Biochemical Molecules Flashcards
(101 cards)
1
Q
Type of bonding for water?
A
Polar covalent bonding
2
Q
What do polar and non polar molecules have?
A
Polar molecules have an unequal distribution of charge. Non polar molecules have equally distributed charge throughout its atoms)
3
Q
In water what does the -ve oxygen molecule attract?
A
The +ve hydrogen atoms of other water molecules. This is called hydrogen bonding.
4
Q
What is it that gives water is biological features?
A
The hydrogen bonds
5
Q
Solvent features (water):
A
The tiny charges on the molecules attract other charged molecules or ions. These molecules spread around in between the water molecules- dissolving.
Excellent solvent due to its polar nature (examples are ions carried by plasma and urea in urine).
6
Q
Viscosity and lubrication effect of water
A
Water has a low viscosity, important for the flow of blood. Yet its lubricating nature makes it useful in synovial fluid).
7
Q
Why is water important for living organisms (4)
A
Water is a reactant in chemical reactions: hydrolysis reactions
Water is transport medium: transports glucose and oxygen
It’s a solvent, meaning substances can be dissolved in water and transported
Used in temperature control.
8
Q
Temperature asserts (of water)
A
When heat energy is added to water, a lot of energy is used to break h bonds
Little energy is left to raise the temperature
Water needs a lot of energy to raise its temperature high specific heat capacity
9
Q
Water needs a lot of energy to raise its temperature high specific heat capacity
Why is this important in the body?
A
Stops rapid temperature changes: temperature kept fairly constant
Water is Thermo-stable (high specific heat capacity) meaning that a lot of energy is required to break the hydrogen bonds between the molecules, thus keeping aquatic environments fairly steady despite external fluctuations in temperature.
10
Q
Also a lot of energy is used to break H bonds for evaporation (high latent heat of evaporation)
How is this useful in the body?
A
Water in sweat on the skin surfaces absorbs heat energy from the body as it evaporates. Causing cooling.
11
Q
What does the upthrust in water permit?
A
Enables aquatic animals to be much larger than terrestrial
12
Q
Density features (water):
A
Solid water is less dense than liquid, means cold snap aquatic organisms can survive under the frozen surface (ice floats on water).
13
Q
Transparent features (water):
A
Water is transparent, essential for photosynthesising aquatic plants and enables aquatic animals to see their food and/or predators
14
Q
Cohesion and surface tension features (water):
A
Water molecules stick together due to its polarity.
Allows water to flow easily and transport substances.
Upper most molecules are pulled downwards as they have no water molecules above them.
Pulling force draws them closer together forming strong surface tension
The “sticky” nature of the water makes it a habitat for light invertebrates like pond skaters using the surface tension of water. This polar nature means that water can rise in xylem a considerable distance.
15
Q
Stem cells
A
All cells begin as undifferentiated cells and originate from mitosis or meiosis. They’re not adapted to any particular function (unspecialised) and they have the potential to differentiate and become any one of the range of specialised cell types in the organism. Stem cells are able to undergo cell division again and again, and the source of new cells necessary for growth, development, and tissues repair.
16
Q
What happens once a cell specialises
A
they lose ability to divide, entering the G0 phase of the cell cycle.
17
Q
Describe and explain the activity and replication of stem cells
A
Activity of stem cells are strictly controlled, not divide fast enough, then tissues aren’t efficiently replaced leading to ageing. Uncontrolled division can form masses of cells called tumours, lead to development of cancer.
18
Q
Potency
A
stem cell’s ability to differentiate into different cell types. Stem cells differ depending on the type of cell they can turn into.
19
Q
Totipotent
A
differentiate into any type of cell (e,g is a fertilised egg, or zygote) they’re usually destined to provide a whole organism (can also differentiate into extra-embryonic tissues.
20
Q
Pluripotent
A
can form all tissue types but not whole organisms
21
Q
Multipotent
A
Can only form a range of cells within a certain type of tissue (haematopoetic stem cells in bone marrow are multipotent because this gives rise to various types of blood cells).
22
Q
Differentiation
Why in multicellular organisms, do cells have to specialise?
A
to take on different roles in tissues and organs (adapted and so have different shapes and sizes and contain different organelles).
23
Q
What happens when cells differentiate, and what forms this adaptation/ what’s it dependant on?
A
When cells differentiate they become adapted to their specific role. What forms this adaptation takes is dependent on the function of the tissue, organ and organ system to which the cell belongs.
24
Q
What do cell require energy for? (ATP)
A
three main types of activity: synthesis (of large molecules like proteins), transport (pumping molecules or ions across cell membranes by active transport) and movement (of protein fibres in muscle cells that cause muscle contraction).
25
Inside cells, what molecules are able to supply energy
Adenosine triphosphate
| ATP
26
What’s an ATP molecule composed off?
f a nitrogenous base, a pentose sugar and three phosphate groups. It is a nucleotide. The base is always adenine, and there are three phosphate groups. The sugar in ATP is ribose, as in RNA nucleotides.
27
What is ATP known as?
Universal energy currency
28
What happens when ATP is broken down?
A small amount of energy is needed to break the relatively weak bond holding the last phosphate group in ATP. However a large amount of energy is then released when the liberated phosphate undergoes other reactions involving bond formation. Overall a lot more energy is released than used.
29
As water is involved in the removal of phosphate group (another example of what sort of reaction?)
Hydrolysis reaction
30
Ethics on stem cells
Removal stems cells, destruction of embryo (although techniques being implemented to not damage it). Not only religious objections to the use of embryos, but moral ones too, many believe life begins at conception, so destruction of an embryo is murder. There is a lack of consensus as to when the embryo itself has rights, and also who owns the genetic material that is being used for research (controversy is holding back progress). The use of plant stem cells does not raise the same ethical issues as animal cells.
31
List some uses of stem cells
transplanted into specific areas have the potential to treat certain diseases such as: heart disease (muscle tissues damaged result of heart attack, normally irreparable), type 1 diabetes (body’s own immune system destroys the insulin producing cells in pancreas), Parkinson’s disease (symptoms of shaking and rigidity, caused by the death of dopamine-producing cells in the brain), Alzheimer’s disease (brain cells are destroyed as a result of the build up of abnormal proteins), macular degeneration (blindness in elderly and diabetics), birth defects, spinal injuries, treatment of burns, drug trials and developmental biology (study).
32
What are the sources of animal stem cells?
Embryonic stem cells- present at very early stage of embryo development and are totipotent. After 7 days a mass of cells (blastocyst) forms and the cells are now in a pluripotent state. Tissue (adult) stem cells- present throughout life from birth, found specific areas (bone marrow). They’re multipotent, although there’s growing evidence can be artificially triggered to become pluripotent. Stem cells can also be harvested from the umbilical cord of new borns, for future use for the individual (won’t be rejected).
33
Source of plant stem cells?
present in meristematic tissue (meristems). This tissue is found wherever growth is occurring in the plant (tips or roots and shoots). Also located sandwiched between phloem and xylem tissues (vascular cambium). These cells differentiate to the cells present in the phloem and xylem tissues. In this way the vascular tissues grows as the plant grows. The pluripotent nature of stem cells in meristems continues throughout the plants life.
34
Does hydrolysis of ATP happen in isolation?
does not happen in isolation, but in association with energy-requiring reactions. Reaction are said to be “coupled” as they happen simultaneously. ATP is hydrolysed into adenosine diphosphate (ADP)a and a phosphate ion, releasing energy.
35
What does the instability of the phosphate bonds in ATP mean?
that it is not a good long term energy source (fats and carbohydrates much better).
36
How is ATP created, from ADP
The energy released from the breakdown of fats and carbohydrates (through cellar respiration), used to create ATP, through reattaching a phosphate group to an ADP molecule (phosphorylation). As water is removed in the process, example of condensation reaction.
37
Why do/can’t cells store large amounts of ATP
Due to instability of ATP, cells don’t store large amounts. However ATP is rapidly reformed by the phosphorylation of ADP. Inter conversion of ATP and ADP is constantly happening in living cells, meaning cells do not need a large store of ATP.
38
Inter conversion of ATP and ADP is constantly happening in living cells, meaning cells do not need a large store of ATP, what does this allow?
Allows there to be a good immediate energy store
39
What does the structure and properties of ATP permit?
means that it is well suited to carry out its function in energy transfer.
40
Properties of ATP:
- Small, moves easily into and out of and within cells
- Water soluble, energy requiring processes happen in aqueous environments
- Contains bonds between phosphates with intermediate energy: large enough to be useful for cellular respiration but not so large that energy is wasted as heat.
- Releases energy in small quantities, quantities are suitable to most cellular needs, so that energy is not wasted as heat.
- Easily regenerated, can be recharged with energy.
41
What are lipids?
A mixed group of hydrophobic compounds (non polar)
Composed of oxygen hydrogen and carbon
Insoluble in water, soluble in organic solvents (alcohol and benzene)
42
How do lipids compare to carbohydrates?
much lower proportion to oxygen to hydrogen compared with carbohydrates (more H atoms per molecule)
43
What are the two types of lipids
Simple (steroids, terpenes)
| Complex (triglycerides, phospholipids, waxes)
44
Triglycerides (shape, bonding, reaction)?
E shaped, Ester bonds (esterification is the synthesis and breakdown of ester bonds, triglycerides), the polar parts of the glycerol and the fatty acid give a condensation reaction, therefore becomes non polar (insoluble in water). 3 water molecules are produced.
45
Saturated lipids
no more H atoms could be added, some have double bonds so could therefore take more H atoms, so are called unsaturated. SSS- Single (bonds) saturated (lipids) solid (at room temperature). DUL- Double (bonds) unsaturated (lipids) liquid (at room temperature)
46
Glycerol (structure, polarity)
Is a small molecule (C3H8O3), always same structure and polar because of the -OH molecule.
47
Fatty acid (structure, polarity)
Fatty acids are long molecules with polar, hydrophilic end, non-polar hydrophobic “tail”, general formula CnH2nO2. The hydrocarbon chain can be from 14 to 22 CH2 units long.
48
What are carbohydrates
contain carbon hydrogen and oxygen. The groups contain monomers dimers and polymers.
49
What are carbohydrates also known as?
Saccharides or sugars
50
What are the different carbohydrates
A single sugar unit is known as a monosaccharide (glucose fructose and ribose). When 2 monosaccharides link together form disaccharide (lactose and sucrose). When two or more monosaccharides are linked, form a polymer called polysaccharides (glycogen, cellulose and starch).
51
General formula of carbohydrates
CnH2nO2
52
What are the two structure variations of glucose
Alpha and beta glucose
53
What is the variation of the alpha and beta glucose molecules
The OH group on carbon 1 is in the opposite positions
54
How are disaccharides formed?
when two monosaccharides units join forming a glycosidic bond, by a condensation reaction. Two hydrogen atoms and an oxygen atom are removed from the glucose monomers and join to form a water molecule. A bond forms between carbon 1 and 4 on the glucose molecules and the molecules are now joined. A covalent bond (glycosidic bond) is formed between 2 glucose molecules. Condensation reaction, because a water molecule is formed as one of the products.
55
Example of the formation of some disaccharides
Glucose + glucose -> maltose + water
Glucose + fructose -> sucrose + water
Glucose + galactose -> lactose + water
56
Properties of monosaccharides
White, crystalline solid, sweet tasting and readily soluble in water
57
Functions of monosaccharides
Functions: glucose is an important respiratory substrate and the starting material for more complicated carbohydrates (starch cellulose glycogen are all polymers of glucose).
Fructose is the sugar found in fruits. Ribose and deoxyribose (pentoses) are part of nucleotides (e.g RNA).
58
Starch structure
Structure: consists of 2 different polysaccharides (amylose and amylopectin). Amylose has slinky structure whereas amylopectin has structure of slinky shape with other similar shapes attached to it. Amylose is a long chain of alpha glucose molecules joined together by 1-4 glycosidic bonds. It coils into a helix shape that make it more compact. Each molecule has only 2 accessible ends where the enzymes amylase can bind (so amylose can be broken down slowly). The additional 1-6 glycosidic bond causes amylopectin to have side branches that are more accessible, and hence amylopectin can be broken down more easily when glucose is needed.
59
Starch properties
Properties: Amylose, compact cylindrical polysaccharide composed of many alpha glucose molecules. Glycosides bonds linking the glucose molecules is a 1-4 bond. Amylose is a compact energy storage molecule. Amylopectin composed of 1-6 bonds forming long straight chains (unlike amylose). Amylose more branched, so it has more branched open molecular structure. Starch is insoluble in water as they’re too large to diffuse through the cell membrane and pass out the cell.
60
Starch function
Function: When cell needs glucose, enzymes are used to break the glycosidic bond in starch. This is a hydrolysis reaction and requires water. As amylopectin has a large number of branches this means it has a large number of ends, means enzymes can break down starch rapidly.
61
Glycogen structure
A polymer of alpha glucose. Most of the alpha glucose molecules are joined by the 1-4 glycosidic bond. It contains branches where the points are joined by the 1-6 glycosidic bond. They have the same structure as amylopectin (main difference is glycogen is more branched making glycogen a very compact molecules). Enzymes can then convert it back to glucose very quickly).
62
Glycogen properties
Properties: It’s a storage polysaccharide of animals and it’s highly branched and not coiled. Is made by animals as their storage polysaccharide and is found mainly in muscle and liver. It can be hydrolysed quickly. It breaks downs into alpha glucose monomers by the enzyme glycogen phosphorylase.
63
Glycogen function
Function: Multi branched polysaccharide of glucose that serves as a form of energy store in animals and fungi. The polysaccharide structure represent the minimum storage form of glucose in the body. In humans glycogen serves as energy store for the liver and the skeletal muscles. Two forms of energy reserves it can serve, glycogen being a short term and other form being triglyceride stores in adipose tissue for long term storage.
64
Cellulose structure
Beta molecules are unable to react together like alpha molecules, hydroxyl groups of carbon 1 and 4 are too far to react. Only way they can react is if an alternative beta molecule is turned upside down. When a polysaccharide is formed from glucose this way, it is unable to coil or form branches. A straight chain molecule is formed called cellulose.
65
Cellulose properties
They make hydrogen bonds with each other forming microfibrils. These then join together forming macrofibrils, which combine to produce fibre. These fibres are strong and insoluble (make cell walls). Cellulose important part of diet, very hard to break down into its monomers and forms the “fibre” or “roughage” necessary for a healthy diet.
66
Cellulose function
Function: The main structural component of cell walls due to its strength which is a result of the many H bonds found between the parallel chains of microfibrils. High tensile strength, strength without breaking, cell walls can withstand turgid pressure. Cellulose fibres freely permeable, allows water and solutes to leave or reach the cell surface membrane. Few organisms have the enzyme cellulase to hydrolyse cellulose it’s a source of fibre.
67
How to carry out the extraction of DNA
- Grind sample in a mortar and pestle (breaks down the cell walls)
- Mix sample with detergent(breaks down cell membrane releasing the cell contents into solutions)
- Add salt (break the hydrogen binds between DNA and water molecules
- Add protease enzyme (will break down the proteins associated wit(t he DNA nuclei)
- Add a layer of alcohol (ethanol) on top of sample (it causes the DNA to precipitate out of solution)
- The DNA will be seen as white strands forming between the layer of sample and layer of alcohol. The DNA can be picked up by ‘spooling’ it onto a glass rod.
68
What is TLC used for?
separate the individual components of a mixture (used to separate and identify a mixture of amino acids in solution).
69
What are the two stages in TLC (what happens in each stage)
2 phases, stationary and mobile phase (which involves an organic solvent). The mobile phase pics up the amino acids and moves through the stationary phase and the amino acids are separated.
In the stationary phase a thin layer of silica gel is applied to a rigid surface (e.g sheet of glass or metal). Amino acids are then added to one of the gel. This end, submerged in organic solvent, which then moves through the silica gel (i.e mobile phase).
70
What does the rate of amino acids through the silica gel depend on
the interactions of hydrogen bonds with the silica in the stationary phase, and their solubility in the mobile phase. This results with different amino acids moving different distances in the same time period resulting with them to separate from each other.
71
A triplet code:
The instructions that DNA carries are contained in the sequence of bases along the chain of nucleotides that make up the two strands of DNA. The code in a base sequence is a simple triplet (no overlap). It’s a sequence of three bases (codon). Each codon codes for an amino acid.
72
What’s a gene
A section of DNA that contains the complete sequence of bases (codons) to code for an entire protein is called a gene.
73
What does it mean if the genetic code is universal
all organisms use this same code, although the sequences of bases for each individual protein will be different.
74
How many different types of base triplets are there
There are 4 different bases, so there are 64 different base triplets/ codons possible. This includes one start codon, when it comes to the beginning of a gene, signalling the start of a sequence. If it’s in the middle of the gene, it codes for the amino acid methionine.
There are three stop codons that don’t code for an amino acids and signal the end of the sequence.
75
Why is it important to have a start codon
Having a single codon to signal start ensures that triplet of bases are read “in frame” (from base 1 instead of 2 or 3). So the genetic code doesn’t overlap.
76
Meaning of the term degenerate code
As there are 20 different amino acids that regularly occur in biological proteins, there are a lot more codons then amino acids, meaning that many amino acids can be coded for by more than one (the code is known to be degenerate).
77
What is DNA
DNA is a polynucleotide. It is built up of basic building blocks called nucleotides. There are four different nucleotides in DNA and these join in pairs by hydrogen bonds, and the sugar phosphate is bonded by phosphodiester bonds.
This forms a long, strong sugar-phosphate ‘backbone’ with a base arranged to each sugar. The phosphodiester bonds are broken by hydrolysis, releasing the individual nucleotides.
78
Differences of RNA and DNA
The sugar (ribose, not deoxyribose)
Uracil instead of thymine
RNA usually single stranded
79
RNA role
Ribonucleic acid plays an essential role in the transfer of genetic info from DNA to the proteins that make up the enzymes and tissues of the body.
80
Why is RNA important
DNA of each chromosome very long molecule, compromising many hundreds of genes, and DNA can’t leave the nucleus to supply information directly to site of protein synthesis.
81
What happens when sequence of bases aren’t matched correctly
Sequence of bases not always matched exactly, incorrect sequence in newly-copied strand. These errors occur randomly and spontaneously, and lead to a change in sequence of the base, known as mutation.
82
Semi-conservative replication (steps)
(half kept the same).
Double helix structure has to unwind and then separate into 2 strands (so hydrogen bonds are broken).
Free DNA nucleotides then pair with their complementary bases (have been exposed as the strands separate)
Hydrogen bonds formed between them.
Finally, the new nucleotides join to their adjacent nucleotides with phosphodiester bonds.
2 new molecules of DNA are produced, each consists of one old strand of DNA and one new strand
83
rRNA tRNA and mRNA roles
rRNA are responsible for reading the order of amino acids and linking amino acids together. They do this through a highly complex sequence. tRNA carries amino acids to the ribosomes. For each kind of amino acid, there is a specific kind of tRNA molecule that will recognize and transport it. mRNA is a single-stranded molecule that carries genetic code from DNA in a cell's nucleus to ribosomes.
84
Name off proteins
Polypeptides
85
State some functions of polypeptides
transport, regulation, enzyme reactions, and cell and tissue structure.
86
Protein
Proteins are often very large, composed of thousands of amino acid monomers (there are 20 different types of amino acids found in proteins).
87
What is undertaken to create a peptide bond
| amino acid + amino acid -> dipeptide
Condensation reaction
88
What breaks a peptide bond (polypeptides)
Introducing a water molecule (hydrolysis reaction)
89
Polypeptides (primary structure)
is a sequence of a chain of amino acids. The amino acid sequence of a protein determines the higher levels of structure of the molecule.
90
Polypeptide (secondary structure)
polypeptides don’t lie straight, chain can form either one of two:
Alpha Helix, twisted shape like a spring with hydrogen bonds between C=O and -NH groups to stabilise.
Beta Fold, pleated sheets with hydrogen bonds in parallel chains
91
Polypeptides (tertiary structure)
polypeptide chains bend to produce 3 dimensional shapes. Chemical bonds and hydrophobic reactions between R groups keep this final tertiary structure. It’s a precise and unique shape. There are 1 of 2: Fibrous proteins, long coiled chains (e,g collagen, keratin and tendons). Globular proteins- spherical shape (e,g enzymes and haemoglobin). There are 4 types of bonds that can take place (ionic bonds between R groups with positive or negative charges quite strong, hydrophobic interactions occur between R groups and are non polar, disulfide linkages/bridges are covalent S-S bonds between two cysteine amino acids which are strong, and hydrogen bonds, weak).
92
Polypeptides (Quaternary structure)
a protein may be made up of several polypeptides chains held together (e.g is haemoglobin- 4 chains held together). They are held together by the same bonds as tertiary, forming a biological active molecule.
93
What are globular proteins
are compact, water soluble, and usually roughly spherical in shape. They form when proteins fold into their tertiary structure in such a way that the hydrophobic R- groups on the amino acids are kept away from the aqueous environment. The hydrophilic R-groups are on the outside of the proteins. This means the proteins are soluble in water.
94
What are globular proteins important for?
Solubility important for many functions, they are essential for regulating many processes essential for life (I.e chemical reactions, immunity, muscle contraction)
95
What are fibrous proteins
are formed from long, insoluble molecules, due to the presence of a high proportion of amino acids with hydrophobic R-groups in their primary structures. They contain a limited range of amino acids, usually with small R-groups. The amino acid sequence in the primary structure is usually repetitive. This leads to very organised structures reflected in the roles fibrous proteins have.
96
Conjugated proteins
are globular proteins that contain a non-protein component called a prosthetic group. Proteins without prosthetics groups are called simple proteins.
97
Insulin
a globular protein. It’s a hormone involved in regulation of blood glucose conc. Hormones are transported in the bloodstream so they need to be soluble. They also need to be able to fit into specific receptors on cell surface membranes to have their effect and therefore need to have a precise shape.
98
Haemoglobin
is the red, oxygen-carrying pigment found in red blood cells. A quaternary protein made from four polypeptides, (2 alpha and 2 beta subunits). Each subunit contains a prosthetic haem group. The iron ll ions present in the haem groups are each able to combine reversily with an oxygen molecule (this is what allows haemoglobin to transport oxygen).
99
Keratin
group of fibrous proteins present in hair, skin and nails. It has a large proportion of the soulful-containing amino acid, cysteine. Resulting in many strong disulfide bonds (bridges) forming strong, inflexible and insoluble materials. Flexibility is determined by the degree of disulfide bonds (hair contains fewer bonds than nails making it more flexible). Unpleasant smell formed when skin or hair is burnt is due to the presence of relatively large quantities of sulphur in the proteins.
100
Elastin
is a fibrous protein found in elastic fibres (along with small protein fibres ). Elastic fibres are present in the walls of blood vessels and in the alveoli, they give theses structures the flexibility to expand when needed, and to return to their normal size. Elastin is quaternary protein made from many stretchy molecules, called tropoelastin.
101
Collagen
Collagen is another fibrous protein, it’s a connective tissue found in skin, ligaments, tendons and the nervous system. Number of differ forms but all made from three polypeptides wounded together in a long and string rope-like structure. Like rope, collagen has flexibility.
