Proteins and Nucleic acids

What are Proteins and their general functions?

1. EX (-ase): lactase, amylase, pancreatic lipase, lysozyme, Rubisco.

2. X Proteins: Collagen (skin), keratin (hair), dystrophin (muscle)

3. StX / NX proteins: Albumin (egg white), Zein (corn kernels),

Casein (milk), Glutein (wheat), Soya (soy protein), Globulin (peanuts)

4. TrX proteins: Aquaporins, hemoglobin, electron transport

5. HX / ReX proteins: Insulin, growth hormone, prolactin

6. MX proteins: Actin and myosin: muscle

7. PrX proteins: Antibodies.

Proteins are ~#% or more of a cell’s dry weight.

The instructions for making proteins come from X.

How to spot an Amino Acids: the X.

ALL amino acids have 5 main parts:

1. Alpha X

2. X end

3. X end

4. X

5. X group: there Are # different R groups that can be grouped chemically:

Polar = Hydrophilic

Charged = Usually Have a charged X or X group within R group

- Nonpolar R: no Oxygen, could be S but surrounded by methyl groups, no charge, X is considered nonpolar tho, because the R group is just a hydrogen

- Polar R: has a lot of oxygen in R, hydrophilic, 

- Polar R and electrically charged: hydorphillic and can be X or X. X: X charged (pick up proton or release OH); X (donate hydrogens or pick up OH-): X charged

What are Proteins and their general functions?

1. Enzymes (-ase): lactase, amylase, pancreatic lipase, lysozyme, Rubisco.

2. Structural Proteins: Collagen (skin), keratin (hair), dystrophin (muscle)

3. Storage / Nutritive proteins: Albumin (egg white), Zein (corn kernels),

Casein (milk), Glutein (wheat), Soya (soy protein), Globulin (peanuts)

4. Transport proteins: Aquaporins, hemoglobin, electron transport

5. Hormonal / Regulatory proteins: Insulin, growth hormone, prolactin

6. Motile proteins: Actin and myosin: muscle

7. Protective proteins: Antibodies.

Proteins are ~50% or more of a cell’s dry weight.

The instructions for making proteins come from genes.

How to spot an Amino Acids: the monomer.

ALL amino acids have 5 main parts:

1. Alpha Carbon

2. Carboxyl end

3. Amino end

4. Hydrogen

5. R group: there Are 20 different R groups that can be grouped chemically:

Polar = Hydrophilic

Charged = Usually Have a charged carboxyl or amino group within R group

- Nonpolar R: no Oxygen, could be S but surrounded by methyl groups, no charge, glycine is considered nonpolar tho, because the R group is just a hydrogen

- Polar R: has a lot og oxygen in R, hydrophilic, 

- Polar R and electrically charged: hydorphillic and can be basic or acidic. Basic: positively charged (pick up proton or release OH); acidic (donate hydrogens or pick up OH-): negatively charged

Proteins need to fold properly to function properly: Four Levels of Protein Structure

1° Primary structure of a protein = unique X of X X (X bonds)

2° Secondary structure = X-bonding that coils and folds the X chain (X-bonds)

3° Tertiary structure = determined by interactions among various side chains (R groups)

4° Quaternary structure = protein functions as multiple X chains (#+ subunits)

- Amino acids there are # of them, they are like pop beads, when you put them together

The Peptide Bond: Making a polymer / X chain

(X end) N-C-C-N-C-C (X end)

- What does it look like when you put two amino acids together, The X group from one amino acid’s X acid and the X part of the X group from the other amino acids come together, and a X bond is made X-X. Everytime you join two amino acids you remove a X, a X bond is made (same with ester, glycocidic, peptide). How do you know if it is a peptide bond, look for the NC (carboxylic acid’s C and the amine’s N). Two amino acids is called a X. 

- NutraSweet (Aspartame) is a X (Phe- Asp), one molecule of X joined to one molecule of X acid: super sweet we do not get nutritional calories tho

- There are some people born with the genetic condition called X, you are unable to drink nutrasweet because they cannot metabolize X

Exploring levels of protein structure 

- You make peptide bonds: in our X, they will help make the 3D proteins

Denaturation and renaturation of a protein.

Denaturation: High X, X, X, X, high X, etc.

Renaturation (sometimes possible): Unboil an egg? (denatured)

Denatured protein

(usually non-X)

- Some proteins need X to fold properly. Sometimes the Heat Chaperonins will grab those proteins and X them.

Proteins need to fold properly to function properly: Four Levels of Protein Structure

1° Primary structure of a protein = unique sequence of amino acids (Peptide bonds)

2° Secondary structure = H-bonding that coils and folds the polypeptide chain (H-bonds)

3° Tertiary structure = determined by interactions among various side chains (R groups)

4° Quaternary structure = protein functions as multiple polypeptide chains (2+ subunits)

- Amino acids there are 20 of them, they are like pop beads, when you put them together

The Peptide Bond: Making a polymer / polypeptide chain

(amino end) N-C-C-N-C-C (carboxyl end)

- What does it look like when you put two amino acids together, The OH group from one amino acid’s carboxylic acid and the H part of the amine group from the other amino acids come together, and a covalent bond is made C-N. Everytime you join two amino acids you remove a H2O, a peptide bond is made (same with ester, glycocidic, peptide). How do you know if it is a peptide bond, look for the NC (carboxylic acid’s C and the amine’s N). Two amino acids is called a dipeptide. 

- NutraSweet (Aspartame) is a dipeptide (Phe- Asp), one molecule of phenylalanine joined to one molecule of aspartic acid: super sweet we do not get nutritional calories tho

- There are some people born with the genetic condition called PKU, you are unable to drink nutrasweet because they cannot metabolize phenylalanine

Exploring levels of protein structure 

- You make peptide bonds: in our ribosomes, they will help make the 3D proteins 

Denaturation and renaturation of a protein.

Denaturation: High heat, acids, bases, alcohols, high fever, etc.

Renaturation (sometimes possible): Unboil an egg? (denatured)

Denatured protein

(usually non-functional)

- Some proteins need chaperonins to fold properly. Sometimes the Heat Chaperonins will grab those proteins and protect them.

- Primary (1°) Structure: X Bonds make X amino acid sequence, there will always be one at the end which is the X of the first amino acid, the last amino acid will have the X X you have 29 amino acids together, you will have # peptide bonds. But a protein is not a long stick like that in the cell, the moment it enters the cytoplasm you will have hydrophobic amino acids and hydrophilic amino acids

Glucagon has 29 amino acids, in this exact order. (DNA RNA Protein)

- Secondary (2°) structure: This is because the protein has now been inside the X, results from X bonds between different parts of the amino acid backbone (the NCCNCC, as they come in contact with eachother, with the hydrogen bonds on the either end is going to create X regions, and in the same region you can have an X helix or a X pleated sheet. -helix: elastic (wool, keratin)) The X helix is elastic it is for things like wool and keratin. The X pleated sheet is very strong and flexible is used for silk

- Tertiary (3°) structure:

Not talking about the amino acid backbone, but how the X groups react Results from all types of bonds between different R-groups of the amino acid!:

R-group interactions ‘rivet’ different parts of the same protein together to make a

X shape needed for function. The X-containing amino acids come together, this is the only time you are able to make a covalent bond:X X, these X bonds are very strong, so a lot of proteins are stabilized by a X X. Two charged amino acids can create an X bond with the X and X R groups, they will be attracted to each other. There is also amino acids that will create a X bonds. Finally, ones where both the R groups are X and will interact through X X X interactions, referred to as a “X” 

Quaternary (4°) structure: Interactions between 2 or more different

protein X (X chains). How are they held together?

- This is when the protein has different protein subunits, so they don’t function as a X protein, there is no specific bond but sometimes those units are held together by X bond, some by X interactions 

- Hemoglobin: # alpha and # beta chains, these are binded together by X 

- Collagen: X 

What happens when 3D shape is altered?

A single X change  Amino acid X in hemoglobin causes X-X disease (Malaria)

- A proteins shape is everything, 3D shapes are very important

- Primary (1°) Structure: Peptide Bonds make Linear amino acid sequence, there will always be one at the end which is the amine of the first amino acid, the last amino acid will have the carboxylic acid, you have 29 amino acids together, you will have 28 peptide bonds. But a protein is not a long stick like that in the cell, the moment it enters the cytoplasm you will have hydrophobic amino acids and hydrophilic amino acids

Glucagon has 29 amino acids, in this exact order. (DNA RNA Protein)

- Secondary (2°) structure: This is because the protein has now been inside the cytoplasm, results from Hydrogen bonds between different parts of the amino acid backbone (the NCCNCC, as they come in contact with eachother, wieth the hydrogen bonds on the either end is going to create elastic regions, and in the same region you can have an alpha helix or a beta pleated sheet. -helix: elastic (wool, keratin)) The alpha helix is elastic it is for things like wool and keratin. The beta pleated sheet is very strong and flexible is used for silk

- Tertiary (3°) structure:

Not talking about the amino acid backbone, but how the R groups react Results from all types of bonds between different R-groups of the amino acid!:

R-group interactions ‘rivet’ different parts of the same protein together to make a

final shape needed for function. The sulfure-containing amino acids come together, this is the only time you are able to make a covalent bond:disulfide bridge, these covalent bonds are very strong, so a lot of proteins are stabilized by a disulfide bridge. Two charged amino acids can create an ionic bond with the acidic and basic R groups, they will be attracted to each other. There is also amino acids that will create a hydrogen bonds. Finally, ones where both the R groupsare hydrophobic and will interact through van der waal interactions, referred to as a “pocket” 

Quaternary (4°) structure: Interactions between 2 or more different

protein subunits (polypeptide chains). How are they held together?

- This is when the protein has different protein subunits, so they don’t function as a single protein, there is no specific bond but sometimes those units are held together by ionic bond, some by hydrophobic interactions 

- Hemoglobin: two alpha and two beta chains, these are binded together by heme 

- Collagen: trimer 

What happens when 3D shape is altered?

A single nucleotide change  Amino acid substitution in hemoglobin

causes Sickle-cell disease (Malaria)

- A proteins shape is everything, 3D shapes are very important

What are nucleic acids? 

Monomer: X 

1. There is a #-carbon X like X (X: RNA and X=DNA)

2. X base (X, X, X, X(tRNA), X) 

3. X group 

Pentose sugars identifying 

- Ribose will have both an X group on the # carbon, however on the # carbon is where they differ, for ribose the 2 C with have an X

- Deoxyribose will have only an X on the 2nd carbon hence deoxy

Nitrogeous base

Pyramidines

- X nitrogenous base, # ring 

- X, X (DNA), X (RNA)

Purines 

- # rings, X and X Pure As Gold

- The DNA helix is held togetehr by X bonds, if there are # hydrogen bonds then that is an AT (or U if RNA) base pair, if there are # then G C base pair. 1 X to 1 X

What are nucleic acids? 

Monomer: nucleotide 

1. There is a 5-carbon sugar like pentose (ribose: RNA and deoxyribose=DNA)

2. Nitrogenous base (A, C, G, T(tRNA), A) 

3. Phosphate group 

Pentose sugars identifying 

- Ribose will have both an OH group on the 3 carbon, however on the two carbon is where they differ, for ribose the 2 C with have an OH

- Deoxyribose will have only an H on the 2nd carbon hence deoxy

Nitrogeous base

Pyramidines

- Single nitrogenous base, 1 ring 

- Cytosine, Thymine (DNA), Uracial (DNA)

Purines 

- Two rings, Adenine and Guanine Pure As Gold

- The DNA helix is held togetehr by hydrogen bonds, if there are two hydrogen bonds then that is an AT (or U if RNA) base pair, if there are 3 then G C base pair. 1 purine to 1 pyramidine

What is the DNA double helix? 

Monomers are connected by X: 

The # X + #’ X creates a X bond. 

- new nucleotides are added to the #’ X during DNA replication

- What is the enzyme that is going to make polymer out of RNA? RNA X, the enzyme that makes more DNA is DNA X. 

- The monomers are connected through X X. You think the # prime X to the # prime X

Can protein/gene sequences determine relatedness between organisms? X

- DNA and protein sequences are X measures of X–document hereditary background of organisms 

- We all have beta globin because we are aerobic organisms and mammals 

- The organisms that tend to have fewer changes are closely X in X sense, ones that diverge more in the amino acid sequence, probably diverge more on their evolutionary history. 

Of course you X DNA everytime you eat food that came from cells!

- Traditional plant breeding has resulted in our staple crops; GMO crops have been on the market in the 90s. Clones animals are common

What is the DNA double helix? 

Monomers are connected by condensation: 

The 5 P + 3’ OH creates a phosphodiester bond. 

- new nucleotides are added to the 3’ OH during DNA replication

- What is the enzyme that is going to make polymer out of RNA? RNA polymerase, the enzyme that makes more DNA is DNA polymerase. 

- The monomers are connected through dehydration synthesis. You think the 5 prime phosphate to the 3 prime OH

Can protein/gene sequences determine relatedness between organisms? Yes

- DNA and protein sequences are Tape measures of Evolution–document hereditary background of organisms 

- We all have beta globin because we are aerobic organisms and mammals 

- The organisms that tend to have fewer changes are closely related in evolutionaryy sense, ones that diverge more in the amino acid sequence, probably diverge more on their evolutionary history. 

Of course you eat DNA everytime you eat food that came from cells!

Practice structures