Bio Lecture 2: Genes

Mcat Prep 1 with Mcat at Georgia Institute of Technology

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By: Ivie Manalo
Created: 2011-05-16
Size: 79 flashcards
Views: 91

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Central Dogma

DNA -(transcribed to)-> RNA -(translated to)-> amino acids to form PROTEIN

Gene

Series of DNA nucleotides that generally codes for the production of a single polypeptide:

- mRNA

- rRNA

- or tRNA

Genes in Prokaryotes vs. Eukaryotes

Prokaryotes: only have one copy of each gene

Eukaryotes:

- unique-sequence DNA (genes) dominate (found in heterochromatin)

- but regions of non-coding DNA (repetitive sequences of DNA) can also be found (in euchromatin)

Genome

Entire DNA sequence of an organism, only 1% of human genome actually codes for protein

4 Nitrogenous bases in DNA

Purines:Pyrimidines

(A)denine:(T)hymine (2-bonds)

(G)uanine:(C)ytosine (3 H-bonds)

Hint: Pyrimidines contain the letter "y"

Phosphodiester Bond

Binds nucleotide to the next between the 3rd C of one deoxyribose and the phosphate backbone of a single strand of DNA with a 5' --> 3' directionality

Two DNA strands in a single DNA

Lie antiparallel to each other and are bound together by hydrogen bonds between the nitrogenous bases

DNA

Polymer of nucleotides, each nucleotide made up of 3 parts:

1. Phosphate group

2. 5-carbon sugar

3. Nitrogenous base

DNA Replication

- One time in a cell's life cycle

- Semi-conservative: 1 strand from original DNA + 1 newly synthesized strand

- Governed by a group of proteins called a replisome

DNA Replication Directions

1. Replication begins @ middle of DNA (called the "origin of replication")

- Eukaryotic chromosome contains multiple origins on each chromosome

2. Bidirectional: 2 replisomes proceed in opposite directions, producing a leading and a lagging strand

Prokaryotic Replisome

Replication has 5 steps:

Helicase unzips the double helix
RNA Polymerase builds a primer
DNA Polymerase assembles the leading and lagging strands
Primers are removed
Okazaki fragments are joined

DNA Helicase

Unwinds the double helix separating the 2 strands

DNA Polymerase

Enzyme that builds the new DNA strand. Cannot initiate a strand from 2 nucleotides, but can only add to an existing strand.
Reads parental strand in only 3' --> 5' direction (upstream), creating new complementary strand in 5' --> 3' direction

Primase

An RNA polymerase. Creates an RNA primer approximately 10 ribonucleotides long to initiate the strand.

Okazaki Fragments

Series of disconnected strands in the lagging strand. DNA ligase (Latin ligare: to fasten or bind) binds the fragments. Causes DNA replication to be "semidiscontinuous".

DNA Ligase

Moves along the lagging strand and ties the Okazaki fragments together to complete the polymer.

Exonuclease (subunit in DNA polymerase)

Automatically proofreads each new strand, and makes repairs when it discovers any mismatched nucleotides. DNA replication in eukaryotes is extremely accurate!

Telomeres

Repeated 6 nucleotide units from 100 to 1000 units long to protect the chromosomes from being eroded through repeated rounds of replication (at the ends of eukaryotic chromosomal DNA).

DNA vs. RNA Locations

DNA: only in nucleus and mitochondrial matrix

RNA: also in cytosol

RNA

Identical to DNA except:

C number 2 on pentose is not deoxygenated (it has hydroxyl group)
single-stranded
Uracil instead of Thymine
Can move thru nuclear pores, not confined to nucleus
3 forms: mRNA, rRNA, tRNA

mRNA

Delivers DNA code for amino acids to the CYTOSOL where PROTEINS are manufactured

rRNA

Combines with proteins to form ribosomes, the cellular complexes that direct the synthesis of proteins.

rRNA is synthesized in the nucleolus

tRNA

Collects amino acids in the cytosol and transfers them to the ribosomes for incorporation into a protein

Promoter vs. Primer

Replication requires a PRIMER, whereas

Transcription requires a PROMOTER.

A promoter is a spot on the DNA that tells RNA polymerase where to begin transcription. A primer is a short piece of RNA that jump starts replication.

Initiation

Beginning of transcription

Initiation factors find a promoter on the DNA strand and assemble a transcription initiation complex, which includes RNA polymerase.

Transcription

Only one strand in a molecule of double stranded DNA is transcribed.

- The template/antisense strand is transcribed

- The coding/sense strand protects its partner against degradation

RNA Polymerase

Moves along DNA strand in 3' --> 5' direction, building the new RNA strand in the 5' --> 3'.

Does NOT contain a proofreading mechanism (rate of errors is higher than in replication).

Termination

The end of transcription, requires a special termination sequence

Activators and Repressors

Bind to DNA close to the promoter, and either activate or repress the activity of RNA polymerase.

Operon

The generic unit usually consisting of the operator, promoter, and genes that contribute to a single prokaryotic mRNA.

Primary Transcript - processed in 3 ways

Initial mRNA nucleotide sequence arrived at through transcription.

Processed in 3 ways:

Addition of nucleotides
Deletion of nucleotides
Modification of nitrogenous bases

Before leaving nucleus, it is cleaved into introns and exons

5' cap

Attachment site in protein synthesis, protects against degradation by exonucleases

3' poly A tail

3' end is polyadenylated to protect it from exonucleases

Spliceosome

Introns are looped, bringing exons together. Introns are then excised by the spliceoscomes and exons are spliced together to form the single mRNA strand that codes for a polypeptide.

REMEMBER: Introns remain in the nucleus, and exons exit the nucleus to be translated. Most of a typical gene consists of introns, removed by snRNPs in the nucleus

Denaturing DNA

Done by heating or immersing DNA in high [salt] solution or high pH solution

The H-bonds connecting the two strands are disrupted and separate

Since G-C has 3 bonds while A-T has 2 bonds, DNA with more G-C will be harder to melt

Nucleic Acid Hybridization

DNA prefers to be double stranded & will look for a complementary partner.

DNA-DNA, DNA-RNA, and RNA-RNA strand combinations, enable scientists to identify nucleotide sequences by binding a known sequence with an unknown sequence.

Methylation of DNA

Technique some bacteria use to defend themselves from viruses by cutting the viral DNA into fragments with restriction enzymes

Restriction enzymes/endonucleases

Digest (cut) nucleic acid only at certain nucleotide sequences along the chain

Typically, a restriction site will be a palindromic sequence 4 to 6 nucleotides long

Recombinant DNA

Artificially recombined DNA from two DNA fragments cleaved by the same endonuclease, joined together regardless of the origin of the DNA

How do you make a DNA library?

Take your DNA fragment and use a vector (typically a plasmid or infective virus) to insert it into a bacterium
Reproduce that bacterium like crazy

Now you have a clone of bacteria with your DNA fragment

Use antibiotics to screen for desired clones.

cDNA (complementary DNA)

Product of reverse transcribing mRNA using reverse transcriptase
Useful because it lacks the introns that would normally be found in eukaryotic DNA
Adding DNA polymerase to cDNA produces a double strand of the desired DNA fragment

Polymerase Chain Reaction (PCR) method

Fast method of cloning

Target DNA is denatured and mixed with many complementary primers
Primers hybridize with DNA fragments
Specialized polymerase replicates DNA fragments

Southern Blotting

Identifies fragments of DNA...
...via nucleic acid hybridization

Chop up some DNA
Use an electric field to spread out pieces according to size
Blot it onto a membrane
Add a radioactive probe made from DNA or RNA
Visualize with radiographic film

Northern Blotting

Identifies fragments of RNA...
...via nucleic acid hybridization

*Same technique as Southern Blotting, but identifies RNA fragments, not DNA fragments*

Western Blotting

Detects a protein using antibodies

Genetic Code

mRNA nucleotides strung together, translating to an amino acid sequence and ultimately to a protein
Degenerative bc several codes can code for an amino acid
Unambiguous bc a single series of 3 nucleotides will code for only one amino acid

Start Codon

AUG (Methionine)

Stop Codons

Signal an end to protein synthesis

A polypeptide contains 100 amino acids. How many possible amino acid sequences are there for this polypeptide?

20 possible amino acids (you should know that) and 100 positions gives 20¹⁰⁰ possible sequences

Codons

4³=64 possible codons but for only 20 diff amino acids
Codon = 3 consecutive mRNA nucleotides
Written 5' --> 3'

Translation

Protein synthesis:

mRNA - template that carries the genetic code from the nucleus (where posttranscriptional processing occurred) to cytosol
tRNA - contains and sequesters anticodon to an mRNA's codon
rRNA - ribosome

Process: Initiation, Elongation, and Termination

Ribosome

Composed of small & large subunits
Prok's (30S_small+50S_large=70S_combined) are smaller than Euk's (40S+60S=80S)
Manufactured in nucleolus, and small & large subunits are exported separately to cytoplasm

When tRNA possessing the 5'-CAU-3' anticodon sequesters the amino acid methionine and settles in at the ribosome's P-site
Signals the large subunit to join and form the initiation complex

Translational Elongation

A tRNA with its corresponding amino acid attaches to the A site (aminoacyl site) at the expense of 2 GTPs (N-terminus of the new aa attaches to C-terminus of starting methionine)
Translocation: ribosome shifts 3 nucleotides along mRNA toward 3' end

E-site

Where the tRNA exits the ribosome

Order tRNA attaches to ribosome's sites

A-site
P-site
E-site

Translational Termination

When a stop codon (or nonsense) reaches the P-site.
The ribosome breaks up into its 2 subunits to be used again later.

Post-translational Modifications

- Sugars, lipids, or phosphate groups may be added to amino acids
- The polypeptide may be cleaved

Where does translation occur?

Translation may take place on:

a free floating ribosome in cytosol
or a ribosome may attach itself to the rough ER during translation and inject proteins into the ER lumen

These are destined to become membrane bound proteins or secreted from cell

Signal Peptide

Signal near the front of a polypeptide that is recognized by signal-recognition particle (SRP) that carries the entire ribosome to a receptor protein on the ER

Mutations

Mutations in somatic cells are not passed to offspring, mutations in germ cells are.

Can be spontaneous (random errors in replication and genetic recombination) or induced (occurring due to physical/chemical agents called mutagens)

Gene Mutation vs. Chromosomal Mutation

Gene mutation: alteration in the sequence of DNA nucleotides in a single gene
Chromosomal mutation: when the structure of a chromosome is changed

Point Mutation 1 - Base-pair mutations

Mutation that changes a single base-pair of nucleotides

Types:

Base-pair substitution mutation: one base-pair replaced by another
Missense mutation: occurs in the aa coding sequence of a gene (may or may not be serious) e.g. Sickle cell

Point-mutation 1 - Insertion or Deletion

May result in a frameshift mutation (results when insertions/deletions occur in multiples other than 3)

Nonsense Mutation

If a base-pair substituion or an insertion or deletion creates a stop codon

Usually VERY SERIOUS

Transposons

DNA segments that can excise themselves from a chromosome and reisert themselves at another location

Forward Mutation vs Backward Mutation

Refer to an organism already mutated then mutated again:

Forward - changes the organism even more from its original state

Backward - tending to revert the organism back to its original state (wild type)

Histones

Globular proteins that tightly wrap sections of DNA that are not in use
8 histones wrapped in DNA form a nucleosome, which wrap into coils called solenoids, which wrap into supercoils

This condensed form of chromatin is called heterochromatin

An animals cells, where can DNA be found?

Nucleus
or Mitochondria

How many chromosomes are there?

In the nucleus of human cells, there are 46 chromosomes (46 double stranded DNA molecules) before and after replication. The duplicates are called sister chromatids.

Diploid means...

that the cell has homologous pairs!

Homologous

Two chromosomes possessing codes for the same traits

Although the traits are the same, the actual genes may be different: i.e. trait - eye color, gene - blue or brown

Mitosis

PMAT!

Results in genetically identical daughter cells

Meiosis

PMAT x2!

Double nuclear division producing four haploid gametes (germ cells)
In human cells, only the spermatogonium and oogonium undergo meiosis

(All other cells are somatic and undergo mitosis only)

You must know the names of the cells at the different stages and whether or not those cells are haploid or diploid.
Recognize that, under the light microscope, metaphase in mitosis would appear like metaphase II in meiosis and not like metaphase I.

Spermatogenesis

In order:

1 Spermatogonium (2n: 46 chromosomes)

1 Primary Spermatocyte (2n: 46 chromosomes)

--Meisosis I first division--

2 Secondary Spermatocytes (n: 23 chromosomes each)

--Meisosis II second division--

4 Spermatids (n: 23 chromosomes each)

4 Spermatazoa

Oogenesis

In order:

1 Oogonium (2n: 46 chromosomes)

1 Primary Oocyte (2n: 46 chromosomes)

--oocytes stay in this form until fertilization--

--after fertilization: Meisosis I first division--

1st polar body (much smaller) divides from Primary Oocyte and degenerates

The first polar body may or may not go through meiosis II producing two polar bodies.

1 Ovum is formed (before fertilization)

About this deck

By: Ivie Manalo
Created: 2011-05-16
Size: 79 flashcards
Views: 91

About StudyBlue

“I have been getting MUCH better grades on all my tests for school. Flash cards, notes, and quizzes are great on here. Thanks!”
Kathy