Freshman grades do not count towards your CSU/UC GPA, but you can fulfill your a-g course requirements with some of your Freshman classes.
You will need to retake AP Biology and Environmental Science to replace your F and D or those grades remain in your UC GPA calculation especially since you may not be able to retake until Summer or Senior year. They have to be the exact same class or grade replacement will not work. You need a minimum of 2 years laboratory science for the UC’s, so passing Honors Biology and Chemistry will fulfill this requirement for CSU but UC’s recommend 3 years.
UC’s are very GPA focused and if you plan to pursue an Engineering degree, your stats need to be above the averages.
At the end of Junior year, you need to calculate your UC/CSU GPA: https://rogerhub.com/gpa-calculator-uc/
Here is some Freshman admit numbers by GPA range and Campus to give you some targets to aim for:
Freshman Admits for UC GPA of 3.0-3.39:
UCM: 42%
UCR: 25%
UCSC: 10%
Freshman admit rates for UC GPA of 3.40-3.79:
UCSC: 47%
UCR: 64%
UCM: 80%
UCSC is not possible for Chemical Engineering since they do not offer this major. UC Riverside is the only UC on your list where you can major in Chemical Engineering. The other UC’s that offer this major would not be possible with your grades.
I suggest you apply to UCR and UCSC (Chemistry major perhaps) but concentrate on the Cal States since your GPA will be an issue.
Cal Poly Pomona and San Jose State are the only Cal states where you would have the best chances. If you apply to CSUN, you would have to again select another major since Chem E is not available.
Here is a link for California Schools that offer ChemE:
http://educatingengineers.com/states/california/chemical-engineering
Right now, work on doing well on your classes, work with your counselor to try and makeup the bad grades and re-evaluate your goals and college list at the end of Junior year.