Need some good resources to learn about Protein function and structure

Need some good resources to learn about Protein function and structure

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I'm taking a course on biochemistry at edx. Since I'm a computer science student, I'm having some trouble in understanding many biochemical concepts. While the first module was just fine, I found the second module really hard to understand. I have problems to learn and understand about amino acids and proteins, so I would like to study apart from some good resources.

Which is a good resource to learn about amino acids and macromolecules? Also, please let me know if this book is up to date?

Given your background (not a biologist or chemist) you would probably find the introductory material in a biochemistry "lite" textbook more accessible/useful than a hardcore text for specialists. As a co-author of a biochemistry textbook, I can tell you that there are essentially three different classes, or types of texts.

  1. Comprehensive textbooks, of which I think Voet & Voet is an outstanding example, are designed for biochemistry majors who will be taking a full year, in-depth course, typically in the 3rd year of their undergraduate studies.
  2. The general introductory texts are usually thinner, and are designed to whip through the same material in half a year--aimed at life-science students in other majors. Some of these books that I described as "lite" are further targeted to, for example, nursing, medical, or dental school students.
  3. The third category of text tries to be multi-purpose, and appeal to both markets. The current versions of Stryer and Lehninger fall into this class (they are both excellent in my opinion); the instructors can cherrypick the readings if they want to use the book for a half-year course.

Voet, Voet, and Pratt (mentioned in the comments above) is a very good diluted version of Voet & Voet. As you can also tell from the comments, different texts have different flavors, and so which one is best depends on the reader.

It sounds like a more general "concept" based book might be useful for you (to provide background and context). The very thick "Molecular Biology of the Cell" by Alberts et al., has a lighter cousin named Essential Cell Biology which would be well worth looking into.

Keep in mind that when tackling a university-level biochemistry course the instructor has to assume that you have passed university level introductory courses in general chemistry and in organic chemistry. Biochemistry majors typically complete full year courses in both these subjects, as well as a watered-down version of physical chemistry.

I want to add a book to the list that may be easier for you since it takes it from the perspective of Physics:

Finkelstein & Ptitsyn, Protein Physics, Academic Press (2002). ISBN 0-12-256781-1.

It covers structure, thermodynamical processes in proteins, mechanism of folding, function, a bit of bioinformatics. It is designed as a master level course in Biophysics, but it takes most things from the beginning: it even explains what the partition function is (but it helps if you know it already). No prior knowledge in biochemistry is required.

Proteins are organic molecules made up of amino acids – the building blocks of life. These amino acids are joined together by chemical bonds and then folded in different ways to create three-dimensional structures that are important to our body’s functioning.

There are two main categories of amino acids in the body. First, we’ve got essential amino acids – those that the body can’t manufacture, and thus we must consume in our diets.

Some amino acids are conditionally essential, which means that our bodies can’t always make as much as we need (for example, when we’re under stress).

Next, kinda obviously, we’ve got nonessential amino acids – those that the body can usually make for itself.

  • Histidine
  • Isoleucine
  • Leucine
  • Lysine
  • Methionine
  • Phenylalanine
  • Threonine
  • Tryptophan
  • Valine
  • Arginine
  • Cysteine
  • Glutamine
  • Tyrosine
  • Alanine
  • Asparagine
  • Aspartic acid
  • Glutamic acid
  • Proline
  • Serine

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Amino Acids

Amino acids are the fundamental building blocks of protein. Long chains of amino acids, called polypeptides, make up the multicomponent, large complexes of protein. The arrangement of amino acids along the chain determines the structure and chemical properties of the protein. Amino acids consist of the following elements: carbon, hydrogen, oxygen, nitrogen, and, sometimes, sulfur. The general structure of amino acids consists of a carbon center and its four substituents, which consists of an amino group (NH 2 ), an organic acid (carboxyl) group (COOH), a hydrogen atom (H), and a fourth group, referred to as the R-group, that determines the structural identity and chemical properties of the amino acid. The first three groups are common to all amino acids. The basic amino acid structure is R-CH(NH2)-COOH.

There are twenty different forms of amino acids that the human body utilizes. These forms are distinguished by the fourth variable substituent, the R-group, which can be a chain of different lengths or a carbon-ring structure. For example, if hydrogen represents the R-group, the amino acid is known as glycine, a polar but uncharged amino acid, while methyl (CH 3 ) group is known as alanine, a nonpolar amino acid. Thus, the chemical components of the R-group essentially determine the identity, structure, and function of the amino acid.

The structural and chemical relatedness of the R-groups allows classification of the twenty amino acids into chemical groups. Amino acids can be classified according to optical activity (the ability to polarize light), acidity and basicity, polarity and nonpolarity, or hydrophilicity (water-loving) and hydrophobicity (water-fearing). These categories offer clues to the function and reactivity of the amino acids in proteins. The biochemical properties of amino acids determine the role and function of protein in the human body.

Of the twenty amino acids, eleven are considered nonessential (or dispensable ), meaning that the body is able to adequately synthesize them, and nine are essential (or indispensable ), meaning that the body is unable to adequately synthesize them to meet the needs of the cell. They must therefore be supplied through the diet . Foods that have protein contain both nonessential and essential amino acids, the latter of which the body can use to synthesize some of the nonessential amino acids. A healthful diet, therefore, should

Name Abbreviation Linear structure formula (atom composition and bonding)
SOURCE: Institute for Chemistry
Alanine ala CH 3 -CH(NH 2 )-COOH
Arginine arg HN=C(NH 2 )-NH-(CH 2 )3-CH(NH 2 )-COOH
Asparagine asn H 2 N-CO-CH 2 -CH(NH 2 )-COOH
Aspartic acid asp HOOC-CH 2 -CH(NH 2 )-COOH
Cysteine cys HS-CH 2 -CH(NH 2 )-COOH
Glutamine gln H2N-CO-(CH 2 )2-CH(NH 2 )-COOH
Glutamic acid glu HOOC-(CH 2 )2-CH(NH 2 )-COOH
Glycine gly NH 2 -CH 2 -COOH
Histidine his NH-CH=N-CH=C-CH 2 -CH(NH 2 )-COOH |____________| (nitrogen bonded to carbon)
Isoleucine ile CH 3 -CH2-CH(CH 3 )-CH(NH 2 )-COOH
Leucine leu (CH 3 )2-CH-CH 2 -CH(NH 2 )-COOH
Lysine lys H 2 N-(CH 2 )4-CH(NH 2 )-COOH
Methionine met CH 3 -S-(CH 2 )2-CH(NH 2 )-COOH
Phenylalanine phe Ph-CH 2 -CH(NH 2 )-COOH
Proline pro NH-(CH 2 )3-CH-COOH |__________|
Serine ser HO-CH 2 -CH(NH 2 )-COOH
Threonine thr CH 3 -CH(OH)-CH(NH 2 )-COOH
Tryptophan trp Ph-NH-CH=C-CH 2 -CH(NH 2 )-COOH |_________|
Tyrosine tyr HO-Ph-CH 2 -CH(NH 2 )-COOH
Valine val (CH 3 )2-CH-CH(NH 2 )-COOH

consist of a sufficient and balanced supply of both essential and nonessential amino acids in order to ensure high levels of protein production.

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Biomolecules - The Proteins does not work. It disappears.

Posted by Emerson Hayman on 1/21/2020 8:45:46 AM Reply

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what are proteins constructed from?

Proteins are constructed from chains of amino acids.

Proteins are made up of smaller building blocks called amino acids, joined together in chains. There are 20 different amino acids. Some proteins are just a few amino acids long, while others are made up of several thousands. These chains of amino acids fold up in complex ways, giving each protein a unique 3D shape.

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Need some good resources to learn about Protein function and structure - Biology

Welcome to -- the Web site for Ms. Foglia's Biology classes at Division Avenue High School, Levittown and for her collection of resources to help other Biology teachers. There's a lot to see here. So please look around!

  • Your Assignment in Detail: Produce a presentation of some sort that teaches other students the anatomy and function of ALL the cell organelles. You can use any online tool to create or post your presentation, like VoiceThread, Scrapblog, Prezi, create a movie (iMovie on Mac or MovieMaker for PC) and post it on Vimeo or YouTube, create a fake online community of organelles on FaceBook, etc. This can be creative. For example, one class I know did a pirate movie. You CANNOT produce a PPT presentation since that is the form your resources are in. We want you to learn a new tool. Here is an article on free movie making software.
    : Worksheets that you received in class, but can download again if you need. Included in the worksheets is an illustration of an animal and a plant cell that you can fill out with the "Baby Bio" PPT listed below. Fill out the blank chart while you watch the AP PPTs and then add from textbook reading.
    : An introductory PPT that I use in "Baby Bio". It's a good place to start, but don't stop there! Fill out the worksheets with the animal and plant cell diagrams while watching this. : The first of the AP lectures. It's about the organelles involved in making proteins. Fill out the blank chart worksheet while watching this. : The second of the AP lectures. It's about the organelles involved in making energy. Fill out the blank chart worksheet while watching this. : The third of the AP lectures. It's about the organelles involved in making new cells. Fill out the blank chart worksheet while watching this.
  • I have also included links to PDF versions of the PPTs, in case you do not have a working copy of PowerPoint. But it is much better to watch the PPTs with the animations. Try to go to the Public Library (Click here for their hours) and use their computers


Been There, Done That, Got The T-shirt!

How to Explain Basic Nutrition Concepts

According to a 2015 Academy of Nutrition and Dietetics survey of health professionals with experience in Central America, populations in developing areas of this region lack basic knowledge of biology and physiology. Beginning with a discussion of basic health concepts and then explaining how nutrition affects our bodies is a good strategy.

Explaining Organ Functions

  • Lungs: provide oxygen to blood
  • Heart: circulates blood throughout the body
  • Stomach: helps digest food
  • Intestines: absorb nutrients from food
  • Liver: removes toxins from blood and processes nutrients from food
  • Kidneys: filter blood of waste and extra fluid

Explaining Nutrition

Nutrition is how food affects the health of the body. Food is essential&mdashit provides vital nutrients for survival, and helps the body function and stay healthy. Food is comprised of macronutrients including protein, carbohydrate and fat that not only offer calories to fuel the body and give it energy but play specific roles in maintaining health. Food also supplies micronutrients (vitamins and minerals) and phytochemicals that don't provide calories but serve a variety of critical functions to ensure the body operates optimally.

Explaining Macronutrients: Protein, Carbohydrate and Fat

Protein: Found in beef, pork, chicken, game and wild meats, fish and seafood, eggs, soybeans and other legumes included in traditional Central America cuisine, protein provides the body with amino acids. Amino acids are the building blocks of proteins which are needed for growth, development, and repair and maintenance of body tissues. Protein provides structure to muscle and bone, repairs tissues when damaged and helps immune cells fight inflammation and infection.

Carbohydrates: The main role of a carbohydrate is to provide energy and fuel the body the same way gasoline fuels a car. Foods such as corn, chayote, beans, plantains, rice, tortilla, potatoes and other root vegetables such as yucca, bread and fruit deliver sugars or starches that provide carbohydrates for energy.

Energy allows the body to do daily activities as simple as walking and talking and as complex as running and moving heavy objects. Fuel is needed for growth, which makes sufficient fuel especially important for growing children and pregnant women. Even at rest, the body needs calories to perform vital functions such as maintaining body temperature, keeping the heart beating and digesting food.

Fat: Dietary fat, which is found in oils, coconut, nuts, milk, cheese, meat, poultry and fish, provides structure to cells and cushions membranes to help prevent damage. Oils and fats are also essential for absorbing fat-soluble vitamins including vitamin A, a nutrient important for healthy eyes and lungs.

Explaining Micronutrients: Vitamins and Minerals

Vitamins and minerals are food components that help support overall health and play important roles in cell metabolism and neurological functions.

Vitamins aid in energy production, wound healing, bone formation, immunity, and eye and skin health.

Minerals help maintain cardiovascular health and provide structure to the skeleton.

Consuming a balanced diet including fruits, vegetables, dairy, protein foods and whole or enriched grains helps ensure the body has plenty of nutrients to use. Providing a few examples of specific micronutrient functions can enhance the effectiveness of nutrition education:

  • Vitamin A helps the eyes to see
  • Calcium and magnesium help muscles and blood vessels relax, preventing cramps and high blood pressure
  • Vitamin C helps wounds heal and the body&rsquos ability to fight off germs
  • Iron helps the blood transport oxygen throughout the body and prevents anemia

Explaining the Concept of Nutrients as Building Blocks

Building blocks include protein for growing babies in utero, for child and adolescent growth, and for repairing damaged skin, blood, and other body parts in adults who aren't growing. Some parts of the body are replaced regularly, like blood and skin, so even adults are building new body parts regularly. Calcium is also a building block for building bones. Iron is a building block for blood. Since blood cells only last a few months, the body constantly needs more iron and protein to make new blood.

Using Metaphors to Explain Nutrition

According to registered dietitian nutritionists with experience teaching nutrition in developing areas of Central America, metaphors and simple concepts are useful in teaching basic nutrition. An example of this could be conveying foods rich in carbohydrate as "go" foods, protein-rich foods as &ldquogrow&rdquo foods and colorful produce as "glow" foods. Health educators should emphasize that good nutrition requires eating at least one serving of these three types of food at each meal:

Foods Simple Concept of Function
Carbohydrate-rich foods Fuel
Protein-rich foods Building blocks
Fruits and Vegetables Helpers and protectors

Using Illustrations to Convey Basic Nutrition Concepts

Using actual local foods for hands-on meal planning and for teaching food categories helps low-literacy adults and children to understand nutrition. Health educators should try to acquire local foods to use in nutrition education in addition to laminated illustrations.

Due to minimal literacy among Central Americans, illustrations are as important as words in all visual materials. The following are examples of symbols that can represent the three basic reasons why the body needs a variety of foods:

Good sources of high-quality protein

Fish. Most seafood is high in protein and low in saturated fat. Fish such as salmon, trout, sardines, anchovies, sablefish (black cod), and herring are also high in omega-3 fatty acids. Experts recommend eating seafood at least twice a week.

Poultry. Removing the skin from chicken and turkey can substantially reduce the saturated fat. In the U.S., non-organic poultry may also contain antibiotics and been raised on GMO feed grown with pesticides, so opt for organic and free-range if possible.

Dairy products. Products such as skim milk, cheese, and yoghurt offer lots of healthy protein. Beware of added sugar in low-fat yoghurts and flavored milk, though, and skip processed cheese that often contains non-dairy ingredients.

Beans. Beans and peas are packed full of both protein and fiber. Add them to salads, soups and stews to boost your protein intake.

Nuts and seeds. As well as being rich sources of protein, nuts and seeds are also high in fiber and “good” fats. Add to salads or keep handy for snacks.

Tofu and soy products. Non-GMO tofu and soy are excellent red meat alternatives, high in protein and low in fat. Try a “meatless Monday,” plant-based protein sources are often less expensive than meat so it can be as good for your wallet as it is for your health.