Introduction to Cells, Biochemistry and Biological Molecules Notes

Monomer of carbohydrates

monosaccharides

What is a model organism? How are model organisms used in cell biology?

A model organism is a species that has been widely studied, usually because it is easy to maintain and breed in a laboratory setting and has particular experimental advantages such as low cost and short life spans. They are used to help scientist study different biological processes.

Cellular functions of proteins

Act as enzymes, structural components, transport, transmitting information, defense against infection.

Give a specific example of a biological molecule that utilizes each type of noncovalent interaction (ionic, hydrogen, hydrophilic, and hydrophobic, skip Van der Waals forces).

Amino acids use H bonding and the R group could be either hydrophobic or hydrophilic. Carbohydrates are hydrophilic. Monosaccharides have hydrogen bonding. Lipids have hydrophilic heads and hydrophobic tails.

Structure of proteins

Amino acids which consist of carboxyl group, an amino group, side chain, and a central carbon atom bonded to a hydrogen. 3D conformations

Peroxisome

Breaks down long chains of fatty acids by using oxidative reactions.

What is the difference between a covalent bond and a noncovalent bond? Which bonds are the strongest and which are the weakest?

Covalent bonds share valence electrons such as C-C or C-H Non-covalent bonds aka ionic bonds are the transfer of electrons between atoms such as NaCl. Ionic bonds are generally stronger than covalent bonds.

Which biological molecules are polar? Which are nonpolar?

Carbohydrates: Polar Lipids: Nonpolar Nucleic acids: Polar Proteins: Both

What is the basic structure of an amino acid?

Carboxyl group, an amino group, side chain, and a central carbon atom bonded to a hydrogen.

Cellular functions of nucleic acids

Carry and stores information and control most cellular activities.

Structure of carbohydrates

Contains carbon, hydrogen and oxygen

Polymer of lipids

Do not form polymers

Cellular functions of lipids

Energy storage, major components of cell membranes, and cell signaling.

What distinguishes a prokaryotic cell from a eukaryotic cell?

Eukaryotic cells contain a nucleus and membrane bound organelles unlike prokaryotic cells. Prokaryotic cells are generally smaller and less complex than eukaryotic cells.

T/F: All four biological molecule polymers are broken down by hydrolysis reactions.

False. Phospholipids are not broken down by hydrolysis because they are non-covalently linked.

What are the differences between glycogen and starch? Why do you think we (and other animals) store glucose as glycogen instead of starch? Don't worry about the specific linkages, just focus on the overall structure.

Glycogen is found in animals and starch is found in plants. Glycogen is more branched and is easier to breakdown which causes a quicker metabolism. The more branched structure allows there to be a faster harvesting of glucose molecules to be used for energy. Starch is better for long term storage.

What are the properties of water that make it important in cell biology?

It exists naturally in all three states, it has hydrogen bonding, polarization, abundant, non-toxic, can interact with positively and negatively charged ions.

Cytoskeleton

It provides the structural framework of the cell and is responsible for cell movements.

What does pH represent and why is it important for the structure of biological molecules?

It represents the acidity of a solution. It can help explain how molecules interact with each other.

Nucleus

It stores the cell's heredity material/DNA and it coordinates the cell's activities.

Smooth ER

Makes cellular products such as hormones and lipids.

Structure of nucleic acids

Nitrogenous base (Purines and pyrimidines), phosphate group, 5 carbon sugar

Cellular location of nucleotides

Nucleus and ribosomes.

Structure of lipids

Phospholipids: Hydrophobic tails (2 hydrocarbon chains) and hydrophilic heads (phosphate group and polar attachments) See page 52 for other structures.

There are several types of amino acids (see pp. 57). Which type(s) would you expect to interact with water? Which type(s) would you expect to be buried on the inside of a protein, away from water?

Polar amino acids, basic amino acids and acidic amino acids interact with water because they are hydrophilic. Nonpolar acids are buried inside and away from water because they are hydrophobic

Describe the difference between polar and nonpolar covalent bonds by including electronegativity in your answer.

Polar covalent bonds have unequal sharing of the electrons while nonpolar have equal sharing. If the two atoms have different electronegativity's, then they are polar. If the electronegativity is the same, it is nonpolar.

Describe the relationship between monomers and polymers of biological molecules. How are polymers synthesized? How are monomers liberated from polymers?

Polymers are created by the joining of many monomers. Polymers are broken down by hydrolysis where water is added to break apart a bond (except lipids). Polymers are formed by dehydration when a water molecule is taken away to form a bond.

Protein structure is critical for its function. Briefly describe the levels of protein structure and the bonds that mediate the structures. Which level of structure determines all other levels of structure?

Primary: sequence of amino acids. Peptide bonds. Structure that determines all other levels of structure. Secondary: regular arrangement of amino acids within localized regions of the polypeptide. (α and β helixes) Hydrogen bonds. Tertiary: overall folding of single polypeptide chain as a result of interactions between the side chains of amino acids that lie in different regions of primary sequence. Quaternary: interactions between different polypeptide chains in proteins composed of more than one polypeptide.

Lysosome

Removes waste by breaking down biological polymers.

Mitochondria

Responsible for synthesis of most of the ATP in eukaryotic cells by oxidative phosphorylation.

Cellular location of proteins

Ribosomes

Plasma membrane

Separates the interior of the cell from the outside which controls the movement in and out of the cell.

Proteins have more diverse roles in cells than the other types of biological molecules. Why is this?

Since there are 20 different amino acids that can make up a protein, there is a lot of variation in proteins. This causes there to be more diverse and complex groups which have a variety of tasks they perform.

Cellular location of lipids

Smooth ER

Cellular functions of carbohydrates

Source of cellular energy, major nutrients of cells, and the starting material for the synthesis of other constituents.

Cellular location of carbohydrates

They are found on the outer surface of all eukaryotic cells and are usually attached to phospholipids.

What makes a fatty acid saturated vs. unsaturated? Describe other ways the lipid hydrocarbon chain can differ between fatty acids.

Unsaturated fatty acids contain one or more double bonds between carbon atoms. Saturated fatty acids have all of the carbon atoms bonded to the maximum number of hydrogen atoms. Phospholipids can differ by the length of the chain and number of double bonds. The longer the chain, the more intermolecular interactions can occur.

Rough ER

Uses ribosomes to sort proteins

Monomer of proteins

amino acid

Glycosidic bond

bond/linkage joins a carbohydrate to another group, which may or may not be another carbohydrate

Monomer of lipids

fatty acids and glycerol

Monomer of nucleic acids

nucleotides

Polymer of nucleic acids

polynucleotides

Polymer of proteins

polypeptides

Polymer of carbohydrates

polysaccharides