BIO Midterm 1-5 - Lecture notes 1-5 PDF

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Study Guide Midterm Exam Ch. 1 – Foundations of Biology •

List and explain the common themes in biology -

There are 5 common themes in biology; Organization, Information, Energy and Matter, Interactions, and Evolution. All these themes allow us to understand the complexity and similarities that all life, whether big or small, share in the universe. Organization refers to properties, structures, and functions of organisms at different levels in the biological ladder. Beginning with the cell and making its way up to an organism at each level new roles emerge. This simple explanation of organization supports the actual complexity of life. A cell can be unimportant at its lowest level but when combined with other elements at a higher level can mean the difference between a human or an animal. Information refers to genetic information, or DNA, that can be expressed and transmitted. Information can also refer to the, less specific, genome; which is the complete sequence of genetic material that each organism carries. Energy and matter refers to the cycle of life. How energy from our sun is absorbed by organisms and transferred as we move through the food chain. Everything plays a crucial role in existence; no sacrifice is too small. Interactions between cells, plants, and animals, whether harmful or beneficial, are important in sustaining life. Every actions helps another move along. The interactions in an ecosystem trigger a domino effect that allows life to thrive. Evolution refers to the process of time in which organisms develop into better versions of themselves. Evolution allows us to develop with helpful modifications that benefit our survival. Evolution also explains the connection every living organism shares. A universal genetic code means that each organism comes from a common ancestor

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Explain the concept of emergent properties and how it applies to living things -

Emergent properties refers to the phenomena that while you “zoom out” of things, such as cells, you will find more complex connections. The individual member does not have these properties or abilities on its own but as a complex group it can perform more complex routines. •

Explain the difference between hypothesis and theory -

A hypothesis is a possible scientific explanation or inquiry that can be tested; it is based on observations. A theory, on the other hand, is a shared explanation for something in the scientific community. It has been tested and supported numerous times. This does not mean it can not be disproven. •

Outline the scientific method -

You must first make an observation. Then, ask a question about the observation. Go on to form a hypothesis, a possible scientific explanation based on the available evidence. This will either be a scientific hypothesis or a statistical hypothesis which consists of a null and alternative hypothesis. After this, you will make a prediction about the outcome of the scientific experiment. Then proceed to design and conduct an experiment. The experiment will have an independent, dependent, and control variable. The independent variable is the one you are manipulating while the dependent variable is the one that you are observing. The control variable is the one that stays constant throughout the entire experiment. In your experiment you may also have a control group which is used as a comparison. There are two types of control groups: positive and negative. You will not expect a response from the negative control group; however, you will expect a known response from the positive control group. After the experiment is complete, you will collect and analyze the data. You will reject or fail to reject your null hypothesis. Then, in order to form a theory, you must explore different ways to verify your data. This will involve creating new hypotheses and performing other experiments until you have a good understanding of what you are testing. After extensive testing and research, if the results align with your hypotheses, then you can form a theory. •

Ch. 2 Sec 2.3 & 2.5 •

Explain the difference between polar and nonpolar bonds -

A bond is considered to be polar or nonpolar based on its electronegativity. In a nonpolar covalent bond, the electrons are shared equally due to the fact that the two atoms have the same electronegativity. In a polar bond, an atom is actually bonded to a more electronegative atom. The electronegativity is not the same because the electrons are not shared equally. It can be compared to a tug-of-war between the two atoms. •

Distinguish molecular bonds from weak bonds -

Weak bonds are those forces of attraction that, in biological situations, do not take a large amount of energy to break. For example, hydrogen bonds are broken by energies. •

Explain what makes a molecule either hydrophobic or hydrophilic -

A hydrophilic molecule has an affinity for water. Polar molecules are hydrophilic. They have partial positive and negative charges due to the unequal sharing of electrons. Most polar molecules easily dissolve in water; however, in some cases, a molecule can be hydrophilic without actually dissolving. Some molecules might just be too big to dissolve. A hydrophobic molecule is a nonionic/nonpolar molecule that does not have an affinity for water. Ch. 3 – Molecular diversity

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Categorize the main macromolecules living beings are composed of Carbohydrates, Proteins, Nucleic acids - *Lipids are not a macromolecule because they are not generally large enough to be considered a one.* For each macromolecule type, name the polymer they form, the monomers that composed them, and identify an example:

-Carbs: The monomer of carbohydrate is monosaccharide or also known as glucose. When two or more monosaccharides form they make either a disaccharide or a polysaccharide. A good example of a polysaccharide is cellulose. -Proteins: Monomers of proteins are amino acids and the polymer is a polypeptide. Although amino acids are essential they are just simply the building blocks of proteins so providing a single example for this would be difficult same goes for the polypeptide chain for it to be considered a protein it has to be one or more polypeptide chains that have to be twisted and folded and coiled into a unique shape to serve as a functional protein. A single polypeptide is known as a tertiary structure while a functional protein is tertiary or quaternary structure. -Nucleic acids: Monomers of nucleic acids are nucleotides and the polymer is the nucleic acid itself. The monomers of nucleic acids are typically known as the the building blocks of DNA such as Guanine, Thymine, Uracil, ect. While the actual whole structure is known as DNA or RNA. •

Relate the structure of each macromolecule with its function -

Macromolecule

Carbohydrates

Proteins

Nucleic Acids

Structure

Function

Monosaccharide (Carbon, Hydrogen and Oxygen)

Energy source for cells; can be converted into other molecules or polymers. Cellulose;strength ens plant cell walls

Amino Acids

Building Blocks of the cells. Build, maintain, repair, and catalyze chemical reactions

Nucleotides (Nitrogenous base, Phosphate Group and Sugar)

Stores and carries genetic information from DNA to ribosomes;instructions to create proteins.

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Contrast the structure of DNA and RNA -

DNA and RNA are similar in structure.However, DNA contains the double-stranded molecule, and contains the structure deoxyribose + RNA contains only ribose, and only are single-stranded molecules. DNA is responsible for storing and transferring genetic information while RNA directly codes for amino acids and as acts as a messenger between DNA and ribosomes to make proteins. Also, DNA and RNA base pairing is slightly different since DNA uses the bases adenine, thymine, cytosine, and guanine; RNA uses adenine, uracil, cytosine, and guanine. Uracil differs from thymine in that it lacks a methyl group on its ring.

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Describe the levels of protein structure and how each level is determined -

The four levels of proteins are primary, secondary, tertiary, and quaternary. In the primary structure it is the simple linear chain of amino acids. In the secondary structure hydrogen bonds between atoms are formed in the polypeptide backbone giving it a helix or winding like structure. In the tertiary structure side chains are formed using various amino acids, covalent bonds (disulfide bridges) reinforce the bond to give more of a shape at this level it is noted that the amino acid sequences start to fold. At the quaternary structure two or more polypeptide chains are joined together to form the actual functional macromolecule known as a protein, here the shape of the molecule is more folded than in the previous structure. •

Explain the link between protein structure and protein function -

Proteins are linear polymers built of monomer units called amino acids. The function of a protein is directly dependent on its three-dimensional structure. Proteins spontaneously fold up into three-dimensional structures that are determined by the sequence of amino acids in the protein polymer. Proteins contain a wide range of functional groups. These functional groups include alcohols, and a variety of basic groups. For instance, the chemical reactivity associated with these groups is essential to the function of enzymes, the proteins that catalyze specific chemical reactions in biological systems. Some proteins are quite rigid, whereas others display limited flexibility. Parts of proteins with limited flexibility may act as hinges, springs, and levers that are crucial to protein function, to the assembly of proteins with one another and with other molecules into complex units, and to the transmission of information within and between cells. •

Explain what is denaturation and why it affects protein function

The term denaturation is used when speaking about proteins. Since proteins have weak chemical bonds they can be easily be destroyed causing the protein to unravel and lose its shape. This can happen due to a change in pH, temperature, salt concentration,or any other alterations to the proteins environment.

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Explain the structure of lipids and relate it to their function

There are many forms of lipids but they are more easily characterized by being saturated or unsaturated fats. The saturated fats are characterized by having little to no double bonds in their backbone, while the unsaturated fats are known to have one or multiple double bond in their backbone. The double bond in their backbone causes them to have a kink in their structure making the fat or oil to be more fluid at room temperature. Versus the saturated fat is usually solid.

Ch. 4 – Tour of the cell •

Explain why the size of cells is limited

Cell size is limited because of the ideal surface area to volume ratio. A cell can not be too big as this will cause slower connections between the cell. If a cell is too thick or wide signals will take longer to reach each end of the cell or leave the cell. The rapidness of cell functions is what makes them efficient. Slowing down the process could lead to catastrophic results. •

List the characteristics shared by all cells Plasma membrane, DNA, ribosomes, and cytoplasm.

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Describe the differences between prokaryotic and eukaryotic cells

Prokaryotic cells are single celled organisms, such as bacteria, that contain a nucleoid region where DNA is found.It also has a flagella and pili on its outside. Eukaryotic cells make up multicellular organisms therefore are more complex. They contain a nucleus where DNA is housed and membrane bound organelles that have many different complex functions. •

Describe the difference between bacterial and archaeal cells

The difference(s) between bacterial and archaeal cells are as follows: Majority of bacteria cells have a circular chromosome similar to archaean cells but some bacterial cells have linear chromosomes. Archean cells have histone proteins while bacterial cells do not. Archean cells do not have organelles but some bacteria species have a limited number of organelles. Both bacterial and archaean cells have flagella but structurally they are different. Last, they both have a cell wall but are composed of different substances. Peptidoglycan forms the cell wall of bacteria and polysaccharides compose the cell wall of Archean cells. •

Describe the structure and function of chloroplasts and mitochondria

The structures of these two organelles are easily recognizable. They both have two membranes, and the inside of the chloroplast also has stacks of membrane disks that are individually called thylakoids and collectively called grana. The functions of these two organelles are fundamental opposites:

1. The chloroplast builds glucose in order to store energy for the cell. It uses carbon dioxide and water and releases oxygen during this process of photosynthesis. 2. The mitochondrion breaks glucose down in order to get the energy out to make ATP. ATP is what the cells use directly for energy for any cell processes. The process uses glucose and oxygen and releases carbon dioxide and water during cellular respiration. •

Apply the Theory of Endosymbiosis to explain the origin of mitochondria and chloroplast

A eukaryotic cell is composed of many organelles it depends on to carry out basic functions; such as the mitochondria and chloroplast. These two organelles create energy. The theory of endosymbiosis states that eukaryotic cells emerged from past prokaryotic cells. In other words, cells evolved from other cells. The theory explains that when prokaryotic cells first evolved they played different roles. Some bacteria creates energy from the sun, through photosynthesis, and others created ATP energy. These two cells were somehow ingested by a bigger prokaryotic cell and instead of being digested they began to live in unison. They fed off of each other’s functions to survive. These three distinct cells became one fully functioning eukaryotic cell. The cell that ingested the other two became the eukaryotic cell while the two bacteria became what we know today as mitochondria and chloroplast. The evidence comes from the organelles themselves. Just like prokaryotic cells, Mitochondria have their own cell membrane, DNA genome, and even reproduce in the same manner. •

Explain the organization of the eukaryotic cell and its advantages

The functioning membrane bound organelles that are organized within a eukaryotic cell give it its ultimate advantage. Prokaryotes can carry out similar functions but it is all done within one compartment. These organelles are able to specialize in different functions to allow for maximum efficiency. For example, the nucleus only specializes in DNA replication and translation, the golgi ships proteins, mitochondria creates energy, and the ER makes proteins and carbohydrates. These different compartment can focus on mastering each individual function without having to do any other work for the cell.

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Compare the structure of plant cells to animal cells

Plant and animal cells are both eukaryotes. Their main differences are in the organelles each one houses. They both contain mitochondria, a Nucleus, plasma membrane, and ribosomes. The plant cell contains a cell wall which is special to itself as no other cell contains it. •

Describe the function of the main cellular organelles and cellular structures

Endoplasmic Reticulum: Network of interconnected membranes consisting of sacs and canals. Function: Transports materials within the cell; provides attachment for ribosomes. It is the site of protein synthesis in the cell.

Ribosomes:Particles composed of protein and RNA. Function: Bodies where proteins are synthesized.

Golgi Body: Group of flattened, membranous sacs. Function: Packages protein molecules for secretion; origin of lysosomes.

Mitochondria:Membranous sacs with inner partitions. Function: Site where energy released from food molecules and transformed into usable form.

Lysosomes:Membranous sacs. Function: Contain enzymes for intracellular digestion.

Centrosome:Non-membranous structure composed of two rod-like centrioles. Function: Helps distribute chromosomes to daughter cells during cell reproduction and initiates formation of cilia.

Cilia and Flagella: Hair-like projections attached to basal bodies beneath cell membrane. Function: Propel fluids over cellular surface and enable certain cells to move.

Vesicles:Membranous sacks. Function: Contain various substances after entry to the cell. Microfilaments and Microtubules: Thin rods and tubules. Function: Provide support to cytoplasm and help move objects within the cytoplasm; make up cytoskeleton

Nuclear Envelope: Porous double membrane that separates nuclear contents from cytoplasm. Function: Maintains wholeness of the nucleus and controls passage of materials between nucleus and cytoplasm.

Nucleolus:Dense, non-membranous body composed of protein and RNA. Function: Contains materials to form ribosomes.

Chromatin:Fibers composed of protein and DNA molecules. Function: Contains genetic information for protein synthesis.

Cell Membrane: Membrane composed mainly of protein and lipid molecules. Function: Maintains wholeness of cell and controls passage of materials into and out of cells. Nucleus:Composed primarily of histone protein and deoxyribonucleic acid, or DNA. With the exception of red blood cells, all cells have a nucleus in the human body. The nucleus of human cells is surrounded by a membrane called the nuclear envelope. The nuclear envelope is a double-membrane structure consisting of two layers of phospholipid similar to the plasma membrane. Pores in the nuclear membrane allow the internal nuclear environment to communicate with the cytoplasm of the cell. Within the nucleus are two or more dense masses referred to as nucleoli (singular nucleolus). The nucleolus contains RNA, or ribonucleic acid. This nucleic acid is used to construct the subunits of organelles called ribosomes. The subunits are later assembled into ribosomes in the cytoplasm.

Cytoplasm:The cytoplasm is a semifluid substance representing the foundation of the cell. Within the cytoplasm are a number of microscopic bodies called organelles ("little organs"). Various cellular functions occur within these organelles. An example of an organelle is the endoplasmic reticulum.

Ch. 5 – Membrane transport •

Describe the structure of cellular membranes and explain why cell membranes are modeled as a Fluid Mosaic

The term fluid mosaic is a perfect representation of the cell membrane. Fluid refers to the flowing nature of the membrane. The plasma membrane is semi-permeable; allowing only certain things access. This membrane is constructed of phospholipids. The hydrophilic heads facing out and the hydrophobic tails facing in, as to not come in contact with any water. This chain like membrane is free flowing and somewhat bobbing in place. Mosaic refers to how the surface looks due to all the proteins that become embedded inside and on the surface. These proteins are arranged in such a way they create a pattern that resembles a mosaic. •

Explain the composition of a phospholipid and relate it to its function

Phospholipids consist of two hydrophobic fatty acid "tails" and a hydrophilic phosphate group "head.” This structure is an ideal composition for its ultimate function. Phospholipids make up the cell membrane. They create a bounda...