DAT Booster: Biochemistry Chapter 2

What is matter?

Anything that has mass and takes up space

What is an atom and what is it made up of?

The smallest unit of matter and is made up of protons, neutrons, and electrons

What is a molecule and what is it made up of?

Group of 2+ atoms held together by chemical bonds

The chemical bonds are due to electron interactions between atoms

What is electronegativity?

The ability of an atom to attract electrons

Highly EN atom properties

The electrons are kept close to the nucleus

Low EN atom properties

Electrons are further apart from the nucleus

What is an ionic bond?

Complete transfer of electrons from one atom to another

Atoms with very different electronegativities

What is a covalent bond?

Sharing of electrons with atoms that have similar electronegativities

What is a nonpolar covalent bond?

Equal sharing of electrons with atoms that have identical electronegativities

What is a polar covalent bond?

Unequal sharing of electrons with atoms that have different electronegativities, which ends up forming a dipole

What is a hydrogen bond?

A weak bond that can form between bonds that have a hydrogen atom attached to a N, O, or F that is attracted to a negative charge on another molecule (N, O, or F)

- Can be within a molecule or between molecules

What is a van der Waals interaction?

A weak attraction rather than a true chemical bond. Due to the different distribution of electrons

Why is water an excellent solvent?

The dipoles of H2O break up charged ionic molecules

What is unique about water in its solid form?

It is less dense than its liquid form because the H-bonds become rigid and form a crystal that keeps molecules separated

What is unique about water's phase diagram?

It has a negative slope because ice is less dense than the liquid phase of water

What is cohesion?

Attraction between molecules of the same substance

Cohesion and water

Water is attracted to like substances due to its H bonds

Strong cohesion between H2O molecules produces high surface tension

What is adhesion?

An attraction between molecules of different substances

Adhesion and water

Water is also attracted to unlike substances because its polarity attracts it to substances that have charges

What is capillary action?

The ability of a liquid to flow without external forces

What are minerals?

Inorganic ions that the human body needs to function that are found both intracellularly and extracellularly

What are the functions of minerals?

Bone development, establishing electrochemical gradients for muscle and nerve function, component of hemoglobin in RBC's

What are vitamins?

Organic molecules that the human body needs to function

What are fat-soluble vitamins?

Deposited in the body fat and overconsumption can lead to toxic levels in the body

Vitamin A, D, E, and K

What are water-soluble vitamins?

Excesses are excreted in the urine

Vitamin B and C

What are the B vitamins?

8 in total

Are coenzymes or precursor to coenzymes in metabolic processes

What is the function of vitamin C?

Collagen synthesis which is connective tissue formation

Deficiency leads to scurvy

What is the function of vitamin A?

Visual pigmentation and epithelial maintenance

What is the function of vitamin D?

Aids in calcium and phosphorus absorption for bone health and is synthesized by the skin in the presence of sunlight

What is the function of vitamin E?

Antioxidant

What is the function of vitamin K?

Blood-clotting

What are macromolecules?

Large molecules formed from the bonding of smaller molecules

Types of monomers

monosaccharides, hydrocarbons, amino acids, and nucleotides

What is dehydration synthesis?

Dehydration synthesis is the process of joining two molecules, or monomers, together following the removal of water.

What is hydrolysis?

Hydrolysis is the separation of two macromolecules by adding water.

What are carbohydrates?

Macromolecules containing carbon, hydrogen, and oxygen that form sugars, starches, and fibers

Primary function is to store energy, can also be structural molecules

Monomer for carbohydrates

monosaccharides (simple sugars)

Polymer for Carbohydrates

polysaccharides

Bond type for carbohydrates

Glycosidic bond

What are monosaccharides?

A single sugar molecule (ex glucose, fructose and galactose)

What are disaccharides?

Two sugar molecules joined by a glycosidic linkage (ex maltose, sucrose, and lactose)

What are polysaccharides?

Series of connected monosaccharides (ex glycogen)

What is an alpha glucose?

The -OH group on carbon 1 is pointing below the plane

What is a beta glucose?

On the first carbon of the ring the OH group is on the top

What are alpha glycosidic bonds?

The sugars forming the covalent bond are both alpha glucose molecules (OH groups are both pointing down)

What are beta glycosidic bonds?

The sugars forming the covalent bond are both beta glucose molecules (one OH group forming the bond is pointing up, the other is pointing down)

What are examples of alpha glucose molecules?

Starch and glycogen which are both energy storage units

What are examples of beta glucose molecules?

Cellulose and chitin

What are lipids?

Macromolecules containing long hydrocarbon chains that form hydrophobic, non-polar molecules

What compounds are classified as lipids?

Fats, oils, steroid hormones, and phospholipids

What are the functions of lipids?

Insulation, energy storage, endocrine molecules, and structure

What is unique about lipids?

They do not contain a series of repeating units, so they are not true polymers made up of true monomers

Monomer for lipids

Hydrocarbons (ex fatty acid chain)

Polymer for lipids

Hydrocarbon chain (ex triglyceride)

Bond type for lipids

Covalent bond

What are the types of lipids?

Triglycerides, phospholipids, steroids, and porphyrins

What are triglycerides?

Composed of a glycerol backbone (3 carbon molecule) and 3 fatty acids (long carbon chains)

What is a saturated fatty acid?

Has no double bonds, forming straight chains)

This is the type of fatty acid that is bad for our health

What is an unsaturated fatty acid?

Contains double bonds, forming a branched structure

What is a phospholipid?

Composed of phosphate and glycerol head (hydrophilic) and 2 fatty acid tails (hydrophobic)

What are steroids?

Comprised of three 6-membered rings and one 5-membered ring

What are porphyrins?

Comprised of 4 joined pyrrole rings with a metal atom in the center

Hemoglobin and chlorophyll are porphyrins

What happens with cell membrane fluidity in cold weather?

Cell membrane becomes rigid. Cholesterol functions to add space and unsaturated fatty acids are incorporated to make membrane more fluid

What happens with cell membrane fluidity in hot weather?

Cell membrane becomes fluid and flexible. Cholesterol functions to restrict movement and saturated fatty acids incorporated to make membrane more stiff

What are proteins?

Polymers consisting of amino acids bound together via peptide bonds

Monomer for proteins

amino acids

Polymer for proteins

Polypeptide

Bond type for proteins

Peptide bond

Amino acid structure

Central carbon atom

Amino group

Carboxyl group

Single hydrogen

Variable R group

What is the function of proteins?

enzymes, signals, structural

What is the primary structure of proteins?

Sequence of amino acids connected by peptide bonds

What is the secondary structure of a protein?

3D shape resulting from hydrogen bonding between amino and carboxyl groups of adjacent amino acids

Forms alpha helices or beta pleated sheets

What is the tertiary structure of a protein?

3D folding pattern of a protein due to non-covalent side chain interactions between amino acid R groups

What forces interact in the tertiary structure of a protein?

H bonds, ionic bonds, hydrophobic interactions, and Van der Waals forces as well as disulfide bonds (covalent bonds)

What is the quaternary structure of a protein?

Protein consisting of more than one amino acid chain

What is denaturation of a protein?

When the 3D structure and native shape of a protein is lost due to external factors and reverts to its primary structure

What denaturing agents can denature a protein?

Temperature, pH, salt concentrations, UV light and chemicals

What are nucleic acids?

DNA and RNA which are polymers of nucleotides

What is the function of nucleic acids?

To store, transmit, and express genetic information

Monomer of nucleic acids

Nucleotide

Polymer of nucleic acids

nucleic acids

Bond type of nucleic acids

Phosphodiester bonds

What is a base pair?

Two nucleotides bonded together on opposite strands of DNA

What does an RNA nucleotide have?

Nitrogenous base (A, C, G, and U)

5 carbon sugar (ribose)

Phosphate group

What does a DNA nucleotide have?

Nitrogenous base (A, C, G, T)

5 carbon sugar (deoxyribose which means lacking oxygen group)

Phosphate group

What are the purines?

Adenine and Guanine

Remember the acronym PUR As Gold

What are the pyrimidines?

Cytosine, Uracil and Thymine

Remember the acronym CUT the PYE

What is the structure of the DNA backbone?

A chain of nucleotides on the same strand connected through covalent, phosphodiester bonds.

Bond is between phosphate group of one nucleotide and the 5 carbon sugar of an adjacent nucleotide

How are the base pairs connected?

Weak hydrogen bonds which forms the double stranded structure of DNA

2 H bonds between A+T

3 H bonds between G+C

What does 5' to 3' mean?

5' is the end of DNA with a phosphate, and 3' is the end with a deoxyribose sugar

What is Chargaff's rule?

The total number of purines is always equal to the number of pyrimidines in a double stranded nucleic acid

What is a nucleotide?

Nitrogen base + sugar (ribose or deoxyribose) and phosphate group

What is a nucleoside?

nucleotide without a phosphate group

What is a ribonucleoside?

5-carbon ribose sugar

Nitrogenous base (A, C, G, U)

What is a deoxynucleoside?

5-carbon ribose sugar

Nitrogenous base

one less OH group