Name: proteins, amino acids, and polypeptides
Uploaded: 2020-11-23T11:47:34.000Z
Duration: 2 min 17 s
Channel: JoVE

K12 Standards

Tennessee Academic Standards

High School

Biology

from-molecules-to-organisms-structures-and-processes

From Molecules to Organisms: Structures and Processes

BIO1.LS1.3

What are Proteins?

A protein is a chain of amino acids. At physiological pH, amino acids exist predominantly in a zwitterionic form, carrying both, a positive and a negative charge. Each amino acid contains amine and carboxyl groups, along with a different side group, denoted as R, attached to a core carbon.Amino acids are linked through covalent peptide bonds, and the repeating series of atoms along the core is called the polypeptide backbone.The sequence begins at the N-terminus, with a free amino group, NH3+, and ends with the C-terminus, a free carboxyl group, COO-.Each protein is unique, depending on the number of amino acids and their side chains. For example, thyroid-releasing hormone has 3 amino acids, whereas the elastic muscle protein titin has over 34,000.There are 20 standard amino acids, each with a different side chain, and they fall into one of four groups.Negative polar amino acids, such as aspartic and glutamic acid, have side chains with a carboxyl group. Because of this, they carry a negative charge at physiological pH.Positive polar amino acids carry a positive charge at physiological pH and have nitrogen-containing side chains.Several amino acids are polar but uncharged. They are usually hydrophilic and form the outer portion of a folded protein, where they can interact with the aqueous environment.Lastly, a large group of amino acids has nonpolar side chains.They can be simple, as in glycine, or complex, like proline and tryptophan.Nonpolar side chains generally make the amino acid hydrophobic, forming the core of many proteins.

what are proteins?

Proteins are chains of amino acids that are connected by peptide bonds and folded into a 3-dimensional structure. The side chains of individual amino acid residues determine the interactions among amino acid residues, and ultimately the folding of the protein. Depending on the length and structural complexity, chains of amino acid residues are classified as oligopeptides, polypeptides, or proteins.Amino Acid Residues Are the Building Blocks of ProteinsAn amino acid is a molecule that contains a carboxyl (&#x2013;COOH) and an amino group (&#x2013;NH2) attached to the same carbon atom, the &#x237A;-carbon. The identity of the amino acid is determined by its side chain or side residue, often called the R-group. The simplest amino acid is glycine, where the residue is a single hydrogen atom. Other amino acids carry more complex side chains. The side chain determines the chemical properties of the amino acid. For example, it may attract or repel water (hydrophilic or hydrophobic), carry a negative charge (acidic), or form hydrogen bonds (polar).Of all known amino acids, only 21 are used to create proteins in eukaryotes (the genetic code encodes only 20 of these). Amino acids are abbreviated using a three letter (e.g., Gly, Val, Pro) or one letter code (e.g., G, V, P). The linear chain of amino acid residues forms the backbone of the protein. The free amino group at one end is called the N-terminus, while the free carboxyl group on the other end constitutes the C-terminus. The chemical properties of the side chains heavily determine the final structure of the protein as they interact with each other and with polar water molecules.To form a polypeptide, amino acids are linked together by peptide bonds. Peptide bonds are formed between the amino group (&#x2013;NH2 group) of one amino acid and the carboxyl group (&#x2013;COOH) of the adjacent amino acid. Proteins are formed by dehydration synthesis. Each one water molecule is formed during linkage of two amino acids. The resulting covalent bond is a peptide bond.The pH of the Surrounding Medium Determines the Chemical Function of Amino AcidsAmino acids have both a basic and an acidic group. They can, therefore, act as a base (hydrogen ion recipient) or as an acid (hydrogen ion donor). The chemical property depends on the pH of the surrounding medium. At low pH (e.g., pH2) both the carboxyl and amino groups are protonated (&#x2013;NH3, &#x2013;COOH), so the amino acid acts as a base. At an alkaline pH (e.g., pH13), both the carboxyl and amino groups are deprotonated (&#x2013;NH2, &#x2013;COO-) and the amino acid will act as an acid. At a neutral pH (i.e., most physiological environments, ~pH7.4), the amino group is protonated (&#x2013;NH3) and the carboxyl group is deprotonated (&#x2013;COO-), giving rise to a zwitterion, a molecule with both a positive and negative charge. These chemical properties at physiological pH are essential to creating hydrogen bonds, which in turn contribute to the formation of more complex protein structures.The Length, Structural Complexity, and Functionality Distinguish a Polypeptide from a ProteinPolypeptides are chains of amino acids. Polypeptides with less than 20 amino acids are also referred to as oligopeptides, or simply peptides. A polypeptide chain is referred to as protein when it is folded into a three-dimensional structure, ready to perform its specific cellular function.Proteins Are Essential Building Blocks of LifeTogether with carbohydrates, nucleic acids, and lipids, proteins are fundamental building blocks of life. Proteins exhibit enormous diversity in their composition and, hence, function. Among other functions, they provide structure to a cell (e.g., in the form of collagen), allow movement (e.g., actin and myosin in muscles), catalyze reactions (enzymes), bring molecules across the cell membrane, and defend vertebrates against invaders (antibodies).

Overview

Proteins are chains of amino acids that are connected by peptide bonds and folded into a 3-dimensional structure. The side chains of individual ...

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Education

JoVE Core

Molecular Biology

Unit 1

Protein Structure

KEY TERMS AND CONCEPTS

proteins, amino acids, and polypeptides

Proteins are built from amino acids and form polypeptides. Amino acids are the small building blocks, and a polypeptide is a chain of amino acids joined together. This basic relationship explains how proteins are made and why their structure matters.

Proteins have several important roles in living things. Some proteins help build body structures, while others carry out work inside cells. The transcript also connects proteins to enzymes, which are proteins that speed up chemical reactions. Because of these jobs, proteins are a key part of cell function and growth.

The structure of a protein affects what it can do. Different amino acids can be arranged in many ways, so proteins can have different shapes and functions. Understanding amino acids, polypeptides, and proteins helps explain how cells use molecules for specific tasks.

Proteins, Amino Acids, and Polypeptides

Proteins are built from amino acids and form polypeptides. Amino acids are the small building blocks, and a polypeptide is a chain of amino acids joined together. This basic relationship explains how proteins are made and why their structure matters. Proteins have several important roles in living things. Some proteins help build body structures, while others carry out work inside cells. The transcript also connects proteins to enzymes, which are proteins that speed up chemical reactions.

protein organization

Protein Organization and Folding Levels

Protein organization describes how a protein is arranged at several levels. These levels help explain how a chain of amino acids becomes a working molecule. The main stages are primary, secondary, tertiary, and quaternary structure. Primary structure is the linear order of amino acids in the protein chain. Secondary structure is the first step of folding. In this stage, the chain can form patterns such as helices and sheets. Tertiary structure is the overall three-dimensional shape of one...

protein folding

Protein Folding and Structure

Protein folding is the process that gives a protein its final three-dimensional shape. That shape is essential because a protein’s structure helps determine how it works in the cell. A folded protein is stabilized by several interactions. These include hydrogen bonds, van der Waals interactions, and disulfide bridges. Each one helps hold the protein in the correct form. When a protein does not fold properly, its structure can change. That can affect its function and can interfere with normal...

conservation of protein domains over different proteins

conservation-of-protein-domains-over-different-proteins

Argonaute Protein Domains Across Species

Argonaute proteins have conserved domains that help small RNAs guide gene silencing. These proteins are found across organisms, but the number of Argonaute family members can differ from one species to another. Protein domains are small, structurally independent parts of a single amino acid chain. They can keep their shape on their own, but they may still work together with other parts of the protein. During evolution, domains can duplicate, recombine, and form new combinations. This process,...

globular and fibrous proteins

Protein Shapes: Globular vs Fibrous

Proteins can be grouped by shape into globular proteins and fibrous proteins. These two subtypes also differ in how they dissolve in water and in the jobs they do in cells and tissues. Globular proteins, also called spheroproteins, are usually round in shape. They contain a mix of amino acid types and varied primary sequences. Their shapes support many functions, including enzymes, cellular messengers, and molecular transporters. These roles often need the proteins to stay soluble in the...

intrinsically disordered proteins

Flexible Protein Regions and Binding

Intrinsically disordered proteins are proteins that do not fold into one fixed three-dimensional shape. Their flexible structure helps them work with ordered proteins to do jobs that rigid proteins cannot easily do. They are found more often in eukaryotes than in prokaryotes, and they can be fully disordered or made of both ordered and disordered regions. This lack of a rigid shape is linked to amino acid makeup. These proteins usually have many polar and charged amino acids and fewer...

protein complex assembly

How Proteins Self-Assemble in Cells

Proteins can self-assemble into working complexes inside cells. Some complexes are homomeric, which means they contain more than one copy of the same protein. Others are heteromeric, which means they are built from different protein types. Most protein complexes form through ordered self-assembly. In some cases, assembly factors help guide the proteins into the correct structure. Even in the crowded space inside a cell, proteins usually find the right partners and form functional complexes. <br...

conjugated proteins

Conjugated Proteins and Their Roles

Conjugated proteins are proteins that bond with a non-protein part. Unlike simple proteins, which contain only amino acids, these protein complexes include another chemical moiety attached covalently. That extra part can change how the protein works in the body. Nucleoproteins are conjugated proteins that contain nucleic acids. They are grouped as deoxyribonucleoproteins (DNPs) or ribonucleoproteins (RNPs). A nucleosome is a common DNP example, where nuclear DNA is associated with histone...

amyloid fibrils

Amyloid Fibrils in Brain Disease

Amyloid fibrils are clumps of misfolded proteins linked to brain disease and other disorders. In normal cells, misfolded proteins are usually refolded by chaperone proteins or broken down by the proteasome. But in some mutations or diseases, these proteins can build up into large clusters and then assemble into long fibers called fibrils. Amyloid deposits were seen as early as 1639 in the liver and spleen. In 1854, Rudolph Virchow used iodine staining, a method normally used to identify...

antibody structure

Antibody Heavy and Light Chains

Antibodies are built from heavy and light chains that work together to form a Y-shaped molecule. These chains give the antibody its basic structure and help it bind to specific targets. The two upper arms of the Y contain the variable regions, which differ from one antibody to another. These variable regions help determine which antigen, or foreign molecule, the antibody can recognize. The lower part of the antibody is the constant region. This region is more similar across antibodies and...

protein families

Protein Families and Superfamilies

Protein families are groups of homologous proteins with similar amino acid sequences and three-dimensional shapes. They often appear after gene duplication, when an extra copy of a gene is added to an organism’s genome. Mutations can then change the amino acids, as long as the protein can still be made correctly. If the new proteins keep similar amino acids in key places, their domains and overall three-dimensional structure can stay similar too. Members of the same family can share as little...

key terms and concepts

Learn how amino acids join to form polypeptides and proteins, and how protein structure relates to function, enzymes, and cell work in high school biology.

Proteins, Amino Acids, and Polypeptides | JoVE K12

molecular biology

JoVE Core Molecular Biology showcases the molecular processes of the cell through clear and concise animated video lessons. Additionally, in scientist-in-action videos, these concepts' application is demonstrated through real experiments in modern laboratories.

Arizona Science Standards

Life Science

HS+B.L1

HS+B.L1U1.5

south-carolina-college-and-career-ready-science-standards

South Carolina College and Career Ready Science Standards

B-LS1-1.

Characteristics of Life

Biology is a natural science that studies life and living organisms, including their structure, function, development, interactions, evolution, ...

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Levels of Organization

Biological organization is the classification of biological structures, ranging from atoms at the bottom of the hierarchy to the Earth&#x27;s biosphere. ...

the-tree-of-life-bacteria-archaea-and-eukaryotes

The Tree of Life - Bacteria, Archaea, and Eukaryotes

Prokaryotic Cells

Prokaryotes are small unicellular organisms that include the domains &#8212; Archaea and Bacteria. Bacteria include many common microorganisms, such as ...

Introduction to Virus

Viruses are unique biological entities that blur the boundary between living and non-living systems. Although they lack cellular structure and metabolic ...

Size and Structure of Viral Genomes

Viral genomes exhibit remarkable diversity in size, structure, and composition, influencing their replication strategies and interactions with host cells. ...

Compare and contrast existing models, identify patterns, and use structural and functional evidence to analyze the characteristics of life. Engage in argument about the designation of viruses as non-living based on these characteristics.
EXPLANATION: Students begin to develop patterns of living and non-living organisms in kindergarten and build on detailed characteristics of different classifications of living organisms throughout elementary and middle school. Biology 1 discussions introduce viral particles and viral cycles, building on student understanding of living organisms to engage in an argument regarding the classification of a viral particle as either living or non-living.

BIO1.LS1.1

What are Cells?

Cells are the smallest and basic units of life, whether it is a single cell that forms the entire organism, e.g., in a bacterium, or trillions of them, ...

Eukaryotic Compartmentalization

One of the distinguishing features of eukaryotic cells is that they contain membrane-bound organelles, such as the nucleus and mitochondria, that carry ...

Eukaryotic Evolution

The endosymbiont theory is the most widely accepted theory of eukaryotic evolution; however, its progression is still somewhat debated. According to the ...

Animal and Plant Cell Structure

Animal and plant cells not only differ in their structure, function, and mode of nutrition but also in how they reproduce, specialize, and organize into ...

Evaluate comparative models of various cell types with a focus on organic molecules that make up cellular structures.
EXPLANATION: Students explicitly discuss the structure and function of major cellular organelles in seventh grade. Building on this understanding, Biology I students should shift their focus to the different types of cells found in organisms and how the role of each cell type relates to its composition and the prevalence of different organelles within that cell. An example might include the absence (or enucleation) of the nucleus in red blood cells in mammals providing for increased levels of oxygen transport in organisms or the lack of centrioles in most neurons. Varying cell types can include both prokaryotic and eukaryotic cell types.

BIO1.LS1.2

Nucleic Acids

Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell&#39;s genetic blueprint and carry instructions for its ...

The DNA Helix

Deoxyribonucleic acid, or DNA, is the genetic material responsible for passing traits from generation to generation in all organisms and most viruses. DNA ...

DNA Base Pairing

Erwin Chargaff&#x2019;s rules on DNA equivalence paved the way for the discovery of base pairing in DNA. Chargaff&#x2019;s rules state that in a ...

The Central Dogma

The central dogma explains the flow of genetic information from DNA nucleotides to the amino acid sequence of proteins.
RNA is the Missing Link Between ...

DNA Packaging

Overview

Eukaryotes have large genomes compared to prokaryotes. In order to fit their genomes into a cell, eukaryotes must pack their DNA tightly inside ...

Organization of Genes

Overview

The genomes of eukaryotes can be structured in several functional categories. A strand of DNA is comprised of genes and intergenic regions. ...

Karyotyping

Describing the number and physical features of chromosomes can reveal abnormalities that underlie genetic diseases. This description is facilitated by ...

Replication in Prokaryotes

Overview

DNA replication has three main steps: initiation, elongation, and termination. Replication in prokaryotes begins when initiator proteins bind to ...

Replication in Eukaryotes

Overview

In eukaryotic cells, DNA replication is highly conserved and tightly regulated. Multiple linear chromosomes must be duplicated with high ...

Mutations

Overview

Mutations are changes in the sequence of DNA. These changes can occur spontaneously or they can be induced by exposure to environmental factors. ...

Transcription

Overview
Transcription is the process of synthesizing RNA from a DNA sequence by RNA polymerase. It is the first step in producing a protein from a gene ...

Translation

Lesson: Translation
Translation is the process of synthesizing proteins from the genetic information carried by messenger RNA (mRNA). Following ...

RNA Structure

Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form ...

RNA Stability

Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations ...

pre-mRNA Processing

In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or ...

Types of RNA

Overview
Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs ...

MicroRNAs

siRNA - Small Interfering RNAs

Small interfering RNAs, or siRNAs, are short regulatory RNA molecules that can silence genes post-transcriptionally, as well as the transcriptional ...

piRNA - Piwi-interacting RNAs

PIWI-interacting RNAs, or piRNAs, are the most abundant short non-coding RNAs. More than 20,000 genes have been found in humans that code for piRNAs while ...

CRISPR and crRNAs

Bacteria and archaea are susceptible to viral infections just like eukaryotes; therefore, they have developed a unique adaptive immune system to protect ...

lncRNA - Long Non-coding RNAs

In humans, more than 80% of the genome gets transcribed. However, only around 2% of the genome codes for proteins. The remaining part produces non-coding ...

Protein Organization

Protein Folding

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein ...

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.&#160; Although these domains are often structurally ...

Globular and Fibrous Proteins

Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
Globular ...

Intrinsically Disordered Proteins

Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows ...

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.&#160; Most protein complexes ...

Conjugated Proteins

Simple proteins and protein complexes contain only amino acids. In contrast, many other proteins, called conjugated proteins, covalently bond with ...

Allosteric Proteins-ATCase

Binding sites linkages can regulate a protein&#39;s function.&#160; For example, enzyme activity is often regulated through a feedback mechanism where the ...

Amyloid Fibrils

Amyloid fibrils are aggregates of misfolded proteins.&#160; Under most circumstances, misfolded proteins are either refolded by chaperone proteins or ...

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand ...

Antibody Structure

Phosphorylation

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their ...

Protein Kinases and Phosphatases

Proteins undergo chemical modifications that trigger changes in the charge, structure, and conformation of the proteins. Phosphorylation, acetylation, ...

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism&#39;s survival. Most PPIs ...

GTPases and their Regulation

Guanine nucleotide-binding proteins (G-proteins), also known as GTPases, are a superfamily of proteins that regulate many cellular processes, such as cell ...

Conserved Binding Sites

Many proteins&#8217; biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein ...

Covalently Linked Protein Regulators

Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an ...

the-equilibrium-binding-constant-and-binding-strength

The Equilibrium Binding Constant and Binding Strength

The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at ...

protein-complexes-with-interchangeable-parts

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex&#8217;s function. ...

Cofactors and Coenzymes

Mechanical Protein Functions

Proteins perform many mechanical functions in a cell. These proteins can be classified into two general categories- proteins that generate mechanical ...

Allosteric Regulation

Structural Protein Function

Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures ...

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other ...

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other ...

Integrate evidence to develop a structural model of a DNA molecule. Using the model, develop and communicate an explanation for how DNA serves as a template for self-replication and encodes biological information.
EXPLANATION: Discussions of DNA in earlier grades have been limited to discussions of genes and the role of genes in the appearance and activities of an organism. Biology 1 represents a student's introduction to a molecular model of a DNA as well as the organization of DNA into genes and genes subsequently into chromosomes. Students should address interactions between genes in proteins which regulate both the shape and reproduction of DNA molecules. It is important to note that not all segments of DNA are transcribed for proteins. Portions of DNA are involved in regulating the expression of genes or affect the structure of the chromosomes (replication origin, centromeres, and telomeres).

What is the Cell Cycle?

The cell cycle refers to the sequence of events occurring throughout a typical cell&#8217;s life. In eukaryotic cells, the somatic cell cycle has two ...

Interphase

The cell cycle occurs over approximately 24 hours (in a typical human cell) and in two distinct stages: interphase, which includes three phases of the ...

The Cell Cycle Control System

Positive Regulator Molecules

Inhibition of CDK Activity

S-Cdk Initiates DNA Replication

M-Cdk Drives Transition Into Mitosis

Mitogens and the Cell Cycle

Replicative Cell Senescence

Abnormal Proliferation

cells-coordinate-growth-and-proliferation

Cells Coordinate Growth and Proliferation

Mitosis and Cytokinesis

In eukaryotes, the cell division cycle is divided into distinct, coordinated cellular processes that include cell growth, DNA replication/chromosome ...

Chromosome Duplication

Cohesins

Create a model for the major events of the eukaryotic cell cycle, including mitosis. Compare and contrast the rates of cell division in various eukaryotic cell types in multicellular organisms.
EXPLANATION: Students first discuss mitosis in seventh grade, specifically focusing on the role of mitosis in creating genetically identical daughter cells. Biology 1 discussions should connect a student's understanding of gene expression and protein function with the process of mitosis to explore the differentiation of cell types from otherwise identical daughter cells. Discussions should also include varying rates of mitotic division and the relationship between these rates of division and the function of specific cell types within eukaryotic organisms. Examples may include the extremely limited use of mitosis by neurons due to their interconnectedness within neural networks or the rapid rates of mitosis with growing root tips.

BIO1.LS1.6

Proteins, Amino Acids, and Polypeptides

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