Macromolecules: Nucleic acids & proteins

What do membranes do?

form semipermeable barriers

Membranes

essential structures that define the boundaries of cells and organelles, playing crucial roles in transport, signalling, and adhesion.

Polysaccharides function

cell energy, structure, and signaling

polysaccharide

polymer consisting of sugars and sugar derivatives linked together by glycosidic bonds.

Nucleic acids function

store, transmit, and express genetic information (instructions for life)

Proteins function

do almost everything else that cells need

-Virtually everything a cell is or does depends on the genes it express and the proteins it contains

e.g proteins can be enzymes, structural proteins, motility proteins, Regulatory proteins, Transport proteins, Signalling proteins, defensive proteins, and antibody proteins

What is DNA the molecule of?

Heredity

Heredity

The process by which characteristics are passed down from a parent to child through genes

Genes are “written” in what?

DNA

What is the genome?

The genome (all genes in an organism) provide all of the instructions for making that organism

Gene

The basic unit of heredity passed down from parent to child. Genes are made up of sequences of DNA and are arranged, one after another, at specific locations on chromosomes in the nucleus of the cell. They contain information for making specific proteins that lead to the expression of a particular physical characteristic or trait, such as hair colour or eye colour, or to a particular function in a cell.

What does DNA do?

Stores and transmits biological information

What does DNA transmitting information mean?

it carries the instructions (genes) for building and operating a living thing, encoded in its base sequence, and passes these instructions accurately from parent to offspring during reproduction, ensuring continuity and traits from one generation to the next

What does RNA do?

RNA is chemically similar to DNA, but is used to “express” genetic information

Gene expression:

A genes DNA sequence is used to create a functional product, usually a protein or functional RNA, through two main steps: Transcription and Translation

Transcription

process by which RNA polymerase utilizes one DNA strand as a template for guiding the synthesis of a complementary RNA molecule.

Translation

Process by which the base sequence of an mRNA molecule guides the sequence of amino acids incorporated into a polypeptide chain; occurs on ribosomes.

Nucleic acids:

Linear polymers of nucleotides

DNA:

deoxyribonucleic acid

RNA:

ribonucleic acid

Nucleotides:

Basic building blocks of nucleic acids

Nucleotides consist of:

Phosphate group Five-carbon sugar (ribose or deoxyribose) Nitrogen-containing aromatic base ▪ Purine or pyramidine

What is the difference in the sugars of DNA and RNA?

RNA contains the five-carbon sugar ribose in each of its nucleotides, whereas DNA contains the closely related sugar deoxyribose

-Ribose has OH group at C 2’

-Deoxyribose has H group at C 2’

Purine

two-ringed nitrogen-containing molecule; parent compound of the bases adenine and guanine.

Pyrimidine

single-ringed nitrogen-containing molecule; parent compound of the bases cytosine, thymine, and uracil.

DNA purines:

Adenine, Guanine

Dna Pyrimidines

Cytosine, Thymine

RNA purines

adenine, guanine

Rna pyrimidines

Cytosine, Uracil

Nucleoside

molecule consisting of a nitrogen-containing base (purine or pyrimidine) linked to a five-carbon sugar (ribose or deoxyribose); a nucleotide with the phosphate removed.

What can each purine and pyrimidine exist as?

The free base, a nucleoside, or the nucleotide

Adenine; Nucleoside, Nucleotide, Deoxynucleoside, Deoxynucleotide,

Nucleoside: Adenosine

Nucleotide: Adenosine monophosphate (AMP)

Deoxynucleoside: Deoxyadenosine

Deoxynucleotide: Dexoyadenosine monophosphate (dAMP)

Guanine: Nucleoside, Nucleotide, Deoxynucleoside, Deoxynucleotide,

Nucleoside: Guanosine

Nucleotide: Guanosine monophosphate (GMP)

Deoxynucleoside: Deoxyguanosine

Deoxynucleotide: Deoxyguanosine monophosphate (dGMP)

Cytosine: Nucleoside, Nucleotide, Deoxynucleoside, Deoxynucleotide,

Nucleoside: Cytidine

Nucleotide: Cytidine monophosphate (CMP)

Deoxynucleoside: Deoxycytidine

Deoxynucleotide: Deoxycytidine monophosphate (dCMP)

Uracil: Nucleoside, Nucleotide, Deoxynucleoside, Deoxynucleotide,

Nucleoside: Uridine

Nucleotide: Uridine monophosphate (UMP)

Deoxynucleoside: N/A

Deoxynucleotide: N/A

Thyamine: Nucleoside, Nucleotide, Deoxynucleoside, Deoxynucleotide,

Nucleoside: N/A

Nucleotide: N/A

Deoxynucleoside: deoxythymidine

Deoxynucleotide: deoxythymidine monophosphate (dTMP)

a nucleoside monophosphate

has one phosphate group attached to it

Can be diphopshate (2 phosphate groups) Triphosphate (3 phosphate groups)

example: Adenosine Triphisphate (ATP) : 3 phosphate groups, Adenine base, Ribose sugar.

Nucleic acids

Nucleic acids are linear polymers of nucleotides

-formed by linking each nucleotide to the next through a phosphate group

3ʹ,5ʹ phosphodiester bonds:

Nucleotides linked by 3ʹ,5ʹ phosphodiester bonds:

▪ 1 phosphate group linked to 2 adjacent nucleotides via two phosphodiester bonds

What are Nucleotide in polymers are linked by?

phosphodiester bonds

Directionality of nucleotide polymers:

5ʹ phosphate at one end

▪ 3ʹ hydroxyl at the other end

▪ Nucleotide sequences written in 5ʹ to 3ʹ direction

Nucleic acid synthesis requires what?

Information and energy

Information:

A pre-existing template

template:

a nucleic acid whose base sequence serves as a pattern for the synthesis of another (complementary) nucleic acid.

phosphodiester bridge

covalent linkage in which two parts of a molecule are joined through oxygen atoms to the same phosphate group.

To provide the energy needed to form each new phosphodiester bridge:

each successive nucleotide enters as a high-energy nucleoside triphosphate

Energy:

Nucleotides enter as high energy triphosphates

RNA: nucleotide triphosphates:

(NTPs; e.g., ATP)

DNA: deoxynucleotide triphosphates:

(dNTPs)

In nucleic acid synthesis, what ensures correct order?

Correct base pairing between the template and the incoming nucleotide ensures correct order

base pairing

complementary relationship between purines and pyrimidines based on hydrogen bonding that provides a mechanism for nucleic acids to recognize and bind to each other; involves the pairing of A with T or U, and the pairing of G with C.

Base pairs form between:

complementary bases:

▪ A forms two hydrogen bonds with T

▪ G forms three hydrogen bonds with C

How many hydrogen bonds between Cytosine and Guanine?

3

How many Hydrogen bonds between Thymine and Adenine?

2

Base pairing is

Complimentary

between purine (little name big base) and Pyrimadine (big name, little base)

Describe the structure of DNA

DNA forms a double-stranded helix

• One strand base-pairs with the other= Complementary

• The two strands are in opposite orientations = Antiparallel

DNA replication

Each strand of Dna acts as a template for DNA replication

Explain Base Pairing and RNA:

▪ RNA is normally single stranded

▪ RNA structure also depends on base pairing ▪ RNA base pairing is usually between bases in different areas of the same molecule and is less extensive than that of DN

Explain Proteins

• Polymers of Amino Acids

• 20 amino acids are used in proteins

Amino Acid Structure

• α (central) carbon which the following is attached to:

• amino (NH3) group

• Carboxyl group

• A hydrogen atom

• R group (different for each amino acid)

• Most have two enantiomers (L and D) ▪ Only the L enantiomer is used in proteins

What do specific properties of amino acids depend on?

the nature of their R groups

Polypeptide:

product of amino acid polymerization

Protein synthesis

The process of elongating a chain of amino acids

A polypeptide does not become a protein until it has assumed a stable, three-dimensional shape and is biologically active

What are the classes of amino acid R groups?

• 9 amino acids have hydrophobic (nonpolar) R groups

• 11 amino acids have hydrophilic R groups

In regards to the 11 amino acids have hydrophilic R groups:

• 6 are polar and uncharged

• 5 are charged at neutral pH

Acidic amino acids

have negative charges

basic amino acids

have positive charges

What kind of side groups do hydrophobic (nonpolar) R groups have?

hydrophobic (nonpolar) R groups

-e.g phenyl groups, just H, CH, ect

What kind of side groups do hydrophilic R groups have?

• the R group is polar e.g has OH, NH2,

• R group is acidic or basic and thus is charged at cellular pH e.g NH+, O-

Where are Hydrophilic and hydrophobic amino acids found?

Hydrophilic amino acids tend to be found on the water-facing surfaces of proteins; hydrophobic tend to be on the interior

Amino acids in a polypeptide and are linked by what?

peptide bonds

How do peptides have directionality?

the chain of amino acids formed has an intrinsic directionality because it always has an amino group at one end and a carboxyl group at the other end

The end with the amino group is called the N- (or amino) terminus ▪ Beginning of the protein

▪ The end with the carboxyl group is called the C- (or carboxyl) terminus ▪ End of the protein

peptide bond

a covalent bond between the amino group of one amino acid and the carboxyl group of a second amino acid

he initial folding of a polypeptide into its proper shape, or conformation, depends on what?

several different kinds of bonds and interactions including the covalent disulfide bond and several noncovalent bonds and interactions

Label a) b) c) d) and explain this figure

a)Disulfide bonds: Covalent bonds. Very stable bond ▪ Formed between sulfur atoms in cystein residues ▪ Intra- or Inter-molecular

b)Hydrogen bonds

c) Ionic bonds

d)van der Waals interactions ▪ Hydrophobic interactions

b, c, and d are all Noncovalent bonds/interactions

Individually weaker than bonds, but collectively strong

What determines the determine the 3D shape of the protein?

Bonds/interactions between R groups

Primary structure basis:

Amino acid sequence

Primary structure bonds/interactions:

Covalent peptide bonds

Secondary structure basis:

Folding into alpha helix or beta sheet, or random coiling *Local folding

Secondary structure bonds/interactions:

Hydrogen bonds between NH and CO groups of peptide bonds in the backbone.

Tertiary structure basis:

Three dimensional folding of a single polypeptide chain

Tertiary structure bonds/interactions:

Disulfide bonds, hydrogen bonds, ionic bonds, van der Waals interactions, hydrophobic interacrions

Quaternary structure basis:

Association of multiple polypeptide to form a multimeric protein

Quaternary structure bonds/interactions:

Disulfide bonds, hydrogen bonds, ionic bonds, van der Waals interactions, hydrophobic interacrions

Secondary Structure

• Local regions of structure

• Readily predictable, and determined by the primary structure

• Results from hydrogen bonding between NH and CO groups along the polypeptide backbone

• Two major patterns ▪ α helix and β sheet

• Result from localized folding of a segment of the polypeptide ▪ Alpha helices are usually ~10-20 amino acids long ▪ Beta sheets have multiple strands with variable length

Result from localized folding of a segment of the polypeptide ▪ Alpha helices are usually ~10-20 amino acids long ▪ Beta sheets have multiple strands with variable length

The α Helix

Helix is spiral in shape ▪ R groups jut-out from the spiral ▪ Some amino acids have strong propensities toward forming helices; other amino acids disrupt helices

The β Sheet

Sheet-like conformation formed by multiple polypeptide strands ▪ Extensive but variable hydrogen bonding between backbones ▪ R groups jut-out on alternating sides of the (pleated) sheet ▪ Classified based on relative directionality of strands (N-to-C) ▪ Parallel: same directions ▪ Antiparallel: opposite directions

Tertiary Structure:

3D folding of a polypeptide ▪ Depends upon interactions between R groups; prediction enabled by new AI platforms (AlphaFold)

Tertiary Structure is determined by

1. Hydrophobic residues avoiding water 2. Hydrophilic residues interacting with water 3. Repulsion of similarly charged residues 4. Attraction between oppositely charged residues

quaternary structure

• level of organization concerned with subunit interactions and assembly

• The term only applies to multimeric proteins (composed of two ore more polypeptides)

• Some multimeric proteins consist of multiple identical subunits; others, such as hemoglobin, contain two or more types of polypeptides