Bio 311C Concept Map

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Biological Molecules: Key Terms

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par Kunnapa Yokluean

Comparing

par Nikina Bear-Lowen

BIO 311C Concept Map

par Long H Nguyen

Cellular Processes

DNA Replication

Three Steps of DNA Replication

DNA polymerase I removes the RNA bases from the 5' end

The primer begins the leading strand. The existing strand is now the template strand. DNA polymerase III begins putting down the new bases. The lagging strand is synthesized in okazaki fragments. DNA ligase puts together the okazaki fragments.

Initiation

Replication begins at the ORI, where helices begins to unwind the DNA. Topoisomerase releases tension ahead of the replication fork. The RNA primers are created to begin elongation.

Structure of DNA

Complementary Bases

Cytosine

Guanine

Thymine

Adenine

Semi-Conservative Nature of DNA

DNA was discovered to be Semi-Conservative though the experiments by Messleson and Stahl. Both strands of parental molecule separate and each template synthesizes a new, complementary strand.

Cell Division

Cell Communication

Cells Signal one another frequently to tell other cells to begin replication, beginning at the phospholipid-bilayer.

This involves the Phospholipid-bilayer; where signal molecules activate cellular process, beginning with the attachment to a receptor.

DNA Synthesis

Origin of Replication

the point in the DNA at which replication begins

Replication Fork

point at which the two DNA strands begin to separate for replication

Lagging Strand

Synthesizes in a direction away from the fork

Leading Strand

Synthesizes in a direction toward the replication fork

Enzymes of DNA and their Functions

Topoisomerase

Prevents DNA from "overwinding" by releasing tension ahead of the replication

Ligase

Connects fragments of DNA

DNA Pol I

Removes RNA primer and replaces it with DNA

DNA Pol III

Synthesizes new DNA strands by adding nucleotides to 3' end of RNA primer

Primase

Creates RNA primer and places one at 5' end of leading strand and several on lagging strand

Helicase

Unwinds parental double helix at replication forks

Gene Expression

RNA Modifications after Transcription in Eukaryotic Cells

RNA Splicing

During RNA processing, the introns are cut out and the eons are spliced together.

5' Cap and Poly A Tail

A 5' cap and a Poly A tail are added to the two ends of a eukaryotic pre-mRNA molecule in order to 1.) facilitate the export of mature RNA from the nucleus 2.) protect the mRNA from degrading 3.)help ribosomes attach to the 5' end of the mRNA when it is in the cytoplasm.

3 Steps of Transcription

Termination

The RNA transcript is release and the polymerase detaches from the DNA

Elongation

The polymerase moves downstream, unwinding the DNA and elongating the RNA transcript in 5' to 3' direction.

1. The initiation of Transcription

RNA polymerase binds to the promote, the DNA strands unwind, and the polymerase initiates RNA synthesis at the start point on the template strand

Eukaryotes

3. Other transcription factors bind to the DNA along with RNA polymerase II, forming the transcription initiation complex.

2. Transcription factors bind to the DNA before RNA polymerase II can bind to it.

1. The eukaryotic promoter has a TATA box which is a nucleotide sequence containing TATA.

3. Termination of Tranlastion

3.The two ribosomal subunits and the other parts dissociate.

2. The release factor promotes hydrolysis of the bond between tRNA in P site and the last amino acid. Therefore, it frees the polypeptide from ribosome.

1. A ribosome reached the stop codon and the A site of the ribosome accepts a "release factor".

An rRNA molecule of a large ribosomal subunit catalyzes the formation of a peptide bond. This step removes the polypeptide from tRNA in the P site and attaches it to the amino acid on the tRNA in the A site.

1. The Initiation of Translation

2. A large ribosomal subunit arrives to complete the initiation complex. The initiation factors are in charge of connection all the translation components. Hydrolysis of GTP gives off energy to the assembly. The initiator tRNA is in the P site while the A site is free for the tRNA who carries the next amino acid.

1. A small ribosomal unit binds to an mRNA molecule. Then, an initiator tRNA, with anticodon UAC, pairs with the start codon, AUG, which carries the amino acid methionine (Met).

Translation

Molecule of mRNA is moved in a ribosome where codons are translates into amino acids. tRNA molecules interpret each type of nucleotide in sets of 3. A tRNA adds its amino acid to a growing polypeptide chain once the anticodon hydrogen bonds to the complementary codon on the mRNA.

2. Elongation Cycle of Translation

3. Translocation

Ribosome translocates tRNA in the A site to the P site. The empty tRNA in the P site is moved to the E site where it gets released. The mRNA moves with its bound tRNAs, which bring the next codon to the A site so it can be translated.

2. Peptide Bond Formation

1. Codon Recognition

Anticodon of aminoacyl tRNA base pairs with complementary mRNA codon in A site. Hydrolysis of GTP is present in this step. The aminoacyl tRNA with the appropriate anticodon binds and proceeds with the cycle.

Cellular Components

Golgi Apparatus

Gives instructions to proteins and transports them

Endoplasmic Reticulum

Focuses on synthesizing protein (rough) and lipids (smooth).

Rough ER

Smooth ER

Ribosomes

Synthesizes proteins, made of RNA and proteins.

free or bound

proteins

Lysosome

A vesicle which breaks down molecules and recycles them.

Endocytosis

Pinocytosis

Phagocytosis

Receptor Mediated

Nucleus

The component of a cell which contains the genetic material of a cell.

Vacuole

Contains water or various liquids in the cell.

Food Vacuole

Central Vacuole

Cytoplasm

An aqueous solution where the cellular components reside in.

Cell Wall

A protective wall that is made from cellulose and chitin

Mitochondria

Supplies energy to the cell through various cellular processes

Phospholipid Bilayer

A membrane made up of two fatty acid tails and a hydrophillic head.

Glycerol

Fatty Acids (Fats)

Lipids

Present in plants, a layer of cellulose and chitin which protects the cell.

Triglycerides (Fats)

Unsaturated

Oils

Saturated

Cell Signaling

Membrane Receptors

Ion channel receptor

A membrane-bound receptor which undergoes a conformational change once the signal molecule attaches to the receptor. Allows for the passage of ions.

Tyrosine kinase receptor

Allows for the transfer of phosphate from ATP to the tyrosine kinase regions of a dimer, once a signal molecule binds to it.

G protein coupled receptor

A cell surface transmembrane receptor that works with the help of a G protein.

Types of Signal Molecules

Receptor on/in Cell (Plasma) Membrane

Hydrophobic Signal Molecule

Receptor in Cell Nucleus

Receptor in Cell Cytoplasm

Types of Cell Signaling

Long-Distance Signaling

Exocrine/Hormonal Signaling

Hormone must travel through the blood stream

Local Signaling

Synaptic Signaling

Neurotransmitters released which diffuses across the synapse, stimulating the target cell.

Paracrine Signaling

Involves direct signaling: affects nearby cells

3 Stages of Cell Signaling

Cellular Response: The transduced signal triggers a cellular response

Transduction: The receptor protein changes in some kind of way when the signaling molecule binds to it. The signal is conveyed to a form that can bring about a specific cellular response. Transduction usually occurs in a series of steps-signal transduction pathway.

AKA: Amplification (involves Second Messengers)

Reception: A signal molecule binds to a receptor protein located at the cell's surface.

Gene Regulation

Transcription Factors

Specific transcription ,like activators, lead to increased expression (high levels of transcription)

Distal control elements are enhancers that are located upstream or downstream of a gene

Activators bind to the enhancer sequence and bends the sequence

General transcription factors leads to low(basal) levels of transcription

Proximal control elements are sequences in DNA close to promoter

Transcription factors binds to the proximal elements and transcription is low level

allows RNA pol II to bind weakly

Repressor binds to the enhancer sequence and bends but prevents RNA poly II to bind

Tryptophan

When tryptophan is present, the repressor is active which means it can bind to the operator, operon is off

When tryptophan is absent, the repressor is inactivated which means it can't bind to the operator,operon is on

A negative regulator because it binds to a repressor

an amino acid

cAMP Levels

Lactose is present, glucose is present, cAMP levels are low and CAP is inactivated

Lactose is present, glucose is absent, cAMP levels are high and the CAP is activated

Operon is on!

Lactose is present, repressor is inactive(allolactose inactive the repressor), operon on

Operon is off!

Lactose is absent, repressor is on(repressor binds to the operator), opreron is off

Lac Operon

Lactose operon is an operon required for the transport and metabolism of lactose in bacteria.

Lac I is the lac repressor (regulatory gene)

Can switch off the operon when binding to the operator and it is active by itself.

Lac A adds an acidicyl group to lactose

Enzyme responsible is transacetylase

Lac Y takes in the lactose

Enzymes responsible is permase

Lac Z is a gene that forms mRNA

Enzymes responsible is galactosidase

Prokaryotes

Operator is not in Eukaryotes it is in Prokarytoes

Multiple genes are controlled by the same promoter.

In prokaryotes, genes are organized as operons.

DNA Packaging

The DNA is packaged with proteins in an elaborate complex known as chromatin (the basic unit of the nucleosome).

Histone core: a protein that bind the DNA twice

Nuclesomes are formed when the DNA wraps around the histones twice.

The looped domains coil further.

The 30-nm fiber forms looped domains that attach to proteins.

Interactions between nucleosomes cause the thin fiber to coil or fold into this thicker fiber.

The tight helical fiber needs help of the H1 which is outside the nucleosome.

Nuclesomes are strung together like beads on a string by linker DNA.

Only the H2A, H2B, H3, H4 form the histone core. The H1 is outside and not apart of the code.

Different types of Histones: H1, H2A, H2B, H3, H4

Think of "beads on a string"