Chapter 1: Molecules and Fundamentals of Biology Flashcards
Matter is anything that …
Takes up space and has mass.
An element is a __________ that has ____________ and cannot be ____________.
An element is a PURE SUBSTANCE that SPECIFIC PHYSICAL/CHEMICAL PROPERTIES and cannot be BROKEN DOWN INTO A SIMPLER SUBSTANCE.
An atom is the ___________ that still retains what?
An atom is the smallest unit of matter that retains the chemical properties of the element.
A molecule is what?
Two or more atoms joined together.
What is the difference between inter and intra-molecular forces?
INTRA-molecular forces are attractive forces WITHIN molecules.
INTER-molecular forces are attractive forces BETWEEN molecules that affect the physical properties of the substance.
Monomers are ________ that can potentially ___________.
Monomers are single molecules that can potentially polymerize.
What are polymers?
Polymers are substances made up of many monomers joined together.
What are carbohydrates made of? What forms do they come in?
Carbon, hydrogen, and oxygen. They come in the form of monosaccharides, disaccharides, and polysaccharides.
What are monosaccharides and what is their chemical formula?
Monosaccharides are CHO monomers with the empirical formula (CH2O)n (Where n = the number of carbons)
What are the 3 common monosaccharides?
fructose, glucose, and ribose (glucose and fructose are isomers)
What is an isomer?
Isomers are molecules with the same chemical formulas but different arrangements of atoms.
Ribose is a ____ Carbon monosaccharide.
Glucose is a ____ Carbon monosaccharide.
Fructose is a ____ Carbon monosaccharide.
5
6
6
What are disaccharides? What are they joined by?
Disaccharides are TWO monosaccharides joined together by glycosidic bonds.
Sucrose
Lactose
Maltose
What reaction is the glycosidic bond that forms disaccharides the result of?
Result of a dehydration reaction (condensation), where a water molecule leaves and a covalent bond forms.
What is a hydrolysis reaction?
The opposite of a dehydration reaction. A covalent bond is broken by the addition of water.
Disaccharide: What is sucrose made up of?
Glucose + Fructose
Disaccharide: What is lactose made up of?
Galactose + Glucose
Disaccharide: What is Maltose made up of?
Glucose + Glucose
What are polysaccharides?
They contain many monosaccharides connected by glycosidic bonds into a long polymer.
Starch is ________ for plants and is an ______ bonded polysaccharide.
Starch is ENERGY STORAGE for plants and an ALPHA bonded polysaccharide.
What is linear starch called?
Amylose
What is branched starch called?
Amylopectin
Glycogen is ________ for humans and is an _____ bonded polysaccharide. Glycogen has much more ________ than starch.
Glycogen is ENERGY STORAGE for humans and is an ALPHA bonded polysaccharide. Glycogen has much more BRANCHING than starch.
Cellulose is a _______ in plant cell walls and is a _____ bonded polysaccharide.
Cellulose is a STRUCTURAL component in the plant cell walls, it is BETA bonded polysaccharide. Linear strands are packed rigidly in parallel.
Chitin is a _______ in _______ cell walls and insect ________. It is ____ bonded polysaccharide with _______ added to each monomer.
Chitin is a STRUCTURAL component in FUNGI cell walls and insect EXOSKELETON. It is BETA bonded polysaccharide with NITROGEN added to each monomer.
What are proteins composed of?
CHON Carbon, hydrogen, oxygen, and nitrogen.
Protein atoms combine to form what?
Amino acids (monomers of protein), which link together to build polypeptides (proteins).
What is an amino acid structure?
Amino group (N-H2,H+), hydrogen, carboxyl group (C=O,O), and R group attached to Carbon.
How many different amino acids are there?
There are 20 different amino acids, each with a different R group.
What are polypeptides? What types of bonds are they joined by? What reactions are they formed by? What reactions break them?
These are polymers of amino acids. These are joined by polypeptide bonds formed through dehydration (condensation) reactions. Hydrolysis reactions break these bonds. The polypeptide becomes an amino acid chain that contains two end terminals on opposite sides.
The N-terminus of a polypeptide is the side that what?
(amino terminus) The N-terminus is the side that ENDS with the last amino acid’s amino group. START with N-terminus.
The C-terminus of a polypeptide is the side that what?
(carboxyl terminus) The C-terminus ENDS with the last amino acid’s carboxyl group. End with C-terminus.
The primary structure of a protein is…
A sequence of amino acids.
The secondary structure of a protein is…
These are due to _______ bonding and form what?
INTERmolecular forces between the polypeptide backbone (not R-groups) due to HYDROGEN BONDING, and form alpha-helices or beta-pleated sheets.
What are the tertiary structures of proteins due to?
These are three dimensional structures due to interactions between the R-groups and can create hydrophobic or hydrophilic spaces based on the R-groups.
How are disulfide bonds created?
From tertiary structures… Disulfide bonds are created by covalent bonding between the R-groups of two CYSTEINE amino acids (sulfur-sulfur bond).
What is the quaternary structure of proteins?
Multiple polypeptide chains come together to form one protein.
Proteins can also be classified based on structure as what three things?
Fibrous, globular, or intermediate.
When looking at protein composition, they can be what two things?
Simple (amino acids only) or conjugated (amino acids + other components).
What is protein denaturation?
Describes the loss of protein FUNCTION and higher-order STRUCTURES. Only the primary structure is unaffected.
What are some reasons why a protein might denature?
High or low temperatures, pH changes, and salt concentrations. (Example: when an egg is cooked in high heat, it will disrupt the intermolecular forces in the egg’s protein, causing it to coagulate).
What are the 7 functions of proteins?
Storage, hormones, receptors, motion, structure, immunity, enzymes.
Explain how proteins function as storage.
Proteins are a reserve of amino acids.
Explain how proteins function as hormones.
Signaling molecules that circulate through the body to regulate physiological processes.
Explain how proteins function as receptors.
Proteins in cell membranes, which bind to signal molecules to trigger changes inside the cells.
Explain how proteins function in motion.
Movement generation for individual cells or entire organisms.
Explain how proteins function as structure.
Provide strength and support to tissues.
Explain how proteins function in immunity.
Prevention and protection against foreign invaders.
What are catalysts and how do they work?
Catalysts INCREASE reaction rates by lowering the ACTIVATION ENERGY of a reaction.
What is the transition state? What do catalysts do to the transition state?
This is the unstable conformation between the reactants and the products. Catalysts reduce the energy of the transition state.
Catalysts do NOT ________ a chemical reaction and they do NOT affect ________.
They do not SHIFT chemical reactions, nor do they affect SPONTANEITY.
Enzymes act as biological ______ by binding to _________ and converting them to _________.
Enzymes act as biological catalysts by binding to substrates (reactants) and converting them into products.
Enzymes bind to substrates at an _______, which is what? Most enzymes are _______.
Bind at an active site that is specific for the substrate that it acts upon. Most enzymes are proteins.
The specificity constant measures what?
It measures how efficient an enzyme is at binding to the substrate and converting it to a product.
What is the induced fit theory?
It is the theory that describes how the active site molds itself and changes shape to fit the substrate when it binds. The outdated theory was the “key and lock” model.
What is a ribozyme?
A ribozyme is an RNA molecule that can act as an enzyme (a non-protein enzyme).
What is a cofactor? What is a coenzyme?
A non-protein molecule that helps enzymes perform reactions. A coenzyme is an organic co-factor such as vitamins. Inorganic co-factors are usually metal ions.
Holoenzymes are enzymes that are bound to their _______ while apoenzymes are enzymes that are ___________.
Holoenzymes are enzymes that are bound to their co-factors, and apoenzymes are enzymes that are not bound to their co-factors.
Prosthetic groups are cofactors that are ______ or _____ _______ to their enzymes.
Prosthetic groups are cofactors that are TIGHTLY or COVALENTLY BOUND to their enzymes.
Protein enzymes are susceptible to ______. They require optimal ______ and _____ for function.
Denaturation; temperature and pH
Competitive inhibition occurs when a competitive inhibitor competes ______ with the substrate for the _________. The rate of enzyme action can be increased by what?
Competitive inhibition occurs when a competitive inhibitor competes DIRECTLY with the substrate for the ACTIVE BINDING SITE. The rate of enzyme action can be increased by adding more substrate.
Noncompetitive inhibition occurs when a noncompetitive inhibitor binds to an ________ site, this does what? The rate of enzyme action can be increased by what?
When a non-competitive inhibitor binds to an ALLOSTERIC site (location on the enzyme that is different from the active site), MODIFYING THE ACTIVE SITE. The rate of enzyme action CANNOT be increased by adding more substrate.
What can an enzymatic kinetics plot be used for?
Can be used to visualize how inhibitors affect enzymes.
What do the x- and y-axis represent in a kinetics plot?
The x-axis is the concentration of the substrate and the y-axis is the velocity of the reaction. (Reaction rate)
What is Vmax?
The maximum reaction velocity.
What is Michaelis Constant (Km)?
The substrate concentration (x) when the velocity (y) is at 50% of the Vmax.
What is saturation?
This occurs when all active sites are occupied, so the rate of the reaction does not increase anymore despite increasing substrate concentration (graph plateaus).
What happens to the Km and Vmax in competitive inhibition?
Compared to a normal enzyme, the Km increases, and the Vmax stays the same. (You require a higher concentration of substrate with competitive inhibition to be at 50% of the Vmax.)
What happens to the Km and Vmax in non-competitive inhibition?
Km stays the same and Vmax decreases.
The graph shows the normal enzyme (highest), competitive inhibition, then non-competitive inhibition (lowest). Non-competitive inhibition is the lowest because when a substrate binds to an allosteric site, the active site is altered.
What are lipids composed of?
CHO and long hydrocarbon tails. They are very hydrophobic.
Triacylglycerol (triglyceride) is a lipid molecule with a _______________.
Glycerol backbone (three carbons and three hydroxyl groups) AND three fatty acids. Glycerol and the three fatty acids are connected by ester linkages.
What are saturated fatty acids?
They have NO double bonds and as a result, pack tightly (solid at room temperature).
What are unsaturated fatty acids?
They HAVE double bonds and they are liquid at room temperature. They can be divided into monounsaturated fatty acids (one double bond) and polyunsaturated fatty acids (two or more double bonds).
What are cis-unsaturated fatty acids?
These have kinks that cause the hydrocarbon tails to bend. As a result, they do not pack tightly.
What are trans-unsaturated fatty acids?
These have straighter hydrocarbon tails, so they can pack tightly.
What are phospholipids composed of?
A glycerol backbone, a phosphate group (hydrophilic/polar), and two fatty acids (hydrophobic/non-polar). Thus they are amphipathic (both hydrophobic and hydrophilic).
What do phospholipids spontaneously do?
Form lipid bilayers.
Cholesterol is a lipid molecule that is a component of what? It is the most common precursor of what? Cholesterol is also the starting material for what two things?
(Have 4 hydrocarbon rings) It is a component of cell membranes and it is amphipathic. It is the most common precursor to steroid hormones. Starting material for VITAMIN D and BILE ACIDS.
High temperatures _______ membrane fluidity.
Low temperatures _________ membrane fluidity.
Increase; decrease
Cholesterol does what at high temperatures? At low temperatures?
At high temperatures, cholesterol holds the membrane together. At low temperatures, it keeps the membranes fluid.
Degrees of unsaturation also affect membrane fluidity… Saturated fatty acids _________ than unsaturated fatty acids.
Pack more tightly. Unsaturated fatty acids introduce kinks.
What do lipoproteins allow?
They allow the transport of lipid molecules in the bloodstream due to an outer coat of PHOSPHOLIPIDS, CHOLESTEROL, and PROTEINS.
HDLs vs. LDLs?
High-density lipoproteins are the good cholesterol that takes cholesterol away from the peripheral tissues to the liver where bile can be made to reduce the blood lipid levels.
LDLs are low in protein content and they are the bad cholesterol as they deliver cholesterol to the peripheral tissues, they can cause vessel blockage.
Waxes are simple lipids that have _______ connected to _____ through _______ linkages. What are they mainly used for?
Long fatty acids connected to mono-hydroxy alcohols through ester linkages. They are mainly used as hydrophobic protective coatings.
Carotenoids are lipid ______ containing long _________ with _______ ___________ and __________ at each end.
These are lipid derivatives containing long carbon chains with conjugated double bonds (double bond every other) and six-membered rings at each end. They function mainly as pigments.
What are nucleic acids composed of? They contain _______ monomers.
(CHONP) Carbon, hydrogen, oxygen, nitrogen, and phosphorus atoms. They contain nucleic monomers that build DNA and RNA polymers.
Nucleosides vs nucleotides.
Nucleosides: Sugar + nitrogenous base.
Nucleotides: Sugar + nitrogenous base + phosphate group.
Deoxyribose sugars (in DNA) contain a _______ at the ___’ carbon with ribose five-carbon sugars (in RNA) contain a ________ at the ___’ carbon.
Deoxyribose sugars (in DNA) contain a hydrogen at the 2’ carbon with ribose five-carbon sugars (in RNA) contain a hydroxyl at the 2’ carbon.
What does U replace in RNA?
U replaces T in RNA… U now binds to A.
What are purines? Pyrimidines?
PUR As Gold = Adenine and Guanine are purines (two-ring structure)
CUT the Py = Cytosine, Uracil, and Thymine are pyrimidine (one-ring structure).
A can only bond to T, how many hydrogen bonds?
2
G can only bond to C, how many hydrogen bonds?
3
Phosphodiester bonds connect the _______ of one nucleotide at the ___’ carbon to the _________ of another nucleotide at the ___’ carbon.
Phosphodiester bonds connect the phosphate group of one nucleotide at the 5’ carbon to the hydroxyl group of another nucleotide at the 3’ carbon.
A series of phosphodiester bonds create what?
This creates the sugar-phosphate backbone, with a 5’ end (free phosphate) and a 3’ end (free hydroxyl).
How does nucleic acid polymerization proceed?
Nucleoside triphosphates are added to the 3’ end of the sugar-phosphate backbone.
RNA is single-stranded after being what?
After being copied from DNA.
Modern cell theory states what 7 things?
- All lifeforms have one or more cells.
- The cell is the basic structural, functional, and organizational unit of life.
- All cells come from other cells (cell division).
- Genetic information is stored and passed down through DNA.
- An organism’s activity is dependent on the total activity of its independent cells.
- Metabolism and biochemistry (energy flow) occur within cells.
- All cells have the same chemical composition within organisms of similar species.
What is the central DOGMA of genetics?
Information is passed from DNA –> RNA –> Proteins. There are a few exceptions (reverse transcriptase and prions).
What does the RNA-world hypothesis state?
It states that RNA dominated earth’s primordial soup before there was life. RNA developed self-replicating mechanisms and later could catalyze reactions such as protein synthesis to make more complex macromolecules. Since RNA is reactive and unstable, DNA later became a better way of reliability storing genetic information.
