Topic 1 Flashcards
1
Q
What are receptors
A
Proteins on the cell surface or interior will respond to the target cell as it has the right shape.
Hormones can only bind to cells with the correct receptor.
2
Q
How is the structure of a protein determined?
A
By it’s the unique sequence of amino acids
3
Q
What does haemoglobin do
A
transport oxygen and carbon dioxide in the blood
4
Q
What is a primary structure
A
sequence of amino acids joined by peptide bonds
5
Q
Describe the side chains
A
side chains of amino acids determine the type of interaction with other amino acids
6
Q
what is a secondary structure
A
small regions within the polypeptide consisting of alpha-helix and beta-sheet formed by hydrogen bonding
7
Q
What is a tertiary structure
A
Final 3D folded structure of the polypeptide.
folding and coiling due to interactions between amino side chains and surrounding water
8
Q
What is a quaternary structure
A
interactions with another polypeptide (2 or more)
9
Q
how is the sequence of amino acids determined
A
by the sequence of codons in the gene
10
Q
when do sulphide bridges form
A
when two cysteine amino acids are opposite each other in the polypeptide chains. consists of a covalent bond which is very strong compared to other bonds in tertiary structure. sulphide bridges can happen within a polypeptide or join two together.
11
Q
What is denaturation?
A
a structural change in a protein that results in the loss (usually permanently) of its biological properties = can no longer function. usually caused by two key conditions - temperature and pH
12
Q
What are enzymes
A
Molecules that carry out biological reactions increasing the rate of chemical reactions in cells.
13
Q
why is the 3D shape of an enzyme critical to it’s function
A
The active site of an enzyme recognises and binds a substrate, but the shape of the substrate and the shape of the active site must be complementary.
14
Q
Describe the induced fit model of an enzyme
A
Catabolic/breakdown reaction
- upon binding the enzyme undergoes a conformational change (induced fit) lowering the activation energy of the reaction by stressing the bonds holding the substrate together
- products are released and the enzyme is free to catalase another reaction
15
Q
Describe induced fit of enzyme-substrate binding
A
Anabolic reaction
Combine monosaccharides to form polysaccharides.
upon binding the enzyme-substrate complex creates a bond between the two substrates to produce the product.
16
Q
What is activation energy
A
the energy required to initiate a chemical reaction
17
Q
How do anabolic reactions lower the activation energy
A
by aligning the substrates so that the bonds can be more readily made to create the product
18
Q
How do catabolic reactions lower the activation energy
A
by stressing the bonds holding the substrate together so that the substrate is more readily broken to form the products
19
Q
How does temperature effect enzyme activity
A
LOW TEMPERATURE
enzyme is in a good state, the rate of reaction is too low to locate the substrate to allow for binding
OPTIMAL TEMPERATURE
molecular motion is more rapidly resulting in more successful collisions between enzyme and substrate resulting in more product being formed
HIGH TEMPERATURE
colliding too fast and the enzyme is denaturing.
20
Q
How does pH effect enzyme activity
A
LOW PH
excess H+ ions. charges become positive resulting in repulsion.
OPTIMAL PH
charges are opposite allowing for the substrate molecules to be attracted to the enzymes active site.
HIGH PH
lack of H+ ions. charges between active site and substrate become negative resulting in repulsion.
21
Q
What happens at non-optimal pH?
A
change in charges of amino acids can change the shape of the active site. the ionic bonds in the enzyme are broken leading to unfolding of the polypeptide.
22
Q
How do competitive inhibitors effect enzyme activity?
A
the inhibtor is similar enough in shape to a substrate that it can bind to the active site and simple block the substrate from binding. the rate of reaction will slow down.
23
Q
How do non competitive inhibitors effect enzyme activity?
A
inhibitor molecule binds to the enzyme at a location other than the active site. These inhibitors change the conformation of the enzyme as well as the enzyme’s active site, so the substrate is not able to bind.
24
Q
How does concentration of reactions effect enzyme activity
A
the rate of reaction increases with increasing substrate concentration. eventually, the concentration will exceed the availability of active sites and the rate of reaction will plateau and remain constant.
25
What is feedback inhibition
The process which the end product of a metabolic pathway acts on the first enzyme of that pathway, to prevent more product from being made.
excess products can bind to the enzyme and prevent substrate binding by altering the shape of the active site.
26
what are hormone receptors
proteins that allow hormones to recognise and bind because of the 3D shape of the hormone that is complementary to the 3D shape of the receptor binding site
27
What are antibodies
proteins with a quaternary structure that recognise and bind to a particular antigen on the surface of a cell to be destroyed
28
How do antibodies bind
to the antigen binding site that is complementary to the shape of the antigen. hence, each antibody is specific to a particular antigen
29
Explain how it is possible for each different protein molecule to have a unique primary structure
The primary structure is determined by the number, type and sequence of amino acids. Each protein differs in regards to these three factors.
30
Explain how the different shapes and chemical properties of hormones enable molecules to control metabolic pathways
Hormones have a complementary shape to their receptors therefore when this binding occurs it initiates a response
31
Explain why adrenaline doesn't affect all cells in the organism
As only particular cells will possess that particular receptor that can bind to adrenaline
32
relate the complementary shape of an antibody to its role in destroying or inactivating invaders
antibodies are complementary to the antigens and bind to the invaders. this assists in the destruction of the bacteria and virus (invaders).
33
describe the importance of a primary structure determining the pleat sheet arrangement
It is the bonding of the amino acids in the primary structure that determine the arrangement of a secondary structure, pleated sheet.
34
explain how such a secondary structure may be important for the function of lysozyme enzyme
The secondary structure determines the 3D structure which is responsible for the action of lysozyme.
35
Why do all cells have the same DNA but are all capable of producing different types of protein molecules
Not all genes are active in all cells. some genes are turned off while others are switched on and active.
36
Why could the same cell produce different proteins at different times
Gene activity is carefully controlled. There is a range of factors that determine which proteins are made and at which time.
37
definition of induced fit model
describes the substrate is capable of inducing the proper alignment of the active site to the substrate
38
name four properties of enzymes
1. biological catalysts
2. not used up in a reaction
3. bind to substrate at the active site
4. lower the activation energy
39
how do enzymes lower activation energy for a reaction
two enzymes could be brought together by binding at the active site. nonds may be stressed during enzyme substrate binding and this may lower the activation energy.
40
explains what it means to say that enzymes are biological catalysts
because they control the rate of reaction in cells and organisms
41
name on physical and one chemical factor that changes the activity of enzymes and explain how they do this
1. physical - temperature = at optimum temperature the substrate and enzymes have kinetic energy allowing to collide and bind more frequently.
2. chemical - pH = incorrect pH may alter the shape of the active site reducing enzyme substrate binding
42
name three external factors that could affect the activity of the enzyme catalase
pH, temperature, inhibitor
43
why would catalase be specific for a reaction
It will only catalase this reaction and nothing else.
44
describe what it means to say that enzymes "lower the activation energy required for a reaction to proceed"
activation energy is the energy chemical reactions need for a reaction to occur. Enzymes lower this making it easier for the reaction to start.
45
explain the most likely reason for a plateu in the graph
all of the enzymes active sites are occupied by substrates therefore there are no more available for enzyme-substrate binding
46
what is the biological significance of the optimum temperature
this temperature is the best for it to catalyse the the conversion of substrate to products.
47
Describe the Polymerase Chain Reaction
- heating to 95 to seperate strands
- cooling to 55 to allow primers to bind by complementary base pairing to the start of the target DNA strand
- heating again to 75 for DNA polymerase to use free nucleotides to synthesise new DNA
48
What are primers
short stretches of nucleotides complementary to the ends of the opposite strands of the region to be amplified
49
What are primers used for
2 primers ar required for the Polymerase Chain Reaction. These bind to the strand in cooling to 55 stage and they become part of the new DNA
50
What are the requirements for PCR?
- DNA sample to act as template for new DNA synthesis
- 2 DNA primers complementary to the ends of the region to be amplified
- DNA nucleotides to be incorporated into new DNA
- Heat resistant DNA polymerase to synthesise the new DNA
- Buffer, for optimum pH for DNA polymerase
- Thermal cycler to do heating/cooling
51
What is the role of temperature in PCR
- heated to 95 to seperate strands and break the weak hydrogen bonds
- cooled to 55 to allow primers to bind by complementary base pairing to identify DNA polymerase
- heated to 72 to allow DNA polymerase to join free nucleotides onto ends of primers
52
What is electrophoresis
A technique commonly used to seperate charged molecules such as DNA, RNA and proteins
53
Describe the process of electrophoresis
- Agarose and buffer mixed to create a gel which is poured into a mould with a comb inside.
- Restriction enzymes used to cut DNA
- DNA samples inserted into wells using micropipette
- Electrical current is turned on. A negative charge on the sugar phosphate backbone attracted to the positive electrode.
DNA fragments separated according to size
54
What is DNA sequencing
The process of determining the nucleic acid sequence
55
What are VNTRs and STRs
VNTR regions are short regions of DNA where a short sequence of nucleotides is repeated.
STR is made up of multiple copies of short tandem.
56
What is microinjection
When either plasmids or chromosomes are injected into a eukaryotic cell
57
What are probes
Short stretches of DNA or RNA complementary to the gene of interest used to select a gene
58
Describe how particular genes can be selected using probes
A probe is labelled with either fluorescent or radioactive tag so that it can be detected when it binds by complementary base pairing
59
What are restriction enzymes
Enzymes that recognise specific sequences in DNA due to their active site cut the DNA at recognition sites to create sticky ends.
60
Why do restriction enzymes cut before or after end
So that the full gene is obtained as this results in a non-functional gene.
61
What are sticky ends
Overhanging base sequences formed when a restriction enzyme cuts the DNA at an angle
62
Describe the plasmid method
- Extract plasmid from bacteria
- Cut plasmid with restriction enzyme
- Cut human DNA with same restriction enzyme
- Join cut pieces together with DNA ligase
- Allow recombinant bacteria to divide and isolate the recombinant bacterium producing the human insulin
63
What are plasmids
Small circular pieces of DNA found in bacteria
64
Describe the process of making genetically modified bacteria
- Foreign gene is removed and plasmid cut with the same restriction enzyme
- Plasmid and gene of interest joined by DNA ligase
- The transformation of recombinant plasmid back into a bacterium to produce the recombinant bacterium
- Grow genetically modified bacteria in culture
65
What is electroporation
The process of introducing DNA or chromosomes into bacteria or other cells using a pulse of electricity to open the pores in the cell membranes briefly. Cells are placed in a solution and DNA is subjected to an electrical pulse creating membrane pores. The DNA fragments enter through the pores into the cytoplasm.
66
How does DNA store information
In sequences of 4 bases in the nucleus
67
How does DNA transmit information from parent to offspring
Through processes like mitosis
68
State the reason that chromosomes are not visible in cells that are dividing
They are too loosely packed
69
Name two organelles, other than the nucleus, in which DNA might be found in a eukaryotic cell. Suggest one possible reason for the presence of this DNA.
MITOCHONDRIA AND CHLOROPLAST
| As they once were free-living unicellular organisms capable of independent existence
70
Compare a chromosome in a eukaryotic cell with a chromosome in a prokaryotic cell
Located in the nucleus of a eukaryote and in the nucleoid of a prokaryote
71
Explain the significance of different species having different numbers and types of chromosomes
Different species have different features and characteristics therefore different numbers and types of chromosomes
72
Discuss the likely reasons that chromosomes are often referred to as 'structural units of information in organisms'
Because it is a visible structure in the form of bases like DNA
73
A section of a DNA molecule is found to be 30% guanine. Using your knowledge of complementary base pairing, predict the percentage of bases that would be thymine
20%
74
Why is DNA replication essential for the production of new cells
When cells reproduce, they usually produce daughter cells that are identical to the parent. Therefore they must have equal and identical copies of the chromosomes. Hence, DNA replication.
75
What is the exon of a gene
The coding portion of the gene
76
What is the intron of the gene
The non-coding portion of the gene
77
What is RNA splicing
The removal of non-coding sequences of genes (introns)
78
Explain what it means when it is stated that a particular gene is linked to a specific chromosome
When genes are close together therefore they are said to be linked
79
Name 3 different types of an RNA molecule
Messenger RNA
Transfer RNA
Ribosomal RNA
80
Describe what it means when a gene is said to be the 'unit of heredity'
Genes are sections of DNA, they are inherited from one generation to the next, hence the term 'unit of heredity'
81
State the approximate percentage of exons found in eukaryotic DNA
1.1%
82
State the approximate percentage of introns found in eukaryotic DNA
24%
83
Which appropriate nucleic acid has a double helical structure
DNA
84
Which appropriate nucleic acid is only found in the cytosol
tRNA
85
Which appropriate nucleic acid is found primarily in the nucleus of the cell
DNA
86
Which appropriate nucleic acid contains thymine
DNA
87
Which appropriate nucleic acid contains uracil
RNA
88
Which appropriate nucleic acid carries amino acids to the ribosomes
tRNA
89
Which appropriate nucleic acid has triplets of bases called codons
mRNA
90
Which appropriate nucleic acid is found in both the nucleus and cytoplasm
mRNA
91
Which appropriate nucleic acid has three bases which comprise the anticodon
tRNA
92
If there are 12,300 amino acids in a particular protein how many codons are needed for the protein
4100 (divide by 3)
93
If there are 12,300 amino acids in a particular protein, how many mRNA nucleotides are required to code for the protein
36,900 (multiply by 3)
94
Outline why the complementary strand is most similar to the mRNA molecule made during transcription
The mRNA molecules are made during transcription when mRNA nucleotides are complementary to DNA nucleotides bind to these exposed bases
95
State two ways why the mRNA molecule would differ from the complementary strand
- mRNA contains uracil instead of thymine
| - mRNA has ribose sugar instead of deoxyribose sugar
96
Compare the processes of transcription and DNA replication
Transcription occurs so that cells can produce the protein molecules that are required for a range of needs. This is in comparison to DNA replication which makes an exact copy of the DNA that is necessary for cell division. DNA transcription involves making a mRNA molecule for a gene, whereas DNA replication involves copying 2 full strands, the template and the complementary strand
97
Explain why it is necessary to remove the intron sections of pre-mRNA molecules
They are de-coding strands therefore need to be removed to ensure only exons are transcribed
98
Predict how different combinations of exons could code for different forms of the protein coded by one gene
The exons are sections of DNA transcribed into polypeptides. This alternative means that different axon sections can be transcribed, leading to different polypeptides of different lengths and with different amino acids.
99
Explain how the structure of a tRNA molecule enables it to function in the process of translation during protein synthesis
tRNA molecules have two critical binding sites. One is the anti-codon which binds to a specific mRNA codon ensuring it can bring the correct amino acid into position. The other binding site is where an amino acid binds to it, each tRNA molecule can carry only one specific amino acid
100
Define the term 'phenotype'
The set of observable characteristics of an individual
101
How do cells become specialised
By changing or differentiating which genes are turned on or off
102
What is cellular differentiation
A process in which a stem cell becomes a specialised cell with a specific structure and function by the expression of selected genes
103
What are housekeeping genes
Genes required for essential functions in every cell such as DNA replication and protein synthesis
104
What can alter gene expression
Methylation
105
What is epigenetics
The study of what happens to your DNA after you inherit it. In other words, which genes are turned on in your cells and which ones are turned off.
106
What can epigenetic changes lead to
Differences between identical siblings, phenotypic differences between clones, may cause human diseases.
107
How does methylation effect gene expression
If the promotor region is not methylated this allows transcription factors and RNA polymerase to bind and so the gene will be expressed.
If the promotor region is methylated, this prevents transcription factors and RNA polymerase from binding.
108
What happens when DNA is methylated
Inhibits the ability of RNA polymerase to bind to promotors to allow for the DNA to be transcribed
109
State the difference between hypo-methylation and hyper-methylation
hypo-methylated DNA can be expressed and therefore the gene is turned on whereas hyper-methylated DNA can not be expressed and therefore the gene is turned off.
110
How does cancer connect with DNA methylation
Studies have shown that cancer cells were substantially hypo-methylated or hyper-methylated compared with normal cells
111
What two genes is cancer linked to
Proto-oncogenes and tumor-suppressed genes
112
What do proto-oncogenes do
Code for proteins that speed up cell division. Hypo-methylation activates them to become oncogenes which over-produce the proteins leading to uncontrolled cell division. Cells are essentially being triggered to divide all of the time.
113
What so tumour suppressed genes do
Code for proteins that slow down cell division
114
What are mutations
Permanent changes in the DNA sequence of an organism
115
What can increase the rate of mutation
Mutagens
116
What are point mutations
The change of a single base in the DNA usually to the 3rd base of the codon
117
What are silent mutations
Point mutations that do not change the order of amino acids in the polypeptide chain
118
What are missense mutations
Point mutations that change the amino acid which may change the folding of the protein
119
What are nonsense mutations
Point mutations that produce a stop codon which results in a non-functional protein
120
Why are mutations silent
There is more than 1 codon that codes for certain amino acids thus, a bade change can change without affection the amino acid
121
What is a frameshift mutations
Mutations caused by insertions of deletions of a base pair in the DNA resulting in a different amino acid sequence after the mutation
122
What are germ-line cells
Cells that produce gametes by meiosis that only have 1 copy of each chromosome
123
What are somatic cells
Cells that re produced my mitosis and are all genetically identical to the parent cell and have a full set of genes
124
Can genes be inherited
Yes but only if they have occurred in the gametes of the parent. There are referred to as germ-line cells
125
How can inheritable mutations lead to changes in characteristics of descendants
If the mutations affects the production of a protein then it will affect the phenotype of the individual
126
What is a promotor
A sequence of DNA to switch the gene on or off
127
What is an activator
A molecule that increases the activity of enzymes and productions of genes
128
What is a repressor
A protein that turns off genes
129
What is a transcription factor
Proteins involved in transcribing DNA into RNA
130
What is methylation
When methyl groups are added to DNA, changing the activity but not the sequence
131
State the difference in DNA that is able to be expressed and DNA that is not able to be expressed
DNA that is able to be expressed the DNA is more exposed and not wound up tightly by histones. Genes that are switched off, are wound up tightly and unaccessible to RNA polymerase therefore unable to be transcribed
132
Describe what genes being expressed continuously means and give an example
Genes that are expressed continuously are active genes and frequently transcribed to produce polypeptides and protein molecules. An example is housekeeping genes
133
Explain how it is possible for some cells to have the same DNA but very different structures and functions
This is the process of cell differentiation. Where cells become specialised for particular roles in the organism. The cell ends up with these special structures and functions as the same genes are not expressed in each cell
134
Describe the process most likely to be responsible for shutting down genes so they remain inactive
DNA methylation is when DNA has methyl groups bound to it that tend to prevent RNA polymerase from carrying out transcription
135
Explain why stem cells are unlike specialised cells and retain their genetic potential
Because stem cells don't have gene sequences or genes that ae permanently switched off
136
Compare the likely differences between methylation in a normal cell compared to a cell that is cancerous
Cancer cells have abnormal methylation depending on the gene. Genes involved are suppressor genes and oncogenes.
137
Predict the likely reasons that changes in methylation could lead to cancerous cells
An example could be a gene involved in DNA repair. If these genes were suppressed (over methylated) then DNA would be slowed and some abnormal DNA may lead to cancerous cells
138
Point out the likely reason why activators and repressors in their mode of action, why they act in opposite ways in gene expression
Repressors are likely to bind to the DNA and prevent the action of RNA polymerase. Activator works in the opposite fashion.
139
Name two types of genes where hyper-methylation could possibly lead to tumour formation
Oncogenes and DNA repair genes
140
What is gene expression
The process where genes are turned on or off in a cell
