Ch. 3 Flashcards
What is an Organic Molecule?
Molecules that contain Carbon.
Example: Glucose (C6H12O6)
What is an Inorganic Molecule?
Do not contain Carbon.
Example: Water (H2O)
What is a Hydrocarbon?
A molecule that contains one Carbon and Hydrogen.
Example: Methane (CH4)
Even charge distribution (Non-polar)
What are Function Groups?
The C-H backbone and specific groups of many organic molecules.
What does it mean when molecules have similar functional groups?
They often have similar properties.
What are some common functional groups?
- OH Hydroxyl Group
- C=O Carbonyl Group
- COOH Carboxyl Group
- PO4 Phosphate Group
- NH2 Amine Group
What are Polymers?
Large aggregates of smaller sub-units.
Can be thought of as long trains that are made by linking together many individuals.
What are monomers?
The individual sub-units that make up a polymer.
What are 4 main types of macromolecules?
Proteins
Nucleic Acids
Lipids
Carbohydrates
What are 2 types of proteins?
Globular and structural
What is the sub-unit of proteins?
Amino Acids
What are the functions and examples of proteins?
Enzymes (Hemoglobin) and support (Keratin, Collagen)
What are 2 types of Nucleic Acids?
DNA and RNA
What is the sub-unit of Nucleic Acids?
Nucleotides
What are the function and example of Nucleic Acids?
Gene coding (Chromosomes) and Gene Expression (mRNA).
What are 3 types and sub-units of lipids?
Fats (Glycerol, 3 fatty acids)
Phospholipids (Glycerol, 2 fatty acids)
Steroids (Carbon rings)
What are the Function and example of each type of lipid?
Fats (Energy storage; Butter, Olive Oil)
Phospholipids (Cell Membranes; Lipid Bilayer)
Steroids (Hormones; Estrogen)
What are 3 types of Carbohydrates and their sub-units?
Starch (Glucose, simple sugar)
Cellulose (Glucose, simple sugar)
Chitins (Modified glucose)
What are the function and examples of each of the 3 types of carbohydrates?
Starch (Energy storage; potatoes)
Cellulose (Cell walls (plants); celery strings)
Chitins (Structural; Crab shells)
What does Dehydration Synthesis do?
Used to build macromolecules. An -OH from one molecule and an H+ from another are removed and the sub-units are joined.
Cells expend energy to assemble the macromolecules.
What is Hydrolysis?
The breakdown of macromolecules by breaking the bonds by adding an -H to one end and a -OH to the other.
-Lysis means break
What are six functions of proteins?
- Enzyme Catalysis
- Defense
- Transport
- Support
- Motion
- Regulation
What is an example of Enzyme Catalysis?
-Help to speed up chemical reactions.
What is an example of protein defense?
Globular proteins attach to foreign molecules forming the basis for the immune system.
What is an example of protein transport?
Hemoglobin transporting Oxygen in the bloodstream.
What are examples of protein support?
- Fibrous, structural proteins help keep us together.
- Keratin makes hair
- Fibrin makes blood clots
- Collagen makes skin, ligament, cartilage, and bones
What is an example of protein motion?
Actin and Myosin are contractile proteins that are responsible for moving materials in cells and the motion of muscles.
What is an example of protein regulation?
Some hormones are small proteins that are used to send messages between cells. These turn on and off certain genes are used to regulate growth, development, etc.
What groups are proteins comprised of?
All amino acids have an amine group, a carboxyl group and a side group {R}.
In amino acids, what does the R group determine?
The chemical properties.
How many common amino acids are there, and how many classes?
20 common amino acids, and they are broken into 5 classes of R groups.
What are the 5 classes of R Groups?
Non-polar amino acids; R groups with -CH2 or -CH3
-Example: Alanine, Valine
-These are hydrophobic
Polar, uncharged amino acids; R groups contain Oxygen
-Example: Glutamine
-These are hydrophilic
Ionizable amino acids; R groups contain acids or bases
-Example: Glutamic acid
-These are hydrophilic
Aromatic amino acids; R groups contain benzene ring
-Example: Phenylalanine
Special amino acids
-Methionine, first amino acid in polypeptide
-Proline, causes kinks in protein chains
-Cysteine, bonds with itself to bend protein
How do amino acids join together?
By undergoing condensation (dehydration synthesis)
What are peptide bonds?
The bond between two amino acids.
It isn’t a flexible bond which allows for the protein to maintain a tight shape which in turn determines function for many proteins.
What are polypeptides?
Give an example.
Long chains of amino acids joined together by peptide bonds.
Example: hemoglobin is comprised of 4 polypeptide chains.
What amino acids tend to be on the surface of the protein?
Charged, polar amino acids.
In a protein, how many levels of structure are there, and what are they?
- 6 levels of structure
- Primary (Amino Acid Sequence), Secondary (Coils and sheets), Motifs (Combinations of secondary), Tertiary (3-D shape), Domains (Exons), & Quaternary (Arrangement of polypeptide chains)
What is the primary structure of proteins?
The specific amino acid sequence
- Determined by the nucleotide sequence of the gene that codes for the protein.
- A protein can consist of any amino acid sequence since the R groups aren’t involved in the peptide bonds.
If a polypeptide is 100 amino acids long, how many possible combinations are there?
20^100 possible combinations.
What is the secondary structure of proteins?
The folding of the polypeptide chain into the characteristic shapes.
The -COOH and the -NH3 ends can form hydrogen bonds with each other
- The hydrogen bonds causes patterns in the protein shape.
- Alpha helix (a-helix); looks like a spring
- Beta pleated sheet (B-pleated sheet); looks like a curled up sheet.
What is the motif level of structure of proteins?
Combinations of secondary structure.
-Also called super secondary structure.
What is the tertiary structure of proteins?
The final folded shape of the protein (3D shape).
- Hydrophobic interaction help determine the tertiary structure.
- Chemical nature of the side groups {R-Groups} helps to determine the final shape.
- The different size of the R-groups of the non-polar amino acids allow for a very exact fit. Helps to keep the final shape of the protein very stable.
- Disulfide bonds between Cysteine (R-Group= CH2SH)
What are Van Der Waal’s forces?
Weak intra-atomic forces caused by the slight change in polarity of atoms as the electrons move about the nucleus of the atoms.
-Affects the tertiary structure of proteins.
What are domains of a protein?
- Contain exons (functional unit)
- A single polypeptide chain consists of several linked domains.
- Domains have independent functions:
* One domain will bind to a cofactor
* Another will help bind to substrate
What are exons?
- Genes encoded in functional sectionals.
- Exons are typically 100 to 200 amino acids long and fold into a structurally independent unit.
What are the quaternary structure of a protein?
Arrangement of polypeptide chains
-Each polypeptide chain is a sub-unit of the quaternary structure.
Example: Hemoglobin is made of 4 chains (2 alpha chains, and 2 beta chains)
-Interfaces between sub-units are often non-polar amino acids that help hold the protein together.
What are chaperonins?
About how many kinds are there?
Special proteins that help in the assembly of other proteins.
About 17 kinds
-Thought to work by fixing proteins that are incorrectly folded.
What diseases may be linked to Chaperonin deficiencies?
Cystic fibrosis and Alzheimer’s disease
What is Denaturation?
The process of a protein changing shape, or unfolding.
What can cause a protein to undergo denaturation?
- Changes in pH
- Changes in temperature
- Changes in ionic concentration
What happens when a protein is denatured?
It is usually biologically non-active.
What is the tolerance range of an enzyme?
The range of pH, temperature, [ions], within which they work fine, outside of it, they are often denatured and non-functional.
What happens if an unfolded protein returns to normal conditions?
Many proteins will spontaneously refold, however larger proteins often cannot do this.
What is dissociation?
If polypeptide chains of a protein disengage from each other but are not individually denatured, it can reassemble. If the chains are denatured, it won’t refit.
What are Nucleic acids?
Information molecules (cellular blueprints)
What are two varieties of nucleic acids?
DNA: Deoxyribonucleic acid
RNA: Ribonucleic acid
What is DNA responsible for?
What is DNA often called?
Encodes the instructions for building proteins and serves as a template for copying itself to pass along to the net generation of cells.
A Hereditary Molecule
What is RNA responsible for?
Reading DNA code and direct the synthesis of the proteins.
What two processes are involved with RNA?
Transcription and translation
What is transcription?
The process of making an mRNA from the DNA template.
What is translation?
The process of making a protein from the mRNA.
What is a nucleotide?
The sub-unit of a nucleic acid (polymer)
What three parts is a nucleotide composed of?
1) A five-carbon sugar
a) Ribose for RNA
b) Deoxyribose for DNA
2) A phosphate group
3) A nitrogenous base
i) Adenine (A)
ii) Guanine (G)
iii) Cytosine (C)
iv) Thymine (T), only in DNA
v) Uracil (U), only in RNA
What is a phosphodiester bond?
Links the five-carbon sugars by the phosphate group
How many kinds of nitrogenous bases are there?
1) Purines
- Large, double ringed molecules found in both DNA and RNA (A,G)
2) Pyrimidines
- Smaller, single ringed molecules (C,T,U)
- T is found in DNA only, U is found in RNA only.
What are the nitrogenous bases found in DNA?
A, G, T, C
What shape does DNA take?
Double helix
Double stranded molecule that is twisted.
In DNA, what are the complimentary base pairs?
What are they held together by?
Adenine (A) bonds Thymine (T), and Guanine (G) bonds to Cytosine (C)
The base pairs are held together by hydrogen bonds.
What are the two differences between RNA and DNA?
1) The 5-carbon surge is ribose instead of deoxyribose
2) The pyrimidine thymine is replaced with uracil (Tells the cell which of the molecules is used for storage of information and which is to be used for protein synthesis)
3) RNA is single stranded
How does information flow between DNA, RNA and proteins?
DNA to RNA to proteins
What other function does Adenine (A) have in the cell?
It is a component of ATP (Adenosine triphosphate), which is the energy currency of the cell.
What are lipids?
Loosely defined as a group of molecules that are insoluble in water.
Have long chains of non-polar C-H bonds.
What are phospholipids responsible for?
The formation of membranes
What 3 parts are phospholipids made of?
1) Glycerol - A 3-carbon alcohol that forms the backbone of the lipid molecule.
2) Fatty Acids - Long chains of C-H bonds, ending in a carboxyl group. Two are present in a phospholipid.
3) Phosphate group - Attached to one end of the glycerol molecule is a phosphate group with a charged organic molecule.
In regards to polarity, how are phospholipids composed?
A polar head (phosphate group) with two non-polar tails.
What do phospholipids form?
A lipid bilayer.
What is a lipid bilayer?
A double layer of lipids with non-polar tails pointing at each other, and polar heads facing out.
What are lipid bilayers the basic framework for?
Cell Membranes.
What are fats?
Fats are lipids that do not have a polar head.
What 2 parts do fats consist of?
1) Glycerol - 3-carbon alcohol
2) Fatty Acid Chain - 3 chains instead of 2, all non-polar
Why are fats called triglycerides?
Because they have 3 fatty acid chains.
They don’t all have to be the same; often they are different from each other.
What are triglycerides used for?
Energy storage in many organisms.
When is a fat considered saturated?
If all of the carbon atoms in the fatty acid chains have at least 2 hydrogens bonded to them.
-It contains the highest amount of hydrogen atoms possible. (no double bonds)
When is a fat considered unsaturated?
If the carbon atoms in the fatty acid chains have less than 2 hydrogen atoms (double bonded)
What is a polyunsaturated fat?
If there are lots of double bonds in a fatty acid chain.
Do unsaturated fats have a higher or lower melting point?
What does this mean to unsaturated fats at room temperature?
Give an example of an unsaturated fat at room temp.
Lower melting points.
They are often liquid at room temp.
Example: Corn oil
Do saturated fats have a higher or lower melting point?
What does this mean to saturated fats at room temperature?
Give an example of a saturated fat at room temp.
Higher melting point.
Solid at room temp.
Example: Butter
What are terpenes?
Long chains of lipids.
What are steroids?
Another type of lipid.
Example: Cholesterol, testosterone, and estrogen.
About how many carbon atoms do most fats have?
About 40 carbon atoms.
Compared to carbohydrates, do fats how more or less energy storing bonds?
Fat have about twice as many energy storing bonds.
Do animals produce saturated or unsaturated fats?
Saturated fats (except fish)
Do plants produce saturated or unsaturated fats?
Unsaturated fats (except for coconut and palm oil which are saturated)
How can unsaturated fats be converted into saturated fats?
By hydrogenating them.
Example: Done to peanut butter to keep the peanut oils from separating in the jar.
What do carbohydrates function as?
Energy storage molecules and structural elements.
What are carbohydrates?
Loosely defined as a group of molecules that contain carbon, hydrogen, and oxygen in a 1:2:1 ratio.
Why are carbohydrates considered an energy storage molecule?
Because they contain many C-H bond that release energy when broken.
What are sugars considered?
Simple carbohydrates.
What is the simplest form of carbohydrates?
Give an example, and how many carbons is it comprised of?
Simple sugars called monosaccharides.
Example: Glucose, Fructose and Galactose (typically a 6-carbon sugar)
What is glucose used for?
Energy storage.
What are disaccharides?
Give 2 examples.
What are the combinations of simple sugars to comprise them?
When two sugar molecules are joined together by covalent bonds.
Example:
Sucrose- Glucose and Fructose.
Lactose- Glucose and Galactose.
What are polysaccharides?
Give 2 examples.
What are their functions?
Long chains of sugars linked together.
Examples:
Starch- Store energy.
Cellulose- Build the cell walls in plants.
What are isomers?
How many kinds of isomers are there, and what are they?
Compounds that have the same empirical formula, but different structure.
2 kinds of isomers.
Structural isomers and stereoisomers.
What are structural isomers?
Give an example.
The arrangement of molecules is different.
Example: Fructose and Glucose.
Fructose has a double bond (=) at carbon #2, Glucose has a double bond (=) at carbon #1
What are stereoisomers?
Give an example.
Change in orientation of groups.
Example:Glucose and Galactose
Hydroxide (-OH) at carbon #4 are mirror images.
What is the real world name for sucrose?
What monosaccharides combine to make sucrose?
Table sugar
Glucose + Fructose = Sucrose
How are glucose and fructose broken apart in the body when the glucose is needed?
A special enzyme will be present to break open the disaccharide.
Why are glucose and fructose combined?
To transport glucose so it won’t get metabolized before it’s needed.
Give examples of transport disaccharides.
Sucrose and Lactose.
What is an example of a storage polysaccharide?
Give an example.
Carbohydrates are often used for energy storage.
Example: Starch
What are starches?
Long polymers of glucose located in plants.
What is the simplest starch?
What is its basic structure?
Amylose
Long un-branched chains of glucose.
Name a second starch other than amylose.
What is its basic structure, and where can it be found?
Amylopectin.
A polymer of glucose, but instead of a long chain, it has branches.
Found in potatoes.
Where can glycogen be found?
What is the function of glycogen?
What is the basic structure of glycogen?
In animals.
Carbohydrate storage.
A branched chain of glucose.
How forms of glucose are there?
Name the forms of glucose.
What determines if a glucose is alpha or beta?
2 forms
Alpha and Beta
The position of the hydroxyl group on the #1 carbon.
What are alpha and beta glucose examples of?
Stereoisomers.
What is the basic structure of cellulose?
The linking together of only beta glucose.
How are cellulose and amylose different in regards to animal digestion?
Most animals lack the enzymes to break down cellulose.
What is an animal that is able to break down cellulose?
Cows
What is the basic structure of chitin?
Where can it be found?
Basically a cellulose molecule (linking together of only beta glucose) with some nitrogen groups attached to it.
Can be found in many invertebrates and in the cell walls of fungi.
