Unit 1 - Biochem Flashcards
Carbohydrates - Building Blocks
Monosaccharides which are simple sugars
Carbohydrates - Use
energy, structure, and for storing/transporting energy
What do animals store glucose as? What do plants store glucose as?
Animals store glucose as glycogen which is a carbohydrate
Plants store glucose as starch which is a carbohydrate
Carbohydrates - Structure
- Made up of only carbon, hydrogen, and oxygen MUST be in a 1:2:1 ratio
- Monosaccharides (single rings), disaccharides (double rings)
Monosaccaride
Simple sugars, serve as a major nutrients for cells and as raw material for building carbohydrates
Polysaccarides
Polymers. Also known as complex carbs, since they contain many monomers. Have storage and structural roles. The structure and function of a polysaccharide are determined by its sugar monomers and the positions of glycosidic linkages (sugar and another molecule). Can be branched or in straight chains.
Disaccharide
Two monosaccharides bonded together. A disaccharide is formed when a dehydration reaction joins two monosaccharides. This covalent bond is called a glycosidic linkage.
Cellulose
Carbohydrate. Made of repeating monomers of glucose. Make up cells walls in plants - structure. Does not dissolve in water, and is not easily broken down because it has so many links. Most herbivores require special bacteria in their gut to digest cellulose.
Chitin
Carbohydrate. Similar to cellulose. Forms chains linked by hydrogen bonds. Forms structural materials. Durable, translucent, and flexible. Strengthens hard parts of animals like insects and arachnids. Forms the cell walls in fungi.
Starch
Carbohydrate. Different covalent bonding patterns between glucose monomers makes a chain that can coil up into a spiral. Not very soluble in water, but more unstable than cellulose. Ideal for storing glucose in plants, but cannot be transported easily- must be broken up first. Humans have enzymes that can break down starch
Glycogen
The covalent bonding pattern in this molecule produces a highly branched polysaccharide. The sugar storage molecule in animals. Stored in muscle and liver cells. Can be broken down to access glucose for energy.
Amphipathic (meaning and why its important)
Amphipathic means both hydrophobic and hydrophilic parts. In a phospholipid, the amphipathic nature is crucial for its function in forming biological membranes. The polar head is hydrophilic, meaning it is attracted to water, while the nonpolar tails are hydrophobic, repelling water. This dual characteristic allows phospholipids to form a bilayer in aqueous environments, like the cell membrane. The hydrophilic heads face outward, interacting with the watery environments inside and outside the cell, while the hydrophobic tails face inward, away from water, forming a stable barrier. This arrangement is essential for regulating what enters and exits the cell, maintaining its selective permeability.
Lipids - Structure
Made of carbon, hydrogen, and oxygen. Sometimes phosphorus.
Fatty acids are composed of both polar and nonpolar regions, leading to both hydrophilic and hydrophobic properties
Hydrocarbon “tails”: hydrophobic (nonpolar)
Carboxyl group “head” : hydrophilic (polar)
Fatty Acids: Simple organic compounds with a carboxyl group joined to 4 to 36 carbon atoms
Does NOT have 1:2:1 ratio (way more carbons than oxygens)
Glycerol attched to each carboxyl group of each fatty acid tail
Lipids - Use
long term energy storage, structural foundation of cell membranes
Lipids - Building Blocks
Glycerol and fatty acids
Lipids - Saturated vs Unsaturated
Saturated fatty acids: have the maximum number of hydrogen atoms possible and no double bonds, flexible and can stack up at room temperature, forming a solid. The absence of carbon-carbon double bonds in molecules, such as in saturated fats, allows them to pack closely together. Ex: animal fat
Unsaturated fatty acid: have one or more double bonds in the hydrocarbon tail, less flexible due to bend and cannot stack together. The double bonds have to be in the hydrocarbon tail for it to be unsaturated. Forms a liquid ex: vegetable oil
Steroids
Lipids with a rigid backbone of four carbon rings and no fatty acid tails, The most common steroid in animal cell membranes (helps maintain cell structure). Forms bile salts that help us digest fats, forms vitamin D which is needed by bones and teeth, steroid hormones like estrogen and testosterone which govern reproduction and reproductive system development. Steroids can be recognized by their multiple rings of carbon atoms connected together. Steroids are included in lipid category because they are also hydrophobic and insoluble in water.
Waxes
Lipid. Complex molecules with a varied mixture of lipids with long fatty acid tails bonded to long chain alcohols or carbon rings, molecules pack tightly, so wax is firm and water resistant. Generally solid at room temp.
Phospholipid
Molecules with a polar head containing a phosphate and two nonpolar fatty acid tails, Head = polar + hydrophilic, Tails = nonpolar + hydrophobic, most abundant lipid in cell membranes. Phospholipids make up the semipermeable membrane of the phospholipid bilayer.
Triglyceride
A lipid. The carboxyl group of a fatty acid easily forms bonds with other molecules. 3 fatty acids attach to glycerol via the carboxyl group, which then loses its hydrophilic properties. The new molecule is hydrophobic and does not dissolve easily in water. They are the most common type of fat in your body. Circulate in your blood.
Trans Fats
The arrangement of hydrogens around the carbons have a significant effect on our bodies ability to process the lipids. Trans fats are difficult for our body to break down leading to its health dangers, made through hydrogenation of oils
Proteins - Use
Structure, nutrition, enzymes, transport, communication, cellular defense
Proteins - Structure
Made of amino acids: amine group, a carboxyl group, and an R group
The R groups (or functional groups) give the amino acid unique properties, like being polar, non-polar, acidic, etc.
Consists of carbon, hydrogen, oxygen, nitrogen, and sometimes sulfur.
Lots of oxygen + nitrogen in R group made a protein polar
If it just has carbon and hydrogen in the R group then there is nothing pulling the electrons strongly so it is nonpolar
If it has sulfur, it is special. Sulfur is polar but its not that strong so it still makes it nonpolar
S-S bonds are nonpolar and lead to more stability
Protein structure is important because the structure of the protein determines its function
Proteins - Building Blocks
Amino acids
Secondary Structure
The polypeptide chain folds and forms hydrogen bonds between the amino acids. Hydrogen bonds can cause the polypeptide to make two kinds of shapes, Alpha Helices: Coils, Beta Pleated Sheets: Flat Sheets
Polypeptides
A linear chain of amino acids joined by peptide bonds (covalent)
Primary Structure
The unique amino acid sequence of a protein (polypeptide chain), Amino acids are covalently bonded by peptide bonds
Tertiary Structure
Protein is compacted into structurally stable units called domains. Based on R-Group interactions (hydrophobic, hydrophilic). Can lead to: Hydrogen bonds, Hydrophobic Interactions, Disulfide Bridges (two sulfur atoms, keep an eye out for two S’s), Ionic Bonds
Quaternary Structure
Some proteins consist of two or more folded polypeptide chains in close association - can involve hydrogen bonds
What happens if an amino acid gets deleted in a protein?
If an amino acid gets deleted in a protein then it will affect the primary, secondary, and tertiary structures
Nucleic Acids - Building Blocks
Nucleotides. Nucleotides are made up of a nitrogenous base (Adenine, Thymine, Cytosine, Guanine in DNA; Uracil replaces Thymine in RNA), a five-carbon sugar (Deoxyribose in DNA, Ribose in RNA), one or more phosphate groups.
Nucleic Acids - Structure
Made of carbon, hydrogen, oxygen, nitrogen, and phosphorus. Has a phosphate base, sugar group, and nitrogenous base. The backbone of DNA is made of alternating sugar (deoxyribose in DNA, ribose in RNA) and phosphate groups. The phosphate groups link the 3’ carbon of one sugar to the 5’ carbon of another, creating the sugar-phosphate backbone.
Nucleosides
Nucleic acids without the phosphate group are called nucleosides.
Nucleic Acids - Use
Nucleic Acids store, transmit, and help express hereditary information. Make either DNA or RNA.
Pyrimidine vs Purine
Pyrimidines (C, U, T, with single rings) always bond with purines (A, G, with double rings) in nucleic acids
CUT the Py → C, U, T are Pyrimidines
PUR As Gold → A and G are Purines
adenine (A) and thymine (T) pair together (A-T) for DNA and adenine (A) and uracil (U) pair together (A-U) in RNA, and cytosine (C) and guanine (G) pair together (C-G).
DNA vs RNA
DNA:
carries genetic information
double stranded
contains 1 less oxygen in the 5 carbon sugar group than RNA
RNA:
mRNA carries genetic information from DNA in the nucleus to ribosomes in the cytoplasm, where proteins are synthesized.
rRNA is a structural and functional component of the ribosome, which is the site of protein synthesis. It helps to catalyze the assembly of amino acids into protein chains.
tRNA carries amino acids to the ribosome and matches them to the codons in the mRNA template during protein synthesis.
single stranded
contains 1 more oxygen in the 5 carbon sugar group than DNA
Properties of Water
polar, high specific heat capacity, high heat of vaporization, cohesion, adhesion
Polar: Water is a polar molecule, meaning it has a partial positive charge on the hydrogen atoms and a partial negative charge on the oxygen atom. This results from oxygen’s higher electronegativity, which pulls shared electrons closer to itself, creating a dipole. Due to water’s polarity, the partially positive hydrogen atoms of one water molecule are attracted to the partially negative oxygen atoms of another, forming hydrogen bonds. Each water molecule can form up to four hydrogen bonds, giving water its unique properties.
Cohesion: Water molecules stick to each other due to hydrogen bonding. This property allows for the formation of water droplets and contributes to surface tension, enabling small organisms (like water striders) to move on the water’s surface.
Adhesion: Water molecules also stick to other polar or charged surfaces/molecules The adhesion of water is best explained as the ability of water to stick to other surfaces through the creation of weak surface bonds. This is critical for capillary action, where water moves up thin tubes like plant xylem, helping transport nutrients from roots to leaves.
High Specific Heat Capacity: Specific heat capacity is the amount of heat energy required to raise the temperature of a substance per unit of mass. Water can absorb or release large amounts of heat with only slight temperature changes, which helps regulate temperature in environments. This is due to hydrogen bonds absorbing heat before breaking.
High Heat of Vaporization: It takes significant energy to turn water into vapor because the hydrogen bonds must first be broken. This makes water a good coolant (e.g., through perspiration in humans), as evaporation removes excess heat.
Electronegativity
Electronegativity is the measure of the ability of an atom to pull shared electrons to itself.
nonpolar covalent vs polar covalent vs ionic bonds
Nonpolar covalent is the bond between a nonmetal and a nonmetal and the electrons are evenly distributed. Polar covalent is the bond between a nonmetal and a nonmetal and the electrons are unevenly distributed. Ionic bonds is the bond between a metal and a nonmetal where electrons are given not shared.
intramolecular vs intermolecular
Intramolecular: Bonds that occur within a molecule, holding the atoms together to form the molecule. Includes covalent bonds (where atoms share electrons), ionic bonds (where atoms transfer electrons, resulting in oppositely charged ions), and metallic bonds (where electrons are shared in a “sea” among metal atoms). Typically stronger than intermolecular bonds because they involve the actual sharing or transfer of electrons between atoms.
Intermolecular: Bonds that occur between molecules, governing how molecules interact with each other. Includes hydrogen bonding, dipole-dipole interactions, and London dispersion forces (van der Waals forces).
how many bonds do A-T/U and G-C make?
The Adenine - Thymine/Urucil base pair is held together by 2 hydrogen bonds while the Guanine - Cytosine base pair is held together by 3 hydrogen bonds. They are hydrogen bonds.
5’ and 3’ orientation
5’ and 3’ refer to the orientation of the 5 carbon sugar group in DNA and RNA. The 5th carbon in DNA and RNA (going clockwise from the top center aka the single oxygen atom) has a phosphate group attached to it and the 3’ refers to the 3rd carbon having a hydroxyl group (-OH) attached to it. Obviously RNA has one more hydroxyl group because it is a ribose sugar, but 5’ and 3’ orientation just emphasizes what DNA and RNA have in common.
