ATOMS/MOLECULES, WATER, BIOCHEM Flashcards
Matter
Anything that occupies space and has mass
How many naturally occurring elements are there?
92 and elements cannot be broken down by ordinary chemical means
Which 4 elements are essential for life in our human body, give the %
Oxygen 56%, carbon 18.5%, hydrogen 9.5%, nitrogen 3.2%
Trace elements and examples (14)
Minerals present in living tissues in small amounts, usually as catalysts in enzyme systems. It can lead to serious physiological conditions if they are lacking in diet (eg. boron, chromium, cobalt, copper, fluorine, iodine, iron, manganese, molybdenum, selenium, silicon, tin, vanadium, zinc)
Molecule
Combination of two or more atoms joined by a chemical bond (eg. N2, H2O, O2, CH4N2O)
Compound
Substance containing at least two DIFFERENT elements joined by a chemical bond (eg. H2O, CH4N2O, C6H12O6)
Organic compounds
Contains carbon and hydrogen (eg. C6H12O6, CH4N2O)
Inorganic compounds
Does not contain both carbon and hydrogen (eg. H2O, CO2)
Importance of carbon
Chemically versatile as carbon has the ability to form 4 covalent bonds with other atoms; can combine with other major elements to form an endless variety of organic compounds (eg. Carbohydrates, lipids, proteins, nucleic acid).
Protons
Positive charge, found in nucleus, and has one unit of mass
Electron
Negative charge, orbits nucleus in the cloud because they are attracted to protons, and has almost no mass
Neutrons
No charge, found in the nucleus, and has one unit of mass
Atomic number
Number of protons and electrons in a NEUTRAL ATOM
Mass number
Number of protons and neutrons combined; subtract the atomic number from the mass to find the number of neutrons
Electron shells
Outside portion of an atom around the atomic nucleus that electrons occupy at a distinct energy level
Maximum number of electrons in each shell
2, 8, 18, 32, 32
Octet rule
Tendency of atoms to have 8 electrons in valence shell which makes them non reactive
Valence shell
Outermost electron shell; if the valence shell is not full, the atom will tend to be reactive with other atoms to fill its valence shell
All atoms except ___ and ___ are stable when there are exactly 8 electrons in the valence shell
Hydrogen and helium
Ionic bonds
Attraction between nonmetal and metal; two oppositely charged ions and COMPLETE transfer of electrons
Cation
Positive charge ion formed when it loses one or more electrons
Anion
Negative charge ion formed when it gains one or more electrons
Covalent bond
Attraction between two nonmetals; shares electrons in a mutually stabilizing relationship (no gain or loss of electrons). They are very stable as electrons move back and forth between atoms and are not broken apart in water
Nonpolar covalent bond
Bond that occurs when two atoms share a pair of electrons with each other
Single covalent bond
Two atoms sharing one pair of electrons
Double covalent bond
Two atoms sharing two pairs of electrons
Polar covalent bond
Bond that occurs when there is an unequal sharing of electrons which results in a slight negative charge at one end of molecule and a slight positive charge at other end
What is a good example of a polar molecule
Water; The atomic nucleus of oxygen (8 protons) exerts a charge eight times greater than that of each hydrogen (1 proton). Oxygen region has a partial negative charge and the hydrogen region has a partial positive charge
Hydrogen bond
Attraction between two atoms that already participate in other chemical bonds. One of the atoms is hydrogen, while the other may be any electronegative atom, such as oxygen, chlorine, or fluorine usually represented by dotted lines and WEAKER than ionic and covalent bonds (eg. Water)
Chemical properties of water (3):
- Water is polar; oxygen has partial negative charge and hydrogen has partial positive charge
- The opposing partial electrical charges pull the atoms in a way and creates a triangular shape
- Hydrogen bonds form between the hydrogen of one molecule and the oxygen of another
Physical properties of water (3):
- Liquid water is MORE DENSE than ice even though for most substances, the solid state is more dense
- Water has a boiling point of 100 degrees C
- Formation of hydrogen bonds leads to surface tension where the attraction between the water molecules allows a film of water to resist changes in shape
Functions of water as a lubricant & cushion (4):
- Synovial fluid lubricates actions of body joints
- Water in pleural fluid helps lungs expand and recoil
- Water fluids help keep food flowing through digestive tract and friction free
- Water protects cells and organs from physical trauma
3 ways listed from the lecture that water protects cells and organs from physical trauma:
- Cushions the brain with the cell
- Protects the delicate nerve tissue in eyes
- Cushions a developing fetus in mother’s womb
Heat sink
Absorbs and dissipates heat without experiencing a corresponding increase in temperature
Water as a heat sink (3):
- When temperature rises in the environment, the water stored in our body plays a crucial role in regulating our body temperature by aiding the cooling process
- Warm blood from body’s core flows to capillaries in the skin and radiates heat to the environment
- Sweat evaporates from skin, breaking hydrogen bonds that use up heat energy and cools the blood in the capillaries
Mixture
Combination of two or more substances, each of which maintains its own chemical identity
Water as a component of liquid mixtures:
Cells are kept in a moist water based liquid called a solution to survive in the body
Dehydration synthesis
Monomers become a polymer and water is PRODUCED = larger formation (one reactant gives up an atom of H and another reactant gives up a OH in synthesis of new product)
Hydrolysis
Uses water to break apart polymers into monomers (molecule of water disrupts a compound and breaks its bond = water split into H and OH)
Body water content in age (4):
- 75% of body mass water in infants
- 45% of body mass water old age
- 50% of body mass water women
- 60% of body mass water men
Intracellular fluid (6):
- Includes all fluid enclosed in cells by their plasma membranes
- Lies within cells and principle component of cytosol/cytoplasm
- Makes up 60% (2/3) of total water in human body and about 25L (7 gal) in adult males
- Very stable because the amount of water in the cell is highly regulated
- Too little water = cytosol becomes too concentrated and cant operate normally
- Too much water = cell may burst
Extracellular fluid (4):
- Surrounds all the cells in the body and has two major components –> blood plasma (fluid component of blood), and interstitial fluid (surrounds all cells not in blood)
- 1/3 of body’s water content
- 20% found in blood plasma and travels through body in blood vessels and transports materials throughout the body such as blood cells, proteins, electrolytes, nutrients, gases, waste between capillaries and interstitial fluid
- Cells are separated from the interstitial fluid by a selectively permeable cell membrane
Cerebrospinal fluid
Bathes the brain and spinal cord
Lymph
In vessels of the lymphatic system
Synovial fluid
In some articulating joints
Pleural fluid
Surrounds lungs
Pericardial fluid
Surrounds heart
Peritoneal fluid
Surrounds the abdominopelvic organs
Aqueous bumor
Eyes
Water content of body’s organs and tissues (10):
- Brain 80-85%
- Teeth 8-10%
- Lungs 75-80%
- Heart 75-80%
- Bones 20-25%
- Liver 70-75%
- Kidneys 80-85%
- Blood 80%
- Skin 70-75%
- Muscles 70-75%
Carbon (4):
- Forms the fundamental components of most biological molecules
- Carbon atom contains four electrons in its valence shell = can form four single covalent bonds
- Carbon skeletons can then form the basis for an endless array of molecules
- Carbon atoms can bind with atoms of other elements, such as nitrogen, oxygen, and phosphorus, the molecules can also form rings which can link with other rings
What element does carbon covalently bond with the most
Hydrogen
Functional groups
A group of atoms linked by strong covalent bonds and tending to function in chemical reactions as a single unit (think of tightly knit cliques whose members cant be parted)
5 functional groups important in human physiology
Hydroxyl, carboxyl, amino, methyl, phosphate
Hydroxyl (-OH)
Polar, components of all 4 types of organic compounds, involved in dehydration synthesis, hydrolysis, and hydrogen bonding
Carboxy (-COOH)
Found within fatty acids and amino acids + organic acids
Amino (-NH2)
Found within amino acids = the building blocks of protein
Methyl (-CH3)
Component of amino acids? + fatty acids
Phosphate (-PO4^2-)
Found within phospholipids and nucleotides
Monomers
” one “ and “part”
Polymers
Macromolecules made up of multiple copies of single units called monomers
Use of dehydration synthesis and hydrolysis in monomers and polymers
- Monomers link together to form polymers through dehydration synthesis
- Polymers are split into monomers through hydrolysis
Carbohydrate functions (5):
- The carbohydrates that the body uses for energy originates mostly from plant-based foods
- Polysaccharides such as starch play a role as a primary energy source, especially glucose
- Short chains of carbohydrates can be used for the glycocalyx that surrounds most animal cells
- Human body stores glucose in body as glycogen
- Pentose sugars are critical components of ATP and the nucleotides of DNA and RNA
“Generic” carbohydrate molecule
“Hydration of carbon” (CH2O)
Monosaccharides (4):
- Monomer of carbohydrates
- Simple sugars, usually glucose C6H12O6
- Number of carbon atoms ranges from 3 to 6
- Exists as linear chain or ring shaped
5 important monosaccharides:
- Glucose (hexose sugar)
- Fructose (hexose sugar)
- Galactose (hexose sugar)
- Deoxyribose (pentose sugar)
- Ribose (pentose sugar)
Hexose sugar
6 atoms of carbon
Pentose sugar
5 atoms of carbon
Glucose
Important source of energy. Organisms use the energy released from glucose to make ATP
Disaccharide
Chemical reactions of two monosaccharides joined together through dehydration synthesis and bonds of glycosidic (glyco = sugar) bonds
3 important disaccharides:
- Glucose + glucose: Maltose (malt sugar)
- Glucose + fructose: Sucrose (table sugar) - Galactose + glucose: Lactose (milk sugar)
- Dissacharides are split into monosaccharides through hydrolysis in digestive tract
Polysaccharide
Long chain of monosaccharides. Can be a few to a thousand monosaccharides
3 important polysaccharides:
- Starch
- Glycogen
- Cellulose
Starch
Polymers of glucose occurring in long chains called amylose or branched chains called amylopectin and are stored in plant-based foods and easy to digest
Glycogen
Polymers of glucose stored in tissues of animals especially in muscles and livers and are NOT considered a dietary carbohydrate but human body stores excess glucose as glycogen
Cellulose
Polysaccharide made of glucose and is the primary component of cell wall of green plants or fibers in humans. Cellulose is NOT digestible
Lipid
Highly diverse group of compounds made up of mostly hydrocarbons. All lipids are at least partly hydrophobic
Types of lipids (4):
- Fatty acids (unsaturated/saturated)
- Phospholipids
- Steroids
- Neutral fats
Emulsion
Mixture of liquids that do not dissolve in each other and having droplets of one liquid scattered throughout the other
Triglycerides structure
One of the most common dietary lipid groups most abundantly found in body tissues and consist of a glycerol molecule covalently bonded to three fatty acids
Glycerol structure
Organic compound with 3 carbon atoms
Fatty acid structure
Long chain of hydrocarbons with an acid carboxyl group on the end; Each fatty acid is covalently bound to one of the 3 oxygen atoms of the glycerol molecule through dehydration synthesis, producing three molecules of wate
Saturated fatty acid structure
Lacks double bonds between carbon atoms in the hydrocarbon chain
Unsaturated fatty acid structure
At least one double bond between carbon atoms in the hydrocarbon chain
Saturated fat example
Tend to pack tightly in fatty acid chains and therefore solid at room temperature. They are of animal origin (eg. Butter, lard)
Unsaturated fat example
Double bond causes bend in the fatty acid chain and prevents them from packing tightly, therefore they are considered oils and liquid at room temperature (eg. Vegetable oil, palm oil)
Triglyceride function (4):
- Major fuel source for body and used when glucose storages are low, and also fuels long and slow physical activities
- Assists the absorption of the non-polar-fat-soluble vitamins A, D, E, and K
- Protects and cushions body’s bones and internal organs and acts as insulation
- Components of glycolipids
Glycolipids
Sugar-fat compounds found in cell membrane
Phospholipids
Class of lipids that are constituent of plasma membrane. Contains a hydrophilic (water loving) head made of a phosphate group and two hydrophobic (water hating) tails made from fatty acids joined by a glycerol molecule
Membrane
All cells are surrounded by a membrane composed of a bilayer of phospholipids. Fatty acids of both layers of phospholipids face towards each other, away from the water inside and outside cell and the hydrophilic head faces towards the watery fluid
Steroids
Class of lipids with a molecular structure containing four rings of carbon and a short hydrocarbon tail that are most known for hormones and cholesterol
Steroid functions (3):
- Synthesized by the liver and present in most animal-based foods
- Component of bile acids to help emulsify dietary fats
- Building blocks of hormones
Proteins
Organic molecule always composed of amino acids linked by peptide bonds dehydration synthesis. Critical components of all tissues and organs and play key structural and chemical roles in the body
Microstructure of proteins
Polymers made up of nitrogen-containing monomers (amino acids)
How many types of amino acids are there
20 but proteins in our body contain a unique combination of a few dozen to a few hundred
Amino acid general structure
Molecule composed of an amino group and a carboxyl group together with a variable side chain
What do all 20 of the amino acids contain:
- Hydrogen atom
- Alkaline (basic) amino group NH2
- Acidic carboxyl group COOH
- Variable group
R group
Remainder group that determines the type of amino acid it becomes
1 amino acid
amino acid
2 amino acid
dipeptide
3 amino acid
tripeptide
More than 5 amino acids
polypeptide
50-70 amino acids
protein
Peptide bond
Covalent bond between two amino acids that forms by dehydration synthesis
Why do all proteins have different shapes
They have different shapes because proteins have different functions
Primary structure
Linear sequence of amino acids, it looks like a chain held by peptide bonds
Secondary structure
Twisting of helix held by hydrogen bonds. Most common patterns are beta pleated sheet and alpha-helix
Tertiary structure
3D globular shape produced by the folding of the already coiled and folded chain of amino acids from 1 and 2 level structure of proteins.
Quartenary structure
More than one tertiary protein together into a globular mass
Denaturation
Process where a protein’s shape is altered causing it to lose its function
8 main protein functions:
- Mechanical support: Some proteins forms structural basis of cells, tissues, and organs (eg. Keratin found in skin cells and hair, and collagen found in almost all tissues)
- Movement: Some proteins change shape to allow movement (eg. Actin and myosin used in muscle contraction)
- Regulate metabolism: Some proteins act as hormones and cause regulatory effects on body systems (eg. Oxytocin produced by hypothalamus, and insulin used to lower blood sugar)
- Regulate body fluid pH: Some proteins act as acids or bases to buffer solutions (eg. Albumin and hemoglobin)
- Defend the body: Some proteins assist in fighting off organisms that invade the organism (eg. Antibodies)
- Transport: Some proteins carry molecules throughout the boy (eg. Hemoglobin transporting oxygen and CO2 in circulatory system)
- Molecular chaperone: Some proteins are essential to the production of other proteins and the appropriate breakdown of damaged proteins (eg. Heat-shock proteins produced in response to environmental stress)
- Catalytic action: Some proteins act as enzymes to speed up chemical reactions (eg. Salivary amylase used to break down starch into maltose)
Nucleotides and nucleic acids
Carry genetic blueprint of a cell and carry instructions for the functioning of the cell and contains a nitrogenous base, a pentose (5-carbon) sugar, and a phosphate group. The nitrogenous base is attached to the sugar and the sugar is attached to the phosphate group
2 main types of nucleic acids
DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) constructed from monomers called nucleotides
DNA
Found in the nucleus for genetic material found in all living organisms and directs protein synthesis and double stranded
RNA
Found in the cytoplasm (cell area outside nucleus) and carries out genetic instructions for protein synthesis and is single stranded
DNA structure
Double helix composed of alternating sugar and phosphate groups outside of each strand forming the backbone, and the nitrogenous bases stacked in the interior with the nitrogenous bases from one strand binding to those of the opposite strand held by hydrogen bonds forming base pairs
DNA bases
Adenine, guanine, cytosine, thymine
RNA bases
Adenine, guanine, cytosine, uracil
ATP (Adenosine tri-phosphate) (4):
- Important nucleotide not part of a nucleic acid
- It is composed of ribose sugar, adenine base and 3 phosphate groups
- High energy compound because the two covalent bonds linking its three phosphates store a significant amount of potential energy and the breaking of the bonds help fuel the body’s activities
- Powered by mitochondria
Phosphorylation
Addition of a phosphate group to an organic compound, in this case, resulting in ATP
