Cell Biology:Cell Compounds and Biological Molecules

Lesson 4 – Proteins and Nucleic Acids (Inquiry into Life pg. 37-41)

Today’s Objectives Analyze the structure and function of biological

molecules in living systems, including carbohydrates, lipids, proteins, nucleic acids List the major functions of proteins Draw a generalized amino acid and identify the amine, acid

(carboxyl), and R-groups Identify the peptide bonds in dipeptides and polypeptides Differentiate among the different levels of protein organization

with respect to structure and bond type, including: primary, secondary, tertiary, quaternary

Name the four bases in DNA and describe the structure of DNA using the following terms: nucleotide (sugar, phosphate, base), complementary base pairing, double helix, hydrogen bonding

Relate the general structure of the ATP molecule and its role as “energy currency”

2.7 - Proteins Proteins have many functions:

Proteins such as keratin and collagen have structural roles.

Proteins are also enzymes that speed up the chemical reactions of metabolism.

Proteins such as hemoglobin are responsible for the transport of substances within the body.

Proteins transport substances across cell membranes. Proteins form the antibodies of the immune system

that defend the body from viruses and disease. Proteins such as insulin are hormones that regulate

cellular function. Contractile proteins such as actin and myosin allow

parts of cells to move and muscles to contract.

What are proteins? Contain carbon, hydrogen, oxygen, and

nitrogen Also often contain sulfur, and sometimes

phosphorus and iron The basic structure of a protein is a chain of

amino acids (polypeptides) There are about 20 different amino acids

What are amino acids? Proteins are polymers with amino acid

monomers An amino acid has a central carbon atom

bonded to a hydrogen atom and three groups:

One of the three groups is an amino group (-NH2),

One of the groups is an acidic group (-COOH) Hence called an amino acid!

The third group is called an R Group Amino acids differ from one another by their R

group

What are R groups? An R group is a variety of atoms attached to

amino acids R group = radical group or remainder group An R group distinguishes one amino acid

from another

Examples of amino acids

Formation of Proteins An amino acid can be referred to as a peptide Dehydration synthesis of amino acids result in

the bonding of amino acids together and the release of water molecules

When two amino acids bond together, they produce a dipeptide

Example: amino acids glycine and alanine bond to form the dipeptide gly-ala

Formation of proteins The bond that connects amino acids is called

a peptide bond A dipeptide has one peptide bond holding

together two amino acids A Tripeptide would have two peptide bonds

holding together three amino acids A polypeptide would have numerous peptide

bonds holding together numerous amino acids A polypeptide is a single chain of amino acids

The order or combination of these amino acids determines which protein is produced

Dehydration synthesis of amino acids

Dehydration synthesis of amino acids

Dehydration synthesis of amino acids

Formation of proteins This process when repeated form

long sequences of amino acids, or proteins

These sequences take on specific features and characteristics of the individual amino acids that are bonded together

Protein Structure There are three to four levels of protein

structure Primary structure – sequence of amino acids

(polypeptide) Secondary structure – orientation of

polypeptide Tertiary structure – final 3-D shape of

polypeptide Quaternary structure* - arrangement of

multiple polypeptides *not all proteins have multiple polypeptides

Primary Structure Simply the sequence of

amino acids Because there are twenty

amino acids, it is easy to see that there are literally millions of different possible amino acid sequences

Consequently, there are millions of proteins

Secondary Structure As the amino acid chains

(polypeptides) get longer, they begin to twist or fold

This is a result of stress on the peptide bonds

Two types of secondary structure: Alpha helix – like a spiral Beta pleated sheet –

like folded paper The alpha helix is most

common

Secondary Structure – alpha helix As the polypeptide bends into a spiral,

hydrogen bonds form between the hydrogen of one amino acid and an oxygen further down the chain

This hydrogen bond helps the alpha helix hold its shape

An alpha helix contains 3.6 amino acids per spiral

Secondary Structure – Beta pleated sheet Hydrogen bonds can form between parallel

lengths of the polypeptide chain creating beta pleated sheets

Secondary Structure

Tertiary Structure The third level of protein structure or tertiary

structure is described as the bending and folding of the alpha helix

As the helix gets longer there are some amino acids that cannot fit the configuration and therefore cause kinks

New bonds will form to hold it into a three dimensional (3-D) shape

These bonds can be ionic, covalent, and/or hydrogen bonds

Tertiary Structure

Alpha helix

Quaternary Structure Only occurs in proteins with more than one

polypeptide The quaternary structure is where different

3-D (tertiary) configurations are associated with and function with each other Imagine multiple kinked helixes tied up with each

other in knots An example of a protein with quaternary

structure is hemoglobin which transports substances through our body in our blood

Quaternary Structure

Levels of Protein Structure

More about Protein Functions Enzyme proteins speed up chemical reactions

in our body Reactions that normally would take several hours

will take only a fraction of a second Proteins such as hemoglobin transport

nutrients and other substances through our body

Antibody proteins fight infections and attack viruses

The protein keratin is the main structural component of fingernails and hair

Collagen makes up the connective tissues in our muscles

Actin/myosin make up muscle fibers that allow for movement

2.8 Nucleic Acids Nucleic Acids are polymers made up of

monomers called nucleotides There are two types of nucleic acids:

DNA – deoxyribonucleic acid RNA – ribonucleic acid

Some functions of Nucleic Acids: They form genetic material and are involved in the

functioning of chromosomes and protein synthesis DNA stores genetic information DNA codes for the order of amino acids in a protein RNA is an intermediary in the sequencing of amino

acids into a protein

What are Nucleotides? Nucleotides are made from a pentose sugar,

a phosphate group, and a nitrogen containing base

Nucleotides There are five basic nucleotides: Adenine and Guanine

Double ring structure purines Cytosine, Uracil, and Thymine

single ring structure pyrimidines

These bases are found in DNA and RNA DNA contains A,G,T and C RNA contains A,G,U and C

DNA structure compared to RNA structure

Nucleotides The bases found in

DNA form complementary base pairs (the same two bases always bond with each other)

The structure of DNA is a double helix (we will talk more about DNA later this year

Complementary Base Pairs in DNA

ATP (Adenosine Triphosphate) One particularly important nucleic acid is the modified

nucleotide known as ATP ATP is an RNA nucleotide with an adenine (A) base (adenine

+ ribose = adenosine) attached to 3 phosphate groups

ATP is a very high energy molecule When ATP undergoes hydrolysis, large amounts of energy are

released

ATP: The energy currency of cells ATP is a high energy molecule because the last two

phosphate bonds are unstable and easily broken A lot of energy is required to maintain these bonds If the bonds are broken, this energy is released

When an ATP molecule loses a phosphate, it becomes the molecule ADP (adenosine diphosphate) and a phosphate molecule

With the addition of energy, this process can be reversed, creating the ATP cycle

Muscle cells use the energy for muscle contraction Cells use the energy to synthesize carbohydrates

and proteins More on this later in the year

ATP Cycle

Pop Quiz! An amino acid is a central hydrogen atom attached to

a hydrogen atom and what? What are the monomers called that make up proteins? Describe primary protein structure Describe secondary protein structure What are the two main types of secondary structure Describe tertiary protein structure Describe quaternary protein structure What are 3 main functions of proteins? What are the monomers called that make up nucleic

acids? How do cells get energy from the hydrolysis of ATP? What are the 4 bases found in DNA?