Biol 190 Unit 2 Lecture 7

What is a gene?

DNA sequence that encodes a specific protein

What is a genome?

Complete set of DNA in a living organism

How many genomes does every living organism have?

1 genome

Identify the macromolecule, polymer, monomer, and building block of monomer.

Macromolecule: nucleic acid

Polymer: polynucleotide (ex. DNA and RNA)

Monomers: nucleotide

Building block of monomer: sugar, phosphate, and base

What are the biological uses of DNA?

\-Permanent storage of genetic information

\-stored in the chromosomes

\-transmission of genetic info

What are the biological uses (roles) of RNA?

Temporary; Transmits the genetic information from DNA to the protein synthesizers in the cell

Together, what do DNA & RNA do?

Use the genetic information to direct the creation of new proteins

What are the building blocks of nucleotides?

1. Nitrogenous base
2. A five-carbon sugar (ribose or deoxyribose)
3. Phosphate (mono, di, or tri) group

What are the two classes for the five nitrogenous bases?

Pyrimidine (single rings): Cytosine, Thymine (unique to DNA), Uracil (unique to RNA); Purines (double ring): Adenine, Guanine

What are the two sugars of nucleotides?

1. Deoxyribose (in DNA)- without oxygen 2. Ribose (in RNA)

What type of monomer is this? Identify its name.

Nucleotide; ATP (Adenosine TriPhosphate)

What is ATP?

Multifunctional: Builds nucleic acids (DNA & RNA) & energy source for cells

Which part of the nucleotide is rich with potential energy?

Phosphate functional group (5 covalent bonds)

How is energy released from ATP?

Remove a phosphate group (breaks the bond between a phosphate group)

What molecule is this?

ADP (Adenosine Diphosphate)

What molecule is this?

AMP (Adenosine Monophosphate)

Which monomer has the least energy out of ATP, ADP, and ADP? Which monomer has the most?

ADP; ATP

What is a nucleoside?

Nitrogenous base + sugar

What is a nucleotide?

Nucleoside + phosphate group

DNA and RNA have \____________

Directionality

What is the beginning of a polynucleotide called? What is the end called?

5' end; 3' end

Where does the beginning and end of a polynucleotide come from?

5' \= fifth carbon on sugar; 3' \= third carbon on sugar (has a free hydroxyl group attached)

What direction are nucleic acids synthesized?

5' to 3' direction

How is a nucleotide linked to form a polynucleotide?

Remove water (dehydration reaction) from OH from 3' end and OH from phosphate group

What is the covalent bond that holds polynucleotides together?

Phosphodiester bonds

What do the covalent bonds between the sugar and phosphate of monomers form?

Strong, stable sugar-phosphate backbone

What are the attributes of DNA vs. RNA?

\-DNA: double-stranded, deoxyribose sugar (lacks an oxygen), Thymine

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\-RNA: single-stranded, ribose sugar, Uracil

What is the shape of DNA?

Double helix- two DNA strands coil around each other

What is the complementary base pairing?

Adenine pairs with Thymine (Apple Trees)

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Cytosine pairs with Guanine (Chewing Gum)

How are nitrogenous bases held together?

Hydrogen bonds

Why does uracil not have a complementary base pairing?

Uracil is unique to RNA; RNA is single-stranded

What are the properties of a DNA double helix?

\-DNA strands are antiparallel

\-DNA has polarity (head is different from the tail)

\-complementary strands

\-there are base stacking interactions

\-hydrogen bonds hold together the two strands (can be broken to unzip the DNA)

Where does the stability of DNA come from?

Covalent bonds of the sugar-phosphate backbone

What force holds the 2 strands of DNA together?

Hydrogen bonds

What force holds the 1 strand of DNA together?

Covalent bonds

Why would you want to unzip the bonds between 2 strands of DNA?

To make proteins (so cell can see the instructions from the unzipped DNA); DNA is zipped back to protect itself

What are the three types of RNA?

mRNA, rRNA, and tRNA (all are involved in gene expression)

What is the first type of RNA?

Messenger RNA (mRNA)- temporary copy of the gene (the instructions)

What is the second type of RNA?

Ribosomal RNA (rRNA)- site/location of gene expression

What are ribosomes made of?

Proteins and ribosomal RNA

What is the third type of RNA?

Transfer RNA (tRNA)- carries around amino acids needed to make proteins

What is the central dogma of molecular biology?

1. Replication (DNA-> DNA)- entire DNA double helix is duplicated
2. Transcription (DNA->RNA)- information to produce a single gene is copied
3. Translation (RNA->Protein)- Functional protein is made

Does all of the DNA go through gene expression?

No, just a gene from DNA will go through transcription to make mRNA; mRNA goes through translation to make proteins

Identify the macromolecule, polymer, monomer, and building block of monomer.

Macromolecule: Proteins

Polymer: polypeptides

Monomers: amino acid

Building block of monomer: C-H, Amino, Carboxyl, (20) R groups (side-chains)

What is the most common macromolecule?

Proteins

What are the eight protein functions?

1. Enzyme
2. Defensive proteins
3. Storage proteins
4. Transport proteins
5. Hormonal proteins
6. Receptor proteins
7. Contractile and motor proteins
8. Structural proteins

Name the function and example of the first type of protein.

Enzymes:

\-Function: Selective acceleration of chemical reactions

\-Example: Digestive Enzymes

Name the function and example of the second type of protein.

Defensive proteins:

\-Function: Protection against disease

\-Example: Antibodies

Name the function and example of the third type of protein.

Storage proteins:

\-Function: Storage of amino acids

\-Examples: Casein, milk protein; Ovalbumin (egg white)

Name the function and example of the fourth type of protein.

Transport proteins:

\-Function: Transport of substances; transporters across cell membranes

\-Examples: Hemoglobin, iron-containing protein in RBC

Name the function and example of the fifth type of protein.

Hormonal proteins:

\-Function: Coordination of life activities

\-Example: Insulin, pancreatic hormone

Name the function and example of the sixth type of protein.

Receptor proteins:

\-Function: Cell response to stimuli

\-Example: Receptors built into nerve cell membranes detect signaling molecules released by other nerve cells

Name the function and example of the seventh type of protein.

Contractile and motor proteins:

\-Function: Movement

\-Example: Motor proteins allow movement of cilia and flagella

Name the function and example of the eighth type of protein.

Structural proteins:

\-Function: Support

\-Example: Keratin is the protein of hair, horns, feathers, etc.; collagen and elastin

What are polypeptides?

Polymers built from amino acid monomers

What does a protein consist of?

One or more properly folded polypeptides; proteins are made by stringing together 20 different amino acids

What is an attribute of amino acids?

All amino acids have the same structure except for the R group

How many amino acids are there?

20 different amino acids

What are the rules to identifying whether an amino acid is hydrophobic or hydrophilic?

1. Find one polar covalent bond in the R group (one PCB makes the entire amino group polar); polar= hydrophilic
2. Charged= hydrophilic

Define essential amino acids

Essential- something your body cannot synthesize for itself; must be consumed; amino acids (8) that must be consumed

How is an amino acid linked to form a polypeptide?

Place a backbone next to another backbone-\> Remove water (dehydration reaction) from OH of carboxyl group and H of amino group

What is the covalent bond that holds polypeptides together?

Peptide bond

What is the backbone of a polypeptide?

Amino group, carboxyl group, C-H

Does a polypeptide have directionality?

Yes, so does DNA and RNA

What is the beginning of a polypeptide called? What is the end called?

N-terminus (free amino group NH2); C-terminus (free carboxyl group )

What are the four levels of folding for protein structure?

Primary, Secondary, Tertiary, Quaternary

What is the first level of protein structure?

Primary: the unique sequence of amino acids bonded together by covalent peptide bonds

What is the second level of protein structure?

Secondary: stabilized by hydrogen bonds within the backbone; Two types: 𝛂 helix and pleated sheet

What is the third level of protein structure?

Tertiary: first time using R groups, polar amino acids are exposed to water while nonpolar amino acids form the inside

What do proteins have?

A 3D shape (all using R-groups)

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Bonds involved:

Hydrogen bonds, hydrophobic interactions, van der Waals interactions, ionic bonds, disulfide bridges

What is protein folding?

An energy independent process; usually to the most energetically favorable structure

What is the fourth level of protein structure?

Quaternary: 2 or more polypeptides that interact together to make a functional protein (e.g. hemoglobin)

What are chaperonins?

Proteins that aid the proper folding of other proteins (protection)

What is a denatured protein?

Secondary, tertiary, quaternary structure bonds broken due to change in: pH, salt content, temperature, and high concentrations of polar or nonpolar substances

Is a denatured protein active or inactive?

Inactive

What is renaturation?

When the denaturant (e.g. heat) is removed, proteins can refold to the correct structure

What is X-ray crystallography?

Method used to determine 3D structure of protein