Biological Molecules Flashcards
What are the two types of Glucose that make up nearly every sugar?
Alpha Glucose and Beta Glucose.
What super weird analogy do you use to remember how to draw alpha and Beta glucose.
Santa! Santa is the biggest alpha of them all, so for alpha glucose you use the catchphrase “ho ho ho” but spell it “HHO HOH HOH” these are 1 top and 2 bottom molecules bonded to the bottom three carbons (the fourth, in between HHO and HOH, is always OHH). Beta Glucose is HHO HOH OHH, the oh representing the underwhelming nature of a beta.
How do you form Maltose?
By the condensation of 2 beta glucose molecules. Therefore, it is a disaccharide.
How do you form Sucrose?
By the condensation of 1 glucose and 1 fructose molecule. Therefore, it is a disaccharide.
How do you form Lactose?
By the condensation of 1 glucose and 1 galactose molecule.Therefore, it is a disaccharide.
How do you form fructose?
fructose is a monosaccharide, made up of 6 carbons, with the formula C6 H12 O6.
How do you form Galactose?
Galactose is a monosaccharide, made up of 6 carbons, with the formula C6 H12 O6.
How do you form Glycogen?
By the condensation of many alpha glucose molecules. Therefore, it is a polysaccharide with the formula C180 000 H360 000 and O180 000. It is only found in animals.
How do you form Starch?
By the condensation of many alpha glucose molecules. Therefore, it is a polysaccharide.
How do you form Cellulose?
By the condensation of many beta glucose molecules. Therefore, it is a polysaccharide. It is only found in plants.
What is a condensation reaction?
When two monosaccharides react with each other and release a hydrogen forming a hydrogen bond and creating the disaccharide/polysaccharide product.
What is a Hydrolysis reaction?
The breaking down of poly/disaccharides into monomers via reacting a hydrogen molecule with it, forming it to break the hydrogen bond.
What is a reducing sugar?
A sugar that can donate electrons to (reduce) another chemical.
How can you test for reducing sugars? (give method)
Using the Benedict’s test. Add 2cm cubed of the food sample in liquiud form to a test tube. Add an equal volume of benedict’s reagent. Heat the mixture in a water bath for five minutes. In terms of concentration of sugars, the colour of the solution can indicate this.
Clear-none, Green-very low, yellow-low, orange-medium, red-high. The concentration goes up in order of the colour spectrum.
Why is starch a good storage molecule?
Because it is coiled, it can be densely packed into small areas. It is also insoluble, so it does not cause osmosis and is therefore not likely to cause cells to become damaged or burst. Has many short branches so lots of enzymes can access and break it down into glucose monomers at one time.
Why is glycogen a good storage molecule?
It is insoluble so therefore does not tend to draw water into the cell via osmosis and doesn’t diffuse out of cells. It is compact so a lot can be stored in a small space. It has more branches than starch so more enzymes can be reacted on it at one time to form glucose monomers. This is important, as animals are more active than plants so have a higher respiratory and metabolic rate.
Why is Cellulose a good structural molecule?
Forms long, straight and unbranched chains,which lie parallel to each other and form hydrogen bonds between the layers. These molecules are grouped to form microfibrils, which then form fibres, which give it even more structural strength.
What are the two main types of lipids we need to know about?
Triglycerides and phospholipids.
What is the structure of a triglyceride?
A glycerol head with three fatty acid tails.
What makes Triglycerides such good stores of energy?
- They have high energy because of all the carbon and hydrogen bonds.
- They have a low mass to energy ratio, meaning they release more energy per gram than carbohydrates.
- They have large insoluble molecules
- Release water when oxidised as of high ratio to hydrogen to oxygen
What is the main difference between phosphate molecules and triglycerides?
Phosphate molecules still have a glycerol molecule, however, one of the fatty acid tails is replaced by a phosphate molecule.
Name one use of Phospholipids.
They are used to make up cell membranes, alongside glycoproteins and glycolipids.
What is a glycolipid?
A phospholipid combined with carbohydrates. It is important in cell recognition.
Are phospholipids polar or non-polar? Why?
Polar. This is because they have hydrophillic heads and hydrophobic tails (the head is the phospholipid).
How do phospholipids react in water?
They form spherical, bilayer membranes.
What are proteins?
Proteins are usually large molecules made up of amino acids.
Why are fats better for energy storage?
They have a higher energy:mass ratio, meaning they release more energy per gram. They also are good for waterproofing as they are insoluble.
What is the structure of wax?
A long chain alcohol bonded to fatty acids with ester bonds.
What are the uses of wax?
Waxes are found in nature as coatings on leaves and stems. Wax waterproofs the leaves of the plant.
Describe how to draw an amino acid molecule.
In the centre is an alpha carbon, with a solitary h bond directly above it and the variable “R” group directly below it. This vertical column is called the side chain. To the left is the amino group. The alpha carbon is bonded to a nitrogen, with a hydrogen atom above it and a hydrogen atom to the left of the nitrogen. So it kind of looks like a right angle triangle, with N as the right angle and the 2 Hs as the other two corners. To the right is the Carboxyl group. This also looks like a right angle triangle, but mirror reflected (the other way round). It has a carbon bonded to the alpha carbon, with an oxygen double bonded just above it and an OH molecule just to the right.
What is the formula of a basic amino group?
-NH2
What is the formula of a basic Carboxyl group?
-COOH
Describe the primary structure of protein.
Primary structure is the sequence of amino acids into a polypeptide chain. It is vital in the function of the protein as it is determined by what amino acids are present, how many acids there are and what order they are in. If any of these change, it could change the structure of the protein.
Describe the secondary structure of protein.
The peptide bond that forms amino acids into polypeptides is an ionic bond. Because of this, the polypeptide molecules move round as they are attracted to the opposite charge. this draws them into a shape, most often an alpha helix or a beta pleated sheet.
Describe the Tertiary structure of protein.
Tertiary structure is the result of further twisting of the secondary structure. This occurs because of different bonds forming within the structure. These bonds are either disulfide bonds, ionic bonds between loose/unreacted carboxyl and amino groups and hydrogen bonds.
Describe the Quartinary structure of protein.
When all the polypeptides bond to make a large protein molecule. However, some smaller proteins stop at tertiary bonds.
Name the two main categories of proteins and give an example of each type.
Fibrous proteins e.g. Collagen
Globular Protein e.g. haemoglobin
Why do fibrous proteins form such strong tissues?
The proteins form into long parallel chains and these chains are then linked into cross-bridge hydrogen bonds, which are weak on their own, but make the molecules very strong because of their multitude.
Describe the structure of Collagen.
The primary structure of a polypeptide chain. The secondary structure is a very tightly coiled alpha helix. The tertiary structure is also a helix shape. The quarternary structure is three of these coiled polypeptide chains twisted together, like a plait or a rope.
What is collagen?
Collagen is a fibrous protein found in tendons and skin of animals. it has a lot of glycerine, so can be visualised as the weird, carnivore-plasm stuff next to animal bones.
What is an enzyme?
An enzyme is a large protein that acts as a biological catalyst.
What is the active site of an enzyme?
The are that a substrate fits with an enzyme and interacts.
What is the Enzyme-substrate-complex?
When the enzyme is completely connected to the substrate.
what is activation energy?
The energy needed to commence a reaction.
What conditions are needed for a reaction to take place?
- reactants must collide with sufficient energy to alter the arrangement of their atoms
- The free energy of the products must be less than that of the substrates/reactants
- their must be sufficient activation energy
Why is the lock and key model now considered a historical/outdated model?
it was inaccurate, because though it did explain how a substrate fitted an active site specifically and broke it into smaller molecules, it eluded that the shape of an enzyme’s active site was rigid and doesn’t change and that an active site only fits one substrate. We have now replaced this with the induced fit model.
Describe the induced fit model.
It describes how an enzyme tends to form the shape of it’s active site whilst it is in Enzyme-substrate-complex.
How does protein structure support the idea of the induced fit model.
The flexibility in the polypeptide chain allows the enzyme to shape it’s active site around the substrate. This also contributes to the idea of denaturing, as the polypeptide chain in enzymes will lose it’s structure/flexibility if the hydrogen bonds in the structure are broken, and these bonds can be broken very easily, the enzyme will not be able to fit around the substrate as easily, which cause it not to be able to fit and perform its function.
how can enzymes help in making bonds between molecules that would usually repel?
It can hold them together with it’s tensile strength, like putting a rubber band around two halves of an apple.
How could you test for a lipid in a sample?
——The emulsion test—–
+ Take a completely dry and grease free test tube
+ Add 5cm^3 of ethanol to 2cm^3 of sample in the test tube and shake thoroughly to dissolve any lipids
+ Add 5cm^3 and shake gently
+ If a white emulsion appears, it indicates the presence of a lipid.
+ As a control, repeat the method using water instead of ethanol– the water should stay clear.
What are nucleotides made up of?
A phosphate group, a 5 carbon sugar and a nitrogenous base.
What are the two main 5 carbon sugars that make up nucleic acids?
Ribose and deoxyribose.
You have a mnemonic for the nitrogenous bases, All Gangsters Carry Tea, what do these letters (AGCT) stand for?
A- adenine G- guanine C- cytosine T- thymine ( uracil in RNA)
What is a chromatid?
One of the two identical X shaped arms of a chromosome.
What is a centromere?
The point at which two chromatids are joined together.
What happens in Interphase?
The cell is still functioning as it grows and the DNA replicates. When you see a cell going through interphase in a cell, you can’t see the chromosomes.
What happens during Prophase?
The chromosomes condense and become visible through a microscope. The centrioles begin to move to opposite ends/poles of the cell. The spindle begins to form.
What happens during Metaphase?
The nuclear envelope breaks down. Chromosomes align along the equator/centre of the cell. Spindle fibres (microtubules) connect centrioles to centrosomes of chromosomes.
What happens during Anaphase?
Centromeres split, allowing chromatids to separate. chromatids move towards poles pulled by the spindle fibres.
What happens during telophase?
Spindle fibres disperse, nuclear envelope reforms, chromosomes decondense/unravel.
What type of proteins are antigens?
Globular proteins
What is the definition of an antigen?
An antigen is any part of the immune system that is recognised as foreign by our immune system.
What are the two types of defence/immune systems animals have?
Non specific and specific.
What are the features of the non-specific immune system?
Physical barriers to prevent the ingestion of antigens and phagocytosis.
What are the features of the specific immune system?
B lymphocytes and T-Lymphocytes.
What is a phagosome?
Where, in a phagocyte, the vesicle carrying the pathogen
What is lysozyme?
The enzyme found in lysosomes that breaks down the pathogen in phagocytosis.
Describe the journey of a pathogen during phagocytosis?
The pathogen travels through the cell membrane, but is then trapped in a vesicle. This vesicle then carris the pathogen to the phagosome, where it is stored to be broken down. Lysosomes are then secreted and they enter the phagosome, and break the pathogen down using lysozymes.
What sort of molecules can diffuse?
Only small, non-polar molecules can diffuse across cell surface membranes, such as oxygen and carbon dioxide.
Define Facilitated Diffusion in 5 features
+ It is a passive process
+ It relies on the kinetic energy of diffusing molecules
+ Occurs through trans membranes and carriers
+ Has to happen at these specific points in a cell membrane
+ Occurs down a concentration gradient
What are protein channels?
Water-filled hydrophilic channels. They only allow specific, water-soluble molecules to pass through. However, these ions are very selective and will remain closed unless specific ions are present. Can be drawn in a diagram to look like a fortune cookie with a hole in the middle (in the middle of a phospholipid bilayer).
What are Carrier Proteins? Four features
+Carry molecules.
+ The molecule has to be specific to the protein
+ The molecule binds to the protein, which causes to change shape, and is then reshaped when the molecule is released
+ Only uses the kinetic energy the molecule already has (Can be drawn in a diagram to look like a fortune cookie with a hole in the middle (in the middle of a phospholipid bilayer)).
What is water potential?
It can help quantify osmosis, as water always moves from a higher water potential to a lower water potential. 100% pure water has has a water potential of 0. Adding solutes reduces the water potential (so it is negative).
What happens when a cell is too hypertonic?
It becomes plasmolyzed. this means the cytoplasm shrinks, so everything inside the cell membrane looks smaller and shrivelled ( though membrane-bound organelles stay the same size). This means the cell membrane looks like it is shrinking away from the cell wall.
What do you call it when a animal cell becomes too hypotonic?What does it look like?
It can cause crenation. This looks like the cell shrivelling.
What do you call it when a animal cell becomes too hypotonic?
It becomes too turgid and can burst, which is called lysis.
Describe DNA replication
DNA replication needs to occur to pass genetic information on to the next generation. When DNA is replicated, it is done semi-conservatively, meaning that each time it is copied, only half of the information is made new.
Describe how to recognise glycolipids in a diagram of a phospholipid
Glycolipids are carbohydrates bound to lipids. The lipid portion/molecule would be embedded in the bilayer, with the chain of carbohydrates extending outside of the membrane. This is helpful because it as the carbohydrates can act as recognition and binding sites.
What is the usual function of a fibrous protein? Give an example
Fibrous proteins usually have structural functions. An example of this would be collagen, which is found in the tendons which join muscle to bone.
Describe the structure of Collagen– Primary, Secondary, Tertiary, Quatinery and random feature
+ The primary structure is a polypeptide chain
+ The secondary structure is very tightly coiled
+ The tertiary structure is also a helix shape
+ The quaternary structure is three of these coiled polypeptide chains linked together
+ The high concentration of glycerine (an amino acid) helps it pack closely together
How do fibrous proteins form fibres?
The proteins form long parallel chains, these chains are then linked with hydrogen bond “bridges”, which help them form very stable molecules.
What is the general function of globular proteins (give two examples)
Globular proteins perform metabolic functions. Enzymes and haemoglobin are examples of metabolic proteins.
What biological molecule controls the cell cycles to try and prevent uncontrolled cell replication (cancer).
Control Genes
Name 5 preventable Cancer causes (Doses)
Diet Obesity Sunlight Exposure Exercise Smoking
What are the three treatments for cancer?
Surgery, Radiotherapy, Chemotherapy
How do the four types of chemotherapy work?
clues–
1) deoxiribo-blockade
2) Pin curls
3) Tying DNA’s Tubes
4) Stopping the “needle on a spinning wheel bran flakes”
1) Blocks enzymes that are necessary for protein synthesis
2) Prevents DNA unwinding (which is required for mitosis), like pinning a curl in place
3) Inhibits the synthesis of new nucleotides (stops mitosis reproduction)
4) Prevents the development of the spindle fibres ( essential for anaphase)
What is the function of smooth endoplasmic reticulum?
The synthesis of lipids and carbohydrates
What is the function of rough endoplasmic reticulum?
Aids the synthesis of proteins.
What is the function of golgi apparatus?
Produce secretory enzymes, such as those secreted by the pancreas. Secretes carbohydrates (i.e. cellulose) lipids, and enzymes like lysozymes.
What is the function of lysosomes?
Aids phagocytosis
Releases enzymes to the outside of the cell, in order to destroy material around the cell
digests worn out organelles to re-use the base components
Completely break down cells after they have died
Basically the over-protective mother of the cell
Name the three most important features of the mitochondria.
Double membrane- outer flat one and inner, heavily folded christae membrane.
Christae- Folded membrane, allows for more reactions to take place as there is a larger surface area
Matrix- The fluid that reactions such as respiration takes place in, thicker than the cytoplasm.
Name the four most important units in the nucleus
The Nuclear envelope
The Nuclear pores - important for molecules such as ribosomes and RNA
Nucleoplasm- goo in the nucleus
Chromosomes
the nucleolous- the largest structure in the nucleus, makes ribosomes
Name the two most important units in the chloroplasts
Grana and Stroma
What is the structure and function of Grana?
Grana are made up of stacks of circular, coin-like discs called thylakoids. These are the site of light- dependant reactions such as photosynthesis.
What is the structure and function of the stroma?
Colourless fluid surrounding the grana, contains the enzymes required for photosynthesis as well as DNA and ribosomes.
What are the maximum magnification and minimum resolution of light microscopes?
Maximum Magnification = x 1500
Minimum Resolution = 200 um
Name three features of light microscopes
Uses waves of light energy
Shows the real object colour in the image
Creates a 2 dimensional image
Name three features/strengths of using a TEM microscope?
+ Highest magnification and resolution as there is a shorter wavelength of electrons
+ Focuses using an electromagnet
+ works by shining a beam of electrons through a thin specimen an then focusing these to form a digital image
name 4 drawbacks of using a TEM microscope
Produces a 2D digital image Can not look at living cells/specimen Must be in a vacuum Complicated preparation may create artefact Does not produce true colour image
how does an SEM microscope work?
It passes a beam of electrons over the surface of the specimen, calles a scanning beam
The specimen will have been coated in heavy metals, so the electrons will be reflected to form an image
this means it produces a 3D image using a condenser electromagnet. This is good as the specimen doesn’t need to be thin.
What are 2 uses of monoclonal antibodies?
Cancer and Pregnancy tests
What does the structure of a monoclonal antibody look like
Antibodies are composed of 4 poly peptide chains: 2 heavy chains, 2 light chains. These chains are joined by disulfide bonds. Overall, this forms a Y shaped structure - The “stem”/vertical bit of the y is the constant region, that stays the same for every antibody, while the “arms”/ v-shaped bit of the y is the variable region, that is specificly shaped for binding to a specific antigen.
Where do T lymphocytes mature?
In the thymus gland
What type of immunity are T cells part of?
Cell-Mediated immunity
What are the 2 types of T cell?
Helper T cells (Th), Cytotoxic T cells (Tc)
what is the role of Th cells in cell-mediated immune response?
Activated T cells divide by mitosis to produce Th cell clones. This is done because, once the original T cell has binded to the antigen-presenting cell, The Th cell clones have receptors specific to that antigen, so it can recognise pathogens with the same antigen. Basically, these cells recognise pathogens, help activate mitosis ( which in turn can activate Tc cells, phagocytosis and B cells) and can form memory cells.
What is the role of Tc cells in cell cell-mediated immune response?
Tc cells are activated by the releasing of Cytokines. They produce the protein perforin which forms “pores” or holes in the target cells membrane. They are triggered by Th cells, and are used to break down pathogens and antigen presenting cells. they can cause cell death.
What are two main features of Cell Mediated immunity?
It requires the use if T cells and it requires antigen Presenting cells
How are T cells adapted for their function?
They have receptor proteins on their outer membranes, which are specific in order to bind to a specific antigen.
What are 2 key features of Humoral Immunity?
B lymphocytes and antibodies.
How can antigens break down a pathogen? (three ways)
Agglutinate cells together or to the pathogen/Antigen-presenting cell
Stop pathogens invading body cells
Bind to free toxin proteins
How is the B cells structure related to what pathogen it engulfs?
The B cell has antibodies on it’s outer membrane. It will only bond with pathogens/Antigen resenting cells with corresponding antigens to the antibodies on their cell surface.
How are Th cells used in humoral immunity?
After the B cell has engulfed the pathogen (so now displays it’s antigens), corresponding receptor proteins on T cells will bind to these antigens and trigger the antigen-presenting B cell to clone by mitosis.
What are the 2 types of B cell an activated B cell will become after mitosis?
Plasma cells- cells that secrete antibodies that are relative to the antigen from the pathogen they engulfed, so can recognise that pathogen in future
Memory Cells- Stay in the blood until the pathogen enters the body in future, as it has the corresponding antibodies to recognise it and break it down.
How are cancer cells recognisable to monoclonal antibodies?
They have specific surface antigens called tumor markers which monoclonal antibodies can bind to.
How can monoclonal antibodies help treat cancer?
Monoclonal Antibodies can be specifically produced to bond to tumor markers on cancer cells. Anti-cancer treatment drugs can be attached to these antibodies, which are released when the antibodies bind to the antigens.
What is one positive of using Monoclonal Antibodies to treat Cancer?
This treatment method reduces side effects as the drugs will only attack cancer cells specifically, whereas chemotherapy and radiotherapy are often not so specific.
What is HcG?
A hormone produced in the placenta of pregnant women, which can be found in her urine.
How can monoclonal antibodies be used to detect pregnancy in pregnancy tests alongside HCG.
Monoclonal Antibodies are immobilised and attached to coloured beads in pregnancy tests
When urine containing HCG hits the stick, the HCG will bind to the antibodies.
This HCG-Antibody-colour complex will then move along the stitch until it is trapped by another type of antibody.
These accumulate and produce a blue line to indicate pregnancy (though the line will not appear without HCG)
Name one ethical issue towards the use of Monoclonal Antibodies
To actually produce this antibody, mice are used. However, these antibodies are cloned by the use of tumor cells. This raises ethical issues as of the exploitation of animals and the fact that tumor cells can mutate uncontrollably and are usually just generally unsafe.
Name an illness Monoclonal antibodies can’t treat
Judging by the failed drug trial of 2006, monoclonal antibodies can not treat multiple sclerosis.
what does the Specific Immune System consist of?
Humoral and Cell Mediated Immunity (T and B lymphocytes)
What does the Non- Specific Immune System Consist of?
Phagocytosis and Physical Barriers such as skin and cilia.
What is Primary Immune Response?
The response that occurs when an unfamiliar pathogen first invades the cell. As the pathogen is unfamiliar, there will not be any pre-existing memory cells or antigens for it, so relatively few specific T and B cells can recognise it, and few clones of these corresponding T and B cells will be made. This is when symptoms are most likely to occur.
What are Memory Cells?
Cells that are produced from activated by specific T and B cells, so have relevant antigens and antibodies to a specific pathogen. They remain in your blood for a number of years, so can recognise the pathogen in future.
What is secondary Immune Response?
Occurs when the same pathogen infects a person for the second time. Memory cells for the pathogen are present, so the pathogen’s elimination is much faster. The memory cells don’t need to specify, so the T cells can immediately divide into Tc cells and the B cells into plasma cells when activated, so the pathogen is broken down much faster, usually before symptoms can set in.
Give an example of active immunity?
Vaccinations
What are the two types of organisms in vaccinations?
Attenuated Microorganisms (The organisms are still alive, but are slightly weakened or diminished), or Dead Microorganisms (would still present the antigens needed to make memory cells).
Give an example of naturally occurring Passive Immunity
Heredity, mother-to-baby immunity, usually due to memory cells being passed through blood from the placenta.
Give an example of artificial passive immunity
Antibodies from the blood plasma of a previously infected person being injected into someone currently infected (or at risk of infection). Though this does assist the body’s natural immune response, these antibodies can’t form long term immunity on their own.
Name a pathogen subject to antigenic variability?
Influenza (hence why we are always getting new vaccines).
Describe antigenic variability
If the antigens on a pathogen remain constant, we remain immune to that pathogen. However, if a pathogen mutates and presents different antigens, the body does not have memory cells that recognise them, so requires new primary response, so people can experience symptoms of infection.
What sort of pathogen is HIV?
A Virus
How is HIV spread?
Via bodily fluids (i.e. blood or sexual fluids).
What does HIV stand for?
Human Immunodeficiency Virus
What is the genetic material within HIV?
RNA
What are the 7 stages of HIV replication?
Binding, Fusion, Reverse Transcription, Integration, Replication, Assembly and Budding.
