Proteins summary

Most cellular jobs are performed by proteins

Proteins interact with other molecules in specific ways to perform cellular functions

Levels of protein structure

• Proteins are amino acid polymers
• The amino acid polymer is called a polypeptide
• Once polypeptides are functional after being folded, the polypeptides are called proteins
• Some proteins are generated by folding more than one chain of polypeptides

Categories of protein structure

• Primary structure-amino acid sequence in the protein
• Secondary structure-are small regions folded into pleated sheets and alpha helices
• Tertiary structure-is the 3D final structure of a single folded chain of amino acids
• Quaternary structure- is a protein structure that consists of two or more chains of amino acids

Primary structure

• Is the amino acid sequence in the protein
• There are twenty amino acids in human cells hence ordering of the amino acids makes up the primary structure
• On every amino acid, a central carbon atom is bonded to various chemical groups
  • Nitrogen-containing  amino group (–NH2 or –NH₃)
  • A hydrogen atom (-H)
  • Carboxyl group(-COOH)
  • Sidechain (R) which varies among the twenty amino acids

Amino acids bond to each other by condensation.

Water is formed as covalent bond forms between two amino acids

The bond being formed is called a peptide bond

Secondary structure

Chains of polypeptide fold into the final structure and some regions of the chain form regular folded patterns

There are two-fold patterns;

• Alpha helix twists around  a spiral-like staircase
• Pleated sheets wound back and forth
• Secondary structure types and number in a protein depends on the protein.

Tertiary structure

• Is the 3D final structure of a single folded chain of amino acids
• Categories of 3D proteins include:
  • Globular proteins-they contain an overall rounded shape or irregular shape. Most enzymes are globular
  • Fibrous proteins-cable like and long proteins.
• The tertiary structure is held together by several types of bonds between atoms of amino acid R groups.
• The  bonds forming between R groups include:
  • Covalent bonds-include the bond formed between to cysteine amino acids.
  • Hydrogen bonds- occur in R groups with polar covalent bonds which create differences in negative and positive charges in atoms.
  • Ionic bonds- formed when R groups that are ionized come close to each other in a folded polypeptide chain
  • Hydrophobic interaction-formed when hydrophobic R groups get pushed together in small pockets inside polypeptide chains that are folded resulting in hydrophobic interactions.

Quaternary structure

• They contain many chains of polypeptides.
• the bonds that attach polypeptide chains to build up a protein are the same ones in the tertiary structure.

Functions of proteins

• proteins are enzymes- enzymes make biochemical reactions faster
• proteins reinforce structures- proteins form the structure of plasma membranes and cytoskeletal proteins strengthen internal cell structures
• proteins transport materials inside and outside cells
• proteins play a big part in cellular identification
• proteins promote cell movements
• proteins help in cell communication
• proteins promote the organization of molecules in cells
• proteins promote immunity
• proteins regulate the use of DNA  in cells

Enzymes and substrates

• enzymes are specific
• the correct enzyme folding creates a region called an active site
• substrate- are molecules that fit correctly into enzymes active sites

Inhibiting enzymes

There are two main types of enzyme inhibition

• Competitive inhibition- occurs from another molecule of the same shape as the substrate competing for the active site on enzymes
• Non-competitive inhibition-occurs if a regulatory molecule binds to another site apart from the active site

Membrane proteins

Proteins on the plasma membrane coordinate  many activities of the plasma membrane

The activities include;

• transport proteins
• receptor proteins
• protein adhesion
• protein identification
• enzymes production

DNA Binding Proteins

• The genetic material contains many functional and structural instructions of the cell
• DNA binding proteins control part of the DNA to be expressed
• Many DNA proteins are known and most of the proteins have repeating units called motifs
• Commonly DNA binding protein motifs are;
  • Helix turn helix motifs- contain 2 alpha-helices which are connected  by short amino acid sequences between the helices
  • Leucine zipper motifs- contain 2 alpha-helices which cross over each other
  • Zinc finger motifs-contain 2 pleated sheats and 2 alpha-helices held by a zinc atom.

Concept/Term	Description/Answer
Most cellular jobs are performed by proteins	Proteins carry out various functions within cells.
Proteins interact with other molecules in specific ways to perform cellular functions	Proteins interact with other molecules through specific mechanisms to carry out their roles in cellular processes.
Levels of protein structure	Proteins have four levels of structure: primary, secondary, tertiary, and quaternary.
Primary structure	The primary structure of a protein refers to the specific sequence of amino acids in the polypeptide chain.
Secondary structure	Secondary structure involves the folding of small regions of the polypeptide chain into patterns like alpha helices and beta sheets.
Tertiary structure	Tertiary structure is the overall 3D structure of a single folded chain of amino acids.
Quaternary structure	Quaternary structure refers to the arrangement of multiple chains of amino acids in a protein.
Functions of proteins	Proteins serve various functions such as enzymatic activity, structural support, transport, cell communication, etc.
Enzymes and substrates	Enzymes are proteins that catalyze biochemical reactions, and substrates are the molecules that bind to the active site of an enzyme.
Competitive inhibition	Competitive inhibition occurs when a molecule competes with the substrate for the active site of an enzyme.
Non-competitive inhibition	Non-competitive inhibition happens when a regulatory molecule binds to a site other than the active site of an enzyme.
Membrane proteins	Membrane proteins are involved in various activities on the plasma membrane, such as transport, adhesion, and identification.
DNA Binding Proteins	DNA binding proteins control gene expression and contain specific motifs, such as helix-turn-helix, leucine zipper, and zinc finger motifs.
Name of the basic unit of proteins	Amino acids are the basic units that make up proteins.
Elements present in all amino acids	Carbon, oxygen, hydrogen, and nitrogen are present in all amino acids.
Basic structure of an amino acid	An amino acid consists of an amino group (-NH2), a carboxyl group (-COOH), a central carbon, a hydrogen atom, and a side chain (R group).
Number of amino acids	There are 20 amino acids, including 9 essential and 11 nonessential amino acids.
Steps of protein synthesis	Protein synthesis involves cell signaling, transcription, and translation.
Steps of protein digestion	Protein digestion involves several steps: gastric acid denaturation, enzyme action, small intestine digestion, and absorption.
Denaturation	Denaturation is the alteration or unfolding of a protein’s 3D structure, often resulting in loss of biological activity.
Deamination	Deamination is the removal of an amino group from an amino acid, leading to the conversion of amino acids to other compounds.
Major functions of proteins	Proteins have various functions, including structural support, enzymatic activity, movement, transport, communication, and more.
Edema and protein’s role	Severe protein deficiency can lead to low levels of albumin, causing fluid accumulation in interstitial spaces and edema.
Complete protein foods	Complete protein foods contain all essential amino acids.
Incomplete protein foods	Incomplete protein foods lack one or more essential amino acids.
Complementary proteins	Complementary proteins are two or more incomplete protein sources that together provide adequate amounts of all the essential amino acids. Every function in the living cell depends on proteins.

Question	Answer
What are the four major classes of biological macromolecules?	Carbohydrates, lipids, proteins, and nucleic acids
What are monomers?	Single subunits or building blocks of macromolecules
What is the process called when monomers combine to form polymers?	Dehydration synthesis or condensation
How are monomers joined together in a dehydration synthesis reaction?	The hydrogen of one monomer combines with the hydroxyl group of another monomer, releasing a molecule of water
How are polymers broken down into monomers?	Through hydrolysis reactions
What are the roles of dehydration and hydrolysis reactions in macromolecules?	Dehydration reactions form new bonds and require energy, while hydrolysis reactions break bonds and release energy
What type of reactions are dehydration and hydrolysis reactions?	They are catalyzed reactions, meaning they are sped up by specific enzymes
What is the role of enzymes in dehydration and hydrolysis reactions?	Enzymes catalyze the reactions and facilitate the formation or breakage of bonds
What is the primary function of proteins?	Proteins have a diverse range of functions in living systems
What are the different types of proteins?	Structural, regulatory, contractile, protective, transport, storage, membranes, toxins, and enzymes
What are structural proteins?	Proteins that make up the cytoskeleton and scaffold of cells
Give examples of structural proteins.	Keratin (skin) and collagen (connective tissue)
What are contractile proteins?	Proteins that allow muscles to contract
Give examples of contractile proteins.	Actin and myosin
What are antibodies?	Proteins that help mount an immune response
What is the role of hemoglobin?	Hemoglobin transports oxygen in the blood
Where can proteins be found in cell membranes?	Proteins can be found as receptors, channels, pumps, and signaling molecules
What are enzymes?	Proteins that catalyze biochemical reactions
What are the four levels of protein structure?	Primary, secondary, tertiary, and quaternary
What is the primary structure of a protein?	The unique sequence of amino acids in a polypeptide chain
What is the secondary structure of a protein?	The local folding of the polypeptide into α-helix or β-pleated sheet structures
What is the tertiary structure of a protein?	The three-dimensional structure of a polypeptide, primarily due to interactions among R groups
What is the quaternary structure of a protein?	The interaction of multiple polypeptide chains or subunits to form a functional protein
What is denaturation?	The loss of a protein’s shape and, in some cases, function
What can cause denaturation?	Changes in temperature, pH, or exposure to chemicals
What are chaperones?	Protein helpers that assist in protein folding