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Flashcards in Chapter 2: Molecular Biology Deck (142):
1

Organic Chemistry

chemistry of carbon compounds

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Anabolism

Building complex molecules from simpler ones. Ex: photosynthesis

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Catabolism

Breaking down organic molecules to release energy. Ex: cellular respiration

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4 groups of molecules

-carbohydrates, lipids, proteins, nucleic acids

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Insulin

protein hormone that facilitates the movement of glucose from the bloodstream to the interior of cells.

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examples of carbohydrates

-Monosaccharides (glucose, galactose, fructose, ribose)
-Disaccharides (maltose, lactose, sucrose)
-Polysaccharides (starch, glycogen, cellulose, chitin)

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Carbohydrate building blocks

Monosaccharides

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Lipids building blocks

Glycerol, fatty acids, phosphate groups

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Proteins (polypeptides) building blocks

Amino Acids

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Nucleic acids building blocks

Nucleotides

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examples of proteins

enzymes, antibodies, peptide hormones

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examples of lipids

Triglycerides: fat stored in adipose cells
Phospholipids: lipids forming a bilayer in cell membrane
Steroids: some hormones

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examples of nucleic acids

deoxyribonucleic acid (DNA), ribonucleic acid (RNA) and adenosine triphosphate (ATP)

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What are the factors determining whether a reaction occurs when two molecules collide

-identity of the colliding molecules
-orientation of the colliding molecules (where they hit each other)
-the speed of the molecules when they collide

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Enzymes

protein molecules that have a specific shape into which a reactant(s) can fit, at a molecular location called the active site of the enzyme. By having an active site, the enzyme increases the likelihood of a reaction

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Examples of reactions in our body

-replication of DNA, in preparation for cell division
-synthesis of RNA, allowing chemical communication between the nucleus and the cytoplasm
-synthesis of proteins, including bonding of one amino acid to another
-cell respiration, with nutrients being converted into ATP
-photosynthesis with light energy being used to create carbohydrates

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Example of catabolism and anabolism

when animals eat foods, food is digested into the building blocks (catabolism). After these building blocks are transported to body cells, they are bonded together to form larger molecules once again (anabolism).

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Hydrolysing

digesting

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Hydrolysis

A reaction involving the breaking of a bond in a molecule using water.

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Condensation reaction

A reaction in which two molecules combine to form a larger molecule, producing a small molecule such as H2O as a by-product

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Covalent bond

the bond formed by the sharing of a pair of electrons by two atoms.

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Hydrogen Bonding

Whenever 2 water molecules are near each other, the positive end of one attracts the negative end of another.

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ephemeral hydrogen bonding explains which variety of events

-why water forms into droplets when it is spilt
-why water has a surface tension that allows some organisms to "walk on water"
-how water is able to move as a water "column" in the vascular tissues of plants

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Adhesion

attraction between 2 unlikely molecules

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Cohesion

The binding together of alike molecules.

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Thermal properties of water

-high specific heat, water can absorb or give off a great deal of heat without chaining temperature very much
-high heat of vaporization, water absorbs a great deal of heat when it evaporates

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Water solvent properties

A liquid in which substances (or solutes) are dissolved forming a solution. Water is an excellent solvent of other polar molecules

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Hydrophilic molecules

molecules that are polar substances, "water loving"

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Hydrophobic molecules

non-polar molecules, "water fearing"

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Fatty acids

Any of the group of a long chain of hydrocarbon derived from the breakdown of fats (through a process called hydrolysis).

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Monomer

a molecule that can be bonded to other identical molecules to form a polymer.

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3 most common monosaccharides

-trioses, containing 3 carbons, C3H6O3
-pentoses, containing 5 carbons, C5H10O5
-hexoses, containing 6 carbons, C6H12O6

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Monosaccharides formula

CnH2nOn

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Functions of Cellulose (a polysaccharide)

Major component of plant cell walls, helps give rigidity/support to plant parts such as roots, stems and leaves

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Functions of Starch (a polysaccharide)

Organic products of photosynthesis are stored in plants as starch, typically as starch granules in chloroplasts or in plant storage areas such as roots or root structures

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Functions of Glycogen (a polysaccharide)

Animals store excess glucose in this form. Glycogen is stored in the liver and in muscle tissue.

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Two subcomponents of starch

Amylose and amylopectin

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Fatty acids structure

have a carboxyl group (-COOH) at one end and a methyl group (CH3-) at the other end. In between is a chain of hydrocarbons usually between 11 and 23

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Saturated fatty acids

the carbons are carrying as many hydrogen atoms as they can, in other words are saturated with hydrogen atoms. No double bonds.

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Monounsaturated fatty acids

If 1 double bond exists in the chain of hydrocarbons, it is no longer saturated, it has 2 empty spaces where hydrogen atoms could be. This unsaturated fatty acid is called monounsaturated.

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Polyunsaturated fatty acids

Have at least 2 double bonds in the carbon chain. 2 or more carbons are not carrying the maximum number of hydrogen atoms (2 or more carbons are double bonded to each other).

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Hydrogenation

the double bonds are eliminated by adding hydrogen atoms. It straightens out the natural bent shape of unsaturated fatty acids.

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Cis fatty acids

Naturally curved fatty acids. (omega-3)

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Trans fatty acids

hydrogenated straightened fatty acids, the result of chemical transformation in food-processing factories.

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Component molecules of triglyceride lipids

glycerol and 3 fatty acids

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Chemical strategies to store molecules in reserve to use for ATP

-storing glucose as the polysaccharide glycogen in liver and muscle tissues
-storing triglyceride lipids within adipose (fat) cells

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Glycogen

A branched polymer of glucose that is mainly produced in liver and muscle cells, and functions as secondary long-term energy storage in animal cells.

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Why are triglyceride lipids good for storing molecules

-can by hydrolysed into 2 carbon segments that can enter into cell respiration, have twice the energy content per gramme compared with other molecules
-long-term energy storage: insoluble in water and do not upset the osmotic balance if solutions

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Body Mass index (BMI)

a number that reflects both the weight and the height of a person

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How to calculate BMI

-using a formula, based on either metric or imperial measurements of weight and height (weight kg/ (height m x height m))
-using a graph known as nomogram
-using an online calculator

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Formation of polypeptides

-20 amino acids to synthesize polypeptides
-each polypeptide created under control of a gene

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Polypeptide

A polymer of amino acids joined together by peptide bond

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Which gene is universal

the genes that code for proteins involved in common cell cell functions (such as the protein components that make up ribosomes as all cells need ribosomes).

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Approximate number of active genes in humans

20 000 to 25 000 genes in each of our cells

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Amino Acids

The building block of protein in which each is coded for by a codon (A set of three adjacent nucleotides, the building blocks of nucleic acids like DNA and RNA) and linked together through peptide bonds (covalent bond joining amino acids).

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Rubisco protein function

the short hand name for the enzyme that catalyses the 1st reaction of the carbon-fixed reactions of photosynthesis

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Insulin protein function

A protein hormone produced by the pancreas that results in a decrease of blood sugar levels and an increase of sugar inside body cells

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Immunoglobulin protein function

Another name for an antibody that recognized an antigen as part of the immune system

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Rhodopsin protein function

a pigment found in the retina of the eye that is particularly useful in low light conditions

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Collagen protein function

the main protein component of connective tissue, which is abundant in skin, tendons, and ligaments

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Spider silk protein function

a fibrous protein spun by spiders for making webs, drop lines, nest building and other uses

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the 4 levels of organization to protein synthesis

primary, secondary, tertiary, quaternary

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Primary protein structure

the sequence of amino acids within the protein, this sequence determines the 3-dimensional shape

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Secondary protein structure

repetitive shapes as either a helix (alpha helix, spiral staircase shape) or a pleated sheet (beta sheet, a sheet with corrugated folds, such as spider silk)

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Tertiary protein structure

a shape often described as globular (enzymes)

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Quaternary protein structure

two or more polypeptides combined together to make a single functional protein (haemoglobin)

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Difference between Protein and Polypeptide

Protein is an organic substance consisting of covalently bonded amino acids, ready to carry out its function.
A polypeptide is a single amino acid chain with its own primary structure. it has a single c-terminal end and a single n-terminal end. If the single polypeptide is able to carry out its function as it is, then the polypeptide is considered to be a protein.

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genome

the specific DNA sequence that is unique to one individual

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proteome

the full complement of proteins that occur within a cell, tissue, or organism. Each individual has a unique set of proteins that he or she is capable of synthesizing.

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What does temperature do to the protein shape

When protein molecules are place into a temperature environment that is higher than their physiological favorable condition, the increased molecular motion puts a great deal of stress on the weak intra-molecular bonds. The primary structure remains intact but the hydrogen bonds cannot stay in place. The protein loses its three dimensional shape and function. A protein's function is directly dependent on its shape. As long as the covalent bonds remain intact, the protein will return to its normal shape when returned to normal temperature

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Endergonic

a process which absorbs energy

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exergonic

a process which releases energy

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Capillary action

water will move up xylem against gravity

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Surface tension

the surface of water is strong enough to support insects and causes drops to form

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Carbohydrate functions

Sugars (small molecules soluble in water):
-maintenance of osmotic balance
-transport of energy reserves
-energy substrate (respiration and photosynthesis)
-energy store (sugar cane)
-flavoring (fruits)
Polysaccharides (large molecules insoluble in water)
-osmotically inactive carbohydrate storage (seeds, roots, chloroplasts)
-structural (cellulose in plants)

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Lipid functions

-Structural: biological membranes (phospholipids, steroids, glycolipids), cushioning (fat deposits around the kidneys)
-Electrical insulation: myelin sheath round axons
-Thermal insulation: subcutaneous fat deposits
-Water proofing: waxes and oils
-Energy store and substrate: very condensed form of energy used by animals and seeds
-Hormones: steroids
-Vitamins: precursor to Vitamin D
-Buoyancy: oil droplets in plankton

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Polar amino acids

Are hydrophilic and tend to be placed outside of the protein

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Non polar amino acids

tend to be placed on the inside of the protein. Hydrophobic

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What does secondary structure produce?

Alpha helix and beta pleating

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Fibrous proteins

Involved in structure (tendons, ligaments, blood clots)
Contractile proteins in movement (muscle, microtubules)

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Globular proteins

Most proteins that move around, they are proteins with binding sites: enzymes, haemoglobin...

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the active site

A specific region of an enzyme where a substrate binds and catalysis takes place (binding site). The part of an enzyme or antibody where the chemical reaction occurs. A structural element of protein that determines whether the protein is functional when undergoing a reaction from an enzyme. this structural element will be accordingly shaped to the structure of the enzyme at work on it. Glove to a hand (glove active site and hand represents substrate or lock and key)

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Enzymes and their substrates

Specific to each other

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Activation energy of the reaction

enzymes lower the activation energy of reactions

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denaturation

A process in which the folding structure of a protein is altered due to exposure to certain chemical or physical factors (e.g. heat, acid, solvents, etc.), causing the protein to become biologically inactive.

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3 major examples of nucleic acids in nature

Adenosine Triphosphate (ATP), deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).

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Coenzymes

a non-protein compound that is necessary for the functioning of an enzyme.

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Polymers

a substance which has a molecular structure built up chiefly or completely from a large number of similar units bonded together

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Monomers

a molecule that can be bonded to other identical molecules to form a polymer.

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5 nitrogenous bases for RNA

Adenine (A), Uracil (U), Cytosine (C), Guanine (G)

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5 nitrogenous bases for DNA

Adenine (A), Thymine (T), Cytosine (C), Guanine (G)

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Sugar in nucleotides of DNA

pentose known as deoxyribose

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Sugar in nucleotides of RNA

ribose

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antiparallel

A term applied to two molecules that are side by side but run in opposite directions. The two strands of DNA are antiparallel. The head of one strand is always laid against the tail of the other strand of DNA.

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polymerase

an enzyme which brings about the formation of a particular polymer, especially DNA or RNA.

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Helicase

The enzyme that initiates this separation into two single strands. It begins at a point in or at the end of a DNA molecule, and moves one complementary base pair at a time, breaking the hydrogen bonds so the double-stranded DNA molecules become two separate strands.

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Transcription

Transcription is the process by which the information in a strand of DNA is copied into a new molecule of messenger RNA (mRNA).

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3 kinds of RNA molecule

mRNA (messenger RNA), rRNA (ribosomal RNA), tRNA (transfer RNA)

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mRNA

messenger RNA, each mRNA is a complementary copy of a DNA gene and has enough genetic information to code for a single polypeptide

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rRNA

ribosomal RNA, each ribosome is composed of rRNA and ribosomal protein

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tRNA

transfer RNA, each type of tRNA transfers one of the 20 amino acids to the ribosome for polypeptide formation

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anticodon bases

they determine which of the 20 amino acids is attached to the tRNA

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Translation

During translation, an mRNA sequence is read using the genetic code, which is a set of rules that defines how an mRNA sequence is to be translated into the 20-letter code of amino acids, which are the building blocks of proteins.

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triplet

any set of three bases containing enough information to code for one of the 20 amino acids.

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codon

when a triplet is found in a mRNA molecule it is called a codon

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The active site of a protein

A region on an enzyme that binds a protein during a reaction. The shape and the chemical environment inside the active site permits a chemical reaction to proceed more easily

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Substrate

The reactants that are activated by the enzyme. Enzymes are SPECIFIC to their substrates, which is determined by the active site

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Lock and key hypothesis

Fit between the substrate and the active site of the enzyme is exact. Temporary structure called the enzyme-substrate complex is former. Products have a different shape from the substrate, and are released from the active site free to become attached to another substrate

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Factors affecting enzymes

Substrate concentration, pH, temperature

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The effect of substrate concentration on enzymes

Increasing substrate concentration increases rate of reaction, at the optimum concentration of substrate molecules, all active sites are full and working at maximum efficiency

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Effect of pH on enzymes

Extreme pH levels will produce denaturation. Structure of the enzyme will change, the active site is distorted and substrate will not fit in. Ionization change when pH values are slightly different from the optimum value, which will affect the binding of the substrate with the active site.

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Essay questions about enzymes?

Enzyme amylase, substrate starch and products glucose

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Activation energy

The amount of energy that must be put into a reaction to make it occur

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What happens when an enzyme goes through a conformational change in the active site to fit the substrate?

An enzyme stresses the bonds in the substrate, reducing the activation energy required for a reaction to occur

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Denaturation

Denaturation is changing the structure of a protein (enzyme) so that it cannot carry out its function (by pH or temperature)

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Why do high temperatures cause denaturation?

The extra energy leads to increased vibration, breaking intra-molecular bonds

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Why do changes in pH cause denaturation?

Hydrogen bonds are broken

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DNA

Deoxyribonucleic acid

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DNA characteristics

-a double helix
-each strand is made of single units called nucleotides
-it has a sugar-phosphate backbone
-bases join the two strands by hydrogen bonds

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Bases

Cytosine, guanine, adenine and thymine

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Basic unit of DNA

Nucleotide

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Polarity

The property of water produced by unequal sharing of electrons

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What kind of bonds join a strand of nucleotides?

Covalent bonds as they are very strong

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Complementary base pairing

A pairs with T and G pairs with C

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Anti-parallel

The two strands run in opposite directions

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Codon

A sequence of three DNA or RNA nucleotides, called a triplet

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Exons

Coding regions with eukaryotic cells

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Introns

Non coding regions which are edited out (junk DNA)

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Genome

The complete set of genes in an organism

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DNA helicases

They separate double-stranded DNA into single strands allowing each strand to be copied during replication.

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DNA polymerase

It collects free nucleotides and attached to the new strand by complementary base pairing.

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Transcription

RNA polymerase makes a mRNA molecule that is complementary to the DNA

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mRNA

A message from the nucleus to the ribosome, instructions for how to put the polypeptide together.

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Genetic code

Sequence of bases on mRNA

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Translation

mRNA is posted out of the nucleus and attaches to the ribosomes. Ribosomes use complementary base-pairing to read codons on the mRNA. tRNA molecules with corresponding anti-codons bring the correct amino acid.

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Anticodon

A sequence of three nucleotides forming a unit of genetic code in a transfer RNA molecule, corresponding to a complementary codon in messenger RNA.

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Cellular respiration

The process by which cells break down glucose to release energy in the form of ATP

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Anaerobic respiration

A form of cellular respiration that occurs when oxygen is absent or scarce. Alcoholic fermentation or lactic acid fermentation

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Aeorobic respiration

A form of cellular respiration that requires oxygen in order to generate energy, generates more ATP than anaerobic.

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Glycosis

Glucose is broken down into two pyravute molecules. 4 ATP molecules generated, net gain is 2 ATP since 2 needed to get started

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Photosynthesis

A light-dependent, anaerobic mode of metabolism by which CO2 and water are used to make sugar. O2 is a waste product.

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Pigment in chloroplasts found in plants

Chlorophyll