Exam 1 Study Guide

Figure legends describe what?

Monday, September 12, 2016 3:08 PM

Exam 1 Study Guide

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Define evolution and apply your basic knowledge of evolution to explain how more complex molecules may have evolved  overtime (continuing objective)

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Evolution is the thought that organisms become more complex over time based off of previous ancestor and all  living things evolved from a common ancestor. More complex molecules may have evolved overtime through  mutations in DNA and reactions of molecules to create new more complex molecules.

∙ Explain how and why the composition and properties of atoms…

o facilitates chemical bonding,  

▪ Review properties of metals, non-metals and valence electrons (ionic bonds and covalent bonds) o impacts the types and properties of chemical bonds that form (describe types of chemical bonds, electronegativity)

Changing amino acids change the structure because of what?

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Hydrogen bond, ionic bonds, covalent bonds. Hydrogen bonds are formed between a hydrogen atom and another  atom, H2O for example is a hydrogen bond. Ionic bonds are formed between metals and non metals because  metals have a low electronegativity and non metals have a high electronegativity. Covalent bonds are formed  between two non metals.

o influences the structures and properties of more complex molecules (e.g., polarity)

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Water is a polar molecule. Polar molecules act this way due to the uneven distribution of electrons. Polar  molecules dissolve in water easily because the two molecules (H2O and the other polar molecule) are both polar  and can easily form hydrogen bonds and so the molecules are pulled apart.

What are the monomers of proteins?

Don't forget about the age old question of a synthetic process combines raw materials or components to create a finished product.

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Predict how and explain why intra and intermolecular forces (including hydrophobicity and bonding) shape the structures of  molecules and or their interactions with themselves and other molecules (Not just with DNA, but RNA and proteins!)

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Intra and intermolecular forces such as hydrophobicity, hydrophilicity and chemical bonding all contribute to the  shape of molecules because hydrophobic molecules tend to stay away from molecules so for example, a protein  will fold to prevent its hydrophobic parts from touching water. These folds contribute to the overall shape of the  molecule.

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Determine the properties/locations of a molecule/structure/amino acid when given information about how said structures  interacts with other molecules/water (and vice versa)

▪ Review amino acids and their properties

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Describe the structure and basic characteristics of DNA, including the structure of the monomers of DNA  (deoxyribonucleotides) If you want to learn more check out food production was not independently invented in the

▪ DNA is made up of monomers of nucleic acids, Adenine, Thymine, Cytosine and Guanine

▪ Thymine and Cytosine are purines and have one ring  

▪ Adenine and Guanine are pyramidines and have two rings

∙ Explain if DNA could have been the initial spark of life!

▪ DNA cannot function as a catalyst, but can only store information. RNA is more of a plausible initial spark.

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Correctly generate a complementary sequence of DNA, including generating the sequence in the appropriate direction and  labeling 3’ and 5’ sides.

∙ Describe the process of DNA replication.

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DNA unwinds and RNA primase is added by RNA polymerase. DNA polymerase adds nucleotides successively to  the 3' end until it encounters the next RNA primer and a different polymerase removes the primer and DNA ligase  connects the two strands together.

∙ Apply your understanding of DNA replication to determine of the Meselson & Stahl hypothesis was supported. We also discuss several other topics like ajay kshemkalyani

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DNA replicates semiconservatively due to the results of the experiment having two different types of DNA  consisting of N15 and N14. If you want to learn more check out french 101 study guide

∙ Describe the structure and basic characteristics of RNA, including the structure of the monomers of RNA (ribonucleotides)

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RNA is made up of ribonucleic acids. Uracil replaces Thymine. RNA is a single strand of nucleic acids  complementary to a template strand of DNA.

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Correctly generate a sequence of RNA, including generating the sequence in the appropriate direction and labeling 3’ and 5’  sides

∙ Describe the process of transcription

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Activator proteins bind to enhancers, general transcription factors and the mediator complex are all brought into  close proximity to RNA polymerase to start transcription. Promoters are the start site of transcription and  terminators are the end of transcription.

∙ Explain if RNA could have been the initial spark of life!

▪ RNA both stores information and can serve as a catalyst so therefore it could be the initial spark of life  Bio 281 Lecture Page 1

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Correctly generate the primary sequence of a protein (next time we’ll add on information as to why mutations in DNA don’t  always produce changes in protein structure and function)  

▪ Amino acids are the complements to a strand of mRNA

∙ Describe the process of translation

Initiation requires a number of protein initiation factorsthat bind to the mRNA. In eukaryotes, one  group of initiation factors binds to the 5' cap that is added to the mRNA during processing. These  recruit the small subunit of the ribosome, other factors bring up tRNA with Met.  If you want to learn more check out good to great study guide

The complex scans mRNA until it encounters the first AUG triplet.  

After AUG is encountered, the large ribosomal subunit joins the complex and the initiation factors are  released, and the next tRNA joins the ribosome at the A site. A bond connects Met to the tRNA which is  then transferred to the amino group, forming a peptide bond. After this the uncharged tRNA shifts to  the E site and is released into the cytoplasm.

Ribosome movement along mRNA and formation of peptide bonds require energy from proteins called  elongation factors.

Elongation continues until a stop codon is reached, then a protein release factor binds to the A site of  the ribosome. This causes the bond connecting the protein to the tRNA to break, creating the carboxyl  terminus and completing the chain. Once finished, the small and large ribosomal units disassociate  from the mRNA and each other. We also discuss several other topics like How to calculate athlete calorie consumption?

In eukaryotes, initiation complex forms at the 5' cap and scans until AUG is encountered.  

In prokaryotes, there is no 5' cap therefore the initiation complex is formed at one or more internal  sequences present in mRNA known as the Shine-Dalgarno sequence. It is followed by an AUG codon  eight nucleotides downstream that serves as the initiation.

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Apply knowledge of DNA replication, transcription, and or translation to predict how a disruption to any one of these  processes will impact replication, transcription and or translation (including protein structure and function) and/or determine  how one might alleviate the symptoms of the disruptive event.

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Review case studies from recitation (diphtheria causes an impact of protein production which affects  transcription eventually)

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Describe the monomers of proteins (amino acids) and their basic characteristics, including how two amino acids bond (these  are on the slides on your handout)

▪ Proteins form when amino acids bond covalently called peptide bonds. The carboxyl group bonds to the amino  group.

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Describe / be able to identify the various structures of a protein and explain how and why intra/intermolecular forces (e.g., hydrogen bonding, hydrophobicity, etc.) shape the structure of molecules (specifically proteins) and their interactions with  other molecules

▪ Proteins fold based off of their bonding between molecules, amino acids determine the folds which determine  function. When fully folded, some proteins contain pockets with positively or negatively charged side chains at  just the right positions to trap small molecules; others have surfaces that can bind another protein or a sequence  of nucleotides in DNA or RNA; some form rigid rods for structural support; and still others keep their hydrophobic  side chains away from water molecules by inserting into the cell membrane.

∙ Predict how and explain why perturbations (e.g., changing amino acids) impacts protein folding and function ▪ Changing amino acids change the structure because different amino acids interact differently with one another.  This is concluded because different proteins have different functions which is determined by structure.  

∙ Generate and interpret figures, including writing figure legends/captions.

▪ Figure legends describe the content of a chart or graph

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Make predictions and interpret experimental evidence to determine if a hypothesis is supported (for example what we did  with the Meselson & Stahl Experiment)

▪ Context based

 Bio 281 Lecture Page 2