AP Biology Unit 6 Gene Expression and REgulation

Vocab from Unit 6 of AP Biology Gene Expression and Regulation

Nucleotide

This is the basic building block of nucleic acids (RNA and DNA). A nucleotide consists of a sugar molecule (either ribose in RNA or deoxyribose in DNA) attached to a phosphate group and a nitrogen-containing base.

The bases in DNA are: Adenine, bonding to Thymine; and Guanine, bonding to cytosine

The bases in RNA are: same as DNA but Uracil takes the place of thymine.

Purine

This a nitrogenous base with a double ring structure, consisting of a six-membered ring fused with a five-membered ring. In other words, it has 2 nitrogen-containing rings. They are larger then pyrimidines

Examples: Adenine and Guanine

Pyrimidines

These are nitrogenous bases with a single six-membered ring structure. These are smaller than purines.

Examples: Cytosine, Thymine, and Uracil

Plasmids

These are small, circular, double-stranded DNA molecule that is distinct from a cell's chromosomal DNA. They naturally exist in bacterial cells, and they also occur in some eukaryotes. Often, the genes carried here provide bacteria with genetic advantages, such as antibiotic resistance.

Polypeptide

This is another word for a strand of amino acids. Although many proteins consist of a single BLANK, some are made up of multiple. Genes that specify BLANKs are called protein-coding genes.

DNA Polymerase

This synthesizes DNA by adding nucleotides one by one to a growing chain. The enzyme always needs a template and adds on to the 3’ end.

The enzyme even proofreads the work to see if it is correct, removing most of the incorrect nucleotides.

DNA Polymerase I

• Removes RNA primers and replaces them with DNA

• Fills gaps in DNA that occur during replication, repair, and recombination

DNA Polymerase II

• Proofreads and edits DNA, mainly in the lagging strand

• Repairs damaged DNA strands

• Catalyzes the repair of nucleotide base pairs

DNA Polymerase III

• The main enzyme responsible for replicating DNA in bacterial cells 

• Extends primers to make the bulk of the new DNA

DNA Ligase

This seals the gaps between DNA fragments after the RNA primers are replaced.

DNA Helicase

This catalyzes the disruption of the hydrogen bonds that hold the two strands of double-stranded DNA together.

aka it opens up the DNA at the replication fork.

DNA Primase

This primes DNA synthesis (gets it started). It makes an RNA primer, or short stretch of nucleic acid complementary to the template, that provides a 3' end for DNA polymerase to work on. A typical primer is about five to ten nucleotides long.

Leading Strand

The strand that runs in the 5' to 3' direction in the replication fork is referred to as the leading strand. This strand is continuously synthesized.

Lagging Strand

Is one of two strands of DNA found at the replication fork, or junction. This strand requires a slight delay before undergoing replication, and it must undergo replication discontinuously in small fragments (Okazaki Segments).

Sliding Clamp

This is a protein that helps out in DNA replication and holds DNA polymerase III molecules in place as they synthesize DNA. It is a ring-shaped protein and keeps the DNA polymerase of the lagging strand from floating off when it re-starts at a new Okazaki fragment.

Topoisomerase

This is an enzyme that assists in DNA replication. This enzyme prevents the DNA double helix ahead of the replication fork from getting too tightly wound as the DNA is opened up. It acts by making temporary nicks in the helix to release the tension, then sealing the nicks to avoid permanent damage.

Gene Expression

the process by which the information encoded in a gene is turned into a function. This mostly occurs via the transcription of RNA molecules that code for proteins or non-coding RNA molecules that serve other functions.

Transcription

This is the first step in gene expression. The goal is to make a RNA copy of a gene's DNA sequence. For a protein-coding gene, the RNA copy, or transcript, carries the information needed to build a polypeptide (protein or protein subunit).

This is performed by RNA polymerases and occurs in 3 steps, initiation, elongation, and termination.

RNA Polymerase

This is the enzyme responsible for copying a DNA sequence into an RNA molecule by adding complementary nucleotides to the growing RNA strand, essentially acting as the main catalyst for the process of transcription.

Specifcally, it builds an RNA strand in the 5’ to 3’ direction, adding each nucleotide to the 3’ end.

Transfer RNA

These are molecular "bridges" that connect mRNA codons to the amino acids they encode. One end of each BLANK has a sequence of three nucleotides called an anticodon, which can bind to specific mRNA codons. The other end of the BLANK carries the amino acid specified by the codons.

Ribosomes

These are the structures where polypeptides (proteins) are built. They are made up of protein and RNA (ribosomal RNA, or rRNA). Each one has two subunits, a large one and a small one, which come together around an mRNA.

They provide a set of handy slots where tRNAs can find their matching codons on the mRNA template and deliver their amino acids. These slots are called the A, P, and E sites. Not only that, but the BLANK also acts as an enzyme, catalyzing the chemical reaction that links amino acids together to make a chain.

Initiation

The ribosome assembles around the mRNA to be read and the first tRNA (carrying the amino acid methionine, which matches the start codon, AUG). This setup, called the initiation complex, is needed in order for translation to get started. is the first step of transcription.

RNA polymerase binds to a sequence of DNA called the promoter, found near the beginning of a gene. Each gene (or group of co-transcribed genes, in bacteria) has its own promoter. Once bound, RNA polymerase separates the DNA strands, providing the single-stranded template needed for transcription.

Elongation

This is the second step of transcription. One strand of DNA, the template strand, acts as a template for RNA polymerase. As it "reads" this template one base at a time, the polymerase builds an RNA molecule out of complementary nucleotides, making a chain that grows from 5' to 3'. The RNA transcript carries the same information as the non-template (coding) strand of DNA, but it contains the base uracil (U) instead of thymine (T).

Termination

This is the third step of transcription. These are sequences that signal that the RNA transcript is complete. Once they are transcribed, they cause the transcript to be released from the RNA polymerase.

pre-mRNA

In bacteria, RNA transcripts can act as messenger RNAs (mRNAs) right away. In eukaryotes, the transcript of a protein-coding gene is called a BLANK and must go through extra processing before it can direct translation.

• Eukaryotic pre-mRNAs must have their ends modified, by addition of a 5' cap (at the beginning) and 3' poly-A tail (at the end).

• Many eukaryotic pre-mRNAs undergo splicing. In this process, parts of the pre-mRNA (called introns) are chopped out, and the remaining pieces (called exons) are stuck back together.

Splicing

Parts of the pre-mRNA (called introns) are chopped out, and the remaining pieces (called exons) are stuck back together. This gives the mRNA its correct sequence. (If the introns are not removed, they'll be translated along with the exons, producing a "gibberish" polypeptide.)

Alternative Splicing

Regular splicing allows for this process, which is when more than one mRNA can be made from the same gene. Through alternative splicing, we (and other eukaryotes) can sneakily encode more different proteins than we have genes in our DNA.

Translation

This takes place in ribosomes. The sequence of the mRNA is decoded to specify the amino acid sequence of a polypeptide. The name indicates that the nucleotide sequence of the mRNA sequence must be translated into the completely different "language" of amino acids.

This is the process of using information in an mRNA to build a polypeptide.

Codons

These are a sequence of three DNA or RNA nucleotides that corresponds with a specific amino acid or stop signal during protein synthesis. DNA and RNA molecules are written in a language of four nucleotides; their are 61 codons that specify amino acids.

In translation, these are read and one BLANK is a "start" BLANK that indicates where to start translation. It specifies the amino acid methionine, so most polypeptides begin with this amino acid. Three other “stop” BLANKs signal the end of a polypeptide. These relationships between BLANKs and amino acids are called the genetic code.

There are three more BLANKs that do not specify amino acids. These stop BLANKs, UAA, UAG, and UGA, tell the cell when a polypeptide is complete.

Genetic Code

This is the relationship between codons and amino acids (stop signals). It is often summarized in a table. Many amino acids are represented in the table by more than one codon. For instance, there are six different ways to "write" leucine in the language of mRNA (see if you can find all six).

Central Dogma

This is a theory stating that genetic information flows only in one direction, from DNA, to RNA, to protein, or RNA directly to protein.

Non-coding Strand

This is the strand of DNA that serves as the template for the synthesis of a matching (complementary) RNA strand by an enzyme called RNA polymerase. This RNA strand is the primary transcript.

Primary Transcript

This is the RNA strand produced by the transcription of DNA. It carries the same sequence information as the non-transcribed strand of DNA, sometimes called the coding strand. However, the BLANK and the coding strand of DNA are not identical, thanks to some biochemical differences between DNA and RNA.