Module 1 - Cells and their Contents Flashcards
Explain why the structure of a protein (or other macromolecule) is important for its function.
A molecule’s biological function is dependent on correct conformation (3D shape). Function usually depends on interaction with other molecules, so shape is important. For example, enzymes have a specific 3D shape at their active site which enables substrate(s) to bind specifically to that enzyme.
Weak interactions are particularly important in the chemistry of living organisms. Write a brief description of each type of interaction listed here:
(a) Hydrogen bonds
(b) Ionic bonds
(c) Hydrophobic interactions
a) weak bond formed when the slightly positive hydrogen atom of a polar covalent bond in one molecule is attracted to the slightly negative atom of a polar covalent bond in another molecule (or in another region of the same molecule).
b) attractive or repulsive interactions between ions in solution or charged parts of a molecule.
c) The tendency for nonpolar molecules to congregate in water.
Write a brief description of the four levels of protein structure and the bonds or interactions that are involved at each level.
Primary = Linear polymer of a unique, specific amino acid sequence of a protein, with covalent peptide bonds
Secondary = REGULAR COILING - Folded into localised shapes due to the hydrogen bonds between the backbone of the chain. Alpha helix (coiled due to hydrogen bonding between H atom from one amino acid to an oxygen atom on the fourth amino acid away). Beta sheet (sheetlike structure due to hydrogen bonding between different polypeptide chains, or between different sections of the same polypeptide.
Tertiary = IRREGULAR FOLDING - The overall 3D shape of the protein. Influenced by the ionic bonds between opposite charged R-groups – hydrogen bonds between R-groups bearing opposite partial charges, and hydrophobic interactions resulting from the tendency of nonpolar R-groups to stay close together in aqueous solution.
Quaternary = Proteins that are made up of more than one polypeptide chain. Not all proteins have quaternary structures.
- Enzymes are biological catalysts.
(a) What class of biological macromolecules do they belong to?
(b) How do they speed up the rate of chemical reactions?
(c) Describe their importance in the cell
a) Proteins
b) They reduce the activation energy required for a reaction to occur, therefore speeding up the overall rate of the reaction
c) They speed up chemical reactions
What are the differences in structure between DNA and RNA?
DNA is a double stranded helix, with a deoxyribose sugar (pentose). This means that there is a H atom bonded to the 2’ C of the sugar. Base pairs are Thymine, Adenine, Guanine and Cytosine.
RNA is single stranded, with a ribose sugar (pentose). This means that there is an OH group attached to the 2’C of the sugar. Base pairs include Uracil, Adenine, Guanine and Cytosine.
- Enzymes are required to add each nucleotide during formation of a nucleic acid. According to the building block principle for biological molecules, they can only be added to one end of the growing nucleic acid polymer.
(a) Which end are they always added to (for both DNA and RNA)?
(b) Each reaction that adds a new nucleotide is either a hydrolysis reaction or dehydration reaction. Which one is it?
a) They are added to the 3’ end, because the enzyme can only extend the chain in the 5’ to 3’ direction, meaning that it can only add new nucleotide to the 3’ end of the strand.
b) Dehydration - because for a new nucleotide to join, a water molecule must be removed.
‘DNA is a double helix’. Explain what this means in terms of the double-stranded DNA molecule.
a) How are the two strands arranged relative to each other?
b) How are the two strands held together in the double helix?
a) They run in opposite direction of one another, in a antiparallel structure. This means that each strand has a 3’ end and a 5’ end.
b) By the complimentary pairing rule, A-T and C-G. They are held together by hydrogen bonds between the base pairs.
Give an example of:
(a) a monosaccharide
(b) a disaccharide
(c) a polysaccharide made by plants
a) Glucose
b) Lactose
c) cellulose and starch
Use base-pairing rules to write the sequence of the DNA strand that is complementary to the strand shown here. Indicate the 5’ and 3’ ends of your new strand.
5’ CAGTAGCTACGGGTACCAA 3’
3’ GTCATCGATGCCCATGGTT 5’
What are integral proteins?
Proteins that are integrated into the lipid layer, permanently in the cell membrane
What are peripheral proteins?
Proteins that are attached to the surface of the bimolecular lipid layer, by electrostatic interactions. They can attach and detach from the cell membrane at different times
What is the self sealing mechanism of the phospholipid layer
The phospholipid molecules are not covalently bonded together; they are kept in place by hydrophobic interactions (to ‘hide’ the hydrophobic tails from the water inside and outside the cell.) and hydrophilic interactions (hydrogen bonds and ionic interactions of the polar groups with water). So, if a hole is made in the bilayer, no covalent bonds are broken, but the hydrophobic tails are exposed. The molecules will rearrange (move) to fill the gap and restore the normal state of the membrane.
What is the Endoplasmic Reticulum (ER)?
List functions etc. (HINT: Rough and Smooth)
Main function is the modification of proteins and synthesis of lipids. It consists of a network of membranous tubules and flattened sacs. The discs and tubules of the ER are hollow, and the space inside is called the lumen.
Rough ER: Has ribosomes attached to its cytoplasmic surface. The ribosomes make proteins, resulting in forming protein chains into the lumen. The proteins fold and undergo modifications, like addition of carbohydrate side chains. The modified proteins are then packaged into vesicles and shipped to the Golgi apparatus. Rough ER also males phospholipids.
Smooth ER: Has few or no ribosomes on its cytoplasmic surface. Functions of the smooth ER include the synthesis of carbohydrates, lipids, and steroid hormones. Detoxification of medications and poison, as well as the storage of calcium ions also occur in the smooth ER.
What is the Golgi apparatus?
List functions etc.
The Golgi apparatus is a organelle made up of flattened discs of membrane. When vesicles bud off from the ER, the lipids and proteins in these transport vesicles need to be sorted and packaged, in order to end up in the correct place. This process takes place in the Golgi apparatus. The receiving side of the Golgi is called the cis face, and the secretion side is called the trans face. The transport vesicles from the ER will travel to the cis face, and fuse with it. This results in them emptying their contents into the lumen of the Golgi. These proteins and lipids can undergo further modification. The modified proteins are sorted, based on markers such as amino acid sequences and chemical tags, and then packaged into vesicles that bud from the trans face of the Golgi.
What are the three principles of cell theory?
- All living organisms are composed of cells
- The cell is the basic unit of life
- Cells arise by division of pre-existing cells
What are the approximate size ranges of prokaryotic and eukaryotic cells?
Prokaryotic (bacterial) cells ~1-10μm
Eukaryotic cells ~10-100μm
What is Light Microscopy?
Define:
- Brightfield Microscopy
- Fluorescence Microscopy
- Confocal Microscopy
Brightfield:
Uses light to illuminate a sample and create an image. Light passes through the sample, and an objective magnifies the image and projects it onto an eyepiece or camera. The sample appears dark against a bright background, hence the name ‘brightfield’.
- simple and inexpensive
- stains can be used
Fluorescence:
- absorption of specific light wavelength (colours) y specimen or fluorescent dyes
- re-emission as another light wavelength (colour).
- optical microscope that uses a mercury arch lamp as a source of UV light
Confocal:
- 3D fluorescence microscopy
- optical sections
- can look at something without slicing it apart
- they are specific, you can only see what you’re looking for
What is Electron Microscopy?
Define:
- Transmission Electron Microscopy (TEM)
- Scanning Electron Microscopy (SEM)
TEM:
- very thin section of sample is used
SEM:
- surface scanning - 3D view is seen
What is a controlled experiment?
One that tests experimental and control groups in parallel.
Express these two dimensions in millimetres (mm).
1 µm =
100 µm =
1 µm = 0.001mm
100 µm = 0.1mm
What are the four classes of biological macromolecules and their general functions?
Proteins - serve as structural support, catalysts, hormones, enzymes, building blocks.
- building blocks are amino acids (20 types)
Polysaccharides (carbohydrates) - serve as a structural organization in animals and plants. Other functions of polysaccharides include: They store energy in organisms. Due to the presence of multiple hydrogen bonds, the water cannot invade the molecules making them hydrophobic
- building blocks are glucose (usually only 1 type)
Lipids - fatty compounds that help with moving and storing energy, absorbing vitamins and making hormones
- they are NOT polymers
Nucleic acids - deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), carry genetic information which is read in cells to make the RNA and proteins by which living things function
- building blocks are nucleotides (4 types)
What is a polymer?
A long chain of covalently bonded building blocks called Monomers.
What is the building block principle for biological polymers?
Dehydration Reaction - when a water molecule is removed, resulting in a covalent bond between two monomers.
Hydrolysis Reaction - when a water molecule is added, resulting in two of the monomers splitting in two for a water molecule to fit in the chain.
What are the functions of building proteins?
Structure, movement, catalysing reactions, transport, storing energy, sending signals, receiving signals.
What does it mean by hydrophobic?
When a protein has a non-polar side chain, (there are 9), it causes the molecule to repel/not mix with water, which is a polar molecule. Remember, “like dissolves like”, as since they have different polarities, they will not react.
What does it mean by hydrophilic?
When a molecule has a polar or electrically charged side chain, it causes the molecule to react with water, due to their similarities in polarity. (“like dissolves like”). Therefore hydrophilic molecules will interact with water.
What is the difference between a protein or a polypeptide?
A polypeptide is a linear polymer of a covalently bonded amino acid.
A protein is one or more polypeptides folded into a specific conformation (3D shape) to enable function
Describe and explain the roles of weak interactions in biological molecules, and distinguish weak interactions from covalent bonds (polar and non-polar).
Weak interactions are important because they maintain the correct structure of biological molecules. The weak interactions allow the polypeptide to fold into a specific 3D structure for the protein to be functional. This ultimately allows the molecules to reversibly interact.
- hydrogen bonds (with the polypeptide or with water)
- ionic interactions (charged side chains and ions in solution)
- hydrophobic interactions (important to final conformation)
- Van der Waals interactions (temporary, permanent etc. These stabilise the structure)
