L4 Proteins 2 + Nucleic acids Flashcards
What does the tertiary structure do?
It finishes the folding of a polypeptide to its final form?
Can proteins be fully formed after the tertiary structure?
Yes, many proteins consist of only one polypeptide so they are fully formed after tertiary structure formation (vs getting to a quaternary form)
Does the formation of a tertiary structure require or release energy?
It releases energy, ie it occurs automatically
What types of interactions contribute to the tertiary structure formation? (4)
- ionic bonds
- hydrogen bonds
- disulfide bonds
- hydrophobic interactions
Where do the ionic bonds, h-bonds, disulfide bonds and hydrophobic interactions occur for the tertiary structure?
Between the amino acid side chains in the interior of the protein
What do the side chain interactions determine? (the ionic bonds, h-bonds, disulfide bonds and hydrophobic interaction in the side chains)
They determine the tertiary structure
Which interaction is the most important determinant of protein folding / tertiary structure?
Hydrophobic interactions because hydrophobic stretches of amino acids automatically rearrange towards the interior of a protein (away from water)
What are coiled coils?
Coiled coils are two alpha-helices wrapped around eachother
How are coiled coils formed? (4)
- Hydrophobic amino acids at every 4th position generates a band of hydrophobicity running along the length of the alpha-helix and slowly rotating around it
- Hydrophobic interactions then ensures that two such alpha helices come together just at that band, which results in the coiled coil
- It is a tertiary structure if both alpha helices are from the same polypeptide
- It is a quaternary structure if the alpha-helices are from two different polypeptides
Where can coiled coils occur ?
In proteins such as keratins giving strength to tendons, hair or feathers
How does curling and uncurling hair work?
- It reduces or breaks the disulfide bonds in keratin which allows for the manipulation of the shape of hair
- Then the disulfide bonds must be oxidised/reformed to keep hair in the new shape
What is a quaternary structure?
A quaternary structure indicates several polypeptides interaction to form a bigger protein complex
Examples of quaternary structures (2)
- hemoglobin → 4 ind. polypeptides
- keratin → 3 alpha helices
What is hemoglobin
Hemoglobin is a protein in red blood cells that carries oxygen to different organs and tissues and transports carbon dioxide from the organs back to the lungs.
What is the importance of the primary structure (the amino acid sequence) ?
The primary structure is sufficient for protein folding, or in other words, all of the information needed about protein folding is encoded in the primary structure.
What are 2 examples that prove that the primary structure (the amino acid sequence) has all of the info needed to fold?
1) A single amino acid mutation in the protein hemoglobin changes the conformation of the hemoglobin, resulting in the shape change of red blood cells, since red blood cells are made up of hemoglobin
2) A typical protein sufficiently diluted in watery solutions denatures (unfolds) at high temperatures, but will renature (refold), when temperature is lowered
SUMMARY what is the primary structure?
the sequence of amino acids in a polypeptide
SUMMARY what is the secondary structure?
the formation of alpha helices and beta pleated sheets in a polypeptide
SUMMARY what is the tertiary structure?
the overall three dimensional shape of a polypeptide (includes contributions from secondary structures)
SUMMARY what is the quaternary structure?
the shape produced by combinations of polypeptides (thus combinations of tertiary structures)
What is protein turnover?
- Protein turnover refers to the replacement of older proteins as they are broken down within a cell
- Breakdown & resynthesis
What is the range of the half life of protein turnover?
It ranges from minutes to weeks
The average is about 2 days
Why is protein turnover important?
Because proteins get damaged often
What are some examples of protein turnover? (3)
- fever
- pH change
- egg becomes hard by boiling bc proteins denature and get all entangled when they try to renature
What are chaperones?
Chaperones are specialized proteins that help keep other proteins (temporarily exposed hydrophobic regions) from interacting inappropriately with one another
How do chaperones keep proteins from interacting inappropriately with other proteins?
They do so by sequestering some newly synthesized proteins to give them time to fold
When do chaperones play their role? (2)
After synthesis or after stress-related unfolding
What are nucleotides?
Nucleotides are made up of a 5-carbon sugar, a nitrogenous base and a phosphate group
What are nucleotides building blocks of?
RNA and DNA
What kind of sugar is in RNA?
Ribose
What kind of sugar is in DNA
Deoxyribose
→ DNA lacks an oxygen at carbon 2
Which nucleotides make up RNA (4)?
- cytosine
- uracil
- guanine
- adenine
Which nucleotides make up DNA (4)?
- cytosine
- thymine
- guanine
- adenine
What are cytosine, uracil, and thymine?
They are pyrimides
What are guanine and adenine
They are purines (which is bigger than pyrimides)
How do nucleotides polymerize?
Nucleotides polymerize via phosphodiester linkages, with 3’ hydroxyl group of the polymer forming a covalent bond with the 5’ phosphate group of the incoming molecule
What does 5’ to 3’ entail
RNA and DNA molecules always start with a 5’ phosphate group and end with a 3’ hydroxyl
What type of reaction is nucleotide polymerization? (condensation or hydrolysis)
Condensation
What is DNA ?
DNA is a self-replicating material that is present in nearly all living organisms as the main constituent of chromosomes. It is the carrier of genetic information.
What is DNA made up of?
DNA is made up of two antiparallel strands held together by hydrogen bonds between the bases
How do the bases pair up? (guanine, adenine, cytosine, thymine)
Gunanine (G) pairs with cycstine (C)
Adenine (A) pairs with thymine (T)
How many H bonds does a G-C (guanine-cytosine) have?
3 H-bonds
How many H bonds does a A-T (adenine-thymine) have?
2 H-bonds
Which base pairing is stronger? G-C or A-T?
G-C (bc it has 3 H bonds while A-T has 2)
How are the sugars, phosphates and bases arranged on the double helix of DNA?
The double helix of DNA has a sugar-phosphate backbone on the outside and the bases on the inside arranged like rungs on a ladder
What does DNA carry?
the genetic information
What is RNA?
RNA is a nucleic acid present in all living cells. Its principal role is to act as a messenger carrying instructions from DNA for controlling the synthesis of proteins
What came first in evolution RNA or DNA?
RNA
How many strands does RNA have?
1
How does RNA work like an enzyme catalyzing certain reactions?
Because it can form into complicated 3D structures similar to proteins
Where does folding occur in RNA?
Folding occurs between nucleotide bases within the same macromolecule pair via H-bonds
What is the stem-loop structure of RNA?
It is a structure that contributes to the regulation of mRNA function
What are the differences between RNA and DNA? (3)
- RNA is 1 strand ; DNA is 2 strands
- DNA is more stable than RNA
- RNA has uracyl and DNA has thymine
