Flashcards in Proteins And Nucleic Acids Deck (35):
What elements do all proteins contain?
What are amino acids?
20 different amino acids are commonly found in cells.
5 are non-essential - we are able to make them.
9 are essential - come from what we eat.
6 are conditionally essential - only needed by infants and growing kids.
What is peptide synthesis?
Amino acids join when the amine and carboxylic groups connected to the central carbon atoms react, forming a peptide bond and water is produced. It is a condensation reaction. This is now a dipeptide.
A polypeptide is a chain of amino acids. The catalyst enzyme is peptidyl transferase.
Different R-groups of the amino acids in the protein are able to interact, forming different types of bonds.
How do you separate amino acids using thin layer chromatography?
1. Draw pencil line 2cm from the bottom of the chromatography plate.
2. 4 equally spaces points marked along pencil line.
3. Amino acid solution spotted onto first dot and allowed to dry.
4. 3 remaining marks spotted with known amino acids and labelled.
5. Plate placed into a jar with solvent no more more than 1cm deep and closed.
Plate left in solvent until it had reached 2cm from the top. Pencil line drawn along solvent front then allowed to dry.
7. Then it’s sprayed in a fume cupboard, with ninhydrin spray so amino acids become purple/brown. Centre of each spot marked with pencil.
What is primary structure?
The sequence in which amino acids are joined.
Only bonds are peptide bonds.
What is secondary structure?
The oxygen, hydrogen, and nitrogen atoms of basic, repeating sequence, interact.
Hydrogen bonds may form within amino acid chain pulling it into an alpha helix. Or a beta pleated sheet.
What is tertiary structure?
The folding of a protein into its final shape. It often includes sections of the secondary structure.
Interactions occur between R-groups:
Hydrophobic and hydrophilic interactions
Ionic bonds - form between oppositely charged R-groups
Disulfide bonds - only between R-groups containing sulfur atoms
What is quaternary structure?
Results from the association of 2 or more individual proteins called subunits. Same kind of interactions as tertiary structure just between different proteins.
Identical or different subunits
What are globular proteins?
They are compact, water soluble, and usually roughly spherical in shape. They fold so that hydrophilic R-groups are on the outside of the protein and the hydrophobic R-groups are on the inside, away from the aqueous environment.
Insulin is a globular protein
What are conjugated proteins?
Globular proteins that contain a non-protein component called a prosthetic group.
There are different types of prosthetic groups: lipids or carbohydrates can combine with proteins forming lipoproteins or glycoproteins. Metal ions and molecules derived from vitamins also form prosthetic groups.
Haem groups are examples of prosthetic groups as they contain iron II ion.
What is haemoglobin?
A red, oxygen-carrying pigment found in red blood cells.
It’s quaternary structure is made up of 2 alpha and 2 beta subunits
Each subunit contains a prosthetic group. iron II ions present in haem groups is are each able to combine reversibly with a oxygen molecule. This is what enables haemoglobin to transport oxygen.
What is catalase?
An enzyme that catalyses reactions. It contains 4 haem prosthetic groups. The iron II ions in the prosthetic groups allow catalase to interact with hydrogen peroxide and speed up its break down.
What are fibrous proteins?
A long insoluble molecule due to the presence of a high proportion of amino acids with hydrophobic R-groups in their primary structure. They are not folded into complex 3D shapes like globular proteins.
What is keratin?
A group of fibrous proteins present in hair, skin, and nails. It has a large proportion of the sulfur-containing amino acid, cysteine. Resulting in many strong disulfide bonds to form strong, inflexible, insoluble materials.
What is elastin?
A fibrous protein found in elastic fibres (along with small protein fibres). Elastic fibres are found in the walls of blood vessels and in the alveoli of lungs, so they can expand when needed.
A quaternary protein made from many stretchy molecules called tropoelastin.
What elements do nucleus acids contain?
What are nucleotides made up of?
A pentose monosaccharide (sugar)
A phosphate group - acidic and negatively charged
A nitrogenous base- one or two carbon rings in its structure as well as nitrogen
How are phosphodiester bonds formed?
Nucleotides linked together by condensation reactions to form a polynucleotide.
Phosphate group at fifth carbon of one and a hydroxyl group at third carbon of another form a covalent bond.
Broken down by hydrolysis
What is deoxyribonucleic acid?
Contains the sugar deoxyribose - one fewer atoms than ribose.
Four different bases:
Pyrimidines- smaller, contain single carbon ring structures - thymine and cytosine.
Purines- larger, contain double carbon ring structures - adenine and guanine.
What is a double helix?
Two strands of polynucleotides cooled into a helix. They are antiparallel.
The pairing between the bases allows DNA to be copied and transcribed
What are the base pairing rules?
Adenine and thymine are both able to form two hydrogen bonds and always join with each other.
Cytosine and guanine form three hydrogen bonds and always bind to each other.
This is complementary base pairing
These rules mean that a small pyrimidine base always bonds to a larger purine base.
What is ribonucleic acid?
Contains the sugar ribose and thymine is replaced with uracil.
Plays an essential role in the transfer of genetic information from DNA to the proteins that make up the enzymes and tissues of the body. DNA is transcribed into a similarly short mRNA molecule so genetic info can go from the nucleus to the ribosome for protein synthesis.
How is DNA extracted from a plant material?
1. Grind sample in pestle and mortar - breaks down cell walls.
2. Mix sample with detergent - breaks down cells membranes.
3. Add salt - breaks the hydrogen bonds.
4. Add protease enzyme - breaks down proteins associated with DNA.
5. Add a layer of alcohol (ethanol) - causes DNA to precipitate out of solution.
DNA will be seen as white strands
What is semi-conservative replication?
The double helix unwinds and separates into two strands so H bonds are broken, free DNA nucleotides will pair with the complementary bases and hydrogen bonds are formed between them.
In short the two new molecules has an original strand and a new strand
What is the role enzymes in replication?
DNA helicase unwinds and separates the two strands of the DNA double helix (unzipping).
DNA polymerase catalyses the formation of phosphodiester bonds between these nucleotides.
What is continuous and discontinuous replication?
The strand that is unzipped from the 3’ end is called the leading strand and can be continuously replicated.
The other strand is unzipped from the 5’ end is called the lagging strand as the DNA polymerase has to wait a second until a section has been unzipped. So it is produced in sections (discontinuously)
How do replication errors occur?
Sequences of bases are not always matched exactly, and may occur in the newly made strand. These errors occur randomly and spontaneously and lead to a change in the sequence of bases. This is a mutation.
What is the triplet code?
A sequence of three bases called a codon. This codes for an amino acid.
What is the degenerate code?
There are 64 different base triplets or codons possible. Including a codon that acts as the start codon and 3 stop codons.
But there are only 20 different amino acids. Therefore many amino acids can be coded for by more than one codon. Due to this, the genetic code is known to be degenerate.
What is transcription?
DNA is contained within a double membrane called the nuclear envelope. Therefore the chromosomal DNA molecule is too large to leave the nucleus.
The sense strand of DNA contains the code for protein synthesis. And the antisense strand is a complementary copy is it so it acts as the template strand.
DNA unzips and free RNA nucleotides will pair with the complementary bases. Then RNA polymerase for phosphodiester bonds between the RNA nucleotides. The completed short strand of RNA is called messenger RNA which detaches from the DNA template and the DNA double helix reforms.
What is translation?
Ribosomes are made up of two subunits one big, one small. They have almost equal amounts of protein and ribosomal RNA. This maintains the structural stability of the protein.
MRNA binds to the small subunit of the ribosome at its start codon.
A tRNA with the complementary codon binds to the start codon of mRNA.
Another tRNA with an anticodon binds to the next codon on the mRNA.
The first amino acid is transferred to the second, forming a peptide bond.
The ribosome moves along the mRNA, releasing the first tRNA. The second tRNA becomes the first.
This process is then repeated until the ribosome reaches the end of the mRNA. Then the polypeptide is released.
What are the main types of activity that requires ATP?
Synthesis - e.g proteins
Transport - e.g active transport across cell membranes.
Movement - e.g protein fibres in muscle cells
What is ATP composed of?
A nitrogenous base
A pentose sugar (ribose)
Three phosphate groups
What are the properties of ATP?
Small - moves easily into, out of and within cells.
Contains bonds between phosphates with intermediate energy - large enough to be used in cellular reactions.
Releases energy in small quantities - no wasted energy.
Easily regenerated - can be recharged with energy.