dna

Chapter 6 - Molecular Biology of Bacteria

6.1 Macromolecules and Genes (You may have to look for some of these answers in Chapter 7 as well)

1.  What do we need to know if we are to understand the biology of microorganisms?

All genes are made up of deoxyribonucleic acid (DNA). It is transferred to the nucleus of a cell where they are located on chromosomes.

3.  Genetic information flow can be divided into 3 steps.  Summarize each.

Replication – " refers to the biological process where a cell creates an exact copy of its DNA molecule, ensuring that each new daughter cell receives a complete set of genetic information before cell division; this process involves unwinding the double helix, using each strand as a template to build a new complementary strand, resulting in two identical DNA molecules

 DNA helicase- unwinds, unzips and breaks the hydrogen bonds. Each has a different starting point 

Semi conservative- you have half of the original and half of the daughter. They spit and fill in so they are identical.

Lagging and leading strands- There is a lagging and leading strand. The leading strand lets the polymerase connect the bases together in one go. The lagging strand has to go section by section. The primer is put on the lagging strand, polymerase reads from the primer to the stopping point, primer is changed to DNA and ligase glues the DNA together on the lagging strand. 

DNA polymerase- 

1. Inserts the appropriate bases.

2. Proofreads

3. Make corrections

Transcription – the process by which a cell makes an RNA copy of a piece of DNA. This RNA copy, called messenger RNA (mRNA), carries the genetic information needed to make proteins in a cell. It carries the information from the DNA in the nucleus of the cell to the cytoplasm, where proteins are made. DNA transcribed into mRNA. Transcription is carried out by the enzyme RNA polymerase. 

Translation – In biology, the process by which a cell makes proteins using the genetic information carried in messenger RNA (mRNA). The mRNA is made by copying DNA, and the information it carries tells the cell how to link amino acids together to form proteins.

4.  What does RNA do?

Single stranded, Uses uracil (U) which binds with adenine (A), the sugar for RNA is ribose. RNA carries out a broad range of functions, from translating genetic information into the molecular machines and structures of the cell to regulating the activity of genes during development, cellular differentiation, and changing environments.

5.  During translation, we learn what a codon is.  What is it?

Codons are in groups of three. These are the parts of the mRNA to touch the DNA. THe tRnA brings the amino acid to the mRNA. The tRNA has anticodons at the bottom of them to connect them to the mRNA. After multiple amino acids are together, they form bonds called peptide bonds. A sequence of three consecutive nucleotides in a DNA or RNA molecule that codes for a specific amino acid. Certain codons signal the start or end of translation. These are called start or stop (or termination) codons.

6.  What is the genetic code?

The genetic code is a set of three-letter combinations of nucleotides called codons, each of which corresponds to a specific amino acid or stop signal.

7.  The tRNA has the amino acid and anticodon attached to it.

8.  When genetic information flows from nucleic acid to protein, it is known as the central dogma of molecular biology.  This is because all living organisms must follow this process.  All genetic and evolutionary processes come from here essentially.  

9.  How does prokaryotic DNA differ from eukaryotic DNA?

Prokaryotic DNA is typically a single, circular chromosome located in the cytoplasm, while eukaryotic DNA is organized into multiple linear chromosomes within a membrane-bound nucleus, often wrapped around histone proteins for compacting; prokaryotic DNA is also usually much smaller and lacks the complex regulatory elements found in eukaryotic DNA. 

10. What is an exon?  An intron?

An intron refers to non-coding sequences found in DNA or RNA. Exons refer to the coding portions of DNA or RNA. Introns are removed via RNA splicing, and exons are joined together to form coding sequences that produce proteins. Found in eukaryotic cells. 

6.2 The Double Helix

11.  Name that base.

A – Adenine

G – Guanine 

C – Cytosine

T – Thymine 

What makes a nucleotide Sugar, Phosphate and base are the three things that make a nucleotide. Phosphodiester bonds join nucleotides together. 

12.  What 2 things make up the backbone of DNA?  

• Made of alternating deoxyribose molecule and phosphate groups 

13.  What does it mean that DNA is complementary?

• Two strands of Dna are referred to as complementary because the sequence 

• of bases on one strand determines the sequence of bases on the other strand 

• A = T 

• C = G

14.  What does antiparallel mean?

• Dna strands are antiparallel run in opposite directions to each other one strand oriented 5’ and 3’ and one strand oriented 3’ and 5’ 

• Prunes: A and G 

• Pyrimidines : C and T 

15.  Compare long DNA to short DNA.

• Short highly accurate for small dna sequences 

• long allows for the study to complete genomes without fragmentation

16.  What is the role of DNA bending?

• Plays a crucial role in gene regulation particularly in transcription. It allows distant regions of DNA to come closer together through looping. 

• Controls gene expression levels

17.  What holds the 2 DNA strands together?

• Held together by hydrogen bonds formed between complementary base pairs. On opposite strands of the DNA molecule. A/T and C/G

18.  How can you melt DNA?

• Can be denatured through heat in a process similar to melting. Heat is applied until it unwinds itself and separated into two single stands. Once they are separate Dna cools down to its normal temperature.

19.  How does this relate to hybridization?

• Is the rebuilding of the strands after they have been melted apart allowing us to analyze the sequence between different DNA based on how easily they rehydrrible at certain temperatures.

Also make sure that you know the importance of phosphodiester and hydrogen bonds in DNA

6.3 Supercoiling (Look in Chapter 7, Section 1 for this as well)

DNA is wound around a protein called histones.  It forms a nucleosome when this happens.  When chromatin coils it becomes chromosomes.  

6.4 Chromosomes and Other Genetic Elements

21.  What is the genome?

A genome is the complete set of genetic information an organism carries, essentially all the DNA present in an organism's cells, organized into chromosomes, which provides instructions for the organism's development and functioning; it's like the entire instruction manual for an organism.

22.  Describe each in regards to genetic elements.

Virus – A virus's genetic elements refer to its nucleic acid, which can be either DNA or RNA, containing the genetic instructions necessary for the virus to replicate within a host cell; this genetic material is considered the core of the virus and is packaged within a protein coat called a capsid

Plasmids – are bacterial DNA molecules that are smaller than the chromosome(s). Generally, they are dispensable for bacterial growth at least under some conditions. Instead, they typically encode properties that allow growth or otherwise give the bacteria selective advantages under niche-specific conditions.

23.  How do plasmids differ from chromosomes?

Plasmids are small, circular DNA molecules that exist separately from the main chromosomal DNA, carrying non-essential genes that can replicate independently, while chromosomes are larger structures containing the essential genetic information for an organism and replicate as part of the cell cycle; essentially, plasmids are considered "extra" DNA that can provide additional benefits under certain conditions, unlike the vital genes carried by chromosomes.

Biotechnology- the ability to manipulate genes. 

Crispr- clustered regularly interspaced short palindromic repeats and is a restriction endonuclease enzyme that is responsible for genetically altering  a cell by affecting a segment of the selected genome. 

Cloning 0 the process where the genome of one organism is importied on another  predicting a genetically identical copy.

6.8 DNA Replication:  Templates and Enzymes

6.9 DNA Replication:  The Replication Fork

Read 6.8 and 6.9 and be able to summarize the process of DNA replication.  This will be discussed in class next week.

Restriction Enzymes and Hybridization (This information will be found throughout the textbook)

24.  What do restriction endonucleases do?

Restriction endonucleases are used by bacteria for self-defense against viral invasions. These bacterial enzymes recognize specific sequences that are not contained in the bacterial genome, so they are very effective at preventing the propagation of viruses that do contain the sequences.

25.  What does the gel electrophoresis process do?

is a laboratory technique used to separate mixtures of molecules like DNA, RNA, or proteins based on their size by applying an electric current through a gel matrix, causing the molecules to travel through the gel at different speeds depending on their size, allowing for their separation and analysis; smaller molecules move faster through the gel pores than larger ones

26.  DNA strands can be separated by “melting” them.  They can then hybridize.  Do you think this hybridization process is important?  Do you think it will play a big role in the future?  (Think about genetic engineering)

Biotechnology- 

6.12 Overview of Transcription

Protein Synthesis and Translation

Again, read all of this material and be able to summarize and take notes on these processes.  This information will be discussed in class.  (This means you should read and take your own notes here)

Protein synthesis is the process by which cells create proteins, occurring in two main steps: transcription and translation. This is the process in which cells create proteins based on the instructions encoded by the DNA. The first step being Transcription the DNA sequence is copied into a messenger RNA (mRNA) molecule in the nucleus. Second mRNA is read by ribosomes, which use transfer RNA (tRNA) molecules to bring the correct amino acids to the growing polypeptide chain. During translation initiation, elongation, and termination occur. In Initiation , the ribosome gets together with the mRNA and the first tRNA so translation can begin. Elongation is the process where amino acids are brought to the ribosome by tRNAs and linked together to form a chain. Finally in the termination stage the finished polypeptide is released to go and do its job in the cell. The fundamental reaction of protein synthesis is the formation of a peptide bond between the carboxyl group at the end of a growing polypeptide chain and a free amino group on an incoming amino acid.