Biochemistry-chemistry

Summary

Biochemistry is a vast, multidisciplinary field that bridges biology, chemistry, and physics. It involves understanding the molecular details of life's processes and involves topics such as enzyme structure, cell metabolism, and the role of essential elements like carbon, nitrogen, oxygen, and hydrogen. These elements form numerous biomolecules, showcasing their importance through chemical bonding and molecular geometry. A strong foundation in organic chemistry is crucial, as it discusses the creation of bonds, functional groups, and protonation states, all of which are vital for understanding biochemical reactions and the complexity of living organisms.

Highlights

• Biochemistry connects biology, chemistry, and physics seamlessly 🌐.
• Key fields benefiting from biochemistry include medicine, agriculture, and biotechnology 🌱.
• Understanding organism functions and ecosystems is crucial 🔍.
• Hierarchical approach in biochemistry helps in understanding complex concepts 📚.
• Knowledge of basic chemistry is essential to grasp biochemistry fundamentals 🔬.
• Core elements in biochemistry: carbon, nitrogen, oxygen, hydrogen, and their bonding properties 🧬.
• Chemical bonds and molecular geometry play a critical role in biomolecules' functions 🎨.
• Functional groups define a molecule's properties and reactivity 🔥.

Key Takeaways

• Biochemistry is interdisciplinary, involving biology, chemistry, and physics 🧬.
• Biochemical knowledge is applicable in fields like medicine, agriculture, and technology 🌽.
• Understanding biomolecules involves hierarchy and complexity 💡.

Overview

Biochemistry is a wonderfully interdisciplinary subject that delves into the molecular heart of life. It combines knowledge from biology, chemistry, and physics to unveil the complex processes that sustain life. In this fascinating field, one explores concepts such as enzyme functions, cellular metabolism, and the fundamental elements that form life’s building blocks—namely, carbon, nitrogen, oxygen, and hydrogen. These elements’ interactions and bonds are pivotal to understanding how biomolecules work within cells.

In approaching biochemistry, we take a hierarchical path. We start from the basics, understanding fundamental concepts from organic chemistry, such as covalent bonds and molecular geometry, which are crucial in forming the diverse biomolecules in living organisms. This knowledge paves the way for exploring how these molecules function together within the complex systems of cells and ultimately organisms, playing critical roles in everything from energy production to the replication of DNA.

Functional groups and their protonation states further enrich the canvas of biochemistry, allowing organic frameworks to acquire unique behaviors and reactivities. These components are the reason behind the specificity and efficiency of biochemical reactions, which are essential for life's processes. Whether your interest lies in biotechnology, medicine, or environmental science, biochemistry unravels the mysteries of life's processes and the natural world's wonders.

Chapters

• 00:00 - 00:30: Introduction to Biochemistry This chapter, titled 'Introduction to Biochemistry,' focuses on two essential components for understanding biochemistry. The first is the hierarchy within biochemistry, and the second is the necessary chemical background needed for success in the field. Emphasizing its multidisciplinary and interdisciplinary nature, the chapter highlights the importance of having a background in physics, biology, and chemistry to truly grasp biochemistry.
• 00:30 - 01:00: The Interdisciplinary Nature of Biochemistry The chapter discusses the broad and interdisciplinary applications of biochemistry across various fields. After gaining an understanding of biochemistry, one could venture into diverse areas such as environmental science, biotechnology, agriculture, pharmaceuticals, and clinical diagnostics. Additionally, there are opportunities in creating commercial products for home or laboratory use, as well as in biomedical research and its applications in medicine and physiology. The chapter highlights the expansive reach of biochemistry in both scientific and practical domains.
• 01:00 - 01:30: Fields Contributing to Biochemistry The chapter 'Fields Contributing to Biochemistry' discusses various areas that contribute to the understanding and learning of biochemistry. It highlights the importance of understanding how organisms function both individually and in ecosystems. Many biology students are particularly interested in these aspects of biochemistry, which adds to the overall knowledge of the subject.
• 01:30 - 02:00: Approaches to Understanding Biochemistry The chapter titled 'Approaches to Understanding Biochemistry' covers the integration of biochemistry into physiology and medical applications. It highlights the use of real-life examples to understand biochemistry and its relevance to everyday life and the environment. The concept of hierarchy is introduced as a foundational starting point in this exploration.
• 02:00 - 02:30: Hierarchy and Complexity in Biochemistry The chapter "Hierarchy and Complexity in Biochemistry" explores the correlation between structure and function as complexity increases. It emphasizes the critical nature of structure-function relationships in biochemistry, particularly in the context of enzymes.
• 02:30 - 03:00: Elements and Macromolecules The chapter 'Elements and Macromolecules' discusses the various groups of molecules and how they combine to form major groups of biomolecules in organisms. It explores the synthesis of larger molecules known as macromolecules, emphasizing the relationship between structure and function. The chapter concludes by explaining how these macromolecules collaborate to execute cellular functions.
• 03:00 - 03:30: Structure-Function Relationship The chapter discusses the concept of metabolism, which involves the various chemical reactions occurring within cells. It aims to help the reader understand these processes by examining the general structure and functions of cells and their organelles. It assumes that the reader has prior knowledge of introductory biology, including basic cell structure and function.
• 03:30 - 04:00: Understanding Chemical Bonds in Biochemistry The chapter 'Understanding Chemical Bonds in Biochemistry' introduces fundamental concepts of organic chemistry that are essential to biology. It begins by discussing key elements that are most prevalent in the human body. The focus is on understanding the composition of the human body in terms of individual elements.
• 04:00 - 04:30: Role of Elements in Biochemistry This chapter discusses the significance of various elements in biochemistry. It emphasizes that carbon, nitrogen, oxygen, and hydrogen are the primary elements constituting biological entities. Despite their dominance, other elements also hold crucial roles in biochemical processes, which will be explored in detail.
• 04:30 - 05:00: Importance of Trace Elements in Biochemistry This chapter discusses the significant role of trace elements in biochemistry, specifically in activating or inactivating enzymes. It highlights how trace elements are crucial in the functioning of various proteins and enzymes. Additionally, the chapter emphasizes the importance of these elements in influencing the structure of different macromolecules.
• 05:00 - 05:30: Forming Biochemical Bonds: Covalent Bonds This chapter introduces the concept of biochemical bond formation, focusing specifically on covalent bonds. Importance of sulfur and phosphorus in biomolecules is highlighted, along with a discussion on the general types of chemical bonds in biochemistry and their occurrence. An example involving covalent bonding is presented to enrich understanding.
• 05:30 - 06:00: Variety and Arrangement in Chemical Bonds The chapter discusses the concept of covalent bonds, wherein electrons are shared between atoms. This is fundamental pre-existing knowledge that is essential for understanding why certain elements, particularly those crucial in biology and biochemistry, behave the way they do. The focus is on major elements like carbon, which can form a maximum of four single covalent bonds due to its four unpaired electrons, and nitrogen.
• 06:00 - 06:30: Molecular Geometry and its Importance The chapter discusses the concept of molecular geometry and its significance, particularly in the context of organic chemistry. It highlights how the unique valency of elements like oxygen and hydrogen allows for the creation of a wide variety of molecules. This forms the basis of understanding organic chemistry, which the reader is expected to have some familiarity with, likely from previous study.
• 06:30 - 07:00: Carbon-Carbon Bonds and Conformations This chapter discusses the significance of carbon-carbon bonds and their role in forming a vast number of compounds essential for life. Key focus is placed on how carbon bonds with hydrogen as well, particularly within the human body, allowing for the formation of various molecular structures. The chapter introduces these concepts using examples, likely touching on different types of carbon-carbon bonds, conformations, and perhaps how these affect the properties and functionality of molecules.
• 07:00 - 07:30: Energy and Reactions in Cells The chapter discusses the formation of covalent bonds, using examples like hydrogen-oxygen, nitrogen-hydrogen (in ammonia), and carbon-oxygen (in carbon dioxide). It explains the concept of double bonds where carbon forms two double bonds with oxygen, involving the sharing of two pairs of electrons. The summary also touches upon carbonic acid to illustrate the use of single and double covalent bonds, emphasizing the visualization of shared electrons as lines representing pairs of shared electrons.
• 07:30 - 08:00: Functional Groups in Biochemistry Functional groups in biochemistry are crucial for understanding the structure and function of molecules within cells.
• 08:00 - 08:30: Characteristics of Functional Groups This chapter explores the concept of molecular geometry, emphasizing how a carbon atom can form up to four single bonds, resulting in a tetrahedral geometry. The significance of this particular structure in understanding molecular shapes and geometry is highlighted.
• 08:30 - 09:00: Protonation States and Their Importance This chapter covers protonation states and their significance in molecular geometry and function. Particularly, it delves into the consistent bond angle of 109.5°, which is crucial for specific molecular jobs. The chapter also explores how variations in shapes, such as carbon-carbon single bonds, permit molecules to perform distinctive functions.

Biochemistry-chemistry Transcription

• 00:00 - 00:30 so today we're going to focus on two key pieces of information that we need to understand biochemistry the first one is looking at the hierarchy associated with biochemistry and then also understanding the chemical background that we need to be successful so biochemistry is very multidisciplinary and interdisciplinary which means you may have background in physics or biology or chemistry and in fact you're going to need all of these
• 00:30 - 01:00 different areas to be successful in understanding and applying biochemistry to the various different types of fields so the types of fields you might go into after understanding biochemistry are things like environmental science biotechnology agriculture pharmaceuticals clinical Diagnostics building or making commercial products for use at home or in labs or simply biomedical research and applying this to medicine and physiology so there's lots
• 01:00 - 01:30 of different areas that you can take the biochemistry so first let's talk a little bit about how we're going to approach understanding and learning about biochemistry most of us are interested in understanding overall how organisms function or maybe how organisms function with one another in ecosystems and two or one important area that many biology students are fascinated with is of
• 01:30 - 02:00 course physiology and how this applies then to medicine and we're going to see some really great examples and apply biochemistry to everyday life examples there's also going to be everyday life examples that are that are tied into understanding our environment as well so we'll see samples of both so to do that we're going to start down at the very bottom in terms of hierarchy and what hierarchy means is that as we move
• 02:00 - 02:30 up we're going to see increasing complexity and with increasing complexity means that we're going to be able to promote new functions okay so our our structure function relationship is really critical when we understand biochemistry we're going to see that especially when we start looking at enzymes so for example we're going to first review what we need to know about different elements and those important to two biochemistry and their functional
• 02:30 - 03:00 groups and they're outlined here we're then going to talk a little bit about how we can put those together to form the major groups of macro or of biomolecules in organisms and then how we can build even larger molecules called macromolecules then we really get to start to understand the structure function relationship when we can talk about how these macromolecules work together in order to get things done in the cell and simply that's just
• 03:00 - 03:30 metabolism that's all of the different chemical reactions that we're carrying out in our cells every day to be able to understand this as well we're going to need to review the general structure of cells and their organelles and how they are put together and there are different general functions and that also is considered to be prior knowledge from intro biology as well so this is prior knowledge as well as your basic
• 03:30 - 04:00 fundamental concepts associated with organic chemistry so let's start at the bottom and what as I mentioned we have a couple of key elements that are essential to biology and if you look at basically in terms of the human body itself what are we composed of most in terms of those individual elements and as you can see if you look at the overall dry
• 04:00 - 04:30 weight you can see we are mostly carbon nitrogen oxygen and hydrogen is four right here so those are the main important elements in biology because we see that you know where were made the most of these different elements now that doesn't mean that the others aren't important in fact a lot of the other elements like key roles we're gonna see especially how some of these play roles
• 04:30 - 05:00 in terms of activating or in activating enzymes we're going to talk about how some of our trace elements are important in the functions of different proteins and enzymes so there's many examples of how these are kind of key in terms of of our body in addition we're gonna see some of these play a major role in the structures of different macromolecules
• 05:00 - 05:30 so mainly sulfur as well as phosphorus are also key components of different biomolecules so the next piece of prior knowledge that we should talk about is understanding the general type of chemical bonds that we see in biochemistry and why they occur so for example what we're looking at here is different types of covalent bonds all
• 05:30 - 06:00 right and then covalent balance we're simply going to be sharing electrons ok so again this should be prior knowledge and if you look at those four major elements again that we talked about before we can see why these are so critical in biology and biochemistry so carbon can has four unpaired electrons that means it can form for maximum of four single covalent bonds nitrogen has
• 06:00 - 06:30 three oxygen has two and hydrogen has one so because of that we can sort of put these elements together in lots of different ways to build a lot of a huge variety of different molecules so if you think about what we mean by organic chemistry and again this is material that you should have gone through in your organic chemistry class okay so organic chemistry means we're talking
• 06:30 - 07:00 about essentially what is associated with forming bonds with carbon and of course in the human body that's typically also going to involve hydrogen's as well and so the way these the way we can can form these maximal number of molecules is due to these bonding characteristics of carbon so we have some examples here water of
• 07:00 - 07:30 course we have two single covalent bonds between our hydrogen and our oxygen ammonia is another example nitrogen is forming three single covalent bonds with hydrogen carbon dioxide here is forming two double bonds with oxygen so sharing two pairs of electrons so each one of those lines represents two pairs of shared electrons in carbonic acid you can see that we have both a double
• 07:30 - 08:00 covalent bond and two single covalent bonds so lots of different arrangements and then if you look at the end here at in terms of the overall structure you can see that these are in fact arranged differently which means they're due to the types of bonding we can have different types of structures that result and in shapes of those structures which are then going to allow them to carry out different jobs in this cell so
• 08:00 - 08:30 when you think about molecular geometry which really is understanding that shape that geometry that occurs in molecules this concept of how a carbon atom can combine up to four single bonds is important because it forms what's called a tetrahedral geometry so you can see this here in terms of the overall shape okay and we know that with this particular structure you have a
• 08:30 - 09:00 consistent bond angle of 109 point five and this shape is importance in allowing it to carry out particular jobs and the differences that can occur in shapes can allow molecules to carry out unique jobs as well so if you look that at a situation here in B where you have a carbon-carbon single bond here these are important
• 09:00 - 09:30 because we actually it allows for rotation to occur around that single bond so you can imagine moving these two end atoms our carbons and rotating so these in this case hydrogen's on either end can freely kind of move around even though those carbons are attached to one another this is different than when you
• 09:30 - 10:00 see a carbon-carbon double bond where there's no rotation because it's sharing two pairs of electrons one here and one here so this gives it a planar conformation which means that within this plane it's like a giant piece of paper you can't twist and turn that paper at all it has to stay flat so we're always going to see these atoms here are going to be within the same plane compared to B where these atoms do
• 10:00 - 10:30 not have to be in the same plane because they are rotating they can freely rotate so this is important because we're going to see that there's different amounts of energy associated with these individual bonds and that energy involved is really going to play a major role in understanding how and when different reactions can occur in a cell our key piece of prior knowledge that's important is understanding functional
• 10:30 - 11:00 groups and these are really what gives a common carbon carbon skeleton it's it's individual or unique roles so these are what we add on to carbon carbon skeletons and they allow us to allow the molecules to change their behavior and they do that because they're going to have particular characteristics they might be positively charged they might be negatively charged they might be
• 11:00 - 11:30 polar or there might be nonpolar and the chemical characteristics of each of these is different for example something that's positive or negatively charged can participate in ionic bonds so these are the main functional groups that we're going to see in this class you should have all of these memorized and be able to draw out and recognize their structures and we're going to see how each of these play a role in forming
• 11:30 - 12:00 unique structural elements of different biomolecules as well as understand how they play a role in a different chemical reactions it's also important to understand that multiple of these functional groups can actually have different protonation states and these different protonation states are are important because their chemical characteristics will alter as well
• 12:00 - 12:30 depending on what protonation state their form found in the one that we don't see that with of course is our methyl groups but for example a carboxyl group can also be written as co- if it's missing its hydrogen