Biochemistry & Cells

Ap Biology

Atoms

• ________ are the basic unit of all matter. • An atom consists of 3 subatomic particles:

– The ________ which has a negative charge and orbits outside the nucleus

– The ________ which has no charge and is in the nucleus of the atom

– The ________ which is in the nucleus and is positively charged

• Atoms bind with each other to form ________

Molecules & Bonds • Molecules are groups of two or more atoms joined by

chemical bonds. • There are three types of bonds:

– ________ bonds- form between two atoms when one or more electrons are ________ from one atom to the other. It occurs because on of the atoms has a stronger pull on the electrons. The atom that gains an electron becomes more negative and the atom that loses the electron becomes more positive- we call these atoms that have charges ________ and they are attracted to each other because of their difference in charge (NaCl) .

Molecules & Bonds– ________ bonds- form when two atoms ________

electrons. The covalent bond can be ________ - where the electrons are shared equally (O2) or ________ -where the electrons are shared unequally (H20).Covalent bonds are the ________ type of bond.

– ________ bonds- are ________ bonds between molecules . They form when a positively charged hydrogen atom on one molecules is attracted to a negatively charged area of another molecule.

Properties of Water that make it important for living things

• ________ - many substances (any that are polar) dissolve in water (called ________ ). Substances that don’t dissolve in water (________ ) are nonpolar. This allows substances to be transported within the body and within cells using water.

• ______________water requires a lot of energy to gain or lose heat. This allows the temperature of large bodies of water to stay very stable. It also allows water to take a lot of heat with it whey you sweat, allowing for ________ _________

• ____________-Unlike most substances that contract and become more dense when they freeze, what expands and becomes more dense- allowing it to float. This allows it to stay on top of lakes and provide insulating during the winter time, rather than sinking to the bottom.

Properties of Water that make it important for living things

• Strong ________ -& high surface tension- Water molecules are attracted to each other because of the hydrogen bonds between them. This creates a high surface tension, creating a water surface that is firm enough to allow insects to walk on.

• Strong ________ -water molecules are also attracted to other substances, such as the walls of narrow tubing or

paper. This helps water to move up the stem of plants.

pH• pH is a measurement of the acidity of a substance. It is measured on

a scale from ________ .• An ________ substance is caused by a high concentration of hydrogen ions. The lower the number on the pH scale, the more acidic the substance. • A ________ substance is caused by a high concentration of hydroxyls- OH. The

higher the number on the pH scale, the more basic (or alkaline) a substance is. • When the number of OH and the number of H are equal, the bind to each other to

form water molecules and the solution is considered ________ . 7 is neutral on the scale.

Organic Molecules

• ________ molecules are molecules that have ________ atoms in them.

• In living things, large organic molecules, called macromolecules or biomolecules, make up cells.

• Macromolecules are polymers, that are made up of many ________ (subunits) repeated many times.

• There are four biomolecules: carbohydrates, proteins, lipids and nucleic acids.

Functional Groups

• Many organic

molecules have similar

properties because they

share similar clusters of

atoms, called ________

________.

Functional Groups• ________ : -OH polar, hydrophillic, many found in sugars• ________ : -COOH polar, hydrophilic, weak acid• Amino: -NH2 polar, hydrophilic, weak base, found in all

amino acids • ________ : -PO3 polar, hydrophilic, acid, found in DNA

nucleotides, phospholipids, and ATP, capable of transferring energy

• ________ : -CH3 nonpolar, hydrophilic, added to DNA to turn off (methylate) genes

• ________ : -COH or -CO polar, hydrophilic

Macromolecules• All macromolecules are built through the process of

________ ________ , also called a condensation reaction. Water is removed to joined the subunits. • All macromolecules are broken apart through the process of

________. Water is added to

snap the monomers apart.

Carbohydrates• Are classified into groups based on the number

of ________ (or saccharide) molecules present:

– _______________-have only a single sugar

molecule, such as fructose or glucose. Consists

of a carbon ring with many hydroxyl groups.

– ___________-consist of two sugar molecules joined by

a covalent bond called a ________ ________ . Example: glucose + fructose= sucrose (table sugar)

Carbohydrates• _________________- consist of a series of monosaccharides, can contain

thousands of them. • They have two main functions-

– Storage of ________ • Starch- stores energy for plant cells• Glycogen- stores energy for animal cells

– Forming ________ parts of organisms

• Cellulose- forms the cell walls of plants and is the major component of wood• Chitin- forms the exoskeleton• of insects and the cell walls of fungi

Lipids• Are all ________ (don’t dissolve) in water because they are nonpolar/hydrophobic. There are three major groups of lipids:

1. ________ -include fats, oils, and waxes. They

consists of three ________ ( a long chain of carbon and hydrogens with a carboxyl group

at one end) joined to a molecule called glycerol. The fatty acid tails are joined to the glycerol molecule through covalent bonds called ________ ________ .

Lipids• Fatty acid tails can be either saturated- where there are single

bonds between the carbon atoms in the tail or unsaturated- where there are one or more double bonds between the carbon atoms.

• A ________ fat is a solid at room temperature (butter and

lard) and an ________ fat

is a liquid at room temperature ( vegetable oil) • Unsaturated fats are “kinked”

Lipids________ have two fatty acids tails and a phosphate group

(instead of a third tail). • The tails of a phospholipids are hydrophobic and the head of the

molecule is hydrophilic. A molecule that has one end that is hydrophilic and one end that is hydrophobic is called

________ . • Phospholipids make up the cell membranes of cells in a bilayer

Lipids3. ________ -are characterized by a backbone

of four fused carbon rings. Examples include cholesterol (a component of the cell membrane) and certain hormones (such as testosterone and estrogen)

Proteins• Proteins have many different functions in organisms:

– ________ -such as keratin that form the hair and horns of animals; collagen in connective tissues; silk in spider webs

– ________ - casein in milk; albumin in egg whites; zein in corn seeds

– ________ - proteins embedded in the cell membrane that allow molecules to move in and out; hemoglobin that carries oxygen in red blood cells

– ________ - antibodies in animals that protect against foreign invaders

– ________ - proteins that regulate the rate of chemical reactions

Proteins• Are made up of subunits called

________ ________ that are joined by

covalent bonds called ________ bonds.• An amino acid consists of an a central carbon, bound to an amino group on one end, a carboxyl group on the other

end and then an “________ ” that varies from amino acid to amino acid• There are ____amino acids that join in different ways to build

proteins.

Proteins• Proteins have 4 levels of structure. • ________ structure- is the order of amino acids. • ________ structure- are repeated folding patterns held

together by hydrogen bonds. Are either alpha helixes or beta pleated sheets.

• ________ structure- three dimentional structure of the protein caused by the following factors: – Hydrogen bonding between R groups – Ionic bonds between R groups– Hydrophobic amino acids– Disulfide bonds- bonds between sulfurs in R groups

• ________ structure- a protein assembled from two or more separate peptide (protein) chains that are already folded into their tertiary structure.

Proteins

Proteins• When a protein loses its shape, we say that it has ________ • This can be caused by changes in heat, environment

(hydrophobic vs. hydrophilic) and chemicals. • When an egg is scrambled its proteins are denatured by

excessive heat.

• When a person chemically perms their hair the keratin protein

in the hair is denatured.

Nucleic Acids• DNA & RNA are nucleic acids. Their function is to store genetic

________. • Both molecules are made of

subunits called ________ . • A nucleotide consists of three parts- a phosphate group, a sugar (deoxyribose in DNA or ribose in RNA) and a base (either adenine, cytosine, guanine, thymine in DNA or uracil in RNA) • The bases in nucleic acids are named based on whether they

have one ring (________ ) or

two rings (________ )

Nucleic Acids• DNA is made of two strands that are ________ (they run

in opposite directions). These two strands are wound together into a shape called a double helix.

• The outsides of a DNA strand consist of sugar-phosphate ________ and in the center the bases pair A-T and C-G.

• The bases are held together by ________ bonds that can be easily broken when the DNA needs to be read to make a protein or to copy the DNA.

• The nucleotides are joined along the backbone through covalent bonds called ______________bonds.

Nucleic Acids

Nucleic Acids• RNA differs from DNA

in the following ways: – Sugar is ________ instead

of deoxyribose– There is no thymine,

but the base ________ instead– RNA is a ________ strand

and doesn’t form a double

helix shape

Chemical Reactions in Metabolic Processes

• In order for a chemical reaction to occur, there must be sufficient ________ ________ to trigger the formation of new bonds.

• ________ lower the activation energy required for a reaction to proceed. They act as catalysts.

• Metabolism is broken down into two types of reactions-– ________ reactions break down molecules and release

energy in the process (they are ________ -release energy)– ________ reactions build molecules and use energy to do so

(they are ________ -require energy)

Endergonic vs. Exergonic Reactions

Enzymes• Enzymes are proteins that act as ________ for reactions. • The ________ is the substance the enzyme acts on. For

example, the enzyme amylase breaks apart starch in your mouth- its substrate is starch.

• Enzymes are ________ to specific substrates. • Some enzymes need non-protein molecules to assist them so

they work- these molecules are called ________ or ________ .• Enzymes are not consumed by a reaction- they just help make

the reaction happen. • Enzyme efficiency is ________ by temperature and pH• Enzymes frequently have the suffix “________ ”

Enzymes

How Enzymes Work • The ____________model

describes how enzymes

work: – Enzymes have an

“________ ________”

made up

of a few amino acids

where a substrate

can bind.

Allosteric Enzymes• ________ enzymes are enzymes that have two kinds of binding sites- one

site for the substrate (the active site) and another site called the allosteric site that allows the enzyme to be controlled.

• Allosteric ________ bind to the allosteric site and stop the enzyme. Allosteric ________ bind to the allosteric site and turn the enzyme on.

• There are two basic ways an enzyme can be inhibited: – ___________ inhibition- the inhibitor molecule binds to the active site and

mimics the substrate. – _____________ inhibition- the inhibitor molecule binds to locations other

than the active site. • In ________ -the enzyme becomes more receptive to substrate molecules

when one substrate molecule attached. Example- when one molecule of oxygen binds to hemoglobin it encourages the molecule to bind to several more molecules of oxygen.

ATP • ATP provides ________ for your cells. It can be used, for

example, to drive reactions and to allow for movement of substances.

• ATP consists of an adenine molecule, a ribose molecule bound to three phosphate groups.

• To deliver energy for a reaction the last ________ group is broken off.

• When ATP has broken off a phosphate it is

called ________ .

Cells• Cells are the basic unit of all living things. • There are two types of cells:

– ________ cells- have a nucleus and organelles. These include animal, plant, and fungal cells.

– ________ cells- have no nucleus or organelles. These include bacteria.

• All cells share a few properties: – They all have ________ that carries their genetic

information– They all have a cell ________

The Plasma Membrane• The plasma membrane is primarily composed of a

________ bilayer. The

membrane is ________ ________ -it only allows some substances to move through freely. In particular, small, non-polar molecules can move through freely. • Embedded in the bilayer are other substances such as:

– ________ -which maintains the fluidity of the membrane – ________ -serve many different functions.

Membrane Proteins

Eukarytotic Cells• Eukarytotic cells have a variety of ________ - structures

that serve to physically separate processes within the cell.

Each organelle has a specific job.

Organelles • ________ -surrounded by the nuclear envelope. Contains DNA. Also

contains nucleoli- structures that make ribosomes. • ________ - make proteins. Some are free floating, others are attached

to the rough endoplasmic reticulum. • ________ -makes lipids and hormones• ________ ________ -flattened sacs that modify and package proteins

and lipids into vesicles that transport them. • ________ -vesicles that bud off of the golgi and contain digestive

enzymes. They break down cellular debris. They are not found in plant cells.

• ________ -are organelles that breakdown substances. They produce hydrogen peroxide (H202) in the process which is then converted to water. They are common in liver and kidney cells where they break down toxic substances and in photosynthesizing plant cells.

Organelles________ -carry out cellular respiration to make ATP. Chloroplasts- found in plant cells. Where photosynthesis occurs.

________, Microfilaments & Intermediate Filaments- protein fibers that establish the shape of a cell. Compose the cytoskeleton. Microtubules for the spindle in a cell that moves chromosomes during mitosis & meiosis.

________ & Cilia- structures that protrude from the cell membrane. Flagella are tails that allow a cell to swim (sperm). Cilia are more like hairs that beat- they are a found in the respiratory system and help to remove debris from your lungs.

________ /Centrosome- produce the spindle. Plants lack these.

Organelles• ________ -are found in pants, fungi, protists and bacteria.

Provide support for the cell and are located outside of the cell membrane. In plants its made of cellulose, in fungi its made of chitin- both are carbohydrates.

• ________ and Vesicles- are fluid filled membrane bodies: – Transport vesicles- move materials – Food vacuoles- temporarily store nutrients – Storage vacuoles- in plants, store starch – Central vacuoles- In plants, are large and in the interior of the cell-

are filled with fluid to put pressure on the cell to maintain its shape. – Contractile vacuoles- specialized organelles in single celled

organisms that pump out excess water

Cell Junctions• ___________ - proteins that attach animal cells to each other• ________ junctions- provide a water tight seal between two

animal cells• ________ junctions- are narrow tunnels that connect the

cytoplasm of two animal cells.

• ______________ - are narrow tunnels that connect two plant

cells.

Cell Transport• Cells need to move nutrients in and wastes out. In

general, there are two types of transport that occur: – ________ transport- requires energy from ATP to occur. – ________ transport- doesn’t require any energy. It can only

be used to move molecules along their concentration gradient (from a high concentration to a lower concentration)

• To compare the concentrations of different solutions we use the following terms: – __________ - has a higher solute concentration– __________ - has a lower solute concentration– __________- has the same solute concentration

Passive Transport• ________ - when molecules move from a high

concentration to a low concentration until they reach equilibrium (when both sides of the membrane are isotonic)

• ________ - when water molecules diffuse. Water will always move to the hypertonic solution to dilute it.

• ________ ________ - when molecules diffuse through a protein channel because they can’t pass through the cell membrane (either because they are too large or they are polar)

Active Transport• ________ - when a vesicle fuses with the cell membrane to dumptheir contents out of the cell. • ________ - when the cell captures substances from outside the cell by pinching in a piece of the plasma membrane to form a vesicle. • There are three types:

– ________ - when undissolved material enters the cell (cellular eating) – ________ - when dissolved enter the cell (cellular drinking) – ________ ________ endocytosis- when specific molecules bind to receptors to signal

to the cell to bring them in

Transport

Water Balance in Cells

Cell Division• There are two types of division that cells go through

to produce new cells: – ________ - occurs in body cells and produces two new,

diploid (two sets of DNA) genetically identical cells. It allows the body to grow larger and repair damage.

– ________ - occurs in germ cells (found in testes and ovaries) and produces four, haploid (only one set of DNA) genetically different cells. It is used only to produce gametes (egg/sperm)

• The life of all cells is describe by the ________ ________ .

Cell Cycle G1, S and G2 are collectively called ________ . This is when the cell is preparing to divide. Cell spend most of their time in interphase.

During s phase the cell ________ its DNA so that the new cell produced will have its own DNA.

Some cells, such as nerve cells, don’t divide and are in G0 phase.

Chromosomes• A chromosome that is unreplicated looks like a straight line, a replicated chromosome is an x shape. The two copies of the chromosome, called sister

________, are joined at a point called

the centromere.• During both mitosis and meiosis, chromosomes are moved by microtubules that

form a structure called the ________ . The spindle is made by ________ /centrioles.

• In a ________ cell, there are two copies of each chromosome. One copy came from the organisms mother and the other copy came from the organisms father. These two copies are called ________ chromosomes or homologues and will line up with each other during cell division.

Mitosis• Is broken into the following phases: – ________ - when the nuclear envelope breaks down, the

spindle forms– ________ - The chromosomes are lined up in the middle

of the cell by the spindle– ________ - The chromosomes are pulled to opposite

ends of the cell. The two sister chromatids are pulled apart.

– ________ - The nuclear envelope comes back- there are now two nuclei. Cytokinesis can occur- when the cell pinches in and divides into two new cells (the division of the cytoplasm and organelles). In animals a cleavage furrow forms and in plants a cell plate forms.

Mitosis

Meiosis• Consists of the following phases:

– Prophase I- nuclear envelope breaks down and spindle forms. Homologous chromosomes pair up in a process called synapsis to form a ________ (group of four sister chromatids). The homologous chromosomes then go through the process of ________ ________ , where they swap segments of DNA to make unique chromosomes.The site of crossing over on the chromosome is called the ________ .

– The rest of the stages proceed as they do in mitosis (metaphase, anaphase, telophase)

– Next, the two cells that are produced each go though a second round of division (prophase, metaphase, anaphase, telophase) but crossing over and interphase do not occur before the second round of division.

Meiosis

Nondisjunction• Sometimes the spindle fibers mess up when separating the

chromosomes during anaphase. • This can lead to cells being produced that have too many or too few chromosomes. • If this occurs during meiosis, and the gamete that is made is fertilized the resulting offspring May not survive or may have a genetic disorder,

Such as ________ ________ .