topic 1 Flashcards
1
Q
what is an lipid
A
- Lipids are a group of biological molecules with shared characteristics:
- They contain Carbon, Hydrogen and Oxygen (with less oxygen than carbohydrates)
- They are insoluble in water but soluble in organic sovents
The main groups of lipids are triglycerides, phospholipids and waxes
2
Q
what are the 4 roles of lipids
A
- Energy – providing up to twice that of carbohydrates (gram-for-gram)
- Waterproofing – waxy cuticles in plants and insects as well as sebaceous oils from mammals
- Insulation – poor conductors of heat, especially seen in polar bears, seals etc.
- Protection – stored around organs such as the kidney, liver etc.
3
Q
how are triglycerides formed
A
4
Q
what are the properities of triglycerides determied by
A
The properties of a triglyceride molecule are determined by variations in the fatty acid molecules
5
Q
what are the main three groups of fatty acids
A
- Saturated – no double bonds between carbon atoms, each has four atoms joined to it.
- Mono-unsaturated – a single C=C double bond
- Polyunsaturated – multiple C=C double bonds
6
Q
what are phospholipids
A
These are lipids in which one of the fatty acids has been replaced by a phosphate group
Whereas the fatty acids repel water (hydrophobic) the phosphate group attracts water (hydrophilic).
We call this behaviour polar
7
Q
how do phosphilipds work
A
•This means the phospholipid will orientate itself in water so that the hydrophilic (phosphate) head is close to water and the hydrophobic (fatty acid) tails are as far away as possible.
8
Q
name lipid test and method and results
A
9
Q
what are the two main categories of protiens
A
There are two main categories of protein:
- Fibrous proteins – structural, e.g. collagen.
- Globular proteins – metabolic functions, e.g. haemoglobin.
- It is their structure that allows them to carry out their functions.
10
Q
what is an amino acid
A
Monomer units of proteins are called amino acids
11
Q
what are polypeptides and how are they formed
A
- Polypeptides are composed of amino acids bonded to each other, like beads on a string.
- The order of these amino acids is known as the primary structure.
- The bond that holds them together is called a peptide bond
- They are formed by loss of water so it is a condensation reaction.
- -OH from carboxyl group
- -H from amino group
12
Q
how are polypeptides formed
A
13
Q
explain the secondary structure of polypeptides
A
- The polypeptide chain folds into localised, three-dimensional structures such as α-helices and β-sheets. These make up the secondary structure of the protein.
- These are held together by hydrogen bonds between the amine hydrogen and the carbonyl oxygen in the backbone of the polypeptide.
14
Q
explain tertiary structure with polypeptides
A
- The polypeptide folds further into a final, large, three-dimensional shape. This is the tertiary structure.
- The tertiary structure is held together by bonds between R-groups on the amino acid residues. These include:
- Hydrogen bonds – Between many R-groups. Numerous and easily broken
- Ionic bonds – Between adjacent R-groups with opposite charge. Readily broken by changes in pH
- Disulphide bonds – Between adjacent cysteine residues forming a strong S=S double bond. Not easily broken
•
•Hydrophobic and Hydrophilic Interactions – In an aqueous environment hydrophilic groups will orientate to the edges and hydrophobic groups to the centre.
15
Q
explain quaternary structure with polypeptides
A
- Some proteins are made of two or more polypeptide chains and/or contain a non-protein prosthetic group. This is called the quaternary structure of the protein.
- The polypeptide chains are held together in a similar way to the tertiary structure.
•An example of such a protein is
haemoglobin which contains four
polypeptide chains (two α-subunits and
two β-subunits) as well as a haem group
(an Fe2+ ion held in a porphyrin ring).
16
Q
explain overview of structures of polypeptides
A
17
Q
explain the test for proteins
A
18
Q
what is starch
A
- Starch is an energy storage molecule found in many parts of a plant, often as microscopic grains.
- This forms the main part of the diet for billions of people around the world (e.g. potatoes and rice)
- The molecule is an unbranched chain of α-glucose residues joined by condensation reactions in 1,4-glycosidic bonds. This forms a tightly-coiled helix structure in the region of 200-5000 residues long.
19
Q
what are the roles of starch that make it suitable for its role as an energy storage
A
- It is insoluble
- It cannot diffuse across cell membranes
- It is quite compact
- It can be readily hydrolysed to form α-glucose
20
Q
What is glycogen?
A
- Glycogen is sometimes known as animal starch due to its similar shape and being found in animals.
- It also is used as a carbohydrate storage and is mostly found in the muscles and the liver.
- The chains are shorter than those in starch and show extensive branching with 1,6-glycosidic bonds.
21
Q
what is cellulose?
A
- Cellulose is a structural polysaccharide found mainly in plant cell walls.
- Unlike starch and glycogen it is formed from β-glucose residues. These are similar to α-glucose except for the –H and –OH groups on the first carbon are inverted.
22
Q
what is the formation of cellulose
A
•Unlike starch and glycogen it is formed from β-glucose residues. These are similar to α-glucose except for the –H and –OH groups on the first carbon are inverted.
- This means that every other glucose residue is ‘upside down’.
- This leads to the formation of long, straight, unbranched chains which lie parallel allowing the formation of hydrogen bonds between them.
23
Q
how is cellulose linked plant cell wall
A
- The cellulose molecules group to form microfibrilswhich bundle together to form fibres.
- The cell wall of a plant is made up many of these fibres held in a matrix. This maintains the rigid structure of the cell and stops it bursting due to osmotic pressure. This allows cells to become turgid.
24
Q
what is an carbohydrate
A
- A carbohydrate is any molecule which contains carbon, hydrogen and oxygen.
- These are biologically very important as they form the body’s main source of energy as well as playing important structural roles.
25
what are the three types of carbohydrate
three types of carbohydrate: monosaccharides, disaccharides and polysaccharides.
26
what is an monosaccharides
* More commonly known as sugars, these are small, sweet tasting molecules with the formula (CH2O)n, where n is between 3 and 7.
* The most common is glucose a molecule with the formula C6H12O6. In solution this forms a ring structure.
27
what are disaccharides
* Disaccharides are pairs of monosaccharides which are joined together.
* Common disaccharides include:
* Maltose = Glucose + Glucose
* Sucrose = Glucose + Fructose
* Lactose = Glucose + Galactose
28
what are condensation reacts and hydrolysis in relation to disaccharides
* The reaction between monosaccharides is a condensation reaction and forms a glycosidic bond.
* When this bond is broken it is known as hydrolysis.
29
what are polysaccharides
* Polysaccharides are where multiple mono- or disaccharides are joined by glycosidic bonds to form much larger structures.
* This makes them well-suited to storage or structural roles in the cell.
* Starch is a storage molecule made up of up to 100,000 α-glucose molecules.
30
how is starch broken down by enzymes
* Starch (from foods such as bread or potatoes) is first hydrolysed in the mouth by salivary amylase (ptyalin) to maltose.
* Pancreatic amylase completes the breakdown of any remaining starch.
* Maltase produced by the wall of the small intestine hydrolyses the maltose to α-glucose.
31
where are sucrase and lactase produced
•Sucrase and Lactase are produced in the small intestine to hydrolyse sucrose (glucose + fructose) and lactose (glucose + galactose).
32
how does lactose intolerance work
* Some people lack the enzyme lactase in their small intestine.
* In these cases lactose is not hydrolysed nor absorbed by the body. Instead it is broken down by bacteria in the small intestine resulting in large volumes of gas being produced.
* This causes discomfort, nausea, diarrhoea and cramps.
* Sufferers avoid milk or add lactase to the product before it is consumed.
33
how are the properties of polysaccharides determined
the different ways polysaccharides are assembled determine the properties
34
what are enzymes
•Enzymes are biological catalysts; this means that they speed up chemical reactions but remain unchanged by the reaction.
35
how do enzymes work
* Enzymes show a high degree of specificity; this means that one type of enzyme will only work on one type of reaction.
* Enzymes can join two molecules together to form one product, break a molecule down into two or more products or change a molecule.
36
how are activation energy and enzymes linked
•Enzymes work by lowering the activation energy of a reaction thus making it more likely to occur.
37
what are enzymes' three possible method of action
•Enzymes have three possible methods of action:
1. The enzyme may distort the shape of the substrate thus lowering the energy required to break the chemical bonds.
2. The enzyme may provides a favourable environment for the reaction e.g. through the charge distribution of the active site.
3. The enzyme my bring the substrates together in the correct orientation to react.
38
what is the lock and key hypothesis
* Suggested by Emil Fischer in 1894 to explain enzyme specificity.
* He thought that the active site and the substrate possess complementary shapes and fit together like a key into a lock.
* This explains the specificity of the enzyme but not other aspects of enzyme activity.
39
what is the induced model
* An improvement to the lock and key hypothesis. Put forward by Daniel Koshland in 1958.
* This allows for the fact that the enzyme is a flexible structure and suggests that the shape of the active site changes to allow the substrate to bind.
This model explains how the activation energy of the reaction is lowered as well as how other molecules can affect enzymes activity.
40
what factors affect enzyme activity
* Temperature
* pH
* Enzyme concentration
* Substrate concentration
* Competitive Inhibitors
* Non-Competitive Inhibitors
* Allosteric Activation/Inhibition
41
how does temperature affect enzyme activity
* Enzymes function best at a specific temperature. For enzymes in the human body this is around 40°C.
* Below this temperature the collisions between enzyme and substrate are less frequent and so fewer reactions occur.
* Above this temperature the tertiary structure of the enzyme becomes unstable and begins to change making the enzyme molecule useless.
* The bacterium Thermus aquaticus has enzymes which function best at around 85-90°C.
42
how does pH affect enzyme activity
* Similarly to temperature, enzymes functions best at a certain pH. This determines where they can function i.e. In the stomach
* Above or below this pH the charge on certain acidic and basic R-groups will change disrupting the tertiary structure of the enzyme (ionic bonds).
* The optimum pH of an enzyme will depend upon the combination of R-groups in the primary structure.
43
how does enzyme concentration affect enzyme activity
* More enzymes mean more active sites to catalyse reactions.
* In the presence of an excess of substrate, increasing the concentration of enzyme will increase the rate of reaction in a linear relationship.
44
explain how substrate concentration affect enzyme activity
* The rate of reaction will initially increase in proportion to the increase in substrate concentration, as long as the amount of enzyme is fixed. This is because the enzyme has “spare capacity” in terms of unused active sites.
* At a point, the rate of reaction will no longer increase as every active site is filled and working at its maximum speed.
* This is the maximum rate of reaction, or Vmax
45
explain how inhibition affects enzyme activity
* Some substances will slow down the rate of reaction of an enzyme. We call these substance inhibitors.
* There are two types of inhibition:
* Competitive
* Non-competitive
* Inhibition may be reversible or irreversible.
46
explain competitive inhibitors
* Competitive inhibitors have a similar shape to the substrate and can bind to active site. This blocks the substrate from reaching the active site and the reaction taking place.
* The inhibitor does not bind permanently and when it leaves the active site may be filled by a substrate molecule or another inhibitor molecule, depending upon their relative concentrations.
* This means the speed of a reaction can be controlled by altering the amount of inhibitor present.
47
explain non-competitive inhibitors
* Non-competitive inhibitors bind to the enzyme at a place other than the active site.
* This is known as an allosteric effect.
* This will ‘deactivate’ a certain number of enzyme molecules. Increasing the amount of non-competitive inhibitor will deactivate more enzyme.
48
explain irreversible inhibition
* Some substances will permanently change the structure of an enzyme in such a way as to render it unable to catalyse reactions.
* This is often through covalent modification of the tertiary structure.
* These can be non-specific, i.e. Heavy metals, extremes of pH or temperature, or specific, i.e. Potassium cyanide, which irreversibly alters the active site of the respiratory enzyme cytochrome C oxidase.
49
explain inhibition in metabolic pathways
•Chemical reactions in cells are very carefully controlled in order to ensure the correct amounts of a given substance are present where they ought to be.
In order to maintain a steady concentration of a substance many metabolic pathways employ end-product inhibition. This is usually non-competitive
50
explain allosteric activation
•Some molecules will bind to enzymes and increase the rate of reaction by increasing their affinity for the substrate.
(some enzymes inactive in natural form (AS not right shape) some molecules can 'turn on' by changing shape)
This is known as allosteric activation
51
explain the basic structure of DNA
* DNA is actually a very simple structure made of three components:
* Deoxyribose (a five-carbon ‘pentose’ sugar)
* Phosphate
* An organic base
Together these join (by condensation reactions) to make up a single mononucleotide
52
what is DNA
* DNA stands for deoxyribonucleic acid. A material found in the cells of all living organisms.
* This molecule contains all of the instructions for building an entire living organism.
53
how is the double helix structure formed with DNA
* DNA is made up of many nucleotides. These join to make a polynucleotide.
* Two polynucleotide strands are joined side by side as a result of hydrogen bonding between their bases.
* This ‘ladder-like’ structure then twist about each other to form a double helix.
54
explain base pairing with DNA
* There are four bases which make up DNA, two single-ring bases and two double-ring bases:
* Single-ring bases – cytosine (C) and thymine (T)
* Double-ring bases – adenine (A) and guanine (G)
* As the double-ring molecules are longer they can only hydrogen bond with the single ring molecules.
* Furthermore, as A and T make two hydrogen bonds and C and G make three they will only bond with each other.
A only pairs with T, C only pairs with G
55
explain the characteristics of DNA
* The DNA molecule is well suited to its function in a number of ways:
* It is very stable and resistant to change enabling it to be passed through generations without loss of information
* It is very large and can therefore carry vast quantities of information
* The two strands are easily separated for replication purposes (due to hydrogen bonds
* The sugar-phosphate backbone ‘protects’ the bases to some degree from external factors which may corrupt it.
56
what characteristics of DNA are provided by the structure of DNA
* It is stable
* The two polynucleotide strands are easily separated for replication
* The genetic information ‘written’ in the sequence of base pairs is, to some extent, protected by the sugar-phosphate backbone.
57
explain the differences between DNA in prokaryotes and eukaryotes
* In Prokaryotic cells (e.g. bacteria):
* The DNA molecule is shorter
* It forms a continuous circle
* It does not have associated structural proteins – hence it does not form chromosomes
* In Eukaryotic cells (e.g. plants, animals, fungi)
* The DNA molecule is larger
* It is linear
* It is associated with histone proteins and forms chromosomes
58
how do chromosomes come about with DNA
* In Eukaryotes, the DNA does not simply float freely about the nucleus. It is associated with proteins.
* Most of the time the DNA is not visible as it is spread throughout the nucleus. However, just before cell division the DNA comes together in structures called chromosomes and is visible using a good light microscope.
* The proteins form the scaffolding around which the DNA is packaged.
59
what is the structure of chromosomes
* The DNA wraps around histone proteins and resembles ‘beads on a string’.
* This structure then coils about itself.
* These coils form loops which then are coiled again.
* This makes the visible chromosome we see in the nucleus.
60
what are the key parts of chromosomes
* Chromosomes have the following key parts:
* Chromatids – these are two identical strands of DNA formed before cell division.
* Centromere – this is the point at which the two chromatids are joined and at which they will be separated during cell division.
61
what are homologous chromosomes
* In most animals and plants, chromosomes occur in pairs called homologous chromosomes.
* These come about as a result of sexual reproduction. You get one from your mother and one from your father.
* The total number of chromosomes is known as the diploid number. In humans this is 46.
62
what are alleles
* Homologous chromosomes code for the same characteristics (i.e. eye colour, blood group) but may have different versions of the gene (i.e. blue/brown, ABO). These versions are known as alleles.
* The genes for the same characteristic will always occur at the same place on each chromosome. This is known as the gene’s locus.
63
why is DNA replication required
* DNA must be copied before a cell divides in order that each of the daughter cells has the required genetic material to function.
* This copying must be exact as changes to the sequence of bases could be catastrophic for the cell resulting in lost functionality or death.
64
explain the two models of DNA replication
* In the early days there existed two models for DNA replication:
* Conservative replication – whereby a new DNA double-helix was assembled in parallel leaving the parent molecule intact and an entirely new daughter molecule.
* Semi-Conservative replication – whereby the double helix split into separate strands and each forms a template for the assembly of the other strand. This leaves two molecules each half ‘new’ and half ‘old’ DNA.
65
what fators does semi conservative replication depend on
* Semi-conservative replication relies on a number of factors:
* There are the four types of nucleotides (ATCG) present
* Each will only bind to one other on the ‘template’ strand (this is a fundamental feature of DNA)
* The enzymes DNA helicase and DNA polymerase are present to catalyse the reaction.
* There is a supply of energy in the form of ATP
66
how does semi conservative replication work
1. DNA Helicase breaks the hydrogen bonds between the polynucleotide chains causing the double helix to ‘unzip’ and separate.
2. Free nucleotides bind to their complementary bases along each strand.
3. Energy (as ATP) ‘activates’ these nucleotides.
DNA Polymerase joins these activated nucleotides to form two new identical DNA molecules
67
what are the three molecules made up of nucleotides
1) DNA (deoxyribonucleic acid)
2) ribonucleic acid (RNA)
3) ATP (adenosine triphosphate)
68
explain DNA bases
bases are nitogenous (contain nitrogen)
- split into 2 groups : purines (two groups) and pyrimidines (one ring)
- 4 possible bases : purines - C and T (cytosine and thymine)
: pyrimidines A and G (adenine and guanine)
69
how are nucleotides linked
- by condesation reactions
- forms a phosphodiester bond and releases a molecule of water
- to make DNA needs 2 polynucleotides which are bonded in opposite directions (antiparallel strands)
70
what is complimentary base pairing
a purine base and a pyrimidine base always go together
- A and T
- G and C
- these antiparallel strands joined at the bases by hydrogen bonds
- 3 between C and G and 2 between A and T
71
how do we describe the direction of the strands
5 prime and 3 prime
- 5 prime used for end with spare phosphate sticking out
72
explain overview of DNA structure
73
what is the sequence of DNA bases actually relating to?
- code to make various proteins
- machinery in cells can read this code and manufacture proteins (protein synthesis)
- every 3 base = amino acid (triplet code)
74
how many base combinations and amino acids combinations are there
- 20 amino acid
- 64 base
- amino acids are usually coded for more than one triplet code
75
what is RNA
* DNA does not leave the nucleus yet protein synthesis occurs on ribosomes in the cytoplasm.
* This means something is required to transfer the information from the former to the latter. This is ribonucleic acid (RNA)
* In particular, the RNA which carries the information is known as messenger RNA or mRNA.
* This is small enough to leave the nucleus through the nuclear pores.
76
give features of the genetic code
* Each amino acid is coded for by a sequence of three bases, a codon.
* The code is degenerate. This means that most amino acids have more than one codon.
* There are three stop codons which mark the end of a polypeptide.
* The code is non-overlapping which means no base is read more than once, i.e. bases 123456 are read as two codons, 123 and 456.
* The code is universal. This means it is the same in the vast majority of organisms.
77
what is the structure of RNA
* The structure of RNA is similar but distinct from the structure of DNA.
* Like DNA it is a polymer made up of repeating mononucleotides. Unlike DNA it is single-stranded.
* The nucleotide is made up of the following sub-units:
* The pentose sugar ribose
* An organic base (Adenine, Guanine, Cytosine and Uracil)
* A phosphate group
78
what is mRNA
* mRNA is made using the DNA as a template in a process known as transcription.
* It forms a single helix which leaves the nucleus and moves to the cytoplasm where it acts as a template by which polypeptides are assembled.
* It is easily broken down and there does not persist in the cytoplasm longer than is necessary.
79
what is tRNA
* tRNA is a small molecule (c. 80 nucleotides) folded into a clover-like shape.
* One arm of the molecule has a binding site for an amino acid and the opposite arm, the anti-codon loop, has a sequence of three bases which are complementary to the codons on the mRNA.
* This structure allows tRNA to assemble the correct sequence of amino acids on the mRNA template in a process known as translation.
80
how does translation happen
ribosomes move along the mRNA
- reading a codon at a time so the corresponding anticodon on a tRNA is selected
- will happen with a second codon too
- peptide bond formed between two amino acids
- the first tRNA can be released and mRNA can move along to next codon
- continues until a stop codon is reached
81
where do the amino acids come from
- amino acids created in seperate cycles in the cell
- exist in the cytoplasm waiting for tRNA
82
what are introns and extons
Introns are sections of DNA that do not code for amino acids and therefore polypeptide chains. These get removed, spliced, out of mRNA molecules Exons are the sections of DNA that do code for amino acids.
83
what is splicing
* Splicing is the process during which introns are removed from the pre-mRNA to leave only the protein coding portion of the gene.
* This only occurs in eukaryotic cells.
* Splicing does more than simply removing introns as the sections can be reformed in many different orders so one gene can code for up to a dozen proteins.
* Some disorders can affect the recombination of these exons and lead to non-functional polypeptides being produced. An example of such a disease is Alzheimer’s disease.
84
what is transcription and how does it work
* Transcription is the process by which pre-mRNA is produced from the DNA template.
* This pre-mRNA is then spliced to remove introns and leave mRNA which diffuses out of the nucleus.
1. DNA helicase acts upon the region of the DNA to be transcribed, breaking the hydrogen bonds and exposing the bases.
2. RNA polymerase moves along the exposed region of the template strand joining RNA nucleotides to the exposed bases as for DNA except free uracil joins to adenine.
3. The DNA reforms behind the RNA polymerase so only around 12 bases are exposed at any one time.
4. When the RNA polymerase reaches a stop triplet code it detaches and the pre-mRNA is complete.
85
show an over view of protein synthesis
86
what is a gene mutation
- occur often because of factors in our environment such as smoking or UV lights (called mutagens)
- however mutations randomly happen all the time its just these mutagens increase the rate of them occuring
- quite often mutations are harmless, but every now and agaij they can cause serious problems
87
what are the three gene mutations we should be aware of
1) substituation
2) deletions
3) insertions
88
what is substitution
- one base changed for another
- not that serious as max one alteration for amino acids
89
what is deletion
- base removed from the sequence
- can be very serious as will effect all amino acids from that point onwards
90
what is insertion
- base inserted into the sequence
- very serious as all bases after that point are affected
91
what is sickle cell disease
- caused by a gene mutation
- base substitution
92
summarise the 8 properties of water which allow adequate function
1) polar solvent, ionic (eg. salt) and covalent (as polar) will dissolve, many chemical reactions will happen here
2) excellent transport medium as many substances will dissolve + others which form colloids (eg. starch)
3) as water cools at 4 degrees it is at max density, when frozen it is less dense due to hydrogen bonds, ice floats forming an insulating layer preventing water under from freezing and will warm easily as only top is ice, life continue under the ice
4) slow to absorb and release heat as hydrogen bonds between molecules need a lot of energy to break. stable temp of lakes making them good habitats
5) liquid so cant be compressed, good for hydraulic mechanisms
6) cohesive molecules as intermolecular forces mean molecules stick together, important for the movement of water from root to leaves
7) adhesive, attracted to other molecules, important in plant transport systems and surface tension.
8) very high surface tension due to intermolecular forces, great importance in plants
