Chapter 3 Flashcards
Organic molecule
Carbon containing molecule found in all forms of life. Among these are lipids and macromolecules such as carbs proteins and nucleic acids
Macromolecule
Large complex compounds
Carbon can form
Four bonds because it has four electrons in its outer shell. This is one reason Carbon is the basis of life. It often forms bonds with hydrogen oxegyn nitrogen and sulfur. They can be double or triple bonded and can be linear, ring like or highly branched.
Hydrocarbons
Molecules with many hydrogen Carbon bonds. Carbon and hydrogen have similar electronegativities so the bond between them is nonpolar and hydrophobic. Carbon+ oxegyn or nitrogen is much more hydrophilic
Carbon and temperature differences
Why can it do that
Carbons bonds are stable in a huge range of temperatures( extreme heat or cold) partly because Carbon is very small so the distance between Carbon to Carbon bonds is very short. Shorter bonds tend to be stronger and more stable .
Functional groups
Most organic molecules and macromolecules have these. They’re groups of atoms with characteristic chemical structures and properties. These chemical properties stay the same no matter what molecule the functional group is in.
Isomers
Wohler
(Usually contain Carbon) two molecules with an identical chemical formula but different structures and characteristics
Wohler discovered that urea and ammonium cyanate contain the exact same ratio of Carbon nitrogen hydrogen and oxegyn but they’re different molecules.
Structural isomers
Contain the same atoms but in different bonding relationships.
Stereoisomers
&
The two types
**look for yellow highlighted passage
Have identical bonding relationships but the spatial positioning of their atoms differs.
- Cis- trans isomers: this is when two hydrogen atoms linked to the two carbons of a Carbon=carbon(double bond) may both be on the same side of one of the carbons. If so this makes the double bond a “Cis double bond”
* *Trans double bond is when the hydrogens are on opposite sides of the c=c.
2.Enantiomer- second type of stereoisomer is when a pair of molecules exist as a mirror image of one another.
Example of a Cis and trans in our body
In our eyes the Cis-retinal dominates during darkness and the trans-retinal takes over in sunlight
Polymer
A large macromolecule formed by linking many smaller molecules called monomers
Monomer
A molecule that consists of many repeating units
Condensation reaction
A chemical reaction where 2 or more molecules combine into one larger molecule by covalent bonding, with the loss of a small molecule
Dehydration reaction
Popular use of it
A type of condensation reaction in which a water molecule is lost
During dna synthesis, dehydration reactions produce strands of linear dna that contain millions of monomers called nucleotides
Hydrolysis reaction
The process where a polymer is broken down into monomers. A molecule of water is added back each time
4 organic/macro molecules all living things have
Lipids carbs proteins and nucleic acids
Carbs Made of: Basic molecular formula Most carbons in a carbohydrate are linked to Sugar is a
A Carbon, hydrogen and oxegyn.
C1(H2O)1. It is a Carbon that is hydrated(Carbo hydrate)😝
Hydrogen atom and a hydroxyl functional group
Small carbohydrate
Monosaccharide
Common ones have how many carbons
Examples of each^
Disaccharide
Polysaccharide
Simplest sugars. Most have 5( pentose ) examples are ribose and deoxyribose
( part of dna and rna)
or 6 carbons(hexose) example is glucose
How is the carbohydrate glucose often used as an energy source
It’s water soluble like all monosaccharides so it dissolves in in fluids so it can be transported across cell membranes. Once inside enzymes breakdown the bonds in glucose which releases energy. The energy is stored in adenosine triphosphate (atp)
Predominant type of structure in living organisms
Ring structure
Disaccharides
Carbs made of 2 monosaccharides joined by dehydration reaction.
The disaccharide sucrose
Maltose and lactose(just where these two come from)
Aka table sugar. Made from glucose and fructose. Sucrose is a major transport form of sugar in plants.
Maltose is formed in the digestive tract of animals
Lactose is from mammal milk
Glycosidic linkage
Usually involves the removal of a hydroxyl group from one of the monosaccharides and a removal of a hydrogen from the other, which gives rise to a water molecule and covalently bonds the two sugars through an oxegyn atom
Polysaccharides Storing energy Starch Glycogen Cellulose
Many monosaccharides linked together.
Some store energy in the cell for times an animal can’t get food/energy
Starch is found in plants. It’s structure is not very branched which makes it less soluble( potatoes and corn)
Found in animals it has extensive branching which creates an open structure which makes it very soluble
Plays a structural role. It’s one of the main ingredients of the primary cell wall in plants and algae. Linear chains of cellulose can form hydrogen bonds with eachother which makes them like sheets of cellulose
Starch vs cellulose and energy
Both starch and cellulose are made of repeating polymers of glucose. Enzymes break down the bonds in starch so it can by hydrolyzed for atp production. Cellulose is not because the enzymes that break down starch don’t recognize the shape of the polymers in cellulose. So, plants can break down starch for energy and keep cellulose intact
Fiber
plant matter that we consume but can’t digest so we just poop it out
Chitin
A tough structural polysaccharide that forms the external skeletons of insects and crustaceans (shrimp, lobster)
Glycosaminoglycans
Large polysaccharides that play a structural role. Found in cartilage and the extra cellular matrix surrounding many cells in an animals body
Lipids
Made of, polar?soluble?
What percentage of organic matter in body
Types
Hydrophobic molecules composed mainly of hydrogen and Carbon and some oxegyn.
Nonpolar, insoluble in water
Includes fats, phospholipids, steroids and waxes
Triglyceride(aka fat)
What’s a glycerol
What’s a fatty acid
Ester bond
The result of 3 fatty acids bonding to a glycerol.
Glycerol is a 3 Carbon molecule with one hydroxyl group bonded to each Carbon.
Fatty acids are made of a chain of Carbon and hydrogen atoms with a carboxyl group at the end.
Triglycerides form when each of the 3 hydroxyl groups in glycerol are linked to the carboxyl group at the end of a fatty acid. This happens by a dehydration reaction that’s called in this case, an ester bond
Fatty acid
A chain of Carbon and hydrogen with a carbonyl group(-COOH) at one end.
Ester bond
How a triglyceride is made; each of the hydroxyl groups in glycerol (-OH) link to a carboxyl group of fatty acids by removing one molecule of water(dehydration process)
Most common fatty acids from nature have how many carbon atoms
16 or 18 and they’re almost always even
Saturated fat
When all the carbons in a fatty acid are linked by a single covalent bond to a hydrogen. They have a high melting point and tend to be solid at room temp.
Unsaturated fatty acid
A fatty acid that has one or more double Carbon to Carbon bond. The c=c makes a kink into the otherwise linear shape of a fatty acid. Because of these links unsaturated fats don’t pack in together as tightly as saturated fats. They have a lower melting point and are liquid at room temperature these are oils. Fats from plants usually have unsaturated fat such as olive oil.
Monounsaturated fats
An unsaturated fat with only one c=c double bond
Polyunsaturated fats
More than on c=c double bond.
Essential fatty acids
Fatty acids we need but don’t make ourselves. An example is linoleic acid
Trans fats
Most fats are cis fats. Trans fats are very bad for health. Formed by a process that makes the fat more compact and linear, giving it a higher melting point. Also extends shelf life and works better for baking. But they narrow the blood vessels that supply the heart with blood(coronary artery disease)
Fat & energy
Fat stores energy. hydrolysis of triglycerides releases the fatty acids from glycerol and these products can then be metabolized to provide energy to make atp. The # of c-h bonds in a molecule of carb or fat determines how much energy it has. Fat has more c-h bonds so it had more energy than carbs.
Phospholipids
Difference in structure from triglycerides
The differences that one change makes
Similar to triglycerides except: the third hydroxyl group of glycerol is linked to a phosphate group instead of a fatty acid. That phosphate is usually attached to a small polar or charged nitrogen containing molecule. The phosphate group and charged molecule make a hydrophilic head at one end of the phospholipid and the fatty acids are like hydrophobic tails.
Phospholipids in water
Organize into bilayers with the polar heads interacting with the water and the nonpolar tails facing inside
Steroids
Chemical structure
3 examples of steroids
Steroids contain ring structures.
Four fused rings of Carbon form the “skeleton” of all steroids
1.cholesterol
All steroid hormones are derived from cholesterol and share similar structures
2. Estrogen one less methyl group and a hydroxyl instead of a keystone group and additional double bonds in one of its rings is what differentiates estrogen from testosterone
Sterols
A steroid with 1 or more polar hydroxyl groups are attached to the ring. But that one polar group isn’t enough to make them very water soluble.
Waxes
Animals/plants
Molecular makeup
Complex lipids that prevent water loss from organisms because they’re very non polar they are a good barrier.
Many plants and animals produce waxes on their surfaces (leaves of plants, cuticles of insects).
All waxes have one or more hydrocarbons and large structures that resemble a fatty acid attached by its carboxyl group to another long hydrocarbon chain.
Proteins
What % of organic material
What are they made of
Are polymers of amino acids.
Play a critical part in nearly all life processes.
Account for 50% of organic material in an animals body.
Made of Carbon, hydrogen oxegyn nitrogen and sulfur
Amino acids
The building blocks of proteins. A simple organic compound containing a carboxyl group (-COOH) and an amino(-NH2) group. Both are linked to the carbon atom which is in the center. ( called the x Carbon) x carbons also linked to a hydrogen and a side gain designated with the letter R
When an amino acid is dissolved in water at neutral ph
When an amino acid is dissolved in water at neutral pH, the amino group accepts a hydrogen ion and is positively charged, whereas the carboxyl group loses a hydrogen ion and is negatively charged. The term amino acid is the name given to such molecules because they have an amino group and also a carboxyl group that acts as an acid
The two isomeric forms of all amino acids(excluding glycine) exist in
The D and L forms are enantiomers(molecules that are mirror images of eachother) only L amino acids are found in proteins D are really only found in cell wall of some bacteria
Peptide bond
Amino acids are joined by a dehydration reaction that links the carboxyl group of one amino acid to the amino group of another amino acid. The covalent bond formed between the carboxyl and amino group is the peptide bond
Polypeptide
N terminus
C terminus
When multiple amino acids are joined by peptide bonds. Linear structure. When two or more amino acids are linked one end of the resulting molecule has a free amino group called “amino end or n terminus” on the opposite side there’s a free carboxyl group called C terminus.
Protein
A functional unit made of one or more polypeptides that have been folded and twisted into a precise 3 dimensional shape.
Glycoproteins
Lipoproteins
Some Proteins have carbs(called glycoproteins) or lipids(called lipoproteins) attached @ various points on the amino chain. This addition gives those proteins unique functions
Structure of proteins
1. Primary
2. Secondary., what causes twist
In a b Pleated sheet what causes zigzag
Page 59 look at notes…
- Primary the amino acid sequence from beginning to end. The primary structure of proteins is determined by genes
- Secondary-the bending or twisting of proteins into x helices or b sheets. In x helix, the polypeptide backbone forms a repeating helical structure that’s stabilized by hydrogen bonds. At regular intervals, a hydrogen will link to a nitrogen which forms a hydrogen bond with an oxegyn that is double bonded to a Carbon causing the backbone to twist.
With a b pleated sheet, parts of the polypeptide backbone lay parallel to eachother. Hydrogen bonds between a hydrogen linked to a nitrogen and a double bonded oxegyn form between the parallel Regions causing the backbone to adopt a zigzag shape
Proteins with stretches of nonpolar amino acids tend to
Anchor themselves into a lipid rich environment such as a plasma membrane
Random coiled regions
Regions on a polypeptide chain that don’t form a helix or pleated sheet
Last two levels of protein structure
- Tertiary structure
- Quaternary
A complex 3D shape a polypeptide chain folds into. Tertiary structures include all the secondary structures plus any interactions involving amino side chains
- When proteins consist of more than one polypeptide they have a quaternary structure. The indiviual polypeptides are called protein subunits.
Factors determining how proteins adopt secondary, tertiary and quaternary structures
1,2&3
- Hydrogen bonds can add up to a strong force that promote protein folding when they’re found in large numbers. These bonds form between atoms in the backbone and atoms in side chains
- Ionic bonds and other polar interactions: positive and negatively charged side chains bind through ionic bonds. Uncharged polar side chains also bind to ionic amino acids.
Hydrophobic effect. As a protein folds non polar hydrophobic amino acids go to the center to avoid water. For long stretches of nonpolar amino acids they’ll stay in the hydrophobic part of the membrane
Factors determining how proteins adopt secondary, tertiary and quaternary structures
4&5
Van der waals dispersion forces. Atoms in molecules have a temporary and weak attraction if they’re the perfect distance apart. Imp for tertiary
5.disulfide bridges- the side chain of amino acid cysteine has sulfhydral group (-SH) which will react with a (-SH) in another cysteine. Resulting in a disulfide bridge or bond linking the two amino side chains. It’s not the most important thing in protein folding but it helps stabilize the structure
Protein to protein interactions
Surface of one protein fits perfectly into surface of the other. Important so cellular processes can happen in defined steps. Also helps build complicated cell structures with shape and organization.
They happen because of hydrogen or ionic bonding the hydrophobic effect can see waals dispersion forces but NOT disulfide bridges
Domain
A defined region of a protein with a distinct structure and function
Nuclear receptors
Proteins that form a group which all have similar roles, regulating how certain genes get turned on in animals, animal development, reproduction,metabolism and homeostasis
Nuclear receptors have 4 or more domains in their structure.
4 domains of a nucleur receptor
- Ligand binding domain, where receptors are activated by a ligand . Differences in the ligand binding domain allow the right ligand to fit and not others
- The dna binding domain binds to dna once the ligand is activated. Different enough that they only bind to certain genes.
- nucleur localization domain facilitates movement of the protein into the cell nucleus where dna is located
- once protein binds to dan the activation domain activates transcription of the target gene
Nucleic acids
Responsible for storage,expression and transmission of genetic information. Genetic info is expressed in the form of specific proteins, determining whether an organism will be human frog or onion.
1 class of nucleic acid Deoxyribonucleic acid (dna)
Stores genetic info coded in the sequence of their building blocks(nucleotides) Consists of two strands of nucleotides coiled around eachother to form double helix held together by hydrogen bonds according to AT/GC rule
Another class of nucleic acid Ribonucleicacid
Made of a single strand of nucleotides.
It’s involved in decoding the information from dna into instructions for linking a specific sequence of amino acids to form a polypeptide
DNA and RNA nucleotides consist of what 3 components
A phosphate group
A five Carbon sugar, either ribose or deoxyribose
And a single or double ring of Carbon and nitrogen atoms known as a base
Bases that can be linked to deoxyribose in dna
Type 1
Type 2
Purine bases: adenine and guanine
^have fused double rings of Carbon and nitrogen atoms
Pyramidine bases cytostine and thymine
^ have a single ring structure
Instead of thymine, rna has
Uracil
Monomers of carbs
Glucose formula
Deoxyribose
Ribose
(C6H12O6).
C5H10o5
C5h10o4
