bio 30 oct exam
how many bonds can carbon form
four covalent bonds
H2O- Covalent or ionic, and electrons
..
H–O :
|
H
dashes represent shared pair or bond, dots are unshared lone pairs.
H2O is covalent.
in h2o, which element has a stronger attraction for the bond electrons
Oxygen has a stronger attraction for the bond electrons than hydrogen.
covalent bond
shares electrons
ionic bond
one atom gives electrons to the other.
how to tell if a bond is covalent or ionic
If a compound is made from a metal and a non-metal, its bonding will be ionic.
If a compound is made from two non-metals, its bonding will be covalent.
why is water polar?
it has a kinda positive side and a kinda negative side
why does water have positive and negative sides
Kinda positive because Hydrogen has a positive charge, and kinda negative becuase oxygen has a negative charge
why is water sticky
it is polar
example of polar and non polar
Water (H20)=polar
Air (NO)=non polar – equal sharing
glucose
C6H12O6 = C.H20
can h2o be individual molecules
H2O can be individual molecules, something like for example NaCl cannot
temperature
average kinetic energy of a substance
density equation
Density: amount/volume = gram/mc = stuff/space
very dense vs less dense
Very dense: lots of stuff/space
Less dense: less stuff/space
density of states of matter
Typically, gas is least dense, liquid is moderate, and solid is most dense
attraction of water states of matter
Gas- no attraction
Liquid- moments of attraction
Solid- attractive forces create a specific geometric arrangement, making space for hydrogen bonds between H2O molecules, pushing them farther apart– ice is less dense than water bc of these
how do lakes freeze
top-down, not bottom-up
Compare and contrast starch and cellulose. Discuss the digestion of these two substances
Starch is an energy-storage polysaccharide made of glucose subunits, commonly found in roots and seeds. It can form unbranched chains of up to 1,000 glucose units or branched chains with up to half a million glucose monomers.
Cellulose, also made of glucose, differs in its bond orientation, where every other glucose is "upside down." This structure gives cellulose strength, forming long, cross-linked fibers that resist tearing. It is a major component of plant cell walls and is more abundant on Earth than any other organic molecule.
While animals easily digest starch, only a few microbes, like those in cows or termites, can digest cellulose due to its unique bond structure, which animal digestive enzymes cannot break down. Microbes produce specific enzymes that can.
Discuss the use of polysaccharides in the structure of exoskeletons. Include which organisms have it; what makes it distinct from other glucose polysaccharides; and how it functions to provide structure.
The exoskeletons of insects, crabs, and spiders are made of chitin, a polysaccharide where glucose subunits are modified with a nitrogen-containing group. Chitin also stiffens the cell walls of fungi. Bacterial cell walls and lubricating fluids in joints contain other modified polysaccharides.
Like cellulose, chitin has alternating "upside down" glucose bonds, but with a nitrogen-containing group replacing a hydroxyl group. This tough, slightly flexible structure supports the soft bodies of arthropods and fungi.
molecules that include carbohydrates
Mucus, hormones, molecules in plasma membrane, nucleic acid
In what three ways are oils, fats, and waxes related?
(1) They contain only carbon, hydrogen, and oxygen; (2) they contain one or more fatty acid subunits, which are long chains of carbon and hydrogen with a carboxyl group (-COOH) at one end; and (3) they normally do not have ring structures.
draw the structure of glycerol
....H
H-C-OH
H-C-OH
H-C-OH
....H
LOOK UP THE DIAGRAM OF TRIGLYCERIDE DEHYDRATION SYNTHESIS
DO IT
Explain why fats are considered an efficient way for animals to store energy for the long term
Because fats store the same energy with less weight than do carbohydrates, fat is an efficient way for animals to store energy.
Distinguish between saturated and unsaturated fatty acids.
Fats have fatty acids with all single bonds in their carbon chains. Hydrogens occupy all the other bond positions on the carbons. it is "saturated" with hydrogens-it has as many hydrogens as possible. Lacking double bonds between carbons, the carbon chain of the fatty acid is straight.
If there are double bonds between some of the carbons, and consequently fewer hydrogens, the fatty acid is said to be unsaturated.
Consider some breakfast fats and oils; butter sits on the counter in block form, while cooking oil runs down the pan. Explain this difference.
Butter has mostly saturated fats, which are straight and pack closely together, keeping it solid at room temperature.
Oil has mostly unsaturated fats, which have kinks that prevent tight packing, making it liquid.
What are some uses of waxes? What properties of waxes give them the qualities to have these uses?
Waxes are chemically similar to fats. They are highly saturated, making them solid at normal outdoor tem-peratures. Waxes form a waterproof coating over the leaves and stems of land plants. Animals svnthesize waxes as waterproofing for mammalian fur and insect exoskeletons and, in a few cases. to build elaborate structures such as beehives
Outline the key chemical difference between a phospholipids and a triglyceride.
Triglycerides have three fatty acids. Phospholipids have two fatty acids plus a phosphate group. Triglycerides store energy. Phospholipids make up cell membranes.
How are steroids structurally different from other lipids.
All steroids are composed of four rings of carbon fused together, with various functional groups protruding from them. They do not contain fatty acids.
what do phospholipids look like
Polar head, non polar fatty acid tails.
phospholipids and water. 3 types
Phospholipids in water keep their head in and stick their legs out.
Phospholipids submerged in water create a micelle, a 3D ball with their legs in the middle that is limited in size
When the micelle starts to fill with water, they create a phospholipid bilayer- a 3D ball with heads on the outside and inside with their legs together. So, there is water outside the bilayer and inside, where it only touches the heads.
What forces are holding the phospholipid bilayer together
Hydrophobic and hydrophilic interactions. Its a love/hate relationship. Phospholipids squirm and wiggle around, they aren’t “cemented” by covalent/ionic bonds.
what does the phospholipid bilayer do
Phospholipid bilayer makes up cell membranes (boundary), allows for an internal and external environment. It is compared to a cantaloupe.
water properties
Important to living things, interacts with many other molecules, it is the polar nature of water that makes it a great solvent for many things, but not all. Can dissolve proteins, salts, and sugars.
Dissolving ionic compounds:
“Negative” pole surrounds positive ions
“Positive” pole surrounds negative ions
dissolving larger polar molecules with water
Water’s “positive” and “negative” poles are attracted to oppositely charged regions of dissolved molecules (hydrophilic things).
Important because many biological molecules including sugars and amino acids are hydrophilic and dissolve readily in water.
Non-polar (hydrophobic) molecules, such as fats and oils, usually dissolve
Water moderates the effect of temperature:
Organisms can survive only within a limited temperature range.
High temperatures damage enzymes/proteins that guide the chemical reactions essential to life.
Low temperatures are also dangerous because enzyme action slows as temperature drops
subfreezing inside is normally lethal, it ruptures membranes
Water forms an usual solid- ice, ice is less dense than liquid
Water molecules tend to stick together:
H bonds interconnect individual water molecules (between different water molecules), giving it high cohesive properties.
is h2o an h bond
no- it is covalent.
h bond
the force of attraction between molecules
intra vs inter
intra is within one molecule, inter is between two molecules
Key physical properties of water (3 types)
-High specific heat, the amount of heat it takes (the amount of energy in joules to raise the temp of a substance by 1 degree) to raise the temperature of something- some things take more than others
-High heat of vaporization (for water) meaning it takes a lot of energy to evaporate it. Sweating-liquid-vapour, all related to stickiness, used heat-cooling effect
-Very high heat of fusion, meaning it moves more slowly and gives off lots of energy to the environment.
This moderates the effects of low temperatures
Because lots of energy must be removed to form the precise crystal arrangement of ice
energy in water cooling and warming
Water warming up- lot of energy in bc its polar
Water cooling down- lot of energy out
Role of carbohydrates
-Important energy source Ex) stored in seeds, sugar in fruit
-Structural support Ex) for individual cells, bodies/organisms, and plants fungi bacteria and insects
Monosaccharides (one sugar) 7
Single unit of sugar
General formula- (CH2O)n
n= number of carbons in backbone
Take ring form in water
Glucose is the main example, Others include fructose and galactose
Some link to form chains in rna and dna
Ribose is 5 carbon sugar: CH2O)5 = C5H10O5
Linked sugars
Disaccharide (2 linked monosaccharides)
Trisaccharide (3 linked…)
Polysaccharide (many…)
Linkage is by dehydration synthesis (take out water, put together)
Disaccharide (two sugar) 5
Two linked single sugars
Short term energy storage (plants)
Ex. sucrose (glucose and fructose, lactose (glucose and galactose),maltose (glucose and glucose)
Polysaccharide (many sugar) 6
Chain of single sugars
Long term energy storage
Usually many glucose linked together
Starch (in plants): roots and seeds up to 100 long, branched, and coiled
Glycogen (in animals): stored in liver and muscles, branched, and shorter
Cellulose (in plants): special bond, strong unbranched structure, and abundent
dehydration synthesis
Dehydration synthesis is a type of chemical* reaction in which molecules of substances bond together to form more complex substances. Water (HO) is released in this type of reaction. For example, two molecules of glucose can join together, with the release of H2O, to form maltose, a double sugar.
hydrolysis
Hydrolysis is the breaking down of large molecules into smaller molecules. Water is used in a hydrolysis reaction. For example, maltose and water react to form two molecules of glucose.
Amino acids 7
Link together to from proteins
Sequence of links controlled by genes (dna)
Over 120 amino acids in a cell
Only 20 usually make up proteins (dna orders them)
Others have roles as intermediates in reactions, neurotransmitters, and hormones
Plants: can make all the amino acids they need from simpler molecules
Animals: must get some ready-made amino acids from their diet
Structure of amino acids
All have a central carbon
Common three attachments to it:
linkers(Amine group (nitrogen containing)
.......... (Carboxyl group (-COOH) make it act like a weak acid because it can give up H atom
A hydrogen atom (placeholder, fills gaps)
The fourth group R makes it structurally unique and gives it functional properties (how does it interact with others- chemical bridge, acidic, basic, hydrophobic, hydrophilic)
CO=acid NH=base
H........R.......O
...\.......|.......//
.....N--C--C
..../......|......\
H........H......OH
Polypeptide chain (string of amino acids) 4
Peptide bonds link amino acids together in long polymers called polypeptide chains- up to several hundred long
These may form part or all of a protein
They may have a function or may need to join others to perform a function
Polymer= linked together
Proteins
Proteins do their job when they are folded up into a 3D structure (affected by temperature and PH, the R group interactions result in the shape)
The 3D arrangement of the R groups of the chain of amino acids gives the protein its unique chemical properties to do its biological job
When a protein loses this precise structure (denaturation), it unusually cannot do its job
Classification of Protein
Primary structure- 1°
Secondary structure- 2°
Tertiary structure- 3°
Quaternary structure- 4°
Primary structure
Sequence of amino acid chain (polypeptide chain); the order of the amino acids
Secondary structure
Folded polypeptide chains (simple)
Two types: coiled (folding), and sheets (simple)
Tertiary structure:
Folding of the secondary structure into a complex and precise shape (3D)
Quaternary structure
Quaternary structure is the combination of two or more polypeptide chains, to form a complete unit
Not all reach this level
Example is hemoglobin
Structural Classification of proteins
Two categories- Fibrous and Globular
Fibrous proteins properties
Water insoluble
Very tough physically, may be supple or stretchy
Parallel polypeptide chains in long fibers or sheets
Fibrous proteins function
Structural role in cells and organisms
E.g. collagen found in connective tissue, cartilage, bones, tendons, and blood vessel walls.
Contractile (contracts)
E.g. myosin, actin
Fibrous example
Collagen is a fibrous protein that consists of three chains wrapped around each other
Globular proteins properties
Easily water soluble (3D)
Tertiary structure critical to function
Polypeptide chains folded into a spherical shape
Globular proteins function
Catalytic (speed up chemical reactions) e.g. enzymes
Regulatory e.g. hormones (insulin)
Transport e.g. hemoglobin
Protective e.g. antibodies
Enzymes 6
Most enzymes are proteins. Non example is ribosomes (rRNA)
They are capable of catalyzing (speeding up) biochemical reactions and are therefore called biological catalysts
Enzymes act on one or more compounds, called the substrate (surface organism is on)
They may break a single substrate molecule down into simpler substances, or join two or more substrate molecules chemically together
The enzyme itself is unchanged in the reaction; its presence merely allows the reaction to take place more rapidly
The part of the enzymes surface into which the substrate is bound and undergoes reaction is known as the active site
enzyme sites
The active site is made of different parts of polypeptide folded in a specific shape so they are closer together
For some enzymes, the complexity of the binding sites can be very precise, allowing only a specific kind of substrate to bind to it (3D)
Some other enzymes have lower specificity and will accept a wide range of substrates of the same general type (e.g. fatty acid chain). this is because the enzyme is specific for the type of bond involved and not an exact substrate
Enzyme structure
-Substrate molecule:
Substrate molecules are the chemicals that an enzyme acts on. They are drawn into the cleft of the enzyme.
-Active sites:
These attraction points draw the substrate to the enzyme's surface. substrate molecule(s) are positioned in a way to promote a reaction: either joining two molecules together or splitting up a larger one (as in this case)
-Enzyme molecule:
The complexity of the active site is what makes each enzyme so specific (i.e. precise in terms of the substrate it acts on)
How enzymes work
The lock and key modeI proposed earlier this century suggested that the substrate was simply drawn into a closely matching cleft on the enzyme molecule. More recent studies have revealed that the process more likely involves an induced fit, where the enzyme or the reactants change their shape slightly.
Metabolism
Catabolic reactions- Some enzymes can cause a single substrate molecule to be drawn into the active site. Chemical bonds are broken, causing the substrate molecule to break apart to become two separate molecules. Examples: digestion, cellular respiration.
Anabolic reactions- Some enzymes can cause two substrate molecules to be drawn into the active site. Chemical bonds are formed, causing the two substrate molecules to form bonds and become a single molecule. Examples: protein synthesis, photosynthesis.
Diffusion (partially permeable membrane)
Molecules constantly move randomly, causing them to spread from high to low concentration in a process called diffusion, which follows a concentration gradient. Diffusion and osmosis are passive, energy-free processes. In diffusion, molecules move freely across permeable membranes, with each type following its own gradient without affecting others. Partially permeable membranes allow some molecules to pass while blocking others. Diffusion plays a key role in exchanging substances with the environment and regulating cell water content. Example: perfume spreading through the air.
Osmosis occurs when water moves to balance concentrations when particles cannot
Concentration gradient
a measurement of how the concentration of something changes from one place to another.
Diffusion of Molecules Along Concentration Gradients (end result)
Diffusion is the movement of particles from regions of high to low concentration (the concentration gradient), with the end result being that the molecules become evenly distributed. In biological systems, diffusion often occurs across partially permeable membranes. Various factors determine the rate at which this occurs
Factors affecting rates of diffusion
-Concentration gradient: Diffusion rates will be higher when there is a greater difference in concentration
-The distance involved: Diffusion over shorter distances occurs at a greater rate than diffusion over larger distances.
-The area involved: The larger the area across which diffusion occurs, the greater the rate of diffusion.
-Barriers to diffusion: Thicker barriers slow diffusion rate.
-Pores in a barrier enhance diffusion.
Diffusion through Membranes (2 types)
Two way diffusion (unaided):
Each type of diffusing molecule (gas, solvent, solute) moves along its own concentration gradient. is common in biological systems, e.g. at the lung surface, carbon dioxide diffuses out and oxygen diffuses into the blood.
Facilitated diffusion:
increases the diffusion rate selectively. occurs when a substance is aided across a membrane by a special moleculed called a lonophore, which allow some molecules to diffuse but not others, speeding up rate of diffusion
Describe two properties of an exchange surface (membrane) that would facilitate (help) rapid diffusion rates
area, pore size
Identify one way in which organisms maintain concentration gradients across membranes
producing/consuming things, pump things across
Active and passive transport
Cells need to move materials in and out for metabolism. Raw materials and molecules needed for cell functions must be gathered from outside, often requiring effort if they are scarce. Waste products and molecules for other parts of the body must be exported. Some substances, like gases and water, use passive transport, which requires no energy. Other molecules, like sugar, are moved via active transport, which requires energy (ATP) and uses oxygen.
Passive transport 5 (what osmosis does)
-Does not require energy
-Moves from high to low
Types:
-Diffusion- molecules of liquids, dissolved solids, and gases are able to move into or out of a cell without any expenditure of energy. These molecules move because they follow a concentration gradient.
-Facilitated diffusion- same as regular diffusion, but has a carrier system. Diffusion involving a carrier system but without any energy expenditure
-Osmosis- water moves. Water can also follow a concentration gradient, across a partially permeable membrane, by diffusion. This is called osmosis. Osmosis causes cells in fresh water to puff up as water seeps in. this water must be continually expelled.
Active transport
Energy is expended (used) by the cell
3 types, 4 categories:
1) Ion pumps- move from low to high. Some cells need to control the amount of a certain ion inside the cell. Proteins in the plasma membrane can actively accumulate specific ions on one side of the membrane. Building up concentration against concentration gradient
2) Exocytosis- vesicles budded off from the golgi apparatus or endoplasmic reticulum can fuse with the plasma membrane, expelling their contents. Common in secretory cells e.g. in glands. Letting things out
3) Endocytosis:
Pinocytosis- ingestion of a fluid or suspension into the cell. The plasma membrane encloses some of the fluid and pinches off to form a vesicle. “Drinking.”
Phagocytosis- ingestion of solids from outside the cell. The plasma membrane encloses a particle and buds off to form a vacuole. Lysosomes will fuse with it to enable digestion of the contents. “Eating.”
the structure of membranes
All cells have a plasma membrane that forms the outer boundary of the cell. In bacteria, fungi, and plants, a distinct cell wall exists outside this membrane. In eukaryotic cells, membranes also surround organelles. The understanding of membrane structure has evolved through various studies. Initially, Davson and Danielli proposed the unit membrane model, where a lipid bilayer was coated with protein. This was later revised to reflect that proteins are embedded within the bilayer. The current accepted model is the fluid mosaic model.
cell membranes (all listed have membranes)
-The nuclear membrane that surrounds the nucleus helps to control the passage of genetic information to the cytoplasm. It may also serve to protect the DNA.
-Mitochondria have an outer membrane (O) which controls the entry and exit of materials involved in aerobic respiration. Inner membranes (l) provide attachment sites for enzyme activity.
-The golgi apparatus comprises stacks of membrane-bound sacs (S). It is involved in packaging materials for transport or export from the cell as secretory vesicles (V).
-The cell is surrounded by a plasma membrane which controls the movement of most substances into and out of the cell.
-phospholipids can move around
The Fluid Mosaic Model
The currently accepted model for the structure of membranes is called the fluid mosaic model. In this model there is a double layer of lipids (fats) which are arranged with their 'tails' facing inwards. The double layer of lipids is thought to be quite fluid, with proteins 'floating' in this layer. The mobile proteins are thought to have a number of functions, including a role in active transport
Cell or Plasma Membrane 2
1) Phospholipid bilayer
2) Proteins on, in, through, and under
The Role of Membranes in Cells
Many important cellular structures and organelles, such as the endoplasmic reticulum, mitochondria, nucleus, Golgi apparatus, chloroplasts, lysosomes, vesicles, and the plasma membrane, are composed of or enclosed by membranes. All eukaryotic cell membranes share the same basic structure as the plasma membrane. They perform critical functions, including compartmentalizing different cell regions, controlling substance entry and exit, and facilitating recognition and communication between cells.