BIO EXAM 2

Protos

Primary importance

Protein

part of every cell and a source of energy in your body, as it builds and repairs tissues, including your skin and muscle, and makes vital substances such as antibodies and insulin

Protein

Complex macromolecules made up of long chains of amino acids. All are constructed from a combination of only 20 types of amino acids

Essential amino acids (indispensable)

Our body cannot make them and must get them in diet. We cannot synthesize them on our own. (9/20 amino acids)

Non essential amino acids (dispensable)

Our body manufactures them when they have enough C, N, H, O (11/20 amino acids)

Complete amino acids

Includes all essential amino acids

Incomplete amino acids

Missing 1 or more essential amino acids

Essential amino acid examples

Isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine

Methionine

The very first amino acid in every protein synthesized from start codon AUG.

Enzymes

Speeding up chemical reaction

Hormones

chemical messengers

Antibodies

Protects us from foreign substrates

Fluid balance

pumping molecules across cell membranes and attracting water to maintain proper hydration levels in the body.

Transport many key substances

Carbon dioxide, vitamins, minerals to target cells throughout the body

Amino acid makeup

Have a central asymmetric carbon to which an amino group, a carboxyl group, a hydrogen atom, and a side chain (r group) are attached

Glycine

is the simplest amino acid, with a hydrogen atom as its side chain

Alanine

amino acid with a methyl group as its side chain

Valine

is a branched-chain amino acid with an isopropyl group as its side chain. (CH- CH3 & CH3)

Nonpolar aliphatic R group

amino acids that have side chains which do not interact favorably with water.

Polar uncharged R group

amino acids which have side chains containing hydroxyl or amide groups that can form hydrogen bonds with water.

Positively charged R group

amino acids which have side chains that hold a positive charge at physiological pH, allowing them to interact favorably with negatively charged molecules.

Negatively charged R group

amino acids which have side chains that carry a negative charge at physiological pH, enabling them to interact favorably with positively charged molecules.

Nonpolar aromatic R group

amino acids which have side chains containing aromatic rings that do not interact favorably with water and are generally hydrophobic.

Peptides

Amino acids link in specific sequences to form standards of protein up to hundreds of amino acids long

Dipeptide

2 amino acids

Tripeptide

3 amino acids

Oligopeptide

4-10 amino acids

Polypeptide

More than 10 amino acids

Dehydration synthesis

Peptide bond formation, the carboxyl group of one amino acid is linked to the incoming amino acids amino group; it releases a water molecule

Protein folding

The process by which a protein acquires its functional three-dimensional structure, determined by its amino acid sequence.

Primary structure

the sequence of amino acids that form one or more polypeptide chains (linear form) ex: cystine

Bovine serum insulin

Protein hormone comprised of two peptide chains (A-21 amino acids) (B-30 amino acids)

Cysteine

has a sulfhydryl group as a side chain and two sulfhydryl groups can react in the presence of oxygen to form a disulfide bond

Secondary structure

The alpha helix or beta sheet are structures of proteins that form because of hydrogen bonding between carbonyl and amino groups in the peptide backbone

Tertiary Structure

Amino acid helices/sheets that are folded over each other to form a three dimensional folding pattern of a protein due to side chain interactions. Some but not all proteins can become functional in three dimensional structures.

Types of chemical reactions for a tertiary structure

Hydrophobic interactions, ionic bonding, hydrogen bonding, and disulfide linkages

Quaternary structure

Two or more proteins associated with each other. All proteins are functional by this step.

Protein denaturation

an alteration in the three dimensional structure of a protein resulting in an unfolded polypeptide chain that usually lacks biological activity (destabilizing a protein’s shape). Caused by acids, bases, enzymes, heat, and others

Sick cell anemia

the hemoglobin beta chain has a single amino acid substitution, causing a change in protein structure and function (valine in the beta chain substitutes the amino acid glutamic). Dramatically decreases lie expectancy.

Change in protein structure and function

Change in nucleotide sequence of the gene’s coding region may lead to adding a different amino acid to the growing polypeptide chain

Hemoglobin molecules

form long fibers that distort the disc-shaped red blood cells and causes them to assume a sickle shape, which clogs blood vessels. Can lead to myriad serious health problems such as breathlessness, dizziness, headaches, and abdominal pain

Why are proteins important?

They serve vital functions in our cells from division to differentiation and everything in between, because enzymes in our digestive pathway are required to break down our food to acquire the nutrients we need to survive

Enzymes

proteins that catalyze (sped up) reactions in our body. Work like a lock and key and can be used to build molecules or break them apart

Enzymatic chemical reaction (dehydration synthesis)

A process where enzymes facilitate the joining of smaller molecules into larger ones while releasing water as a byproduct.

Enzymatic chemical reaction (hydrolysis)

A process where enzymes break down larger molecules into smaller ones by adding water, facilitating the release of energy.

Nucleic Acids

Located in nucleus of cell. They are the hereditary determinants of living organisms. Their elemental composition is carbon, hydrogen, oxygen, nitrogen, and phosphorus. They are polymers that consist of nucleotide residue.

Deoxyribonucleic Acid (DNA)

All living things are made up of cells, with this inside them. In eukaryotes, it resides in the nucleus. It is made up of 5 carbon sugar (deoxyribose), nitrogen base (Adenine, Thymine, Guanine, and Cytosine), and a phosphate (PO4) group. They are the material of inheritance and there are 3 million deoxyribonucleotides

Nucleotides

Long, thread like polymers made up of a linear array of monomers. Three components: pentose sugar, nitrogen base, phosphate residue.

Watson and Crick

Discovered DNA in 1953 by a series of experiments and concluded that DNA is the genetic material present in nucleus of cell and proposed the double helix model of its structure, which illustrated how DNA strands are complementary and held together by base pairing.

Genes

stretch of DNA that carries codes of protein production

DNA structure

Native DNA is an anti parallel double helix, the phosphate backbone is on the outside and the bases are on the inside. Each base from one strand interacts via hydrogen bonding with a base from the opposing strand. The strands are complementary but not identical.

Base pairs

Adenine (A) is always paired with Thymine (T) and Guanine (G) is always paired with Cytosine (C). A and G make purine and T and C make pyrimidine.

RNA

Single stranded and contains uracil (U) instead of thymine (T)

Chromosome

3 billion base pairs of nucleotides in every human cell and 23 chromosome pairs (46 total).

Somatic cells

Chromosomes 1 through 22, don’t include last chromosome which is for gender

Central dogma

process to synthesize amino acids from DNA. Replication (produces exact copy of DNA and occurs prior to every cell division. Transcription (converts a portion of double stranded DNA to a single stranded mRNA and occurs within the nucleus). Translation (converts mRNA code into one or more proteins and takes place in the cytoplasm.)

mRNA

DNA sequence information

tRNA

Helps elongate amino acids

Codon

Every three bases of RNA, each one corresponds to an amino acid.

Methionine

Start codon that always started the protein sequence.

Stop codon

ends the protein sequence (does not correspond to an amino acid)

Conservative hypothesis for DNA replication

The theory that during DNA replication, the two strands of DNA remain together and serve as templates for the formation of new complementary strands.

Semi Conservative Hypothesis for DNA replication

The theory that, during DNA replication, each of the two strands serves as a template for the formation of new strands, resulting in two identical DNA molecules, each containing one old and one new strand.

Random hypothesis for DNA replication

The theory that during DNA replication, the strands of DNA are not preserved but rather randomly reconfigured, resulting in a mix of old and new DNA segments.

Two methods to break down food in mouth

Mechanical: chewing with teeth, tongue, cheeks, hard palate. Chemical: salivary glands produce saliva which contains enzymes to break down food

Digestive Tract

(Input) Mouth → esophagus → stomach → small intestine (Duodenum, Jejunum, Ileum) → through the cecum to large intestine → anus (output)

Peristalsis

Propelling food forward; the muscles of the esophagus contract behind the food bolus. In front of the bolus, the muscles relax. This coordinated contraction and relaxation of muscles allows for the movement of food along the digestive tract.

Sphincter

Circular muscle whose contraction either opens or closes a passages (relaxed=open, contracted=closed). Examples: Mouth, entrance of stomach, exit of stomach, anus.

Esophagus

The muscular tube that connects the throat with the stomach. It transports food and liquids by coordinated muscle contractions known as peristalsis. It divides into the stomach or the trachea (for air) at a divider called the epiglottis.

Acid reflux

inappropriate relaxing of the lower esophageal sphincter, allowing stomach acids to rise into the esophagus.

Job of the stomach

Food storage (brief), digestion; mechanical and chemical, delivery of foods to the small intestine

Small intestine functions

Digestion, absorption of proteins, carbs, lipids, vitamins/minerals, water

Segmentation

Mixing and breaking down food into smaller pieces (segments). Only occurs in small intestine

Chemical digestion in small intestine

Enzymes break down macromolecules into their most basic units. Proteins → amino acids, carbs → monosaccharides, lipids → fatty acids + glycerol, DNA → nucleotides

Duodenum

First region of the small intestine that secrets these enzymes and also gets a supply of enzymes from the pancreas. Primary site for digestion.

3 Helpers of Digestion

Liver: produces bile (water and electrolytes, cholesterol, bile salts, lecithin, and pigments) gallbladder: stores and concentrates bile and delivers bile to the duodenum via the common bile duct. Pancreas: secretes enzymes, produces sodium bicarbonate, and delivers these products to the duodenum via ducts

Jejunum and ileum

Primary sites for absorption in the small intestine

Large intestine function

Absorbs any remaining water and or nutrients. Most of this work has already been done by the small intestine. Also stores waste material until defecation.

Small intestine folds

increase surface area for nutrient absorption.

Mechanical Digestion

Increase the surface area of food through physical processes like chewing and grinding.

Lumen

The space inside the intestine where digestion and absorption occur.

Surface Area

Increased SA of food helps enzymes gain access to macromolecules for digestion, increased SA of the small intestine allows for more opportunity to absorb vital nutrients, macromolecules, and water

Bile

Watery mixture primarily used to emulsify (break up) lipids in the small intestine. Mainly contains water, electrolytes, and cholesterol, also includes other emulsifiers. Lipids must be emulsified into small enough droplets for lipases to be able to digest them.

Colons

Ascending colon, transverse colon, descending colon, sigmoid colon are sections of the large intestine, responsible for absorbing water, electrolytes, and forming waste.

Microvilli

Tiny, finger-like projections on the surface of intestinal cells that increase surface area for nutrient absorption. They play a crucial role in enhancing the uptake of nutrients and minerals from digested food in the small intestine.