as temperature, pH, and aeration.
37
What happens in the stationary phase?
Population stops increasing, number of viable cells remains constant, balance of cell division and cell death.
38
Why does growth stop in the stationary phase?
Due to environmental changes like nutrition depletion, pH change, lack of oxygen, or toxic compound build-up.
39
What happens in the death phase?
Viable cells declines exponentially
Cells dying at a constant rate
Cell division < Cell death
Cells die due to environmental change
* Nutrition depletion
* pH change
* Lack of oxygen
* Toxic compounds build-up
40
What are the methods of measuring bacterial growth?
Turbidity – Absorbance at 600 nm (with a spectrophotometer)
* Dry weight of cells – dehydrate the cells in the liquid they've grown in and measure the dry weight
* Viable cell count – diluting the sample and spreading it on agar plates, incubating the plates, and counting the resulting colonies
* Direct cell count – Directly counting under a microscope/hemocytometer
* Protein measurement – using the protein in the living cells to measure
41
What are the factors that affect bacterial growth?
* Water
* Temperature
* pH
* Oxygen
42
What is a hypertonic solution, and what happens to cells in one?
A hypertonic solution has a lower solute concentration than the cell so water leaves the cell, and it becomes shrivelled
43
What is a hypotonic solution, and what happens to cells in one?
A hypotonic solution has a higher solute concentration than the cell so water goes into the cell, and it is lysed.
44
What are the classifications of bacteria based on water availability?
Halophile
Halotolerant
Nonhalophile
45
What is a halophile?
Requires high level of NaCl (>0.2M)
46
What is a halotolerant bacteria?
Able to tolerate a high concentration of salt in environment
47
What is a nonhalophile?
Unable to grow in high salt concentration
48
How does temperature affect bacteria growth?
It affects the temperature-sensitive enzymatic reactions in the bacteria and affects the membrane structure.
Low temp = membrane solidification
High temp = Lipid bilayer melts and disintegrates.
49
What are the classifications of bacteria based on temperature tolerance?
Psychrophiles, psychrotolerants, mesophiles, thermophiles, and hyperthermophiles
50
Which types of fatty acids help hyperthermophiles survive high temperatures and why?
Saturated fatty acids are solid at room temperature, so they have a higher melting point.
51
What are the classifications of bacteria based on their pH tolerance?
Acidophile, neutrophile, and alkaliphile.
52
How does pH affect bacteria?
It can disrupt the plasma membrane, inhibit enzyme activities, and inhibit transport/uptake systems
53
How can oxygen damage bacteria?
By the formation of reactive oxygen species.
54
What are the classifications of bacteria based on the oxygen requirements?
Obligate aerobe, microaerophile, facultative anaerobe, aerotolerant anaerobe and an obligate anaerobe
55
What is an obligate aerobe?
Requires and use oxygen for respiration
56
What is a microaerophile?
Requires low levels of oxygen (5-10%)
57
What is a facultative anaerobe?
Able to undergo both aerobic and anaerobic growth but prefer the former
58
What is an aerotolerant anaerobe?
Doesn't use but is able to tolerate the presence of oxygen
59
What is an obligate anaerobe?
Anaerobic growth only
60
What are some similarities between DNA and RNA?
Both are made up of nucleotides
Both have a sugar-phosphate backbone
Both are nucleic acids
Both contain the bases A, C, G
Both store genetic information
61
What are DNA and RNA?
They are polymers made up of four different types of nucleotides. DNA contains genetic information
62
What is the monomeric unit, and what does it consist of?
One nucleotide
consists of a phosphate group, a 5-carbon sugar, and a nitrogen-containing base
63
What are the differences between RNA and DNA?
Slightly different nitrogenous bases, different sugars, different structures and bonds.
64
What is the difference between the sugars of DNA and RNA?
The pentose sugar for DNA is deoxyribose; there is a lack of oxygen at the 2-carbon position. RNA uses the pentose ribose; there is oxygen present at the 2-carbon position.
65
What are the differences between the bases of RNA and DNA?
RNA uses adenine, guanine, cytosine and uracil. DNA uses adenine, guanine, cytosine and thymine
66
What bases are pyrimidines?
Thymine, cytosine and uracil.
67
What bases are purines?
Adenine and guanine
68
What is the difference between thymine and uracil?
Thymine has a methyl group at the 5-carbon position and uracil has a hydrogen at the 5-carbon position.
69
What is the difference between purines and pyrimidines?
Purines have two benzene rings, and pyrimidines have a one benzene ring structure.
70
What is the difference in the structures of DNA and RNA?
DNA strands are antiparallel and form double helices. RNA strands are singular and do not form a double helix.
71
What bonds hold DNA and RNA together?
Phosphodiester bonds from sugar to sugar, and hydrogen bonds between base pairs.
72
What are the complementary base pairings for DNA?
A and T
C and G
73
What are the complementary base pairings for RNA?
A and U
C and G
74
What does antiparallel mean?
The strands run in opposite directions, one from 5' to 3' and the other from 3' to 5'.
75
What is transcription?
Process where ribonucleic acid (RNA) is transcribed/synthesised
from DNA
76
Is all DNA transcribed?
No, only DNA that encodes for a gene is transcribed into RNA
77
What is a gene?
A sequence of nucleotides that encodes for a specific protein or functional RNA molecule, influencing an organism's traits and functions.
78
What are the DNA sequences between genes called?
non-coding region
79
What are the three types of RNA?
messenger RNA, ribosomal RNA, and transfer RNA
80
What are the three genes that code for the types of RNA
Protein coding genes – mRNA
Ribosomal RNA gene – rRNA
Transfer RNA gene – tRNA
81
Where does transcription occur in eukaryotes, and what is the exception?
In the nucleus of cells, the exception is erythrocytes because they have no nucleus.
82
Where does transcription occur in prokaryotes?
Adjacent to the nucleoid
83
What's the difference in transcription and translation between prokaryotes and eukaryotes?
The processes are coupled in prokaryotes, but not in eukaryotes
In prokaryotes mRNA is immediately translated without additional processing
The presence of a nucleus in eukaryotes
compartmentalise transcription, which
undergoes RNA processing before leaving
the nucleus for translation
84
What are the four stages of transcription?
* RNA polymerase binding
* Initiation
* Elongation
* Termination
85
What happens during RNA polymerase binding during transcription?
RNA polymerase binds to the promoter region.
86
What is the promoter region?
A specific sequence upstream of the gene that determines which DNA strand will act as the template.
87
What happens during initiation in transcription?
RNA polymerase catalyses the synthesis of RNA from DNA, unwinds and rewinds DNA, and synthesises phosphodiester bonds between nucleotides
88
What direction does RNA polymerase read DNA, and what direction does it synthesise RNA?
Reads DNA in 3' to 5' direction, synthesises
89
What happens during the elongation phase of transcription?
Chain elongation as RNA polymerase moves along the DNA molecule.
90
What happens in the termination phase of transcription, and what causes termination?
At the end of the gene, RNA polymerase receives a termination signal and dissociates from DNA.
91
What are the two termination signals that can occur?
A GC-rich sequence can fold itself into a hairpin loop so no more nucleotides can bind to it, or a protein (rho) structure can attach to the RNA chain and cause dissociation of the DNA-RNA hybrid
92
What is the template strand?
The strand of DNA that serves as a template for DNA formation is the one that is read in the 3' to 5' prime direction
93
What is the non-template strand called, and why is it useful?
The non-template strand is the coding strand, and it is helpful because it is basically the same sequence as the mRNA strand being made, except that T is replaced with U
94
When transcribing DNA, what do you do if given a template strand?
Make sure it reads from 3' to 5'. if it reads 5' -> 3', reverse the sequence.
95
What do you do if given a coding strand from 5' to 3' to transform into a template strand?
Complement the base pairings, and make sure it reads 3' to 5' because the template strand will be antiparallel to the coding one.
96
What do you do if given a coding strand from 3' to 5' to transform into a template strand?
Reverse complement the sequence. It needs to read 5' to 3' first so that when the complements are added for the template strand, the template strand will read 3' to 5'
97
How do you transcribe a template strand into mRNA?
when the strand is in 3' to 5' direction, complement the bases and change T to U, making sure it is synthesized 5' to 3'.
98
What is the difference between RNA polymerase in eukaryotes and prokaryotes?
The RNA polymerase in prokaryotes synthesises all three types of RNA; eukaryotes have three different types .
99
What are the three types of RNA polymerase, and what do they synthesise?
RNA polymerase I – ribosomal RNA
RNA polymerase II - messenger RNA
RNA polymerase III – transfer RNA
100
What is ribosomal RNA and where is it found?
rRNA is the RNA that constitutes the major part of ribosomes, which is where it is found. Produced by the nucleolus, and relatively stable with considerable 2° structure.
101
What is messenger RNA?
mRNA codes for the amino acid
sequence of a protein
102
What makes mRNA less stable than the other two?
Very little 2° structure
Short half-life, rapid turnover
Cells only manufacture protein if needed.
103
What is the size range of mRNA?
300-7000 nucleotides
104
What does transfer RNA do?
* Brings amino acids to site of protein synthesis
* Recognises the coded base sequence of an mRNA
* One amino acid has at least one tRNA
105
What is the relative size of tRNA?
~ 70-90 nucleotides
106
What is an anticodon?
Three specific nucleotides that recognise the mRNA sequence. The anticodon loop is what binds to the specific mRNA codon.
107
What is the structure of tRNA?
It has a generalised 'cloverleaf' structure in 2D form.
In 3D form, when it is folded, it has an inverted L-shape.
108
Where is the amino acid binding site on tRNA?
At the 3' end, with the base sequence -CCA.
109
What is translation?
The process where ribonucleic acid (mRNA) is translated into an amino acid sequence with a protein code (called the genetic code). Polypeptides are produced from mRNA via translation
110
What components are required for translation?
mRNA, tRNA, rRNA, enzymes, and soluble factors.
111
What are the three stages of translation?
Initiation, elongation, and termination
112
What is aminoacylation?
The process where amino acids attach to tRNA
113
What enzyme is used in aminoacylation?
Amino acyl-tRNA synthetase
114
What does amino acyl-tRNA synthetase do?
It catalyses the covalent linkage of amino acids to the 3' end of tRNA. This activates the amino acid, making it ready to be polymerised into a growing peptide chain during translation
115
What do ribosomes do?
They are the site of protein synthesis
116
What makes up ribosomes?
Made up of rRNAs and proteins, they consist of a small and a large subunit.
117
What are the similarities and differences between prokaryotic and eukaryotic ribosomes?
They are both involved in protein synthesis and are structurally similar; however, eukaryotic ribosomes are somewhat larger. The sizes of the subunits differ, and so do the numbers of proteins associated.
118
What is the size of a bacterial ribosome compared to a eukaryotic one?
Bacterial ribosomes are about 70S, made up of 50S and 30S subunits; the eukaryotic ribosomes are about 80S, made up of 60S and 40S subunits.
119
What are the ribosomes' binding sites?
mRNA binding site, aminoacyl binding site, peptidyl binding site, and exit binding site.
120
What does the mRNA binding site do?
Binds to a specific nucleotide sequence to hold the mRNA in position, found in the small subunit
121
What does the A site do?
Holds, tRNA carrying the next amino acid that is to be added to the growing chain
122
What does the P site do?
Holds the tRNA carrying the growing polypeptide chain
123
What happens at the E site?
tRNA leaves the ribosome
124
What happens during the initiation phase of translation?
Binding of mRNA and aminoacyl-tRNA, which is carrying the first amino acid, to the ribosome.
125
What happens during the elongation phase of translation?
The anticodon of an aminoacyl-tRNA base-pairs with the complementary mRNA codon in the A site.
A peptide bond is formed between the amino acid in the A site and the growing polypeptide chain in the P site.
Once the polypeptide chain is attached to the amino acid on the aminoacyl-tRNA in the A site, the ribosome shifts so the empty tRNA is in the E site and can exit the ribosome, the polypeptide chain is now back in the P site, and the A site is empty for the next aminoacyl-tRNA.
126
What enzyme catalyses the formation of peptide bonds between the amino acids?
Peptidyl transferase
127
What happens during the termination of translation?
When a ribosomes reaches a stop codon on mRNA, the A site of the ribosome accepts a release factor, which is a protein shaped like a tRNA. The release factor promotes hydrolysis of the bond between the tRNA in the P site and the last amino acid of the polypeptide, freeing it from the ribosome.
128
What does the genetic code do?
Decodes mRNA into proteins
129
How many amino acids are in the genetic code?
20
130
What is a codon?
Three bases in the mRNA sequence that code for an amino acid.
131
Which direction is the genetic code read?
From 5' to 3'
132
What is the start codon, and what amino acid does it code for?
AUG encodes for methionine (MET).
133
What are the three stop codons?
UGA, UAA, and UAG
134
What are the ends written as in protein instead of 3' and 5'?
NH2- amd -COOH
135
What is the first thing to do when translating RNA?
Make sure the mRNA strand is in the 5' to 3' direction and then find the start codon (AUG). Write NH₂ and COOH at the ands.
136
Why do you not write anything if the mRNA codes for a stop codon?
Because the stop codon do not code for amino acids but release factors instead, which are proteins.
137
Where do post-translational modifications occur?
In eukaryotes it happens in the Golgi apparatus
138
What happens during post-translational modifications?
The Met amino acid is often removed
The formation of disulphide bonds occurs Some amino acids are modified after their incorporation into protein, and some amino acids are cleaved.
139
Why do we have cellular division, and when does it occur?
To prepare for cellular division
(where parent cell give rise to
daughter cells)
Occurs in S phase of cell cycle
(in eukaryotes)
140
How does DNA replicate?
Semiconservative replication
141
Where does DNA replication occur?
In the nucleus
142
What are the four steps of DNA replication?
* Initiation
* Primer binding
* Elongation
* Termination
143
What happens during initiation in DNA replication?
* Starts at origin of replication
* Helicase enzyme unwinding the double helix
* Strands separated by spinning at 10000 rpm
* Hydrogen bonds broken
* Molecule unwinds
* Forms replication fork
* Each strand then acts as a template for the DNA replication process
144
What does the enzyme topoisomerase do?
Prevents supercoiling of DNA strands during replication
145
What do single-stranded DNA binding proteins do?
They prevent the separated DNA strands from coming back together
146
What happens during primer binding in DNA replication?
DNA replication initiated by the binding of short RNA primer to ssDNA
Nucleotides can only be added to the 3’ end of an existing nucleotide chain
147
What enzyme synthesises RNA primer?
Primase
148
What happens during the elongation step of DNA replication?
Adding DNA nucleotide to the primer by DNA polymerase III.
149
What direction are deoxyribonucleoside triphosphates added to the new chain?
5' to 3' direction
150
What are leading and lagging strands?
The leading strand is synthesised as a continuous strand, while the lagging strand is formed from Okazaki fragments that will be stitched together later.
151
What are Okazaki fragments?
Short fragments of DNA that have been synthesised from the lagging strand because DNA must be synthesised from 5' to 3' but this isn't possible for both strands at the same time.
152
What happens during termination of DNA replication?
DNA polymerase I removes the RNA primer; DNA ligase connects fragments to form one continuous strand.
153
What are constitutive and inducible genes?
* Constitutive: Gene that is transcribed at all times
* Inducible: Gene that is only transcribed under certain conditions
154
What is an operon?
Set of genes that encodes a multigenic mRNA by a single promoter
155
What does lac operon do?
Synthesises the necessary
proteins to break down lactose
156
What does permease do?
Allows entry of lactose
into the cell
157
What does β-galactosidase do?
Cleave disaccharide lactose into monosaccharides galactose and glucose
158
