Biochemistry 2280A Lecture Notes - Lecture 3: Protein Folding, Peptide, Protein Structure

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5 May 2018

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Protein Folding

How do proteins get from the linear sequence to their native form (lowest energy state)?

- Folding pathways are likely specified by the linear sequence

- As polypeptides are being translated, they come out as beads on a string but then they fold into the

final 3D structure. This involves thousands of weak interactions (H-bonds, and other bonds) that holds

the protein together.

- In some cases, this occurs spontaneously, no help needed. However, many proteins are very complex

and need some help to fold properly. Chaperones are proteins that help other proteins with folding.

- Protein folding is probably a stepwise process: Hydrophobic Interactions  2° structure  3° structure

Video: Shows polypeptide trying out different energy configurations to see which one is the most

favourable and then it lands on its native state. For this polypeptide, it can go through the different

energy conformations because it is a simple one, but for most proteins are larger polypeptides, it is

more complex because there are more possibilities, so chaperones are involved...

- 2 Types of Chaperone Proteins

(1) (2)

chaperon protein is like a chamber where the partially

folded protein enters in and is somehow able to achieve

the final conformation and then it is released

series of small chaperon proteins that bind

onto partially folded protein and guide it

into the correct final folding conformation

* [Incorrectly folded proteins are toxic to the cell because they have exposed hydrophobic domains

instead of nicely packaging them in the interior. Hydrophobic domains that are exposed on the outside

love to interact with hydrophobic domain on other proteins, which results in incorrectly folded proteins

aggregating – maybe even coming out of solution of the cell. The incorrectly folded proteins are no

longer soluble and will precipitate out of the solution] - Chaperones can mask the exposed hydrophobic

regions to prevent aggregation during the folding process.

Note: Not all proteins must be folded immediately. Proteins that must cross the membrane (e.g.

mitochondrial proteins) must stay unfolded until they reach their destination.

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Document Summary

Folding pathways are likely specified by the linear sequence. As polypeptides are being translated, they come out as beads on a string but then they fold into the final 3d structure. This involves thousands of weak interactions (h-bonds, and other bonds) that holds the protein together. In some cases, this occurs spontaneously, no help needed. However, many proteins are very complex and need some help to fold properly. Chaperones are proteins that help other proteins with folding. Protein folding is probably a stepwise process: hydrophobic interactions 2 structure 3 structure. Video: shows polypeptide trying out different energy configurations to see which one is the most favourable and then it lands on its native state. For this polypeptide, it can go through the different energy conformations because it is a simple one, but for most proteins are larger polypeptides, it is more complex because there are more possibilities, so chaperones are involved

Related Questions

Which of the following is not associated with the folding of a protein into its native conformation?

options:

a)	Molecular chaperones prevent folding intermediates from aggregating.
b)	Folding of proteins is a relatively slow process as the stabilization of the molecular structure depends solely on salt bridge interactions which take time to form.
c)	The major driving force for protein folding is the overall increase in solvent entropy. This increase in solvent entropy is a result of the strong interactions between water molecules that lead to the association of nonpolar side chains and subsequent collapse of the molecule into a more compact shape.
d)	Hydrogen bonds contribute to the cooperativity of folding and help stabilize the native conformations of proteins.
e)	All of the above are associated with the folding of a protein into its native conformation.

2 . A protein of interest needs to be separated from a mixture of proteins for amino acid sequencing. It is known that the protein of interest is highly enriched in lysine residues compared to the other proteins in the mixture. Which of the following techniques will be most effective in isolating this protein?

options:

a)	gel-filtration chromatography
b)	SDS-polyacrylamide gel electrophoresis
c)	mass spectrometry
d)	cation exchange chromatography
e)	anion exchange chromatography

Question 401 pts

Kinetic energy is the stored energy that can be used for motion.

True

False

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Question 411 pts

When an electron is transferred from one atom to another, and the two atoms are then electrically attracted to one another, a(n) ________________ bond is formed.

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Question 421 pts

Changing the number of ____________ of an atom would change the chemical properties of the atom.

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Question 431 pts

Forming molecules and breaking down molecules in biological organisms usually requires the use of _________ to help the reaction proceed faster.

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Question 441 pts

Organic molecules have a core composed of .

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Question 451 pts

The building blocks of carbohydrates are

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Question 461 pts

Water molecules crossing a membrane from high to low concentration is .

active transport

cell fate

facilitated diffusion

osmosis

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Question 471 pts

Choose the membrane molecule responsible for the passage of polar molecules and ions into and out of the cell.

phospholipids

transmembrane channel proteins

cell surface proteins

carbohydrate chains

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Question 481 pts

The simplest cells are .

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Question 491 pts

Which of the following membrane bound organelles are found inside bacterial cells:

nucleus

organelles are not found in prokaryotic cells

mitochondria

chloroplasts

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Question 501 pts

Which of the following is a specialized components of the cell, is associated with the rough endoplasmic reticulum, and is responsible for making proteins.

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Question 511 pts

Proteins are sorted, modified, and packaged by the _____________ and later transported to the outside of the cell.

ribosomes

golgi bodies (golgi apparatus)

nucleus

mitochondria

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Question 521 pts

Dehydration synthesis is a process of linking two smaller subunits together to form a polymer. Which of the following statements below is true of dehydration synthesis?

Oxygen is consumed.

A water molecule is removed from the molecules.

A water molecule is added to the molecules

Carbon dioxide is given off.

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Question 531 pts

Proteins are made up of _________ held together by peptide bonds.

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Question 541 pts

Which of the following gives an amino acid its properties?

NH2

R Group or functional group

COOH

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Question 551 pts

The final three-dimensional shape of a protein that includes the bonding of two or more polypeptide chains is call its _____ structure.

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Question 561 pts

How do DNA and RNA differ?

all statements are differences between DNA and RNA.

DNA is double stranded while RNA is single stranded.

They have different sugars.

Thymine is present in DNA but not in RNA.

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Question 571 pts

Which of the following is a component of a DNA nucleotide?

phosphate

a nitrogen containing base

All are components of a nucleotide.

5-carbon sugar

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Question 581 pts

Cell membranes are made up of several different types of molecules. Select the membrane molecule below that is made up of a polar region and two non-polar fatty acid tails.

transmembrane proteins

carbohydrate chains

phospholipids

cell surface proteins

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Question 591 pts

Two organelles which are believed to have once been free-living bacterial cells are ____________ and ______________.

chloroplasts and mitochondria

golgi apparatus and endoplasmic reticulum

ribosomes and nucleolus

peroxisomes and lysosomes

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Question 601 pts

The is an extensive system of internal membranes responsible for producing carbohydrates and lipids.

smooth endoplasmic reticulum

rough endoplasmic reticulum

nucleolus

mitochondria

sangriarat617

The bacterium E. coli, which is a major model system for the study of genes and DNA, has a singular circular chromosome of about 4x106 bp. In contrast, human diploid cells have __1__ chromosomes, of __2__ different types (donât forget that the X Â¹ Y!). The total amount of DNA found in a haploid cell such as a sperm or egg is called the organismâs âC-valueâ; the human C-value is __3__.

Also in contrast to the E. coli circular chromosome is the fact that eukaryotic chromosomes are not circular, but instead are __4__. Eukaryotic chromosomes are complexed heavily with protein to form a DNA-protein complex generically called __5__. The proteins found can be considered to fall into two general classes: __6__ and __7__. The first class is made up of 5 major proteins called __8__, __9__, __10__, __11__, and __12__. On a weight to weight basis, these proteins make up about __13__% of the total mass of a chromosome. Since these proteins must associate relatively non-specifically with DNA, they are rich in the basic amino acids __13__ and __14__, which gives the proteins a net __15__ charge.

One goal of packaging the DNA into chromatin is to compact the genome so it will fit into a nucleus. The basic unit of chromatin structure is the __16__, which has __17__ base pairs of DNA wrapped around a âcore particleâ composed of __18__ copies each of the core histones. Each nucleosome is separated by a stretch of âlinkerâ DNA so that the repeating unit is approximately 200 bp. Lets do a little arithmetic: If we consider that the nucleosome is approximately __19__ nm in diameter, that there is about 200 bp in this structure, and that 200 bp of DNA would normally occupy __20__ nm if stretched out straight (recall that each base is spaced about 0.34 nm from the next), we can see that the nucleosome alone allows for a __21__-fold compaction ratio.

The nucleosome structure is further compacted by histone __22__, which is not a part of the core particle. Instead, this histone __23__ (does what?) to cause the nucleosomal 10 nm fiber to condense into a higher-order structure referred to as the __24__ nm fiber. In the nucleus, chromosomes do not just float around freely: they are tethered to a proteinaceous structure called the __25__ at specific DNA regions called âSARsâ, which stands for __26__. SARs are rich in topoisomerases, to allow the winding and unwinding of the DNA that accompanies replication and transcription to occur, despite this constraint.

The 30 nm fiber discussed above is the form in which transcriptionally active DNA is believed to exist in the nucleus; however, further condensation leads to a highly condensed inactive form called __27__; in this terminology, the active form is referred to as __28__. The inactive condensed form can be divided into two types: one type is essentially invariant between cell types, and since it is âon all t timeâ, it is referred to as __29__. The other type comes and goes, depending on the expression of the genes present in that region of the chromosome; it is referred to as __30__.

Eukaryotic chromosomes carry the genes, of course, but also have other functional regions. One such region is the place where the spindle apparatus attaches during mitosis and meiosis; this region of the chromosome is called the __31__. Another important part of the linear eukaryotic chromosome is the ends; these are called __32__. In humans, the end of each chromosome is composed of many repeats of the short sequence __33__. One more type of functional region on each chromosome is the place where DNA replication starts; in humans, each chromosome has several of these __34__. Thus, eukaryotic chromosomes carry several different types of functional sequences, which together allow for their __35__ during S phase, __36__ during mitosis and meiosis, and the __37__ of their genes

Biochemistry 2280A Lecture Notes - Lecture 3: Protein Folding, Peptide, Protein Structure

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